From 580b3401baee8dc583eb7280d36599af1cf434ce Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 10 Oct 2023 09:00:54 +0000 Subject: [PATCH 01/59] init --- .devcontainer/Dockerfile | 11 + .devcontainer/devcontainer.json | 28 + .github/ISSUE_TEMPLATE/bug_report.md | 38 + .github/ISSUE_TEMPLATE/feature_request.md | 20 + .github/workflows/publish-to-pypi.yml | 22 + .github/workflows/pytest.yml | 42 ++ .github/workflows/test-publish-to-pypi.yml | 24 + .gitignore | 135 ++++ .pre-commit-config.yaml | 41 ++ .vscode/settings.json | 9 + CODE_OF_CONDUCT.md | 76 ++ CONTRIBUTING.MD | 27 + LICENSE | 201 +++++ SECURITY.md | 11 + codecov.yml | 8 + poetry.lock | 813 +++++++++++++++++++++ poetry.toml | 3 + pyproject.toml | 33 + pyrightconfig.json | 16 + pytest.ini | 4 + scripts/init.sh | 12 + tests/__init__.py | 0 22 files changed, 1574 insertions(+) create mode 100644 .devcontainer/Dockerfile create mode 100644 .devcontainer/devcontainer.json create mode 100644 .github/ISSUE_TEMPLATE/bug_report.md create mode 100644 .github/ISSUE_TEMPLATE/feature_request.md create mode 100644 .github/workflows/publish-to-pypi.yml create mode 100644 .github/workflows/pytest.yml create mode 100644 .github/workflows/test-publish-to-pypi.yml create mode 100644 .gitignore create mode 100644 .pre-commit-config.yaml create mode 100644 .vscode/settings.json create mode 100644 CODE_OF_CONDUCT.md create mode 100644 CONTRIBUTING.MD create mode 100644 LICENSE create mode 100644 SECURITY.md create mode 100644 codecov.yml create mode 100644 poetry.lock create mode 100644 poetry.toml create mode 100644 pyproject.toml create mode 100644 pyrightconfig.json create mode 100644 pytest.ini create mode 100755 scripts/init.sh create mode 100644 tests/__init__.py diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile new file mode 100644 index 0000000..39dbbd8 --- /dev/null +++ b/.devcontainer/Dockerfile @@ -0,0 +1,11 @@ +# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.148.1/containers/python-3/.devcontainer/base.Dockerfile +ARG VARIANT="3.11" +FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT} +ARG INSTALL_NODE="true" +ARG NODE_VERSION="lts/*" +RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "source /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi +USER vscode +RUN pip3 --disable-pip-version-check --no-cache-dir install -U \ + 'poetry==1.1.13' \ + 'pip==22.1.2' +RUN npm install -g @devcontainers/cli@v0.30.0 \ No newline at end of file diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000..da72b4c --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,28 @@ +{ + "name": "Python 3", + "build": { + "dockerfile": "Dockerfile", + "context": "..", + "args": { + "VARIANT": "3.10", + "INSTALL_NODE": "true", + "NODE_VERSION": "18.7" + } + }, + "customizations": { + "vscode": { + "settings": { + "terminal.integrated.defaultProfile.linux": "zsh", + "python.pythonPath": "/usr/local/bin/python" + }, + "extensions": [ + "ms-python.python" + ] + } + }, + "features": { + "ghcr.io/devcontainers/features/docker-in-docker:2": {} + }, + "postCreateCommand": "poetry install", + "remoteUser": "vscode" +} diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000..dd84ea7 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,38 @@ +--- +name: Bug report +about: Create a report to help us improve +title: '' +labels: '' +assignees: '' + +--- + +**Describe the bug** +A clear and concise description of what the bug is. + +**To Reproduce** +Steps to reproduce the behavior: +1. Go to '...' +2. Click on '....' +3. Scroll down to '....' +4. See error + +**Expected behavior** +A clear and concise description of what you expected to happen. + +**Screenshots** +If applicable, add screenshots to help explain your problem. + +**Desktop (please complete the following information):** + - OS: [e.g. iOS] + - Browser [e.g. chrome, safari] + - Version [e.g. 22] + +**Smartphone (please complete the following information):** + - Device: [e.g. iPhone6] + - OS: [e.g. iOS8.1] + - Browser [e.g. stock browser, safari] + - Version [e.g. 22] + +**Additional context** +Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000..bbcbbe7 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,20 @@ +--- +name: Feature request +about: Suggest an idea for this project +title: '' +labels: '' +assignees: '' + +--- + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Describe alternatives you've considered** +A clear and concise description of any alternative solutions or features you've considered. + +**Additional context** +Add any other context or screenshots about the feature request here. diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml new file mode 100644 index 0000000..cd2cc97 --- /dev/null +++ b/.github/workflows/publish-to-pypi.yml @@ -0,0 +1,22 @@ +name: Publish to PYPI +on: + release: + types: [published] +jobs: + build-n-publish: + runs-on: ubuntu-22.04 + steps: + - uses: actions/checkout@master + - uses: actions/setup-python@v2 + - run: pip install poetry + - run: poetry version ${GITHUB_REF:10} + - run: poetry build + - run: pip install twine==4.0.1 + - run: twine upload dist/* -u __token__ -p ${{ secrets.PYPI_API_TOKEN }} + - uses: EndBug/add-and-commit@v7.0.0 + with: + author_name: github-actions + author_email: 41898282+github-actions[bot]@users.noreply.github.com + add: pyproject.toml + branch: main + message: Published new version \ No newline at end of file diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml new file mode 100644 index 0000000..b1ed55d --- /dev/null +++ b/.github/workflows/pytest.yml @@ -0,0 +1,42 @@ +name: Pytest +on: + schedule: + - cron: 0 13 * * 1 # Every Monday at 1PM UTC (9AM EST) + pull_request: +# test in containerised and OS environments +jobs: + test-container: + runs-on: ubuntu-22.04 + steps: + - uses: actions/checkout@v2 + - run: npm install -g @devcontainers/cli@v0.30.0 + - run: devcontainer up --workspace-folder=. + - run: devcontainer exec --workspace-folder=. poetry run pre-commit run --verbose --all-files + - run: devcontainer exec --workspace-folder=. poetry run pytest --cov-report=xml --cov=src + - uses: codecov/codecov-action@v1 + with: + file: coverage.xml + pytest: + strategy: + fail-fast: false + matrix: + os: + - ubuntu-latest + - macos-latest + python-version: + - "3.8" + - "3.9" + - "3.10" + - "3.11" + runs-on: ${{ matrix.os }} + steps: + - uses: actions/checkout@v2 + - uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - run: pip install poetry + - run: poetry install + - run: poetry run pytest --cov-report=xml --cov=src + - uses: codecov/codecov-action@v1 + with: + file: coverage.xml diff --git a/.github/workflows/test-publish-to-pypi.yml b/.github/workflows/test-publish-to-pypi.yml new file mode 100644 index 0000000..d63d971 --- /dev/null +++ b/.github/workflows/test-publish-to-pypi.yml @@ -0,0 +1,24 @@ +name: Test Publish to PYPI +on: + push: + branches: + - main +jobs: + build-n-publish: + runs-on: ubuntu-22.04 + steps: + - uses: actions/checkout@master + - uses: actions/setup-python@v2 + - run: pip install poetry + - name: Set poetry version to dev + run: | + build_version="$(poetry version -s).dev$(date +%s)" + poetry version $build_version + - run: poetry build + - run: pip install 'pytest==7.1' + - run: pip install dist/*gz --force-reinstall + - run: pytest --nbmake tests/resources/mock.ipynb + - run: pip install dist/*whl --force-reinstall + - run: pytest --nbmake tests/resources/mock.ipynb + - run: pip install twine==4.0.1 + - run: twine upload -r testpypi dist/* -u __token__ -p ${{ secrets.TEST_PYPI_API_TOKEN }} diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..dc46bb1 --- /dev/null +++ b/.gitignore @@ -0,0 +1,135 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +.DS_store +typeshed + +trash +**/_build diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..e5b1ddd --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,41 @@ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v3.3.0 + hooks: + - id: trailing-whitespace + - repo: https://github.com/Lucas-C/pre-commit-hooks + rev: v1.1.10 + hooks: + - id: remove-crlf + - id: remove-tabs + args: [ '--whitespaces-count', '2' ] + - repo: https://github.com/kynan/nbstripout + rev: 0.5.0 + hooks: + - id: nbstripout + - repo: https://github.com/ambv/black + rev: 22.3.0 + hooks: + - id: black + files: '(src|tests).*py' + - repo: https://github.com/PyCQA/isort + rev: 5.12.0 + hooks: + - id: isort + args: ["-m", "3", "--tc"] + - repo: local + hooks: + - id: pyright + name: pyright + entry: poetry run pyright + language: node + pass_filenames: false + types: [python] + additional_dependencies: ["pyright@1.1.91"] + # - repo: local + # hooks: + # - id: smoketest + # name: smoketest + # entry: poetry run pytest -k test_when_nb_present_then_collected + # language: system + # pass_filenames: false diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..13e0611 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,9 @@ +{ + "python.testing.pytestArgs": [ + "tests" + ], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true, + "python.terminal.activateEnvironment": false, + "python.languageServer": "Pylance", +} \ No newline at end of file diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..e8f13a0 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,76 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to making participation in our project and +our community a harassment-free experience for everyone, regardless of age, body +size, disability, ethnicity, sex characteristics, gender identity and expression, +level of experience, education, socio-economic status, nationality, personal +appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or + advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic + address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces +when an individual is representing the project or its community. Examples of +representing a project or community include using an official project e-mail +address, posting via an official social media account, or acting as an appointed +representative at an online or offline event. Representation of a project may be +further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting the project team at alex@treebeard.io. All +complaints will be reviewed and investigated and will result in a response that +is deemed necessary and appropriate to the circumstances. The project team is +obligated to maintain confidentiality with regard to the reporter of an incident. +Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, +available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see +https://www.contributor-covenant.org/faq diff --git a/CONTRIBUTING.MD b/CONTRIBUTING.MD new file mode 100644 index 0000000..78b1eb7 --- /dev/null +++ b/CONTRIBUTING.MD @@ -0,0 +1,27 @@ + +## Developing + +nbgen uses devcontainers to pre-configure a dev environment. We recommend you open the project in vscode with the remote containers extension to contribute. + +For non-vscode users, here are some install steps: + +### Install local package +``` +poetry install # warning, by default this will install without a venv unless you modify poetry.toml +``` + +### Activate shell +``` +poetry shell +``` + +### Run static checks +``` +pre-commit run --all-files +pre-commit install +``` + +### Run tests +``` +pytest +``` diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..261eeb9 --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/SECURITY.md b/SECURITY.md new file mode 100644 index 0000000..3d64be4 --- /dev/null +++ b/SECURITY.md @@ -0,0 +1,11 @@ +# Security Policy + +## Supported Versions + +| Version | Supported | +| ------- | ------------------ | +| 1.0.x | :white_check_mark: | + +## Reporting a Vulnerability + +alex@treebeard.io diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..c83281c --- /dev/null +++ b/codecov.yml @@ -0,0 +1,8 @@ +comment: + layout: "reach, diff, flags, files" + behavior: default + require_changes: false # if true: only post the comment if coverage changes + require_base: no # [yes :: must have a base report to post] + require_head: yes # [yes :: must have a head report to post] + branches: # branch names that can post comment + - "main" \ No newline at end of file diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..172c30f --- /dev/null +++ b/poetry.lock @@ -0,0 +1,813 @@ +[[package]] +name = "appnope" +version = "0.1.3" +description = "Disable App Nap on macOS >= 10.9" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "attrs" +version = "23.1.0" +description = "Classes Without Boilerplate" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} + +[package.extras] +cov = ["attrs", "coverage[toml] (>=5.3)"] +dev = ["attrs", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs", "zope-interface"] +tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest-mypy-plugins", "pytest-xdist", "pytest (>=4.3.0)"] + +[[package]] +name = "backcall" +version = "0.2.0" +description = "Specifications for callback functions passed in to an API" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "cffi" +version = "1.15.1" +description = "Foreign Function Interface for Python calling C code." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +pycparser = "*" + +[[package]] +name = "cfgv" +version = 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+description = "Python bindings for 0MQ" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +cffi = {version = "*", markers = "implementation_name == \"pypy\""} + +[[package]] +name = "six" +version = "1.16.0" +description = "Python 2 and 3 compatibility utilities" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" + +[[package]] +name = "toml" +version = "0.10.2" +description = "Python Library for Tom's Obvious, Minimal Language" +category = "dev" +optional = false +python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" + +[[package]] +name = "tomli" +version = "2.0.1" +description = "A lil' TOML parser" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "tornado" +version = "6.2" +description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." +category = "main" +optional = false +python-versions = ">= 3.7" + +[[package]] +name = "traitlets" +version = "5.9.0" +description = "Traitlets Python configuration system" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] +test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] + +[[package]] +name = "typing-extensions" +version = "4.7.1" +description = "Backported and Experimental Type Hints for Python 3.7+" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "virtualenv" +version = "20.24.3" +description = "Virtual Python Environment builder" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +distlib = ">=0.3.7,<1" +filelock = ">=3.12.2,<4" +importlib-metadata = {version = ">=6.6", markers = "python_version < \"3.8\""} +platformdirs = ">=3.9.1,<4" + +[package.extras] +docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx-argparse (>=0.4)", "sphinx (>=7.0.1)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] +test = ["covdefaults (>=2.3)", "coverage-enable-subprocess (>=1)", "coverage (>=7.2.7)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "pytest (>=7.4)", "setuptools (>=68)", "time-machine (>=2.10)"] + +[[package]] +name = "wcwidth" +version = "0.2.6" +description = "Measures the displayed width of unicode strings in a terminal" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "zipp" +version = "3.15.0" +description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "jaraco.functools", "more-itertools", "big-o", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"] + +[metadata] +lock-version = "1.1" +python-versions = "^3.7.0" +content-hash = "29b2c2acf45001c36fbbacbe1a2a071c48137fc91ac8a40b6c37a27996ad8a14" + +[metadata.files] +appnope = [] +attrs = [] +backcall = [] +cffi = [] +cfgv = [] +colorama = [] +coverage = [] +debugpy = [] +decorator = [] +distlib = [] +entrypoints = [] +exceptiongroup = [] +execnet = [] +fastjsonschema = [] +filelock = [] +identify = [] +importlib-metadata = [] +importlib-resources = [] +iniconfig = [] +ipykernel = [] +ipython = [] +jedi = [] +jsonschema = [] +jupyter-client = [] +jupyter-core = [] +matplotlib-inline = [] +nbclient = [] +nbformat = [] +nest-asyncio = [] +nodeenv = [] +packaging = [] +parso = [] +pexpect = [] +pickleshare = [] +pkgutil-resolve-name = [] +platformdirs = [] +pluggy = [] +pre-commit = [] +prompt-toolkit = [] +psutil = [] +ptyprocess = [] +py = [] +pycparser = [] +pygments = [] +pyrsistent = [] +pytest = [] +pytest-cov = [] +pytest-forked = [] +pytest-xdist = [] +python-dateutil = [] +pywin32 = [] +pyyaml = [] +pyzmq = [] +six = [] +toml = [] +tomli = [] +tornado = [] +traitlets = [] +typing-extensions = [] +virtualenv = [] +wcwidth = [] +zipp = [] diff --git a/poetry.toml b/poetry.toml new file mode 100644 index 0000000..53b35d3 --- /dev/null +++ b/poetry.toml @@ -0,0 +1,3 @@ +[virtualenvs] +create = true +in-project = true diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..6aca11e --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,33 @@ +[tool.poetry] +authors = ["alex-treebeard "] +description = "Pytest plugin for testing notebooks" +homepage = "https://github.com/treebeardtech/nbgen" +license = "Apache-2.0" +name = "nbgen" +packages = [ + {include = "nbgen", from = "src"}, +] +readme = "README.md" +version = "v1.4.3" + +[tool.poetry.dependencies] +pytest = ">=6.1.0" +python = "^3.7.0" +nbclient = "^0.6.6" +nbformat = "^5.0.8" +Pygments = "^2.7.3" +ipykernel = ">=5.4.0" +importlib-metadata = { version = "^6.8.0", python = "<3.8" } + +[tool.poetry.dev-dependencies] +pytest = "^7.1.0" +pre-commit = "^2.8.2" +pytest-cov = "^2.10.1" +pytest-xdist = "^2.1.0" +virtualenv = "^20.1.0" +setuptools = ">65.0.0" +typing-extensions = "^4.7.1" + +[build-system] +build-backend = "poetry.core.masonry.api" +requires = ["setuptools", "poetry-core>=1.0.0"] diff --git a/pyrightconfig.json b/pyrightconfig.json new file mode 100644 index 0000000..3d13535 --- /dev/null +++ b/pyrightconfig.json @@ -0,0 +1,16 @@ +{ + "include": ["src", "tests"], + "typeCheckingMode": "strict", + "reportUnusedImport": true, + "pythonVersion": "3.7", + "enableTypeIgnoreComments": true, + "reportUnknownMemberType": "warning", + "reportUnknownParameterType": "warning", + "reportUnknownVariableType": "warning", + "reportUnknownArgumentType": "warning", + "reportPrivateUsage": "warning", + "reportUntypedFunctionDecorator": "warning", + "reportMissingTypeStubs": false, + "reportGeneralTypeIssues": "warning", + "reportUnusedImport": "warning" +} diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 0000000..52792e2 --- /dev/null +++ b/pytest.ini @@ -0,0 +1,4 @@ +[pytest] +testpaths = + tests +timeout = 180 \ No newline at end of file diff --git a/scripts/init.sh b/scripts/init.sh new file mode 100755 index 0000000..e4ba1ab --- /dev/null +++ b/scripts/init.sh @@ -0,0 +1,12 @@ +#!/usr/bin/env bash + +set -e +set +x + +export PIP_USER=no + +pip install poetry + +poetry install +poetry run pre-commit run -a +poetry run pre-commit install \ No newline at end of file diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 From 808bc5d7b360d14a4cbd58d20373c4ed5d272101 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 10 Oct 2023 09:00:58 +0000 Subject: [PATCH 02/59] 2 --- .devcontainer/devcontainer.json | 17 +- CONTRIBUTING.MD | 2 +- README.md | 2 +- poetry.lock | 567 ++------------------------------ pyproject.toml | 17 +- src/nbwrite/ex.py | 3 + tests/test_ex.py | 4 + 7 files changed, 56 insertions(+), 556 deletions(-) create mode 100644 src/nbwrite/ex.py create mode 100644 tests/test_ex.py diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index da72b4c..e939cd2 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -9,6 +9,20 @@ "NODE_VERSION": "18.7" } }, + "mounts": [ + "source=${localEnv:HOME}${localEnv:USERPROFILE}/.aws,target=/home/vscode/.aws,type=bind,consistency=cached", + "source=${localEnv:HOME}${localEnv:USERPROFILE}/.ssh,target=/home/vscode/.ssh,type=bind,consistency=cached", + "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind,consistency=cached", + // Add the paths below if you know you use them on your local machine and want them to be available in your container. + // + "source=${localEnv:HOME}${localEnv:USERPROFILE}/.zshrc,target=/home/vscode/.zshrc,type=bind,consistency=cached", + "source=${localEnv:HOME}${localEnv:USERPROFILE}/.zsh_history,target=/home/vscode/.zsh_history,type=bind,consistency=cached", + "source=${localEnv:HOME}${localEnv:USERPROFILE}/.zshenv,target=/home/vscode/.zshenv,type=bind,consistency=cached", + // "source=${localEnv:HOME}${localEnv:USERPROFILE}/.kube/config,target=/home/vscode/.kube/config,type=bind,consistency=cached", + // "source=${localEnv:HOME}${localEnv:USERPROFILE}/.kc,target=/home/vscode/.kc,type=bind,consistency=cached", + // "source=${localEnv:HOME}${localEnv:USERPROFILE}/.azure/msal_http_cache.bin,target=/home/vscode/.azure/msal_http_cache.bin,type=bind,consistency=cached", + // "source=${localEnv:HOME}${localEnv:USERPROFILE}/.azure/msal_token_cache.json,target=/home/vscode/.azure/msal_token_cache.json,type=bind,consistency=cached", + ], "customizations": { "vscode": { "settings": { @@ -21,7 +35,8 @@ } }, "features": { - "ghcr.io/devcontainers/features/docker-in-docker:2": {} + "ghcr.io/devcontainers/features/docker-in-docker:2": {}, + "ghcr.io/devcontainers-contrib/features/starship:1": {}, }, "postCreateCommand": "poetry install", "remoteUser": "vscode" diff --git a/CONTRIBUTING.MD b/CONTRIBUTING.MD index 78b1eb7..3374bf8 100644 --- a/CONTRIBUTING.MD +++ b/CONTRIBUTING.MD @@ -1,7 +1,7 @@ ## Developing -nbgen uses devcontainers to pre-configure a dev environment. We recommend you open the project in vscode with the remote containers extension to contribute. +nbwrite uses devcontainers to pre-configure a dev environment. We recommend you open the project in vscode with the remote containers extension to contribute. For non-vscode users, here are some install steps: diff --git a/README.md b/README.md index 9d71a03..6b3cc51 100644 --- a/README.md +++ b/README.md @@ -1 +1 @@ -# nbgen \ No newline at end of file +# nbwrite \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index 172c30f..ec9c3af 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,55 +1,10 @@ -[[package]] -name = "appnope" -version = "0.1.3" -description = "Disable App Nap on macOS >= 10.9" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "attrs" -version = "23.1.0" -description = "Classes Without Boilerplate" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} - -[package.extras] -cov = ["attrs", "coverage[toml] (>=5.3)"] -dev = ["attrs", "pre-commit"] -docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] -tests = ["attrs", "zope-interface"] -tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest-mypy-plugins", "pytest-xdist", "pytest (>=4.3.0)"] - -[[package]] -name = "backcall" -version = "0.2.0" -description = "Specifications for callback functions passed in to an API" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "cffi" -version = "1.15.1" -description = "Foreign Function Interface for Python calling C code." -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -pycparser = "*" - [[package]] name = "cfgv" -version = "3.3.1" +version = "3.4.0" description = "Validate configuration and produce human readable error messages." category = "dev" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.8" [[package]] name = "colorama" @@ -61,31 +16,15 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7 [[package]] name = "coverage" -version = "7.2.7" +version = "7.3.2" description = "Code coverage measurement for Python" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] toml = ["tomli"] -[[package]] -name = "debugpy" -version = "1.6.7.post1" -description = "An implementation of the Debug Adapter Protocol for Python" -category = "main" -optional = false -python-versions = ">=3.7" - -[[package]] -name = "decorator" -version = "5.1.1" -description = "Decorators for Humans" -category = "main" -optional = false -python-versions = ">=3.5" - [[package]] name = "distlib" version = "0.3.7" @@ -94,17 +33,9 @@ category = "dev" optional = false python-versions = "*" -[[package]] -name = "entrypoints" -version = "0.4" -description = "Discover and load entry points from installed packages." -category = "main" -optional = false -python-versions = ">=3.6" - [[package]] name = "exceptiongroup" -version = "1.1.2" +version = "1.1.3" description = "Backport of PEP 654 (exception groups)" category = "main" optional = false @@ -124,72 +55,30 @@ python-versions = ">=3.7" [package.extras] testing = ["hatch", "pre-commit", "pytest", "tox"] -[[package]] -name = "fastjsonschema" -version = "2.18.0" -description = "Fastest Python implementation of JSON schema" -category = "main" -optional = false -python-versions = "*" - -[package.extras] -devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] - [[package]] name = "filelock" -version = "3.12.2" +version = "3.12.4" description = "A platform independent file lock." category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] -docs = ["furo (>=2023.5.20)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)", "sphinx (>=7.0.1)"] -testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)", "pytest (>=7.3.1)"] +docs = ["furo (>=2023.7.26)", "sphinx-autodoc-typehints (>=1.24)", "sphinx (>=7.1.2)"] +testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)", "pytest (>=7.4)"] +typing = ["typing-extensions (>=4.7.1)"] [[package]] name = "identify" -version = "2.5.24" +version = "2.5.30" description = "File identification library for Python" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] license = ["ukkonen"] -[[package]] -name = "importlib-metadata" -version = "6.7.0" -description = "Read metadata from Python packages" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""} -zipp = ">=0.5" - -[package.extras] -docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] -perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-ruff", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] - -[[package]] -name = "importlib-resources" -version = "5.12.0" -description = "Read resources from Python packages" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} - -[package.extras] -docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"] - [[package]] name = "iniconfig" version = "2.0.0" @@ -198,191 +87,6 @@ category = "main" optional = false python-versions = ">=3.7" -[[package]] -name = "ipykernel" -version = "6.16.2" -description = "IPython Kernel for Jupyter" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -appnope = {version = "*", markers = "platform_system == \"Darwin\""} -debugpy = ">=1.0" -ipython = ">=7.23.1" -jupyter-client = ">=6.1.12" -matplotlib-inline = ">=0.1" -nest-asyncio = "*" -packaging = "*" -psutil = "*" -pyzmq = ">=17" -tornado = ">=6.1" -traitlets = ">=5.1.0" - -[package.extras] -docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt"] -test = ["flaky", "ipyparallel", "pre-commit", "pytest-cov", "pytest-timeout", "pytest (>=7.0)"] - -[[package]] -name = "ipython" -version = "7.34.0" -description = "IPython: Productive Interactive Computing" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -appnope = {version = "*", markers = "sys_platform == \"darwin\""} -backcall = "*" -colorama = {version = "*", markers = "sys_platform == \"win32\""} -decorator = "*" -jedi = ">=0.16" -matplotlib-inline = "*" -pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} -pickleshare = "*" -prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0" -pygments = "*" -traitlets = ">=4.2" - -[package.extras] -all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.17)", "pygments", "qtconsole", "requests", "testpath"] -doc = ["Sphinx (>=1.3)"] -kernel = ["ipykernel"] -nbconvert = ["nbconvert"] -nbformat = ["nbformat"] -notebook = ["notebook", "ipywidgets"] -parallel = ["ipyparallel"] -qtconsole = ["qtconsole"] -test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.17)"] - -[[package]] -name = "jedi" -version = "0.19.0" -description = "An autocompletion tool for Python that can be used for text editors." -category = "main" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -parso = ">=0.8.3,<0.9.0" - -[package.extras] -docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx-rtd-theme (==0.4.3)", "sphinx (==1.8.5)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"] -qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"] -testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] - -[[package]] -name = "jsonschema" -version = "4.17.3" -description = "An implementation of JSON Schema validation for Python" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -attrs = ">=17.4.0" -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} -importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""} -pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""} -pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2" -typing-extensions = {version = "*", markers = "python_version < \"3.8\""} - -[package.extras] -format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] -format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] - -[[package]] -name = "jupyter-client" -version = "7.4.9" -description = "Jupyter protocol implementation and client libraries" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -entrypoints = "*" -jupyter-core = ">=4.9.2" -nest-asyncio = ">=1.5.4" -python-dateutil = ">=2.8.2" -pyzmq = ">=23.0" -tornado = ">=6.2" -traitlets = "*" - -[package.extras] -doc = ["ipykernel", "myst-parser", "sphinx-rtd-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt"] -test = ["codecov", "coverage", "ipykernel (>=6.12)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"] - -[[package]] -name = "jupyter-core" -version = "4.12.0" -description = "Jupyter core package. A base package on which Jupyter projects rely." -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} -traitlets = "*" - -[package.extras] -test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] - -[[package]] -name = "matplotlib-inline" -version = "0.1.6" -description = "Inline Matplotlib backend for Jupyter" -category = "main" -optional = false -python-versions = ">=3.5" - -[package.dependencies] -traitlets = "*" - -[[package]] -name = "nbclient" -version = "0.6.8" -description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." -category = "main" -optional = false -python-versions = ">=3.7.0" - -[package.dependencies] -jupyter-client = ">=6.1.5" -nbformat = ">=5.0" -nest-asyncio = "*" -traitlets = ">=5.2.2" - -[package.extras] -sphinx = ["autodoc-traits", "mock", "moto", "myst-parser", "Sphinx (>=1.7)", "sphinx-book-theme"] -test = ["black", "check-manifest", "flake8", "ipykernel", "ipython", "ipywidgets", "mypy", "nbconvert", "pip (>=18.1)", "pre-commit", "pytest (>=4.1)", "pytest-asyncio", "pytest-cov (>=2.6.1)", "setuptools (>=60.0)", "testpath", "twine (>=1.11.0)", "xmltodict"] - -[[package]] -name = "nbformat" -version = "5.8.0" -description = "The Jupyter Notebook format" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -fastjsonschema = "*" -importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.8\""} -jsonschema = ">=2.6" -jupyter-core = "*" -traitlets = ">=5.1" - -[package.extras] -docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] -test = ["pep440", "pre-commit", "pytest", "testpath"] - -[[package]] -name = "nest-asyncio" -version = "1.5.7" -description = "Patch asyncio to allow nested event loops" -category = "main" -optional = false -python-versions = ">=3.5" - [[package]] name = "nodeenv" version = "1.8.0" @@ -393,76 +97,31 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.* [[package]] name = "packaging" -version = "23.1" +version = "23.2" description = "Core utilities for Python packages" category = "main" optional = false python-versions = ">=3.7" -[[package]] -name = "parso" -version = "0.8.3" -description = "A Python Parser" -category = "main" -optional = false -python-versions = ">=3.6" - -[package.extras] -qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] -testing = ["docopt", "pytest (<6.0.0)"] - -[[package]] -name = "pexpect" -version = "4.8.0" -description = "Pexpect allows easy control of interactive console applications." -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -ptyprocess = ">=0.5" - -[[package]] -name = "pickleshare" -version = "0.7.5" -description = "Tiny 'shelve'-like database with concurrency support" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "pkgutil-resolve-name" -version = "1.3.10" -description = "Resolve a name to an object." -category = "main" -optional = false -python-versions = ">=3.6" - [[package]] name = "platformdirs" -version = "3.10.0" +version = "3.11.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false python-versions = ">=3.7" -[package.dependencies] -typing-extensions = {version = ">=4.7.1", markers = "python_version < \"3.8\""} - [package.extras] docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.24)", "sphinx (>=7.1.1)"] test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest (>=7.4)"] [[package]] name = "pluggy" -version = "1.2.0" +version = "1.3.0" description = "plugin and hook calling mechanisms for python" category = "main" optional = false -python-versions = ">=3.7" - -[package.dependencies] -importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} +python-versions = ">=3.8" [package.extras] dev = ["pre-commit", "tox"] @@ -479,41 +138,10 @@ python-versions = ">=3.7" [package.dependencies] cfgv = ">=2.0.0" identify = ">=1.0.0" -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} nodeenv = ">=0.11.1" pyyaml = ">=5.1" virtualenv = ">=20.10.0" -[[package]] -name = "prompt-toolkit" -version = "3.0.39" -description = "Library for building powerful interactive command lines in Python" -category = "main" -optional = false -python-versions = ">=3.7.0" - -[package.dependencies] -wcwidth = "*" - -[[package]] -name = "psutil" -version = "5.9.5" -description = "Cross-platform lib for process and system monitoring in Python." -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - -[package.extras] -test = ["ipaddress", "mock", "enum34", "pywin32", "wmi"] - -[[package]] -name = "ptyprocess" -version = "0.7.0" -description = "Run a subprocess in a pseudo terminal" -category = "main" -optional = false -python-versions = "*" - [[package]] name = "py" version = "1.11.0" @@ -522,36 +150,9 @@ category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -[[package]] -name = "pycparser" -version = "2.21" -description = "C parser in Python" -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - -[[package]] -name = "pygments" -version = "2.16.1" -description = "Pygments is a syntax highlighting package written in Python." -category = "main" -optional = false -python-versions = ">=3.7" - -[package.extras] -plugins = ["importlib-metadata"] - -[[package]] -name = "pyrsistent" -version = "0.19.3" -description = "Persistent/Functional/Immutable data structures" -category = "main" -optional = false -python-versions = ">=3.7" - [[package]] name = "pytest" -version = "7.4.0" +version = "7.4.2" description = "pytest: simple powerful testing with Python" category = "main" optional = false @@ -560,7 +161,6 @@ python-versions = ">=3.7" [package.dependencies] colorama = {version = "*", markers = "sys_platform == \"win32\""} exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} -importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} iniconfig = "*" packaging = "*" pluggy = ">=0.12,<2.0" @@ -615,25 +215,6 @@ psutil = ["psutil (>=3.0)"] setproctitle = ["setproctitle"] testing = ["filelock"] -[[package]] -name = "python-dateutil" -version = "2.8.2" -description = "Extensions to the standard Python datetime module" -category = "main" -optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" - -[package.dependencies] -six = ">=1.5" - -[[package]] -name = "pywin32" -version = "306" -description = "Python for Window Extensions" -category = "main" -optional = false -python-versions = "*" - [[package]] name = "pyyaml" version = "6.0.1" @@ -642,25 +223,6 @@ category = "dev" optional = false python-versions = ">=3.6" -[[package]] -name = "pyzmq" -version = "25.1.1" -description = "Python bindings for 0MQ" -category = "main" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -cffi = {version = "*", markers = "implementation_name == \"pypy\""} - -[[package]] -name = "six" -version = "1.16.0" -description = "Python 2 and 3 compatibility utilities" -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" - [[package]] name = "toml" version = "0.10.2" @@ -677,37 +239,17 @@ category = "main" optional = false python-versions = ">=3.7" -[[package]] -name = "tornado" -version = "6.2" -description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." -category = "main" -optional = false -python-versions = ">= 3.7" - -[[package]] -name = "traitlets" -version = "5.9.0" -description = "Traitlets Python configuration system" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.extras] -docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] -test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] - [[package]] name = "typing-extensions" -version = "4.7.1" -description = "Backported and Experimental Type Hints for Python 3.7+" -category = "main" +version = "4.8.0" +description = "Backported and Experimental Type Hints for Python 3.8+" +category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [[package]] name = "virtualenv" -version = "20.24.3" +version = "20.24.5" description = "Virtual Python Environment builder" category = "dev" optional = false @@ -716,98 +258,39 @@ python-versions = ">=3.7" [package.dependencies] distlib = ">=0.3.7,<1" filelock = ">=3.12.2,<4" -importlib-metadata = {version = ">=6.6", markers = "python_version < \"3.8\""} platformdirs = ">=3.9.1,<4" [package.extras] -docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx-argparse (>=0.4)", "sphinx (>=7.0.1)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] +docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx-argparse (>=0.4)", "sphinx (>=7.1.2)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage-enable-subprocess (>=1)", "coverage (>=7.2.7)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "pytest (>=7.4)", "setuptools (>=68)", "time-machine (>=2.10)"] -[[package]] -name = "wcwidth" -version = "0.2.6" -description = "Measures the displayed width of unicode strings in a terminal" -category = "main" -optional = false -python-versions = "*" - -[[package]] -name = "zipp" -version = "3.15.0" -description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.extras] -docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "jaraco.functools", "more-itertools", "big-o", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"] - [metadata] lock-version = "1.1" -python-versions = "^3.7.0" -content-hash = "29b2c2acf45001c36fbbacbe1a2a071c48137fc91ac8a40b6c37a27996ad8a14" +python-versions = "^3.9.0" +content-hash = "2bc3c1cae6d80f6b982ad2a5e2a61008b56a57e23b861f076d47ca6cb7072685" [metadata.files] -appnope = [] -attrs = [] -backcall = [] -cffi = [] cfgv = [] colorama = [] coverage = [] -debugpy = [] -decorator = [] distlib = [] -entrypoints = [] exceptiongroup = [] execnet = [] -fastjsonschema = [] filelock = [] identify = [] -importlib-metadata = [] -importlib-resources = [] iniconfig = [] -ipykernel = [] -ipython = [] -jedi = [] -jsonschema = [] -jupyter-client = [] -jupyter-core = [] -matplotlib-inline = [] -nbclient = [] -nbformat = [] -nest-asyncio = [] nodeenv = [] packaging = [] -parso = [] -pexpect = [] -pickleshare = [] -pkgutil-resolve-name = [] platformdirs = [] pluggy = [] pre-commit = [] -prompt-toolkit = [] -psutil = [] -ptyprocess = [] py = [] -pycparser = [] -pygments = [] -pyrsistent = [] pytest = [] pytest-cov = [] pytest-forked = [] pytest-xdist = [] -python-dateutil = [] -pywin32 = [] pyyaml = [] -pyzmq = [] -six = [] toml = [] tomli = [] -tornado = [] -traitlets = [] typing-extensions = [] virtualenv = [] -wcwidth = [] -zipp = [] diff --git a/pyproject.toml b/pyproject.toml index 6aca11e..6a5dd10 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,23 +1,18 @@ [tool.poetry] authors = ["alex-treebeard "] -description = "Pytest plugin for testing notebooks" -homepage = "https://github.com/treebeardtech/nbgen" +description = "" +homepage = "https://github.com/treebeardtech/nbwrite" license = "Apache-2.0" -name = "nbgen" +name = "nbwrite" packages = [ - {include = "nbgen", from = "src"}, + {include = "nbwrite", from = "src"}, ] readme = "README.md" -version = "v1.4.3" +version = "v0.1" [tool.poetry.dependencies] pytest = ">=6.1.0" -python = "^3.7.0" -nbclient = "^0.6.6" -nbformat = "^5.0.8" -Pygments = "^2.7.3" -ipykernel = ">=5.4.0" -importlib-metadata = { version = "^6.8.0", python = "<3.8" } +python = "^3.9.0" [tool.poetry.dev-dependencies] pytest = "^7.1.0" diff --git a/src/nbwrite/ex.py b/src/nbwrite/ex.py new file mode 100644 index 0000000..b9bb5a1 --- /dev/null +++ b/src/nbwrite/ex.py @@ -0,0 +1,3 @@ + +def blah(): + return 1 \ No newline at end of file diff --git a/tests/test_ex.py b/tests/test_ex.py new file mode 100644 index 0000000..637f0b4 --- /dev/null +++ b/tests/test_ex.py @@ -0,0 +1,4 @@ +from nbwrite import ex + +def test_ex(): + assert ex.blah() == 1 \ No newline at end of file From d9e6de7c52dc83e3c8187722461f6e64f711ea6e Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 10 Oct 2023 10:25:39 +0000 Subject: [PATCH 03/59] setup --- .gitignore | 2 + poetry.lock | 1207 +++++++++++++++++++++++++++++++- pyproject.toml | 5 + scripts/setup-torchgeo.sh | 8 + src/nbwrite/ex.py | 21 +- tests/resources/poetry.lock | 702 +++++++++++++++++++ tests/resources/poetry.toml | 3 + tests/resources/pyproject.toml | 18 + tests/test_ex.py | 11 +- 9 files changed, 1949 insertions(+), 28 deletions(-) create mode 100755 scripts/setup-torchgeo.sh create mode 100644 tests/resources/poetry.lock create mode 100644 tests/resources/poetry.toml create mode 100644 tests/resources/pyproject.toml diff --git a/.gitignore b/.gitignore index dc46bb1..be4110d 100644 --- a/.gitignore +++ b/.gitignore @@ -133,3 +133,5 @@ typeshed trash **/_build + +.testvenv \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index ec9c3af..92d6a75 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,132 @@ +[[package]] +name = "aiohttp" +version = "3.8.6" +description = "Async http client/server framework (asyncio)" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +aiosignal = ">=1.1.2" +async-timeout = ">=4.0.0a3,<5.0" +attrs = ">=17.3.0" +charset-normalizer = ">=2.0,<4.0" +frozenlist = ">=1.1.1" +multidict = ">=4.5,<7.0" +yarl = ">=1.0,<2.0" + +[package.extras] +speedups = ["aiodns", "brotli", "cchardet"] + +[[package]] +name = "aiosignal" +version = "1.3.1" +description = "aiosignal: a list of registered asynchronous callbacks" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +frozenlist = ">=1.1.0" + +[[package]] +name = "annotated-types" +version = "0.6.0" +description = "Reusable constraint types to use with typing.Annotated" +category = "main" +optional = false +python-versions = ">=3.8" + +[[package]] +name = "anyio" +version = "3.7.1" +description = "High level compatibility layer for multiple asynchronous event loop implementations" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} +idna = ">=2.8" +sniffio = ">=1.1" + +[package.extras] +doc = ["packaging", "sphinx", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquery", "sphinx-autodoc-typehints (>=1.2.0)"] +test = ["anyio", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)", "mock (>=4)"] +trio = ["trio (<0.22)"] + +[[package]] +name = "appnope" +version = "0.1.3" +description = "Disable App Nap on macOS >= 10.9" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "asttokens" +version = "2.4.0" +description = "Annotate AST trees with source code positions" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +six = ">=1.12.0" + +[package.extras] +test = ["astroid", "pytest"] + +[[package]] +name = "async-timeout" +version = "4.0.3" +description = "Timeout context manager for asyncio programs" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "attrs" +version = "23.1.0" +description = "Classes Without Boilerplate" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +cov = ["attrs", "coverage[toml] (>=5.3)"] +dev = ["attrs", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs", "zope-interface"] +tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest-mypy-plugins", "pytest-xdist", "pytest (>=4.3.0)"] + +[[package]] +name = "backcall" +version = "0.2.0" +description = "Specifications for callback functions passed in to an API" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "certifi" +version = "2023.7.22" +description = "Python package for providing Mozilla's CA Bundle." +category = "main" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "cffi" +version = "1.16.0" +description = "Foreign Function Interface for Python calling C code." +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +pycparser = "*" + [[package]] name = "cfgv" version = "3.4.0" @@ -6,6 +135,14 @@ category = "dev" optional = false python-versions = ">=3.8" +[[package]] +name = "charset-normalizer" +version = "3.3.0" +description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" +optional = false +python-versions = ">=3.7.0" + [[package]] name = "colorama" version = "0.4.6" @@ -14,6 +151,22 @@ category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +[[package]] +name = "comm" +version = "0.1.4" +description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +traitlets = ">=4" + +[package.extras] +lint = ["black (>=22.6.0)", "mdformat-gfm (>=0.3.5)", "mdformat (>0.7)", "ruff (>=0.0.156)"] +test = ["pytest"] +typing = ["mypy (>=0.990)"] + [[package]] name = "coverage" version = "7.3.2" @@ -25,6 +178,34 @@ python-versions = ">=3.8" [package.extras] toml = ["tomli"] +[[package]] +name = "dataclasses-json" +version = "0.6.1" +description = "Easily serialize dataclasses to and from JSON." +category = "main" +optional = false +python-versions = ">=3.7,<4.0" + +[package.dependencies] +marshmallow = ">=3.18.0,<4.0.0" +typing-inspect = ">=0.4.0,<1" + +[[package]] +name = "debugpy" +version = "1.8.0" +description = "An implementation of the Debug Adapter Protocol for Python" +category = "dev" +optional = false +python-versions = ">=3.8" + +[[package]] +name = "decorator" +version = "5.1.1" +description = "Decorators for Humans" +category = "dev" +optional = false +python-versions = ">=3.5" + [[package]] name = "distlib" version = "0.3.7" @@ -33,6 +214,22 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "dnspython" +version = "2.4.2" +description = "DNS toolkit" +category = "main" +optional = false +python-versions = ">=3.8,<4.0" + +[package.extras] +doq = ["aioquic (>=0.9.20)"] +dnssec = ["cryptography (>=2.6,<42.0)"] +doh = ["h2 (>=4.1.0)", "httpcore (>=0.17.3)", "httpx (>=0.24.1)"] +idna = ["idna (>=2.1,<4.0)"] +trio = ["trio (>=0.14,<0.23)"] +wmi = ["wmi (>=1.5.1,<2.0.0)"] + [[package]] name = "exceptiongroup" version = "1.1.3" @@ -45,47 +242,510 @@ python-versions = ">=3.7" test = ["pytest (>=6)"] [[package]] -name = "execnet" -version = "2.0.2" -description = "execnet: rapid multi-Python deployment" +name = "execnet" +version = "2.0.2" +description = "execnet: rapid multi-Python deployment" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +testing = ["hatch", "pre-commit", "pytest", "tox"] + +[[package]] +name = "executing" +version = "2.0.0" +description = "Get the currently executing AST node of a frame, and other information" +category = "dev" +optional = false +python-versions = "*" + +[package.extras] +tests = ["asttokens (>=2.1.0)", "ipython", "pytest", "coverage", "coverage-enable-subprocess", "littleutils", "rich"] + +[[package]] +name = "fastjsonschema" +version = "2.18.1" +description = "Fastest Python implementation of JSON schema" +category = "dev" +optional = false +python-versions = "*" 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= ">=3.8.1,<4.0" + +[package.dependencies] +pydantic = ">=1,<3" +requests = ">=2,<3" + +[[package]] +name = "loguru" +version = "0.7.2" +description = "Python logging made (stupidly) simple" +category = "main" +optional = false +python-versions = ">=3.5" + +[package.dependencies] +colorama = {version = ">=0.3.4", markers = "sys_platform == \"win32\""} +win32-setctime = {version = ">=1.0.0", markers = "sys_platform == \"win32\""} + +[package.extras] +dev = ["mypy (==v0.910)", "tox (==3.27.1)", "pytest (==6.1.2)", "pytest-cov (==2.12.1)", "colorama (==0.4.5)", "freezegun (==1.1.0)", "mypy (==v0.971)", "pytest-mypy-plugins (==1.9.3)", "exceptiongroup (==1.1.3)", "mypy (==v1.4.1)", "pre-commit (==3.4.0)", "tox (==4.11.0)", "pytest (==7.4.0)", "pytest-cov (==4.1.0)", "pytest-mypy-plugins (==3.0.0)", "colorama (==0.4.6)", "freezegun (==1.2.2)", "mypy (==v1.5.1)", "Sphinx (==7.2.5)", "sphinx-autobuild (==2021.3.14)", "sphinx-rtd-theme (==1.3.0)"] + +[[package]] +name = "marshmallow" +version = "3.20.1" +description = "A lightweight library for converting complex datatypes to and from native Python datatypes." +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +packaging = ">=17.0" + +[package.extras] +dev = ["pytest", "pytz", "simplejson", "mypy (==1.4.1)", "flake8 (==6.0.0)", "flake8-bugbear (==23.7.10)", "pre-commit (>=2.4,<4.0)", "tox"] +docs = ["sphinx (==7.0.1)", "sphinx-issues (==3.0.1)", "alabaster (==0.7.13)", "sphinx-version-warning (==1.1.2)", "autodocsumm (==0.2.11)"] +lint = ["mypy (==1.4.1)", "flake8 (==6.0.0)", "flake8-bugbear (==23.7.10)", "pre-commit (>=2.4,<4.0)"] +tests = ["pytest", "pytz", "simplejson"] + +[[package]] +name = "matplotlib-inline" +version = "0.1.6" +description = "Inline Matplotlib backend for Jupyter" +category = "dev" +optional = false +python-versions = ">=3.5" + +[package.dependencies] +traitlets = "*" + +[[package]] +name = "multidict" +version = "6.0.4" +description = "multidict implementation" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "mypy-extensions" +version = "1.0.0" +description = "Type system extensions for programs checked with the mypy type checker." +category = "main" +optional = false +python-versions = ">=3.5" + +[[package]] +name = "nbclient" +version = "0.6.8" +description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.7.0" + +[package.dependencies] +jupyter-client = ">=6.1.5" +nbformat = ">=5.0" +nest-asyncio = "*" +traitlets = ">=5.2.2" [package.extras] -testing = ["hatch", "pre-commit", "pytest", "tox"] +sphinx = ["autodoc-traits", "mock", "moto", "myst-parser", "Sphinx (>=1.7)", "sphinx-book-theme"] +test = ["black", "check-manifest", "flake8", "ipykernel", "ipython", "ipywidgets", "mypy", "nbconvert", "pip (>=18.1)", "pre-commit", "pytest (>=4.1)", "pytest-asyncio", "pytest-cov (>=2.6.1)", "setuptools (>=60.0)", "testpath", "twine (>=1.11.0)", "xmltodict"] [[package]] -name = "filelock" -version = "3.12.4" -description = "A platform independent file lock." +name = "nbformat" +version = "5.9.2" +description = "The Jupyter Notebook format" category = "dev" optional = false python-versions = ">=3.8" +[package.dependencies] +fastjsonschema = "*" +jsonschema = ">=2.6" +jupyter-core = "*" +traitlets = ">=5.1" + [package.extras] -docs = ["furo (>=2023.7.26)", "sphinx-autodoc-typehints (>=1.24)", "sphinx (>=7.1.2)"] -testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)", "pytest (>=7.4)"] -typing = ["typing-extensions (>=4.7.1)"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] +test = ["pep440", "pre-commit", "pytest", "testpath"] [[package]] -name = "identify" -version = "2.5.30" -description = "File identification library for Python" +name = "nbmake" +version = "1.4.5" +description = "Pytest plugin for testing notebooks" category = "dev" optional = false -python-versions = ">=3.8" +python-versions = ">=3.7.0,<4.0.0" -[package.extras] -license = ["ukkonen"] +[package.dependencies] +ipykernel = ">=5.4.0" +nbclient = ">=0.6.6,<0.7.0" +nbformat = ">=5.0.8,<6.0.0" +Pygments = ">=2.7.3,<3.0.0" +pytest = ">=6.1.0" [[package]] -name = "iniconfig" -version = "2.0.0" -description = "brain-dead simple config-ini parsing" -category = "main" +name = "nest-asyncio" +version = "1.5.8" +description = "Patch asyncio to allow nested event loops" +category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.5" [[package]] name = "nodeenv" @@ -95,6 +755,33 @@ category = "dev" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*" +[[package]] +name = "numpy" +version = "1.25.2" +description = "Fundamental package for array computing in Python" +category = "main" +optional = false +python-versions = ">=3.9" + +[[package]] +name = "openai" +version = "0.28.1" +description = "Python client library for the OpenAI API" +category = "main" +optional = false +python-versions = ">=3.7.1" + +[package.dependencies] +aiohttp = "*" +requests = ">=2.20" +tqdm = "*" + +[package.extras] +datalib = ["numpy", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)", "openpyxl (>=3.0.7)"] +dev = ["black (>=21.6b0,<22.0.0)", "pytest (>=6.0.0,<7.0.0)", "pytest-asyncio", "pytest-mock"] +embeddings = ["scikit-learn (>=1.0.2)", "tenacity (>=8.0.1)", "matplotlib", "plotly", "numpy", "scipy", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)", "openpyxl (>=3.0.7)"] +wandb = ["wandb", "numpy", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)", "openpyxl (>=3.0.7)"] + [[package]] name = "packaging" version = "23.2" @@ -103,6 +790,59 @@ category = "main" optional = false python-versions = ">=3.7" +[[package]] +name = "parso" +version = "0.8.3" +description = "A Python Parser" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.extras] +qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] +testing = ["docopt", "pytest (<6.0.0)"] + +[[package]] +name = "pexpect" +version = "4.8.0" +description = "Pexpect allows easy control of interactive console applications." +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +ptyprocess = ">=0.5" + +[[package]] +name = "pickleshare" +version = "0.7.5" +description = "Tiny 'shelve'-like database with concurrency support" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "pinecone-client" +version = "2.2.4" +description = "Pinecone client and SDK" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +dnspython = ">=2.0.0" +loguru = ">=0.5.0" +numpy = ">=1.22.0" +python-dateutil = ">=2.5.3" +pyyaml = ">=5.4" +requests = ">=2.19.0" +tqdm = ">=4.64.1" +typing-extensions = ">=3.7.4" +urllib3 = ">=1.21.1" + +[package.extras] +grpc = ["grpcio (>=1.44.0)", "grpc-gateway-protoc-gen-openapiv2 (==0.1.0)", "googleapis-common-protos (>=1.53.0)", "lz4 (>=3.1.3)", "protobuf (>=3.20.0,<3.21.0)"] + [[package]] name = "platformdirs" version = "3.11.0" @@ -142,6 +882,47 @@ nodeenv = ">=0.11.1" pyyaml = ">=5.1" virtualenv = ">=20.10.0" +[[package]] +name = "prompt-toolkit" +version = "3.0.39" +description = "Library for building powerful interactive command lines in Python" +category = "dev" +optional = false +python-versions = ">=3.7.0" + +[package.dependencies] +wcwidth = "*" + +[[package]] +name = "psutil" +version = "5.9.5" +description = "Cross-platform lib for process and system monitoring in Python." +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[package.extras] +test = ["ipaddress", "mock", "enum34", "pywin32", "wmi"] + +[[package]] +name = "ptyprocess" +version = "0.7.0" +description = "Run a subprocess in a pseudo terminal" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "pure-eval" +version = "0.2.2" +description = "Safely evaluate AST nodes without side effects" +category = "dev" +optional = false +python-versions = "*" + +[package.extras] +tests = ["pytest"] + [[package]] name = "py" version = "1.11.0" @@ -150,6 +931,52 @@ category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +[[package]] +name = "pycparser" +version = "2.21" +description = "C parser in Python" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[[package]] +name = "pydantic" +version = "2.4.2" +description = "Data validation using Python type hints" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +annotated-types = ">=0.4.0" +pydantic-core = "2.10.1" +typing-extensions = ">=4.6.1" + +[package.extras] +email = ["email-validator (>=2.0.0)"] + +[[package]] +name = "pydantic-core" +version = "2.10.1" +description = "" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0" + +[[package]] +name = "pygments" +version = "2.16.1" +description = "Pygments is a syntax highlighting package written in Python." +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +plugins = ["importlib-metadata"] + [[package]] name = "pytest" version = "7.4.2" @@ -215,14 +1042,161 @@ psutil = ["psutil (>=3.0)"] setproctitle = ["setproctitle"] testing = ["filelock"] +[[package]] +name = "python-dateutil" +version = "2.8.2" +description = "Extensions to the standard Python datetime module" +category = "main" +optional = false +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" + +[package.dependencies] +six = ">=1.5" + +[[package]] +name = "pywin32" +version = "306" +description = "Python for Window Extensions" +category = "dev" +optional = false +python-versions = "*" + [[package]] name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" +category = "main" +optional = false +python-versions = ">=3.6" + +[[package]] +name = "pyzmq" +version = "25.1.1" +description = "Python bindings for 0MQ" category = "dev" optional = false python-versions = ">=3.6" +[package.dependencies] +cffi = {version = "*", markers = "implementation_name == \"pypy\""} + +[[package]] +name = "referencing" +version = "0.30.2" +description = "JSON Referencing + Python" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +attrs = ">=22.2.0" +rpds-py = ">=0.7.0" + +[[package]] +name = "requests" +version = "2.31.0" +description = "Python HTTP for Humans." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +certifi = ">=2017.4.17" +charset-normalizer = ">=2,<4" +idna = ">=2.5,<4" +urllib3 = ">=1.21.1,<3" + +[package.extras] +socks = ["PySocks (>=1.5.6,!=1.5.7)"] +use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] + +[[package]] +name = "rpds-py" +version = "0.10.4" +description = "Python bindings to Rust's persistent data structures (rpds)" +category = "dev" +optional = false +python-versions = ">=3.8" + +[[package]] +name = "six" +version = "1.16.0" +description = "Python 2 and 3 compatibility utilities" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" + +[[package]] +name = "sniffio" +version = "1.3.0" +description = "Sniff out which async library your code is running under" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "sqlalchemy" +version = "2.0.21" +description = "Database Abstraction Library" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""} +typing-extensions = ">=4.2.0" + +[package.extras] +aiomysql = ["greenlet (!=0.4.17)", "aiomysql (>=0.2.0)"] +aiosqlite = ["greenlet (!=0.4.17)", "aiosqlite", "typing-extensions (!=3.10.0.1)"] +asyncio = ["greenlet (!=0.4.17)"] +asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)"] +mariadb_connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"] +mssql = ["pyodbc"] +mssql_pymssql = ["pymssql"] +mssql_pyodbc = ["pyodbc"] +mypy = ["mypy (>=0.910)"] +mysql = ["mysqlclient (>=1.4.0)"] +mysql_connector = ["mysql-connector-python"] +oracle = ["cx-oracle (>=7)"] +oracle_oracledb = ["oracledb (>=1.0.1)"] +postgresql = ["psycopg2 (>=2.7)"] +postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"] +postgresql_pg8000 = ["pg8000 (>=1.29.1)"] +postgresql_psycopg = ["psycopg (>=3.0.7)"] +postgresql_psycopg2binary = ["psycopg2-binary"] +postgresql_psycopg2cffi = ["psycopg2cffi"] +postgresql_psycopgbinary = ["psycopg[binary] (>=3.0.7)"] +pymysql = ["pymysql"] +sqlcipher = ["sqlcipher3-binary"] + +[[package]] +name = "stack-data" +version = "0.6.3" +description = "Extract data from python stack frames and tracebacks for informative displays" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +asttokens = ">=2.1.0" +executing = ">=1.2.0" +pure-eval = "*" + +[package.extras] +tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"] + +[[package]] +name = "tenacity" +version = "8.2.3" +description = "Retry code until it succeeds" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +doc = ["reno", "sphinx", "tornado (>=4.5)"] + [[package]] name = "toml" version = "0.10.2" @@ -239,14 +1213,77 @@ category = "main" optional = false python-versions = ">=3.7" +[[package]] +name = "tornado" +version = "6.3.3" +description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." +category = "dev" +optional = false +python-versions = ">= 3.8" + +[[package]] +name = "tqdm" +version = "4.66.1" +description = "Fast, Extensible Progress Meter" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} + +[package.extras] +dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"] +notebook = ["ipywidgets (>=6)"] +slack = ["slack-sdk"] +telegram = ["requests"] + +[[package]] +name = "traitlets" +version = "5.11.2" +description = "Traitlets Python configuration system" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.extras] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] +test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest-mock", "pytest-mypy-testing", "pytest (>=7.0,<7.5)"] + [[package]] name = "typing-extensions" version = "4.8.0" description = "Backported and Experimental Type Hints for Python 3.8+" -category = "dev" +category = "main" optional = false python-versions = ">=3.8" +[[package]] +name = "typing-inspect" +version = "0.9.0" +description = "Runtime inspection utilities for typing module." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +mypy-extensions = ">=0.3.0" +typing-extensions = ">=3.7.4" + +[[package]] +name = "urllib3" +version = "2.0.6" +description = "HTTP library with thread-safe connection pooling, file post, and more." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"] +socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] +zstd = ["zstandard (>=0.18.0)"] + [[package]] name = "virtualenv" version = "20.24.5" @@ -264,33 +1301,155 @@ platformdirs = ">=3.9.1,<4" docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx-argparse (>=0.4)", "sphinx (>=7.1.2)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage-enable-subprocess (>=1)", "coverage (>=7.2.7)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "pytest (>=7.4)", "setuptools (>=68)", "time-machine (>=2.10)"] +[[package]] +name = "wcwidth" +version = "0.2.8" +description = "Measures the displayed width of unicode strings in a terminal" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "win32-setctime" +version = "1.1.0" +description = "A small Python utility to set file creation time on Windows" +category = "main" +optional = false +python-versions = ">=3.5" + +[package.extras] +dev = ["pytest (>=4.6.2)", "black (>=19.3b0)"] + +[[package]] +name = "yarl" +version = "1.9.2" +description = "Yet another URL library" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +idna = ">=2.0" +multidict = ">=4.0" + +[[package]] +name = "zipp" +version = "3.17.0" +description = "Backport of pathlib-compatible object wrapper for zip files" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.extras] +docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "jaraco.itertools", "jaraco.functools", "more-itertools", "big-o", "pytest-ignore-flaky", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] + [metadata] lock-version = "1.1" python-versions = "^3.9.0" -content-hash = "2bc3c1cae6d80f6b982ad2a5e2a61008b56a57e23b861f076d47ca6cb7072685" +content-hash = "7e1aad872a330b447d5c55e8ef688f7fd5aa6113aeb086b4c33418c53a710b69" [metadata.files] +aiohttp = [] +aiosignal = [] +annotated-types = [] +anyio = [] +appnope = [] +asttokens = [] +async-timeout = [] +attrs = [] +backcall = [] +certifi = [] +cffi = [] cfgv = [] +charset-normalizer = [] colorama = [] +comm = [] coverage = [] +dataclasses-json = [] +debugpy = [] +decorator = [] distlib = [] +dnspython = [] exceptiongroup = [] execnet = [] +executing = [] +fastjsonschema = [] filelock = [] +frozenlist = [] +fsspec = [] +greenlet = [] +huggingface-hub = [] identify = [] +idna = [] +importlib-metadata = [] iniconfig = [] +ipykernel = [] +ipython = [] +jedi = [] +jsonpatch = [] +jsonpointer = [] +jsonschema = [] +jsonschema-specifications = [] +jupyter-client = [] +jupyter-core = [] +langchain = [] +langsmith = [] +loguru = [] +marshmallow = [] +matplotlib-inline = [] +multidict = [] +mypy-extensions = [] +nbclient = [] +nbformat = [] +nbmake = [] +nest-asyncio = [] nodeenv = [] +numpy = [] +openai = [] packaging = [] +parso = [] +pexpect = [] +pickleshare = [] +pinecone-client = [] platformdirs = [] pluggy = [] pre-commit = [] +prompt-toolkit = [] +psutil = [] +ptyprocess = [] +pure-eval = [] py = [] +pycparser = [] +pydantic = [] +pydantic-core = [] +pygments = [] pytest = [] pytest-cov = [] pytest-forked = [] pytest-xdist = [] +python-dateutil = [] +pywin32 = [] pyyaml = [] +pyzmq = [] +referencing = [] +requests = [] +rpds-py = [] +six = [] +sniffio = [] +sqlalchemy = [] +stack-data = [] +tenacity = [] toml = [] tomli = [] +tornado = [] +tqdm = [] +traitlets = [] typing-extensions = [] +typing-inspect = [] +urllib3 = [] virtualenv = [] +wcwidth = [] +win32-setctime = [] +yarl = [] +zipp = [] diff --git a/pyproject.toml b/pyproject.toml index 6a5dd10..d1d6666 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,6 +13,10 @@ version = "v0.1" [tool.poetry.dependencies] pytest = ">=6.1.0" python = "^3.9.0" +pinecone-client = "^2.2.4" +langchain = "^0.0.311" +huggingface-hub = "^0.17.3" +openai = "^0.28.1" [tool.poetry.dev-dependencies] pytest = "^7.1.0" @@ -22,6 +26,7 @@ pytest-xdist = "^2.1.0" virtualenv = "^20.1.0" setuptools = ">65.0.0" typing-extensions = "^4.7.1" +nbmake = "^1.4.5" [build-system] build-backend = "poetry.core.masonry.api" diff --git a/scripts/setup-torchgeo.sh b/scripts/setup-torchgeo.sh new file mode 100755 index 0000000..641a480 --- /dev/null +++ b/scripts/setup-torchgeo.sh @@ -0,0 +1,8 @@ +#! /usr/bin/env bash + +set -e -u -o pipefail + +cd "$(dirname "$0")/.." + +cd tests/resources +poetry install \ No newline at end of file diff --git a/src/nbwrite/ex.py b/src/nbwrite/ex.py index b9bb5a1..c420018 100644 --- a/src/nbwrite/ex.py +++ b/src/nbwrite/ex.py @@ -1,3 +1,20 @@ +from langchain import PromptTemplate -def blah(): - return 1 \ No newline at end of file +template = """Question: {question} + +Answer: """ +prompt = PromptTemplate(template=template, input_variables=["question"]) + +# user question +question = "Which NFL team won the Super Bowl in the 2010 season?" + +import os + +from langchain.llms import OpenAI + +davinci = OpenAI(model_name="text-davinci-003") +from langchain import HuggingFaceHub, LLMChain + +llm_chain = LLMChain(prompt=prompt, llm=davinci) + +print(llm_chain.run(question)) diff --git a/tests/resources/poetry.lock b/tests/resources/poetry.lock new file mode 100644 index 0000000..a003868 --- /dev/null +++ b/tests/resources/poetry.lock @@ -0,0 +1,702 @@ +[[package]] +name = "appnope" +version = "0.1.3" +description = "Disable App Nap on macOS >= 10.9" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "asttokens" +version = "2.4.0" +description = "Annotate AST trees with source code positions" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +six = ">=1.12.0" + +[package.extras] +test = ["astroid", "pytest"] + +[[package]] +name = "attrs" +version = "23.1.0" +description = "Classes Without Boilerplate" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +cov = ["attrs", "coverage[toml] (>=5.3)"] +dev = ["attrs", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs", "zope-interface"] +tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest-mypy-plugins", "pytest-xdist", "pytest (>=4.3.0)"] + +[[package]] +name = "backcall" +version = "0.2.0" +description = "Specifications for callback functions passed in to an API" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "cffi" +version = "1.16.0" +description = "Foreign Function Interface for Python calling C code." +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +pycparser = "*" + +[[package]] +name = "colorama" +version = "0.4.6" +description = "Cross-platform colored terminal text." +category = "main" +optional = false +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" + +[[package]] +name = "comm" +version = "0.1.4" +description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +traitlets = ">=4" + +[package.extras] +lint = ["black (>=22.6.0)", "mdformat-gfm (>=0.3.5)", "mdformat (>0.7)", "ruff (>=0.0.156)"] +test = ["pytest"] +typing = ["mypy (>=0.990)"] + +[[package]] +name = "debugpy" +version = "1.8.0" +description = "An implementation of the Debug Adapter Protocol for Python" +category = "dev" +optional = false +python-versions = ">=3.8" + +[[package]] +name = "decorator" +version = "5.1.1" +description = "Decorators for Humans" +category = "dev" +optional = false +python-versions = ">=3.5" + +[[package]] +name = "exceptiongroup" +version = "1.1.3" +description = "Backport of PEP 654 (exception groups)" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +test = ["pytest (>=6)"] + +[[package]] +name = "executing" +version = "2.0.0" +description = "Get the currently executing AST node of a frame, and other information" +category = "dev" +optional = false +python-versions = "*" + +[package.extras] +tests = ["asttokens (>=2.1.0)", "ipython", "pytest", "coverage", "coverage-enable-subprocess", "littleutils", "rich"] + +[[package]] +name = "fastjsonschema" +version = "2.18.1" +description = "Fastest Python implementation of JSON schema" +category = "dev" +optional = false +python-versions = "*" + +[package.extras] +devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] + +[[package]] +name = "importlib-metadata" +version = "6.8.0" +description = "Read metadata from Python packages" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +zipp = ">=0.5" + +[package.extras] +docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] +perf = ["ipython"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] + +[[package]] +name = "iniconfig" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "ipykernel" +version = "6.25.2" +description = "IPython Kernel for Jupyter" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +appnope = {version = "*", markers = "platform_system == \"Darwin\""} +comm = ">=0.1.1" +debugpy = ">=1.6.5" +ipython = ">=7.23.1" +jupyter-client = ">=6.1.12" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +matplotlib-inline = ">=0.1" +nest-asyncio = "*" +packaging = "*" +psutil = "*" +pyzmq = ">=20" +tornado = ">=6.1" +traitlets = ">=5.4.0" + +[package.extras] +cov = ["coverage", "curio", "matplotlib", "pytest-cov", "trio"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"] +pyqt5 = ["pyqt5"] +pyside6 = ["pyside6"] +test = ["flaky", "ipyparallel", "pre-commit", "pytest-asyncio", "pytest-cov", "pytest-timeout", "pytest (>=7.0)"] + +[[package]] +name = "ipython" +version = "8.16.1" +description = "IPython: Productive Interactive Computing" +category = "dev" +optional = false +python-versions = ">=3.9" + +[package.dependencies] +appnope = {version = "*", markers = "sys_platform == \"darwin\""} +backcall = "*" +colorama = {version = "*", markers = "sys_platform == \"win32\""} +decorator = "*" +exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} +jedi = ">=0.16" +matplotlib-inline = "*" +pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} +pickleshare = "*" +prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0" +pygments = ">=2.4.0" +stack-data = "*" +traitlets = ">=5" +typing-extensions = {version = "*", markers = "python_version < \"3.10\""} + +[package.extras] +all = ["black", "ipykernel", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "docrepr", "matplotlib", "stack-data", "pytest (<7)", "typing-extensions", "exceptiongroup", "pytest (<7.1)", "pytest-asyncio", "testpath", "nbconvert", "nbformat", "ipywidgets", "notebook", "ipyparallel", "qtconsole", "curio", "matplotlib (!=3.2.0)", "numpy (>=1.21)", "pandas", "trio"] +black = ["black"] +doc = ["ipykernel", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "docrepr", "matplotlib", "stack-data", "pytest (<7)", "typing-extensions", "exceptiongroup", "pytest (<7.1)", "pytest-asyncio", "testpath"] +kernel = ["ipykernel"] +nbconvert = ["nbconvert"] +nbformat = ["nbformat"] +notebook = ["ipywidgets", "notebook"] +parallel = ["ipyparallel"] +qtconsole = ["qtconsole"] +test = ["pytest (<7.1)", "pytest-asyncio", "testpath"] +test_extra = ["pytest (<7.1)", "pytest-asyncio", "testpath", "curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "trio"] + +[[package]] +name = "jedi" +version = "0.19.1" +description = "An autocompletion tool for Python that can be used for text editors." +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +parso = 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+[package.dependencies] +attrs = ">=22.2.0" +jsonschema-specifications = ">=2023.03.6" +referencing = ">=0.28.4" +rpds-py = ">=0.7.1" + +[package.extras] +format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] +format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] + +[[package]] +name = "jsonschema-specifications" +version = "2023.7.1" +description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +referencing = ">=0.28.0" + +[[package]] +name = "jupyter-client" +version = "8.3.1" +description = "Jupyter protocol implementation and client libraries" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +importlib-metadata = {version = ">=4.8.3", markers = 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Formerly nbconvert's ExecutePreprocessor." +category = "dev" +optional = false +python-versions = ">=3.7.0" + +[package.dependencies] +jupyter-client = ">=6.1.5" +nbformat = ">=5.0" +nest-asyncio = "*" +traitlets = ">=5.2.2" + +[package.extras] +sphinx = ["autodoc-traits", "mock", "moto", "myst-parser", "Sphinx (>=1.7)", "sphinx-book-theme"] +test = ["black", "check-manifest", "flake8", "ipykernel", "ipython", "ipywidgets", "mypy", "nbconvert", "pip (>=18.1)", "pre-commit", "pytest (>=4.1)", "pytest-asyncio", "pytest-cov (>=2.6.1)", "setuptools (>=60.0)", "testpath", "twine (>=1.11.0)", "xmltodict"] + +[[package]] +name = "nbformat" +version = "5.9.2" +description = "The Jupyter Notebook format" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +fastjsonschema = "*" +jsonschema = ">=2.6" +jupyter-core = "*" +traitlets = ">=5.1" + +[package.extras] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] +test = ["pep440", "pre-commit", "pytest", "testpath"] + +[[package]] +name = "nbmake" +version = "1.4.5" +description = "Pytest plugin for testing notebooks" +category = "dev" +optional = false +python-versions = ">=3.7.0,<4.0.0" + +[package.dependencies] +ipykernel = ">=5.4.0" +nbclient = ">=0.6.6,<0.7.0" +nbformat = ">=5.0.8,<6.0.0" +Pygments = ">=2.7.3,<3.0.0" +pytest = ">=6.1.0" + +[[package]] +name = "nest-asyncio" +version = "1.5.8" +description = "Patch asyncio to allow nested event loops" +category = "dev" +optional = false +python-versions = ">=3.5" + +[[package]] +name = "packaging" +version = "23.2" +description = "Core utilities for Python packages" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "parso" +version = "0.8.3" +description = "A Python Parser" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.extras] +qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] +testing = ["docopt", "pytest (<6.0.0)"] + +[[package]] +name = "pexpect" +version = "4.8.0" +description = "Pexpect allows easy control of interactive console applications." +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +ptyprocess = ">=0.5" + +[[package]] +name = "pickleshare" +version = "0.7.5" +description = "Tiny 'shelve'-like database with concurrency support" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "platformdirs" +version = "3.11.0" +description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.24)", "sphinx (>=7.1.1)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest (>=7.4)"] + +[[package]] +name = "pluggy" +version = "1.3.0" +description = "plugin and hook calling mechanisms for python" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.extras] +dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] + +[[package]] +name = "prompt-toolkit" +version = "3.0.39" +description = "Library for building powerful interactive command lines in Python" +category = "dev" +optional = false +python-versions = ">=3.7.0" + +[package.dependencies] +wcwidth = "*" + +[[package]] +name = "psutil" +version = "5.9.5" +description = "Cross-platform lib for process and system monitoring in Python." +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[package.extras] +test = ["ipaddress", "mock", "enum34", "pywin32", "wmi"] + +[[package]] +name = "ptyprocess" +version = "0.7.0" +description = "Run a subprocess in a pseudo terminal" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "pure-eval" +version = "0.2.2" +description = "Safely evaluate AST nodes without side effects" +category = "dev" +optional = false +python-versions = "*" + +[package.extras] +tests = ["pytest"] + +[[package]] +name = "pycparser" +version = "2.21" +description = "C parser in Python" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[[package]] +name = "pygments" +version = "2.16.1" +description = "Pygments is a syntax highlighting package written in Python." +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +plugins = ["importlib-metadata"] + +[[package]] +name = "pytest" +version = "7.4.2" +description = "pytest: simple powerful testing with Python" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +colorama = {version = "*", markers = "sys_platform == \"win32\""} +exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} +iniconfig = "*" +packaging = "*" +pluggy = ">=0.12,<2.0" +tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} + +[package.extras] +testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] + +[[package]] +name = "python-dateutil" +version = "2.8.2" +description = "Extensions to the standard Python datetime module" +category = "dev" +optional = false +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" + +[package.dependencies] +six = ">=1.5" + +[[package]] +name = "pywin32" +version = "306" +description = "Python for Window Extensions" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "pyzmq" +version = "25.1.1" +description = "Python bindings for 0MQ" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +cffi = {version = "*", markers = "implementation_name == \"pypy\""} + +[[package]] +name = "referencing" +version = "0.30.2" +description = "JSON Referencing + Python" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +attrs = ">=22.2.0" +rpds-py = ">=0.7.0" + +[[package]] +name = "rpds-py" +version = "0.10.4" +description = "Python bindings to Rust's persistent data structures (rpds)" +category = "dev" +optional = false +python-versions = ">=3.8" + +[[package]] +name = "six" +version = "1.16.0" +description = "Python 2 and 3 compatibility utilities" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" + +[[package]] +name = "stack-data" +version = "0.6.3" +description = "Extract data from python stack frames and tracebacks for informative displays" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +asttokens = ">=2.1.0" +executing = ">=1.2.0" +pure-eval = "*" + +[package.extras] +tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"] + +[[package]] +name = "tomli" +version = "2.0.1" +description = "A lil' TOML parser" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "tornado" +version = "6.3.3" +description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." +category = "dev" +optional = false +python-versions = ">= 3.8" + +[[package]] +name = "traitlets" +version = "5.11.2" +description = "Traitlets Python configuration system" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.extras] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] +test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest-mock", "pytest-mypy-testing", "pytest (>=7.0,<7.5)"] + +[[package]] +name = "typing-extensions" +version = "4.8.0" +description = "Backported and Experimental Type Hints for Python 3.8+" +category = "dev" +optional = false +python-versions = ">=3.8" + +[[package]] +name = "wcwidth" +version = "0.2.8" +description = "Measures the displayed width of unicode strings in a terminal" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "zipp" +version = "3.17.0" +description = "Backport of pathlib-compatible object wrapper for zip files" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.extras] +docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "jaraco.itertools", "jaraco.functools", "more-itertools", "big-o", "pytest-ignore-flaky", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] + +[metadata] +lock-version = "1.1" +python-versions = "^3.9.0" +content-hash = "4d06c9090f81c5368171f275d4977bf79f1180d21e61d0bf2df02be1c393a0c6" + +[metadata.files] +appnope = [] +asttokens = [] +attrs = [] +backcall = [] +cffi = [] +colorama = [] +comm = [] +debugpy = [] +decorator = [] +exceptiongroup = [] +executing = [] +fastjsonschema = [] +importlib-metadata = [] +iniconfig = [] +ipykernel = [] +ipython = [] +jedi = [] +jsonschema = [] +jsonschema-specifications = [] +jupyter-client = [] +jupyter-core = [] +matplotlib-inline = [] +nbclient = [] +nbformat = [] +nbmake = [] +nest-asyncio = [] +packaging = [] +parso = [] +pexpect = [] +pickleshare = [] +platformdirs = [] +pluggy = [] +prompt-toolkit = [] +psutil = [] +ptyprocess = [] +pure-eval = [] +pycparser = [] +pygments = [] +pytest = [] +python-dateutil = [] +pywin32 = [] +pyzmq = [] +referencing = [] +rpds-py = [] +six = [] +stack-data = [] +tomli = [] +tornado = [] +traitlets = [] +typing-extensions = [] +wcwidth = [] +zipp = [] diff --git a/tests/resources/poetry.toml b/tests/resources/poetry.toml new file mode 100644 index 0000000..91b4cd5 --- /dev/null +++ b/tests/resources/poetry.toml @@ -0,0 +1,3 @@ +[virtualenvs] +create = true +path = '.testvenv' diff --git a/tests/resources/pyproject.toml b/tests/resources/pyproject.toml new file mode 100644 index 0000000..f30a5af --- /dev/null +++ b/tests/resources/pyproject.toml @@ -0,0 +1,18 @@ +[tool.poetry] +authors = ["alex-treebeard "] +description = "" +homepage = "https://github.com/treebeardtech/nbwrite" +license = "Apache-2.0" +name = "test" +version = "v0.1" + +[tool.poetry.dependencies] +pytest = ">=6.1.0" +python = "^3.9.0" + +[tool.poetry.dev-dependencies] +nbmake = "^1.4.5" + +[build-system] +build-backend = "poetry.core.masonry.api" +requires = ["setuptools", "poetry-core>=1.0.0"] diff --git a/tests/test_ex.py b/tests/test_ex.py index 637f0b4..e3d8d8b 100644 --- a/tests/test_ex.py +++ b/tests/test_ex.py @@ -1,4 +1,11 @@ +import nbmake + from nbwrite import ex -def test_ex(): - assert ex.blah() == 1 \ No newline at end of file + +def test_when_index_then_build_index(): + assert ex.question == "Which NFL team won the Super Bowl in the 2010 season?" + + +def test_when_gen_nbrun_doc_then_nb_output(): + assert ex.question == "Which NFL team won the Super Bowl in the 2010 season?" From c381b023c0fabfb1b538d027a7e7b180cf2edb1e Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 10 Oct 2023 10:50:21 +0000 Subject: [PATCH 04/59] test setup --- .devcontainer/devcontainer.json | 4 ++++ poetry.lock | 27 ++++++++++++++++++++++++++- pyproject.toml | 1 + src/nbwrite/ex.py | 15 +++++++++++++++ 4 files changed, 46 insertions(+), 1 deletion(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index e939cd2..4e4ddb6 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -34,6 +34,10 @@ ] } }, + // "containerEnv": { + // "OPENAI_API_KEY": "${localEnv:OPENAI_API_KEY}", + // "PINECONE_API_KEY": "${localEnv:PINECONE_API_KEY}" + // }, "features": { "ghcr.io/devcontainers/features/docker-in-docker:2": {}, "ghcr.io/devcontainers-contrib/features/starship:1": {}, diff --git a/poetry.lock b/poetry.lock index 92d6a75..4e03d10 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1012,6 +1012,18 @@ toml = "*" [package.extras] testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"] +[[package]] +name = "pytest-dotenv" +version = "0.5.2" +description = "A py.test plugin that parses environment files before running tests" +category = "dev" +optional = false +python-versions = "*" + +[package.dependencies] +pytest = ">=5.0.0" +python-dotenv = ">=0.9.1" + [[package]] name = "pytest-forked" version = "1.6.0" @@ -1053,6 +1065,17 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" [package.dependencies] six = ">=1.5" +[[package]] +name = "python-dotenv" +version = "1.0.0" +description = "Read key-value pairs from a .env file and set them as environment variables" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.extras] +cli = ["click (>=5.0)"] + [[package]] name = "pywin32" version = "306" @@ -1347,7 +1370,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-ena [metadata] lock-version = "1.1" python-versions = "^3.9.0" -content-hash = "7e1aad872a330b447d5c55e8ef688f7fd5aa6113aeb086b4c33418c53a710b69" +content-hash = "d381e745fc6cb47e1c8b007e690598d4c161c7664c4f7af275373dadabe56172" [metadata.files] aiohttp = [] @@ -1426,9 +1449,11 @@ pydantic-core = [] pygments = [] pytest = [] pytest-cov = [] +pytest-dotenv = [] pytest-forked = [] pytest-xdist = [] python-dateutil = [] +python-dotenv = [] pywin32 = [] pyyaml = [] pyzmq = [] diff --git a/pyproject.toml b/pyproject.toml index d1d6666..e334309 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,6 +27,7 @@ virtualenv = "^20.1.0" setuptools = ">65.0.0" typing-extensions = "^4.7.1" nbmake = "^1.4.5" +pytest-dotenv = "^0.5.2" [build-system] build-backend = "poetry.core.masonry.api" diff --git a/src/nbwrite/ex.py b/src/nbwrite/ex.py index c420018..cbfa6c9 100644 --- a/src/nbwrite/ex.py +++ b/src/nbwrite/ex.py @@ -18,3 +18,18 @@ llm_chain = LLMChain(prompt=prompt, llm=davinci) print(llm_chain.run(question)) + +import pinecone + +pinecone.init(api_key=os.environ["PINECONE_API_KEY"], environment="gcp-starter") +index = pinecone.Index("nbwrite") + +index.upsert( + [ + ("A", [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]), + ("B", [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2]), + ("C", [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3]), + ("D", [0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4]), + ("E", [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]), + ] +) From ac4bf6887d9de7ac07d1df0469ea721f2b2157e2 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 10 Oct 2023 11:50:34 +0000 Subject: [PATCH 05/59] openai example --- .pre-commit-config.yaml | 18 +- poetry.lock | 664 ++++++++++++++------------------- pyproject.toml | 12 +- src/nbwrite/ex.py | 46 +-- src/nbwrite/example.py | 0 src/nbwrite/example_helpers.py | 72 ++++ tests/test_ex.py | 52 +++ 7 files changed, 438 insertions(+), 426 deletions(-) create mode 100644 src/nbwrite/example.py create mode 100644 src/nbwrite/example_helpers.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e5b1ddd..d33ab01 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,15 +23,15 @@ repos: hooks: - id: isort args: ["-m", "3", "--tc"] - - repo: local - hooks: - - id: pyright - name: pyright - entry: poetry run pyright - language: node - pass_filenames: false - types: [python] - additional_dependencies: ["pyright@1.1.91"] + # - repo: local + # hooks: + # - id: pyright + # name: pyright + # entry: poetry run pyright + # language: node + # pass_filenames: false + # types: [python] + # additional_dependencies: ["pyright@1.1.91"] # - repo: local # hooks: # - id: smoketest diff --git a/poetry.lock b/poetry.lock index 4e03d10..355f983 100644 --- a/poetry.lock +++ b/poetry.lock @@ -29,32 +29,6 @@ python-versions = ">=3.7" [package.dependencies] frozenlist = ">=1.1.0" -[[package]] -name = "annotated-types" -version = "0.6.0" -description = "Reusable constraint types to use with typing.Annotated" -category = "main" -optional = false -python-versions = ">=3.8" - -[[package]] -name = "anyio" -version = "3.7.1" -description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} -idna = ">=2.8" -sniffio = ">=1.1" - -[package.extras] -doc = ["packaging", "sphinx", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquery", "sphinx-autodoc-typehints (>=1.2.0)"] -test = ["anyio", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)", "mock (>=4)"] -trio = ["trio (<0.22)"] - [[package]] name = "appnope" version = "0.1.3" @@ -167,6 +141,24 @@ lint = ["black (>=22.6.0)", "mdformat-gfm (>=0.3.5)", "mdformat (>0.7)", "ruff ( test = ["pytest"] typing = ["mypy (>=0.990)"] +[[package]] +name = "contourpy" +version = "1.1.1" +description = "Python library for calculating contours of 2D quadrilateral grids" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +numpy = {version = ">=1.16,<2.0", markers = "python_version <= \"3.11\""} + +[package.extras] +docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"] +bokeh = ["bokeh", "selenium"] +mypy = ["contourpy", "docutils-stubs", "mypy (==1.4.1)", "types-pillow"] +test = ["contourpy", "matplotlib", "pillow"] +test-no-images = ["pytest", "pytest-cov", "wurlitzer"] + [[package]] name = "coverage" version = "7.3.2" @@ -179,16 +171,16 @@ python-versions = ">=3.8" toml = ["tomli"] [[package]] -name = "dataclasses-json" -version = "0.6.1" -description = "Easily serialize dataclasses to and from JSON." +name = "cycler" +version = "0.12.1" +description = "Composable style cycles" category = "main" optional = false -python-versions = ">=3.7,<4.0" +python-versions = ">=3.8" -[package.dependencies] -marshmallow = ">=3.18.0,<4.0.0" -typing-inspect = ">=0.4.0,<1" +[package.extras] +docs = ["ipython", "matplotlib", "numpydoc", "sphinx"] +tests = ["pytest", "pytest-cov", "pytest-xdist"] [[package]] name = "debugpy" @@ -215,31 +207,12 @@ optional = false python-versions = "*" [[package]] -name = "dnspython" -version = "2.4.2" -description = "DNS toolkit" -category = "main" -optional = false -python-versions = ">=3.8,<4.0" - -[package.extras] -doq = ["aioquic (>=0.9.20)"] -dnssec = ["cryptography (>=2.6,<42.0)"] -doh = ["h2 (>=4.1.0)", "httpcore (>=0.17.3)", "httpx (>=0.24.1)"] -idna = ["idna (>=2.1,<4.0)"] -trio = ["trio (>=0.14,<0.23)"] -wmi = ["wmi (>=1.5.1,<2.0.0)"] - -[[package]] -name = "exceptiongroup" -version = "1.1.3" -description = "Backport of PEP 654 (exception groups)" +name = "et-xmlfile" +version = "1.1.0" +description = "An implementation of lxml.xmlfile for the standard library" category = "main" optional = false -python-versions = ">=3.7" - -[package.extras] -test = ["pytest (>=6)"] +python-versions = ">=3.6" [[package]] name = "execnet" @@ -278,7 +251,7 @@ devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benc name = "filelock" version = "3.12.4" description = "A platform independent file lock." -category = "main" +category = "dev" optional = false python-versions = ">=3.8" @@ -288,86 +261,34 @@ testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pyt typing = ["typing-extensions (>=4.7.1)"] [[package]] -name = "frozenlist" -version = "1.4.0" -description = "A list-like structure which implements collections.abc.MutableSequence" +name = "fonttools" +version = "4.43.1" +description = "Tools to manipulate font files" category = "main" optional = false python-versions = ">=3.8" -[[package]] -name = "fsspec" -version = "2023.9.2" -description = "File-system specification" -category = "main" -optional = false -python-versions = ">=3.8" - -[package.extras] -abfs = ["adlfs"] -adl = ["adlfs"] -arrow = ["pyarrow (>=1)"] -dask = ["dask", "distributed"] -devel = ["pytest", "pytest-cov"] -dropbox = ["dropboxdrivefs", "requests", "dropbox"] -full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"] -fuse = ["fusepy"] -gcs = ["gcsfs"] -git = ["pygit2"] -github = ["requests"] -gs = ["gcsfs"] -gui = ["panel"] -hdfs = ["pyarrow (>=1)"] -http = ["requests", "aiohttp (!=4.0.0a0,!=4.0.0a1)"] -libarchive = ["libarchive-c"] -oci = ["ocifs"] -s3 = ["s3fs"] -sftp = ["paramiko"] -smb = ["smbprotocol"] -ssh = ["paramiko"] -tqdm = ["tqdm"] - -[[package]] -name = "greenlet" -version = "3.0.0" -description = "Lightweight in-process concurrent programming" -category = "main" -optional = false -python-versions = ">=3.7" - [package.extras] -docs = ["sphinx"] -test = ["objgraph", "psutil"] +all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=15.0.0)", "xattr"] +graphite = ["lz4 (>=1.7.4.2)"] +interpolatable = ["scipy", "munkres"] +lxml = ["lxml (>=4.0,<5)"] +pathops = ["skia-pathops (>=0.5.0)"] +plot = ["matplotlib"] +repacker = ["uharfbuzz (>=0.23.0)"] +symfont = ["sympy"] +type1 = ["xattr"] +ufo = ["fs (>=2.2.0,<3)"] +unicode = ["unicodedata2 (>=15.0.0)"] +woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"] [[package]] -name = "huggingface-hub" -version = "0.17.3" -description = "Client library to download and publish models, datasets and other repos on the huggingface.co hub" +name = "frozenlist" +version = "1.4.0" +description = "A list-like structure which implements collections.abc.MutableSequence" category = "main" optional = false -python-versions = ">=3.8.0" - -[package.dependencies] -filelock = "*" -fsspec = "*" -packaging = ">=20.9" -pyyaml = ">=5.1" 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"pytest-xdist", "pytest-vcr", "pytest-asyncio", "urllib3 (<2.0)", "soundfile", "pillow", "gradio", "numpy", "black (==23.7)", "ruff (>=0.0.241)", "mypy (==1.5.1)", "types-pyyaml", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "hf-doc-builder", "watchdog"] -fastai = ["toml", "fastai (>=2.4)", "fastcore (>=1.3.27)"] -inference = ["aiohttp", "pydantic (<2.0)"] -quality = ["black (==23.7)", "ruff (>=0.0.241)", "mypy (==1.5.1)"] -tensorflow = ["tensorflow", "pydot", "graphviz"] -testing = ["InquirerPy (==0.3.4)", "aiohttp", "pydantic (<2.0)", "jedi", "jinja2", "pytest", "pytest-cov", "pytest-env", "pytest-xdist", "pytest-vcr", "pytest-asyncio", "urllib3 (<2.0)", "soundfile", "pillow", "gradio", "numpy"] -torch = ["torch"] -typing = ["types-pyyaml", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "pydantic (<2.0)"] +python-versions = ">=3.8" [[package]] name = "identify" @@ -388,22 +309,6 @@ category = "main" optional = false python-versions = ">=3.5" -[[package]] -name = "importlib-metadata" -version = "6.8.0" -description = "Read metadata from Python packages" -category = "dev" -optional = false -python-versions = ">=3.8" - -[package.dependencies] -zipp = ">=0.5" - -[package.extras] -docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] -perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] - [[package]] name = "iniconfig" version = "2.0.0" @@ -455,7 +360,6 @@ appnope = {version = "*", markers = "sys_platform == \"darwin\""} backcall = "*" colorama = {version = "*", markers = "sys_platform == \"win32\""} decorator = "*" -exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} jedi = ">=0.16" matplotlib-inline = "*" pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} @@ -464,7 +368,6 @@ prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0" pygments = ">=2.4.0" stack-data = "*" traitlets = ">=5" -typing-extensions = {version = "*", markers = "python_version < \"3.10\""} [package.extras] all = ["black", "ipykernel", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "docrepr", "matplotlib", "stack-data", "pytest (<7)", "typing-extensions", "exceptiongroup", "pytest (<7.1)", "pytest-asyncio", "testpath", "nbconvert", "nbformat", "ipywidgets", "notebook", "ipyparallel", "qtconsole", "curio", "matplotlib (!=3.2.0)", "numpy (>=1.21)", "pandas", "trio"] @@ -496,23 +399,12 @@ qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"] testing = ["django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] [[package]] -name = "jsonpatch" -version = "1.33" -description = "Apply JSON-Patches (RFC 6902)" +name = "joblib" +version = "1.3.2" +description = "Lightweight pipelining with Python functions" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" - -[package.dependencies] -jsonpointer = ">=1.9" - -[[package]] -name = "jsonpointer" -version = "2.4" -description = "Identify specific nodes in a JSON document (RFC 6901)" -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" +python-versions = ">=3.7" [[package]] name = "jsonschema" @@ -552,7 +444,6 @@ optional = false python-versions = ">=3.8" [package.dependencies] -importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" @@ -581,85 +472,32 @@ docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", " test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] [[package]] -name 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"mypy (==1.4.1)", "flake8 (==6.0.0)", "flake8-bugbear (==23.7.10)", "pre-commit (>=2.4,<4.0)", "tox"] -docs = ["sphinx (==7.0.1)", "sphinx-issues (==3.0.1)", "alabaster (==0.7.13)", "sphinx-version-warning (==1.1.2)", "autodocsumm (==0.2.11)"] -lint = ["mypy (==1.4.1)", "flake8 (==6.0.0)", "flake8-bugbear (==23.7.10)", "pre-commit (>=2.4,<4.0)"] -tests = ["pytest", "pytz", "simplejson"] +contourpy = ">=1.0.1" +cycler = ">=0.10" +fonttools = ">=4.22.0" +kiwisolver = ">=1.0.1" +numpy = ">=1.21,<2" +packaging = ">=20.0" +pillow = ">=6.2.0" +pyparsing = ">=2.3.1" +python-dateutil = ">=2.7" +setuptools_scm = ">=7" [[package]] name = "matplotlib-inline" @@ -680,14 +518,6 @@ category = "main" optional = false python-versions = ">=3.7" -[[package]] -name = "mypy-extensions" -version = "1.0.0" -description = "Type system extensions for programs checked with the mypy type checker." -category = "main" -optional = false -python-versions = ">=3.5" - [[package]] name = "nbclient" version = "0.6.8" @@ -757,11 +587,11 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.* [[package]] name = "numpy" -version = "1.25.2" +version = "1.26.0" description = "Fundamental package for array computing in Python" category = "main" optional = false -python-versions = ">=3.9" +python-versions = "<3.13,>=3.9" [[package]] name = "openai" @@ -773,7 +603,16 @@ python-versions = ">=3.7.1" [package.dependencies] aiohttp = "*" +matplotlib = {version = "*", optional = true, markers = "extra == \"embeddings\""} +numpy = {version = "*", optional = true, markers = "extra == \"embeddings\""} +openpyxl = {version = ">=3.0.7", optional = true, markers = "extra == \"embeddings\""} +pandas = {version = ">=1.2.3", optional = true, markers = "extra == \"embeddings\""} +pandas-stubs = {version = ">=1.1.0.11", optional = true, markers = "extra == \"embeddings\""} +plotly = {version = "*", optional = true, markers = "extra == \"embeddings\""} requests = ">=2.20" +scikit-learn = {version = ">=1.0.2", optional = true, markers = "extra == \"embeddings\""} +scipy = {version = "*", optional = true, markers = "extra == \"embeddings\""} +tenacity = {version = ">=8.0.1", optional = true, markers = "extra == \"embeddings\""} tqdm = "*" [package.extras] @@ -782,6 +621,17 @@ dev = ["black (>=21.6b0,<22.0.0)", "pytest (>=6.0.0,<7.0.0)", "pytest-asyncio", embeddings = ["scikit-learn (>=1.0.2)", "tenacity (>=8.0.1)", "matplotlib", "plotly", "numpy", "scipy", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)", "openpyxl (>=3.0.7)"] wandb = ["wandb", "numpy", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)", "openpyxl (>=3.0.7)"] +[[package]] +name = "openpyxl" +version = "3.1.2" +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +et-xmlfile = "*" + [[package]] name = "packaging" version = "23.2" @@ -790,6 +640,56 @@ category = "main" optional = false python-versions = ">=3.7" +[[package]] +name = "pandas" +version = "2.1.1" +description = "Powerful data structures for data analysis, time series, and statistics" +category = "main" +optional = false +python-versions = ">=3.9" + +[package.dependencies] +numpy = {version = ">=1.23.2", markers = "python_version == \"3.11\""} +python-dateutil = ">=2.8.2" +pytz = ">=2020.1" +tzdata = ">=2022.1" + +[package.extras] +test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)", "pytest-asyncio (>=0.17.0)"] +performance = ["bottleneck (>=1.3.4)", "numba (>=0.55.2)", "numexpr (>=2.8.0)"] +computation = ["scipy (>=1.8.1)", "xarray (>=2022.03.0)"] +fss = ["fsspec (>=2022.05.0)"] +aws = ["s3fs (>=2022.05.0)"] +gcp = ["gcsfs (>=2022.05.0)", "pandas-gbq (>=0.17.5)"] +excel = ["odfpy (>=1.4.1)", "openpyxl (>=3.0.10)", "pyxlsb (>=1.0.9)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.3)"] +parquet = ["pyarrow (>=7.0.0)"] +feather = ["pyarrow (>=7.0.0)"] +hdf5 = ["tables (>=3.7.0)"] +spss = ["pyreadstat (>=1.1.5)"] +postgresql = ["SQLAlchemy (>=1.4.36)", "psycopg2 (>=2.9.3)"] +mysql = ["SQLAlchemy (>=1.4.36)", "pymysql (>=1.0.2)"] +sql-other = ["SQLAlchemy (>=1.4.36)"] +html = ["beautifulsoup4 (>=4.11.1)", "html5lib (>=1.1)", "lxml (>=4.8.0)"] +xml = ["lxml (>=4.8.0)"] +plot = ["matplotlib (>=3.6.1)"] +output-formatting = ["jinja2 (>=3.1.2)", "tabulate (>=0.8.10)"] +clipboard = ["PyQt5 (>=5.15.6)", "qtpy (>=2.2.0)"] +compression = ["zstandard (>=0.17.0)"] +consortium-standard = ["dataframe-api-compat (>=0.1.7)"] +all = ["beautifulsoup4 (>=4.11.1)", "bottleneck (>=1.3.4)", "dataframe-api-compat (>=0.1.7)", "fastparquet (>=0.8.1)", "fsspec (>=2022.05.0)", "gcsfs (>=2022.05.0)", "html5lib (>=1.1)", "hypothesis (>=6.46.1)", "jinja2 (>=3.1.2)", "lxml (>=4.8.0)", "matplotlib (>=3.6.1)", "numba (>=0.55.2)", "numexpr (>=2.8.0)", "odfpy (>=1.4.1)", "openpyxl (>=3.0.10)", "pandas-gbq (>=0.17.5)", "psycopg2 (>=2.9.3)", "pyarrow (>=7.0.0)", "pymysql (>=1.0.2)", "PyQt5 (>=5.15.6)", "pyreadstat (>=1.1.5)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)", "pytest-asyncio (>=0.17.0)", "pyxlsb (>=1.0.9)", "qtpy (>=2.2.0)", "scipy (>=1.8.1)", "s3fs (>=2022.05.0)", "SQLAlchemy (>=1.4.36)", "tables (>=3.7.0)", "tabulate (>=0.8.10)", "xarray (>=2022.03.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.3)", "zstandard (>=0.17.0)"] + +[[package]] +name = "pandas-stubs" +version = "2.1.1.230928" +description = "Type annotations for pandas" +category = "main" +optional = false +python-versions = ">=3.9" + +[package.dependencies] +numpy = {version = ">=1.26.0", markers = "python_version < \"3.13\""} +types-pytz = ">=2022.1.1" + [[package]] name = "parso" version = "0.8.3" @@ -802,6 +702,14 @@ python-versions = ">=3.6" qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] testing = ["docopt", "pytest (<6.0.0)"] +[[package]] +name = "pathlib" +version = "1.0.1" +description = "Object-oriented filesystem paths" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "pexpect" version = "4.8.0" @@ -822,26 +730,16 @@ optional = false python-versions = "*" [[package]] -name = "pinecone-client" -version = "2.2.4" -description = "Pinecone client and SDK" +name = "pillow" +version = "10.0.1" +description = "Python Imaging Library (Fork)" category = "main" optional = false python-versions = ">=3.8" -[package.dependencies] -dnspython = ">=2.0.0" -loguru = ">=0.5.0" -numpy = ">=1.22.0" -python-dateutil = ">=2.5.3" -pyyaml = ">=5.4" -requests = ">=2.19.0" -tqdm = ">=4.64.1" -typing-extensions = ">=3.7.4" -urllib3 = ">=1.21.1" - [package.extras] -grpc = ["grpcio (>=1.44.0)", "grpc-gateway-protoc-gen-openapiv2 (==0.1.0)", "googleapis-common-protos (>=1.53.0)", "lz4 (>=3.1.3)", "protobuf (>=3.20.0,<3.21.0)"] +docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"] +tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] [[package]] name = "platformdirs" @@ -855,6 +753,18 @@ python-versions = ">=3.7" docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.24)", "sphinx (>=7.1.1)"] test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest (>=7.4)"] +[[package]] +name = "plotly" +version = "5.17.0" +description = "An open-source, interactive data visualization library for Python" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +packaging = "*" +tenacity = ">=6.2.0" + [[package]] name = "pluggy" version = "1.3.0" @@ -940,42 +850,26 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] -name = "pydantic" -version = "2.4.2" -description = "Data validation using Python type hints" -category = "main" +name = "pygments" +version = "2.16.1" +description = "Pygments is a syntax highlighting package written in Python." +category = "dev" optional = false python-versions = ">=3.7" -[package.dependencies] -annotated-types = ">=0.4.0" -pydantic-core = "2.10.1" -typing-extensions = ">=4.6.1" - [package.extras] -email = ["email-validator (>=2.0.0)"] +plugins = ["importlib-metadata"] [[package]] -name = "pydantic-core" -version = "2.10.1" -description = "" +name = "pyparsing" +version = "3.1.1" +description = "pyparsing module - Classes and methods to define and execute parsing grammars" category = "main" optional = false -python-versions = ">=3.7" - -[package.dependencies] -typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0" - -[[package]] -name = "pygments" -version = "2.16.1" -description = "Pygments is a syntax highlighting package written in Python." -category = "dev" -optional = false -python-versions = ">=3.7" +python-versions = ">=3.6.8" [package.extras] -plugins = ["importlib-metadata"] +diagrams = ["railroad-diagrams", "jinja2"] [[package]] name = "pytest" @@ -987,11 +881,9 @@ python-versions = ">=3.7" [package.dependencies] colorama = {version = "*", markers = "sys_platform == \"win32\""} -exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} iniconfig = "*" packaging = "*" pluggy = ">=0.12,<2.0" -tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] @@ -1076,6 +968,14 @@ python-versions = ">=3.8" [package.extras] cli = ["click (>=5.0)"] +[[package]] +name = "pytz" +version = "2023.3.post1" +description = "World timezone definitions, modern and historical" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "pywin32" version = "306" @@ -1088,7 +988,7 @@ python-versions = "*" name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" -category = "main" +category = "dev" optional = false python-versions = ">=3.6" @@ -1142,56 +1042,65 @@ optional = false python-versions = ">=3.8" [[package]] -name = "six" -version = "1.16.0" -description = "Python 2 and 3 compatibility utilities" +name = "scikit-learn" +version = "1.3.1" +description = "A set of python modules for machine learning and data mining" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" +python-versions = ">=3.8" + +[package.dependencies] +joblib = ">=1.1.1" +numpy = ">=1.17.3,<2.0" +scipy = ">=1.5.0" +threadpoolctl = ">=2.0.0" + +[package.extras] +benchmark = ["matplotlib (>=3.1.3)", "pandas (>=1.0.5)", "memory-profiler (>=0.57.0)"] +docs = ["matplotlib (>=3.1.3)", "scikit-image (>=0.16.2)", "pandas (>=1.0.5)", "seaborn (>=0.9.0)", "memory-profiler (>=0.57.0)", "sphinx (>=6.0.0)", "sphinx-copybutton (>=0.5.2)", "sphinx-gallery (>=0.10.1)", "numpydoc (>=1.2.0)", "Pillow (>=7.1.2)", "pooch (>=1.6.0)", "sphinx-prompt (>=1.3.0)", "sphinxext-opengraph (>=0.4.2)", "plotly (>=5.14.0)"] +examples = ["matplotlib (>=3.1.3)", "scikit-image (>=0.16.2)", "pandas (>=1.0.5)", "seaborn (>=0.9.0)", "pooch (>=1.6.0)", "plotly (>=5.14.0)"] +tests = ["matplotlib (>=3.1.3)", "scikit-image (>=0.16.2)", "pandas (>=1.0.5)", "pytest (>=7.1.2)", "pytest-cov (>=2.9.0)", "ruff (>=0.0.272)", "black (>=23.3.0)", "mypy (>=1.3)", "pyamg (>=4.0.0)", "numpydoc (>=1.2.0)", "pooch (>=1.6.0)"] [[package]] -name = "sniffio" -version = "1.3.0" -description = "Sniff out which async library your code is running under" +name = "scipy" +version = "1.11.3" +description = "Fundamental algorithms for scientific computing in Python" category = "main" optional = false -python-versions = ">=3.7" +python-versions = "<3.13,>=3.9" + +[package.dependencies] +numpy = ">=1.21.6,<1.28.0" + +[package.extras] +test = ["pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack", "pooch"] +doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-design (>=0.2.0)", "matplotlib (>2)", "numpydoc", "jupytext", "myst-nb", "pooch"] +dev = ["mypy", "typing-extensions", "types-psutil", "pycodestyle", "ruff", "cython-lint (>=0.12.2)", "rich-click", "click", "doit (>=0.36.0)", "pydevtool"] [[package]] -name = "sqlalchemy" -version = "2.0.21" -description = "Database Abstraction Library" +name = "setuptools-scm" +version = "8.0.4" +description = "the blessed package to manage your versions by scm tags" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""} -typing-extensions = ">=4.2.0" +packaging = ">=20" +typing-extensions = "*" [package.extras] -aiomysql = ["greenlet (!=0.4.17)", "aiomysql (>=0.2.0)"] -aiosqlite = ["greenlet (!=0.4.17)", "aiosqlite", "typing-extensions (!=3.10.0.1)"] -asyncio = ["greenlet (!=0.4.17)"] -asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)"] -mariadb_connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"] -mssql = ["pyodbc"] -mssql_pymssql = ["pymssql"] -mssql_pyodbc = ["pyodbc"] -mypy = ["mypy (>=0.910)"] -mysql = ["mysqlclient (>=1.4.0)"] -mysql_connector = ["mysql-connector-python"] -oracle = ["cx-oracle (>=7)"] -oracle_oracledb = ["oracledb (>=1.0.1)"] -postgresql = ["psycopg2 (>=2.7)"] -postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"] -postgresql_pg8000 = ["pg8000 (>=1.29.1)"] -postgresql_psycopg = ["psycopg (>=3.0.7)"] -postgresql_psycopg2binary = ["psycopg2-binary"] -postgresql_psycopg2cffi = ["psycopg2cffi"] -postgresql_psycopgbinary = ["psycopg[binary] (>=3.0.7)"] -pymysql = ["pymysql"] -sqlcipher = ["sqlcipher3-binary"] +docs = ["entangled-cli", "mkdocs", "mkdocs-entangled-plugin", "mkdocs-material", "mkdocstrings", "pygments"] +rich = ["rich"] +test = ["build", "pytest", "rich", "wheel"] + +[[package]] +name = "six" +version = "1.16.0" +description = "Python 2 and 3 compatibility utilities" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "stack-data" @@ -1220,6 +1129,14 @@ python-versions = ">=3.7" [package.extras] doc = ["reno", "sphinx", "tornado (>=4.5)"] +[[package]] +name = "threadpoolctl" +version = "3.2.0" +description = "threadpoolctl" +category = "main" +optional = false +python-versions = ">=3.8" + [[package]] name = "toml" version = "0.10.2" @@ -1228,14 +1145,6 @@ category = "dev" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" -[[package]] -name = "tomli" -version = "2.0.1" -description = "A lil' TOML parser" -category = "main" -optional = false -python-versions = ">=3.7" - [[package]] name = "tornado" version = "6.3.3" @@ -1273,6 +1182,14 @@ python-versions = ">=3.8" docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest-mock", "pytest-mypy-testing", "pytest (>=7.0,<7.5)"] +[[package]] +name = "types-pytz" +version = "2023.3.1.1" +description = "Typing stubs for pytz" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "typing-extensions" version = "4.8.0" @@ -1282,16 +1199,12 @@ optional = false python-versions = ">=3.8" [[package]] -name = "typing-inspect" -version = "0.9.0" -description = "Runtime inspection utilities for typing module." +name = "tzdata" +version = "2023.3" +description = "Provider of IANA time zone data" category = "main" optional = false -python-versions = "*" - -[package.dependencies] -mypy-extensions = ">=0.3.0" -typing-extensions = ">=3.7.4" +python-versions = ">=2" [[package]] name = "urllib3" @@ -1332,17 +1245,6 @@ category = "dev" optional = false python-versions = "*" -[[package]] -name = "win32-setctime" -version = "1.1.0" -description = "A small Python utility to set file creation time on Windows" -category = "main" -optional = false -python-versions = ">=3.5" - -[package.extras] -dev = ["pytest (>=4.6.2)", "black (>=19.3b0)"] - [[package]] name = "yarl" version = "1.9.2" @@ -1355,28 +1257,14 @@ python-versions = ">=3.7" idna = ">=2.0" multidict = ">=4.0" -[[package]] -name = "zipp" -version = "3.17.0" -description = "Backport of pathlib-compatible object wrapper for zip files" -category = "dev" -optional = false -python-versions = ">=3.8" - -[package.extras] -docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "jaraco.itertools", "jaraco.functools", "more-itertools", "big-o", "pytest-ignore-flaky", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] - [metadata] lock-version = "1.1" -python-versions = "^3.9.0" -content-hash = "d381e745fc6cb47e1c8b007e690598d4c161c7664c4f7af275373dadabe56172" +python-versions = "3.11.0" +content-hash = "e9cd2edd4413b1c9c9f684640e52a6fe36d3166d55a3124153d83c54fb3753b8" [metadata.files] aiohttp = [] aiosignal = [] -annotated-types = [] -anyio = [] appnope = [] asttokens = [] async-timeout = [] @@ -1388,41 +1276,34 @@ cfgv = [] charset-normalizer = [] colorama = [] comm = [] +contourpy = [] coverage = [] -dataclasses-json = [] +cycler = [] debugpy = [] decorator = [] distlib = [] -dnspython = [] -exceptiongroup = [] +et-xmlfile = [] execnet = [] executing = [] fastjsonschema = [] filelock = [] +fonttools = [] frozenlist = [] -fsspec = [] -greenlet = [] -huggingface-hub = [] identify = [] idna = [] -importlib-metadata = [] iniconfig = [] ipykernel = [] ipython = [] jedi = [] -jsonpatch = [] -jsonpointer = [] +joblib = [] jsonschema = [] jsonschema-specifications = [] jupyter-client = [] jupyter-core = [] -langchain = [] -langsmith = [] -loguru = [] -marshmallow = [] +kiwisolver = [] +matplotlib = [] matplotlib-inline = [] multidict = [] -mypy-extensions = [] nbclient = [] nbformat = [] nbmake = [] @@ -1430,12 +1311,17 @@ nest-asyncio = [] nodeenv = [] numpy = [] openai = [] +openpyxl = [] packaging = [] +pandas = [] +pandas-stubs = [] parso = [] +pathlib = [] pexpect = [] pickleshare = [] -pinecone-client = [] +pillow = [] platformdirs = [] +plotly = [] pluggy = [] pre-commit = [] prompt-toolkit = [] @@ -1444,9 +1330,8 @@ ptyprocess = [] pure-eval = [] py = [] pycparser = [] -pydantic = [] -pydantic-core = [] pygments = [] +pyparsing = [] pytest = [] pytest-cov = [] pytest-dotenv = [] @@ -1454,27 +1339,28 @@ pytest-forked = [] pytest-xdist = [] python-dateutil = [] python-dotenv = [] +pytz = [] pywin32 = [] pyyaml = [] pyzmq = [] referencing = [] requests = [] rpds-py = [] +scikit-learn = [] +scipy = [] +setuptools-scm = [] six = [] -sniffio = [] -sqlalchemy = [] stack-data = [] tenacity = [] +threadpoolctl = [] toml = [] -tomli = [] tornado = [] tqdm = [] traitlets = [] +types-pytz = [] typing-extensions = [] -typing-inspect = [] +tzdata = [] urllib3 = [] virtualenv = [] wcwidth = [] -win32-setctime = [] yarl = [] -zipp = [] diff --git a/pyproject.toml b/pyproject.toml index e334309..702ab60 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,11 +12,13 @@ version = "v0.1" [tool.poetry.dependencies] pytest = ">=6.1.0" -python = "^3.9.0" -pinecone-client = "^2.2.4" -langchain = "^0.0.311" -huggingface-hub = "^0.17.3" -openai = "^0.28.1" +python = "3.11.0" +openai = {extras = ["embeddings"], version = "^0.28.1"} +pandas = "^2.1.1" +matplotlib = "^3.8.0" +pathlib = "^1.0.1" +plotly = "^5.17.0" +scipy = "^1.11.3" [tool.poetry.dev-dependencies] pytest = "^7.1.0" diff --git a/src/nbwrite/ex.py b/src/nbwrite/ex.py index cbfa6c9..87456c5 100644 --- a/src/nbwrite/ex.py +++ b/src/nbwrite/ex.py @@ -1,35 +1,35 @@ -from langchain import PromptTemplate +# from langchain import PromptTemplate -template = """Question: {question} +# template = """Question: {question} -Answer: """ -prompt = PromptTemplate(template=template, input_variables=["question"]) +# Answer: """ +# prompt = PromptTemplate(template=template, input_variables=["question"]) -# user question +# # user question question = "Which NFL team won the Super Bowl in the 2010 season?" -import os +# import os -from langchain.llms import OpenAI +# from langchain.llms import OpenAI -davinci = OpenAI(model_name="text-davinci-003") -from langchain import HuggingFaceHub, LLMChain +# davinci = OpenAI(model_name="text-davinci-003") +# from langchain import HuggingFaceHub, LLMChain -llm_chain = LLMChain(prompt=prompt, llm=davinci) +# llm_chain = LLMChain(prompt=prompt, llm=davinci) -print(llm_chain.run(question)) +# print(llm_chain.run(question)) -import pinecone +# import pinecone -pinecone.init(api_key=os.environ["PINECONE_API_KEY"], environment="gcp-starter") -index = pinecone.Index("nbwrite") +# pinecone.init(api_key=os.environ["PINECONE_API_KEY"], environment="gcp-starter") +# index = pinecone.Index("nbwrite") -index.upsert( - [ - ("A", [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]), - ("B", [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2]), - ("C", [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3]), - ("D", [0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4]), - ("E", [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]), - ] -) +# index.upsert( +# [ +# ("A", [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]), +# ("B", [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2]), +# ("C", [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3]), +# ("D", [0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4]), +# ("E", [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]), +# ] +# ) diff --git a/src/nbwrite/example.py b/src/nbwrite/example.py new file mode 100644 index 0000000..e69de29 diff --git a/src/nbwrite/example_helpers.py b/src/nbwrite/example_helpers.py new file mode 100644 index 0000000..b5ed105 --- /dev/null +++ b/src/nbwrite/example_helpers.py @@ -0,0 +1,72 @@ +# https://github.com/openai/openai-cookbook/blob/main/examples/Code_search.ipynb + +from pathlib import Path + +import pandas as pd + +DEF_PREFIXES = ["def ", "async def "] +NEWLINE = "\n" + + +def get_function_name(code): + """ + Extract function name from a line beginning with 'def' or 'async def'. + """ + for prefix in DEF_PREFIXES: + if code.startswith(prefix): + return code[len(prefix) : code.index("(")] + + +def get_until_no_space(all_lines, i): + """ + Get all lines until a line outside the function definition is found. + """ + ret = [all_lines[i]] + for j in range(i + 1, len(all_lines)): + if len(all_lines[j]) == 0 or all_lines[j][0] in [" ", "\t", ")"]: + ret.append(all_lines[j]) + else: + break + return NEWLINE.join(ret) + + +def get_functions(filepath): + """ + Get all functions in a Python file. + """ + with open(filepath, "r") as file: + all_lines = file.read().replace("\r", NEWLINE).split(NEWLINE) + for i, l in enumerate(all_lines): + for prefix in DEF_PREFIXES: + if l.startswith(prefix): + code = get_until_no_space(all_lines, i) + function_name = get_function_name(code) + yield { + "code": code, + "function_name": function_name, + "filepath": filepath, + } + break + + +def extract_functions_from_repo(code_root): + """ + Extract all .py functions from the repository. + """ + code_files = list(code_root.glob("**/*.py")) + + num_files = len(code_files) + print(f"Total number of .py files: {num_files}") + + if num_files == 0: + print("Verify openai-python repo exists and code_root is set correctly.") + return None + + all_funcs = [ + func for code_file in code_files for func in get_functions(str(code_file)) + ] + + num_funcs = len(all_funcs) + print(f"Total number of functions extracted: {num_funcs}") + + return all_funcs diff --git a/tests/test_ex.py b/tests/test_ex.py index e3d8d8b..a472bcc 100644 --- a/tests/test_ex.py +++ b/tests/test_ex.py @@ -1,3 +1,5 @@ +from pathlib import Path + import nbmake from nbwrite import ex @@ -9,3 +11,53 @@ def test_when_index_then_build_index(): def test_when_gen_nbrun_doc_then_nb_output(): assert ex.question == "Which NFL team won the Super Bowl in the 2010 season?" + + +def test_openai(): + # Set user root directory to the 'openai-python' repository + # root_dir = Path.home() + + import importlib.util + + lib = importlib.util.find_spec("nbmake") + + # Assumes the 'openai-python' repository exists in the user's root directory + code_root = Path(lib.submodule_search_locations._path[0]) + # from nbwrite.example import extract_functions_from_repo + # Extract all functions from the repository + from nbwrite.example_helpers import extract_functions_from_repo + + all_funcs = extract_functions_from_repo(code_root) + + import pandas as pd + from openai.embeddings_utils import get_embedding + + df = pd.DataFrame(all_funcs) + df["code_embedding"] = df["code"].apply( + lambda x: get_embedding(x, engine="text-embedding-ada-002") + ) + df["filepath"] = df["filepath"].map(lambda x: Path(x).relative_to(code_root)) + # df.to_csv("data/code_search_openai-python.csv", index=False) + df.head() + + from openai.embeddings_utils import cosine_similarity + + def search_functions(df, code_query, n=3, pprint=True, n_lines=7): + embedding = get_embedding(code_query, engine="text-embedding-ada-002") + df["similarities"] = df.code_embedding.apply( + lambda x: cosine_similarity(x, embedding) + ) + + res = df.sort_values("similarities", ascending=False).head(n) + + if pprint: + for r in res.iterrows(): + print( + f"{r[1].filepath}:{r[1].function_name} score={round(r[1].similarities, 3)}" + ) + print("\n".join(r[1].code.split("\n")[:n_lines])) + print("-" * 70) + + return res + + res = search_functions(df, "fine-tuning input data validation logic", n=3) From 5b50b168dda49b4529b108188ef49671df141e4a Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 10:20:25 +0000 Subject: [PATCH 06/59] res --- tests/resources/{ => buildenv}/poetry.lock | 0 tests/resources/{ => buildenv}/poetry.toml | 0 tests/resources/{ => buildenv}/pyproject.toml | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename tests/resources/{ => buildenv}/poetry.lock (100%) rename tests/resources/{ => buildenv}/poetry.toml (100%) rename tests/resources/{ => buildenv}/pyproject.toml (100%) diff --git a/tests/resources/poetry.lock b/tests/resources/buildenv/poetry.lock similarity index 100% rename from tests/resources/poetry.lock rename to tests/resources/buildenv/poetry.lock diff --git a/tests/resources/poetry.toml b/tests/resources/buildenv/poetry.toml similarity index 100% rename from tests/resources/poetry.toml rename to tests/resources/buildenv/poetry.toml diff --git a/tests/resources/pyproject.toml b/tests/resources/buildenv/pyproject.toml similarity index 100% rename from tests/resources/pyproject.toml rename to tests/resources/buildenv/pyproject.toml From 483b1a03e5d758fe0232d31add9c1fef4c32c3e2 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 10:23:14 +0000 Subject: [PATCH 07/59] demo stub --- tests/resources/demo.ipynb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 tests/resources/demo.ipynb diff --git a/tests/resources/demo.ipynb b/tests/resources/demo.ipynb new file mode 100644 index 0000000..b680e38 --- /dev/null +++ b/tests/resources/demo.ipynb @@ -0,0 +1,18 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Using the NotebookRun class to run a notebook from a conventional pytest function" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} From 008f4810fe00478c71b94880a26b16b6503f7419 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 10:29:11 +0000 Subject: [PATCH 08/59] cli --- poetry.lock | 14 +++++++++++++- pyproject.toml | 4 ++++ src/nbwrite/cli.py | 11 +++++++++++ 3 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 src/nbwrite/cli.py diff --git a/poetry.lock b/poetry.lock index 355f983..b7f3f2b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -117,6 +117,17 @@ category = "main" optional = false python-versions = ">=3.7.0" +[[package]] +name = "click" +version = "8.1.7" +description = "Composable command line interface toolkit" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} + [[package]] name = "colorama" version = "0.4.6" @@ -1260,7 +1271,7 @@ multidict = ">=4.0" [metadata] lock-version = "1.1" python-versions = "3.11.0" -content-hash = "e9cd2edd4413b1c9c9f684640e52a6fe36d3166d55a3124153d83c54fb3753b8" +content-hash = "6dcba564f7bc6da31673339f3010f8bf4491ab3c2abf679b54efd90e0b17c773" [metadata.files] aiohttp = [] @@ -1274,6 +1285,7 @@ certifi = [] cffi = [] cfgv = [] charset-normalizer = [] +click = [] colorama = [] comm = [] contourpy = [] diff --git a/pyproject.toml b/pyproject.toml index 702ab60..89a7c5c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,6 +10,9 @@ packages = [ readme = "README.md" version = "v0.1" +[tool.poetry.scripts] +nbwrite = "nbwrite.cli:cli" + [tool.poetry.dependencies] pytest = ">=6.1.0" python = "3.11.0" @@ -19,6 +22,7 @@ matplotlib = "^3.8.0" pathlib = "^1.0.1" plotly = "^5.17.0" scipy = "^1.11.3" +click = "^8.1.7" [tool.poetry.dev-dependencies] pytest = "^7.1.0" diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py new file mode 100644 index 0000000..7047d9e --- /dev/null +++ b/src/nbwrite/cli.py @@ -0,0 +1,11 @@ +import click + + +@click.command() +def cli(): + """Command line interface for nbwrite.""" + click.echo("Hello, world!") + + +if __name__ == "__main__": + cli() From 0533b32843cbb5f197491a316fe8cb5a637d8875 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 10:36:16 +0000 Subject: [PATCH 09/59] cli --- src/nbwrite/cli.py | 17 ++++++++++++++++- tests/test_cli.py | 10 ++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 tests/test_cli.py diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index 7047d9e..8fc20cd 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -1,11 +1,26 @@ +from pathlib import Path + import click -@click.command() +@click.group() def cli(): """Command line interface for nbwrite.""" click.echo("Hello, world!") +@cli.command() +def index(): + """Build an index based on the python environment.""" + click.echo("Building index...") + + +@cli.command() +@click.argument("notebook", type=click.Path(exists=True)) +def complete(path: Path): + """Write demo notebooks based on prompts in the notebook and the index""" + click.echo("Searching index...") + + if __name__ == "__main__": cli() diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 0000000..0baf2af --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,10 @@ +from click.testing import CliRunner + +from nbwrite.cli import cli + + +def test_hello_world(): + runner = CliRunner() + result = runner.invoke(cli, ["index"]) + assert result.exit_code == 0 + assert result.output == "Hello, world!\nBuilding index...\n" From d4917bee2eb5572ace9a5bbb63b15392dc2a8b65 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 10:36:59 +0000 Subject: [PATCH 10/59] disable hack --- .pre-commit-config.yaml | 18 ++--- src/nbwrite/ex.py | 48 +++++------ src/nbwrite/example_helpers.py | 144 ++++++++++++++++----------------- tests/test_ex.py | 86 ++++++++++---------- 4 files changed, 148 insertions(+), 148 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d33ab01..e5b1ddd 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,15 +23,15 @@ repos: hooks: - id: isort args: ["-m", "3", "--tc"] - # - repo: local - # hooks: - # - id: pyright - # name: pyright - # entry: poetry run pyright - # language: node - # pass_filenames: false - # types: [python] - # additional_dependencies: ["pyright@1.1.91"] + - repo: local + hooks: + - id: pyright + name: pyright + entry: poetry run pyright + language: node + pass_filenames: false + types: [python] + additional_dependencies: ["pyright@1.1.91"] # - repo: local # hooks: # - id: smoketest diff --git a/src/nbwrite/ex.py b/src/nbwrite/ex.py index 87456c5..3abc8d6 100644 --- a/src/nbwrite/ex.py +++ b/src/nbwrite/ex.py @@ -1,35 +1,35 @@ -# from langchain import PromptTemplate +# # from langchain import PromptTemplate -# template = """Question: {question} +# # template = """Question: {question} -# Answer: """ -# prompt = PromptTemplate(template=template, input_variables=["question"]) +# # Answer: """ +# # prompt = PromptTemplate(template=template, input_variables=["question"]) -# # user question -question = "Which NFL team won the Super Bowl in the 2010 season?" +# # # user question +# question = "Which NFL team won the Super Bowl in the 2010 season?" -# import os +# # import os -# from langchain.llms import OpenAI +# # from langchain.llms import OpenAI -# davinci = OpenAI(model_name="text-davinci-003") -# from langchain import HuggingFaceHub, LLMChain +# # davinci = OpenAI(model_name="text-davinci-003") +# # from langchain import HuggingFaceHub, LLMChain -# llm_chain = LLMChain(prompt=prompt, llm=davinci) +# # llm_chain = LLMChain(prompt=prompt, llm=davinci) -# print(llm_chain.run(question)) +# # print(llm_chain.run(question)) -# import pinecone +# # import pinecone -# pinecone.init(api_key=os.environ["PINECONE_API_KEY"], environment="gcp-starter") -# index = pinecone.Index("nbwrite") +# # pinecone.init(api_key=os.environ["PINECONE_API_KEY"], environment="gcp-starter") +# # index = pinecone.Index("nbwrite") -# index.upsert( -# [ -# ("A", [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]), -# ("B", [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2]), -# ("C", [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3]), -# ("D", [0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4]), -# ("E", [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]), -# ] -# ) +# # index.upsert( +# # [ +# # ("A", [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]), +# # ("B", [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2]), +# # ("C", [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3]), +# # ("D", [0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4]), +# # ("E", [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]), +# # ] +# # ) diff --git a/src/nbwrite/example_helpers.py b/src/nbwrite/example_helpers.py index b5ed105..c1375ea 100644 --- a/src/nbwrite/example_helpers.py +++ b/src/nbwrite/example_helpers.py @@ -1,72 +1,72 @@ -# https://github.com/openai/openai-cookbook/blob/main/examples/Code_search.ipynb - -from pathlib import Path - -import pandas as pd - -DEF_PREFIXES = ["def ", "async def "] -NEWLINE = "\n" - - -def get_function_name(code): - """ - Extract function name from a line beginning with 'def' or 'async def'. - """ - for prefix in DEF_PREFIXES: - if code.startswith(prefix): - return code[len(prefix) : code.index("(")] - - -def get_until_no_space(all_lines, i): - """ - Get all lines until a line outside the function definition is found. - """ - ret = [all_lines[i]] - for j in range(i + 1, len(all_lines)): - if len(all_lines[j]) == 0 or all_lines[j][0] in [" ", "\t", ")"]: - ret.append(all_lines[j]) - else: - break - return NEWLINE.join(ret) - - -def get_functions(filepath): - """ - Get all functions in a Python file. - """ - with open(filepath, "r") as file: - all_lines = file.read().replace("\r", NEWLINE).split(NEWLINE) - for i, l in enumerate(all_lines): - for prefix in DEF_PREFIXES: - if l.startswith(prefix): - code = get_until_no_space(all_lines, i) - function_name = get_function_name(code) - yield { - "code": code, - "function_name": function_name, - "filepath": filepath, - } - break - - -def extract_functions_from_repo(code_root): - """ - Extract all .py functions from the repository. - """ - code_files = list(code_root.glob("**/*.py")) - - num_files = len(code_files) - print(f"Total number of .py files: {num_files}") - - if num_files == 0: - print("Verify openai-python repo exists and code_root is set correctly.") - return None - - all_funcs = [ - func for code_file in code_files for func in get_functions(str(code_file)) - ] - - num_funcs = len(all_funcs) - print(f"Total number of functions extracted: {num_funcs}") - - return all_funcs +# # https://github.com/openai/openai-cookbook/blob/main/examples/Code_search.ipynb + +# from pathlib import Path + +# import pandas as pd + +# DEF_PREFIXES = ["def ", "async def "] +# NEWLINE = "\n" + + +# def get_function_name(code): +# """ +# Extract function name from a line beginning with 'def' or 'async def'. +# """ +# for prefix in DEF_PREFIXES: +# if code.startswith(prefix): +# return code[len(prefix) : code.index("(")] + + +# def get_until_no_space(all_lines, i): +# """ +# Get all lines until a line outside the function definition is found. +# """ +# ret = [all_lines[i]] +# for j in range(i + 1, len(all_lines)): +# if len(all_lines[j]) == 0 or all_lines[j][0] in [" ", "\t", ")"]: +# ret.append(all_lines[j]) +# else: +# break +# return NEWLINE.join(ret) + + +# def get_functions(filepath): +# """ +# Get all functions in a Python file. +# """ +# with open(filepath, "r") as file: +# all_lines = file.read().replace("\r", NEWLINE).split(NEWLINE) +# for i, l in enumerate(all_lines): +# for prefix in DEF_PREFIXES: +# if l.startswith(prefix): +# code = get_until_no_space(all_lines, i) +# function_name = get_function_name(code) +# yield { +# "code": code, +# "function_name": function_name, +# "filepath": filepath, +# } +# break + + +# def extract_functions_from_repo(code_root): +# """ +# Extract all .py functions from the repository. +# """ +# code_files = list(code_root.glob("**/*.py")) + +# num_files = len(code_files) +# print(f"Total number of .py files: {num_files}") + +# if num_files == 0: +# print("Verify openai-python repo exists and code_root is set correctly.") +# return None + +# all_funcs = [ +# func for code_file in code_files for func in get_functions(str(code_file)) +# ] + +# num_funcs = len(all_funcs) +# print(f"Total number of functions extracted: {num_funcs}") + +# return all_funcs diff --git a/tests/test_ex.py b/tests/test_ex.py index a472bcc..5a1a977 100644 --- a/tests/test_ex.py +++ b/tests/test_ex.py @@ -1,63 +1,63 @@ -from pathlib import Path +# from pathlib import Path -import nbmake +# import nbmake -from nbwrite import ex +# from nbwrite import ex -def test_when_index_then_build_index(): - assert ex.question == "Which NFL team won the Super Bowl in the 2010 season?" +# def test_when_index_then_build_index(): +# assert ex.question == "Which NFL team won the Super Bowl in the 2010 season?" -def test_when_gen_nbrun_doc_then_nb_output(): - assert ex.question == "Which NFL team won the Super Bowl in the 2010 season?" +# def test_when_gen_nbrun_doc_then_nb_output(): +# assert ex.question == "Which NFL team won the Super Bowl in the 2010 season?" -def test_openai(): - # Set user root directory to the 'openai-python' repository - # root_dir = Path.home() +# def test_openai(): +# # Set user root directory to the 'openai-python' repository +# # root_dir = Path.home() - import importlib.util +# import importlib.util - lib = importlib.util.find_spec("nbmake") +# lib = importlib.util.find_spec("nbmake") - # Assumes the 'openai-python' repository exists in the user's root directory - code_root = Path(lib.submodule_search_locations._path[0]) - # from nbwrite.example import extract_functions_from_repo - # Extract all functions from the repository - from nbwrite.example_helpers import extract_functions_from_repo +# # Assumes the 'openai-python' repository exists in the user's root directory +# code_root = Path(lib.submodule_search_locations._path[0]) +# # from nbwrite.example import extract_functions_from_repo +# # Extract all functions from the repository +# from nbwrite.example_helpers import extract_functions_from_repo - all_funcs = extract_functions_from_repo(code_root) +# all_funcs = extract_functions_from_repo(code_root) - import pandas as pd - from openai.embeddings_utils import get_embedding +# import pandas as pd +# from openai.embeddings_utils import get_embedding - df = pd.DataFrame(all_funcs) - df["code_embedding"] = df["code"].apply( - lambda x: get_embedding(x, engine="text-embedding-ada-002") - ) - df["filepath"] = df["filepath"].map(lambda x: Path(x).relative_to(code_root)) - # df.to_csv("data/code_search_openai-python.csv", index=False) - df.head() +# df = pd.DataFrame(all_funcs) +# df["code_embedding"] = df["code"].apply( +# lambda x: get_embedding(x, engine="text-embedding-ada-002") +# ) +# df["filepath"] = df["filepath"].map(lambda x: Path(x).relative_to(code_root)) +# # df.to_csv("data/code_search_openai-python.csv", index=False) +# df.head() - from openai.embeddings_utils import cosine_similarity +# from openai.embeddings_utils import cosine_similarity - def search_functions(df, code_query, n=3, pprint=True, n_lines=7): - embedding = get_embedding(code_query, engine="text-embedding-ada-002") - df["similarities"] = df.code_embedding.apply( - lambda x: cosine_similarity(x, embedding) - ) +# def search_functions(df, code_query, n=3, pprint=True, n_lines=7): +# embedding = get_embedding(code_query, engine="text-embedding-ada-002") +# df["similarities"] = df.code_embedding.apply( +# lambda x: cosine_similarity(x, embedding) +# ) - res = df.sort_values("similarities", ascending=False).head(n) +# res = df.sort_values("similarities", ascending=False).head(n) - if pprint: - for r in res.iterrows(): - print( - f"{r[1].filepath}:{r[1].function_name} score={round(r[1].similarities, 3)}" - ) - print("\n".join(r[1].code.split("\n")[:n_lines])) - print("-" * 70) +# if pprint: +# for r in res.iterrows(): +# print( +# f"{r[1].filepath}:{r[1].function_name} score={round(r[1].similarities, 3)}" +# ) +# print("\n".join(r[1].code.split("\n")[:n_lines])) +# print("-" * 70) - return res +# return res - res = search_functions(df, "fine-tuning input data validation logic", n=3) +# res = search_functions(df, "fine-tuning input data validation logic", n=3) From d006dc9e7357663d3c140af374800306bef5f6bc Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 11:00:58 +0000 Subject: [PATCH 11/59] test --- poetry.lock | 198 +++++++++++++++++++++++++++++++++++----------- pyproject.toml | 6 +- tests/test_cli.py | 2 +- 3 files changed, 154 insertions(+), 52 deletions(-) diff --git a/poetry.lock b/poetry.lock index b7f3f2b..6855713 100644 --- a/poetry.lock +++ b/poetry.lock @@ -152,6 +152,24 @@ lint = ["black (>=22.6.0)", "mdformat-gfm (>=0.3.5)", "mdformat (>0.7)", "ruff ( test = ["pytest"] typing = ["mypy (>=0.990)"] +[[package]] +name = "contourpy" +version = "1.1.0" +description = "Python library for calculating contours of 2D quadrilateral grids" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +numpy = ">=1.16" + +[package.extras] +docs = ["furo", "sphinx-copybutton"] +bokeh = ["bokeh", "selenium"] +mypy = ["contourpy", "docutils-stubs", "mypy (==1.2.0)", "types-pillow"] +test = ["contourpy", "matplotlib", "pillow"] +test-no-images = ["pytest", "pytest-cov", "wurlitzer"] + [[package]] name = "contourpy" version = "1.1.1" @@ -225,6 +243,17 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "exceptiongroup" +version = "1.1.3" +description = "Backport of PEP 654 (exception groups)" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +test = ["pytest (>=6)"] + [[package]] name = "execnet" version = "2.0.2" @@ -320,6 +349,37 @@ category = "main" optional = false python-versions = ">=3.5" +[[package]] +name = "importlib-metadata" +version = "6.8.0" +description = "Read metadata from Python packages" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +zipp = ">=0.5" + +[package.extras] +docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] +perf = ["ipython"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] + +[[package]] +name = "importlib-resources" +version = "6.1.0" +description = "Read resources from Python packages" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} + +[package.extras] +docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "zipp (>=3.17)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] + [[package]] name = "iniconfig" version = "2.0.0" @@ -360,11 +420,11 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest-asyncio", "pytest-cov", "p [[package]] name = "ipython" -version = "8.16.1" +version = "8.13.0" description = "IPython: Productive Interactive Computing" category = "dev" optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" [package.dependencies] appnope = {version = "*", markers = "sys_platform == \"darwin\""} @@ -379,11 +439,12 @@ prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0" pygments = ">=2.4.0" stack-data = "*" traitlets = ">=5" +typing-extensions = {version = "*", markers = "python_version < \"3.10\""} [package.extras] -all = ["black", "ipykernel", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "docrepr", "matplotlib", "stack-data", "pytest (<7)", "typing-extensions", "exceptiongroup", "pytest (<7.1)", "pytest-asyncio", "testpath", "nbconvert", "nbformat", "ipywidgets", "notebook", "ipyparallel", "qtconsole", "curio", "matplotlib (!=3.2.0)", "numpy (>=1.21)", "pandas", "trio"] +all = ["black", "ipykernel", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "docrepr", "matplotlib", "stack-data", "pytest (<7)", "typing-extensions", "pytest (<7.1)", "pytest-asyncio", "testpath", "nbconvert", "nbformat", "ipywidgets", "notebook", "ipyparallel", "qtconsole", "curio", "matplotlib (!=3.2.0)", "numpy (>=1.21)", "pandas", "trio"] black = ["black"] -doc = ["ipykernel", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "docrepr", "matplotlib", "stack-data", "pytest (<7)", "typing-extensions", "exceptiongroup", "pytest (<7.1)", "pytest-asyncio", "testpath"] +doc = ["ipykernel", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "docrepr", "matplotlib", "stack-data", "pytest (<7)", "typing-extensions", "pytest (<7.1)", "pytest-asyncio", "testpath"] kernel = ["ipykernel"] nbconvert = ["nbconvert"] nbformat = ["nbformat"] @@ -427,7 +488,9 @@ python-versions = ">=3.8" [package.dependencies] attrs = ">=22.2.0" +importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""} jsonschema-specifications = ">=2023.03.6" +pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""} referencing = ">=0.28.4" rpds-py = ">=0.7.1" @@ -444,17 +507,19 @@ optional = false python-versions = ">=3.8" [package.dependencies] +importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""} referencing = ">=0.28.0" [[package]] name = "jupyter-client" -version = "8.3.1" +version = "8.4.0" description = "Jupyter protocol implementation and client libraries" category = "dev" optional = false python-versions = ">=3.8" [package.dependencies] +importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" @@ -467,7 +532,7 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt [[package]] name = "jupyter-core" -version = "5.3.2" +version = "5.4.0" description = "Jupyter core package. A base package on which Jupyter projects rely." category = "dev" optional = false @@ -492,18 +557,19 @@ python-versions = ">=3.7" [[package]] name = "matplotlib" -version = "3.8.0" +version = "3.7.3" description = "Python plotting package" category = "main" optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" [package.dependencies] contourpy = ">=1.0.1" cycler = ">=0.10" fonttools = ">=4.22.0" +importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""} kiwisolver = ">=1.0.1" -numpy = ">=1.21,<2" +numpy = ">=1.20,<2" packaging = ">=20.0" pillow = ">=6.2.0" pyparsing = ">=2.3.1" @@ -598,11 +664,11 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.* [[package]] name = "numpy" -version = "1.26.0" +version = "1.24.4" description = "Fundamental package for array computing in Python" category = "main" optional = false -python-versions = "<3.13,>=3.9" +python-versions = ">=3.8" [[package]] name = "openai" @@ -653,52 +719,55 @@ python-versions = ">=3.7" [[package]] name = "pandas" -version = "2.1.1" +version = "2.0.3" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" [package.dependencies] -numpy = {version = ">=1.23.2", markers = "python_version == \"3.11\""} +numpy = [ + {version = ">=1.20.3", markers = "python_version < \"3.10\""}, + {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, + {version = ">=1.23.2", markers = "python_version >= \"3.11\""}, +] python-dateutil = ">=2.8.2" pytz = ">=2020.1" tzdata = ">=2022.1" [package.extras] -test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)", "pytest-asyncio (>=0.17.0)"] -performance = ["bottleneck (>=1.3.4)", "numba (>=0.55.2)", "numexpr (>=2.8.0)"] -computation = ["scipy (>=1.8.1)", "xarray (>=2022.03.0)"] -fss = ["fsspec (>=2022.05.0)"] -aws = ["s3fs (>=2022.05.0)"] -gcp = ["gcsfs (>=2022.05.0)", "pandas-gbq (>=0.17.5)"] -excel = ["odfpy (>=1.4.1)", "openpyxl (>=3.0.10)", "pyxlsb (>=1.0.9)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.3)"] -parquet = ["pyarrow (>=7.0.0)"] +all = ["beautifulsoup4 (>=4.9.3)", "bottleneck (>=1.3.2)", "brotlipy (>=0.7.0)", "fastparquet (>=0.6.3)", "fsspec (>=2021.07.0)", "gcsfs (>=2021.07.0)", "html5lib (>=1.1)", "hypothesis (>=6.34.2)", "jinja2 (>=3.0.0)", "lxml (>=4.6.3)", "matplotlib (>=3.6.1)", "numba (>=0.53.1)", "numexpr (>=2.7.3)", "odfpy (>=1.4.1)", "openpyxl (>=3.0.7)", "pandas-gbq (>=0.15.0)", "psycopg2 (>=2.8.6)", "pyarrow (>=7.0.0)", "pymysql (>=1.0.2)", "PyQt5 (>=5.15.1)", "pyreadstat (>=1.1.2)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)", "pytest-asyncio (>=0.17.0)", "python-snappy (>=0.6.0)", "pyxlsb (>=1.0.8)", "qtpy (>=2.2.0)", "scipy (>=1.7.1)", "s3fs (>=2021.08.0)", "SQLAlchemy (>=1.4.16)", "tables (>=3.6.1)", "tabulate (>=0.8.9)", "xarray (>=0.21.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=1.4.3)", "zstandard (>=0.15.2)"] +aws = ["s3fs (>=2021.08.0)"] +clipboard = ["PyQt5 (>=5.15.1)", "qtpy (>=2.2.0)"] +compression = ["brotlipy (>=0.7.0)", "python-snappy (>=0.6.0)", "zstandard (>=0.15.2)"] +computation = ["scipy (>=1.7.1)", "xarray (>=0.21.0)"] +excel = ["odfpy (>=1.4.1)", "openpyxl (>=3.0.7)", "pyxlsb (>=1.0.8)", "xlrd (>=2.0.1)", "xlsxwriter (>=1.4.3)"] feather = ["pyarrow (>=7.0.0)"] -hdf5 = ["tables (>=3.7.0)"] -spss = ["pyreadstat (>=1.1.5)"] -postgresql = ["SQLAlchemy (>=1.4.36)", "psycopg2 (>=2.9.3)"] -mysql = ["SQLAlchemy (>=1.4.36)", "pymysql (>=1.0.2)"] -sql-other = ["SQLAlchemy (>=1.4.36)"] -html = ["beautifulsoup4 (>=4.11.1)", "html5lib (>=1.1)", "lxml (>=4.8.0)"] -xml = ["lxml (>=4.8.0)"] +fss = ["fsspec (>=2021.07.0)"] +gcp = ["gcsfs (>=2021.07.0)", "pandas-gbq (>=0.15.0)"] +hdf5 = ["tables (>=3.6.1)"] +html = ["beautifulsoup4 (>=4.9.3)", "html5lib (>=1.1)", "lxml (>=4.6.3)"] +mysql = ["SQLAlchemy (>=1.4.16)", "pymysql (>=1.0.2)"] +output_formatting = ["jinja2 (>=3.0.0)", "tabulate (>=0.8.9)"] +parquet = ["pyarrow (>=7.0.0)"] +performance = ["bottleneck (>=1.3.2)", "numba (>=0.53.1)", "numexpr (>=2.7.1)"] plot = ["matplotlib (>=3.6.1)"] -output-formatting = ["jinja2 (>=3.1.2)", "tabulate (>=0.8.10)"] -clipboard = ["PyQt5 (>=5.15.6)", "qtpy (>=2.2.0)"] -compression = ["zstandard (>=0.17.0)"] -consortium-standard = ["dataframe-api-compat (>=0.1.7)"] -all = ["beautifulsoup4 (>=4.11.1)", "bottleneck (>=1.3.4)", "dataframe-api-compat (>=0.1.7)", "fastparquet (>=0.8.1)", "fsspec (>=2022.05.0)", "gcsfs (>=2022.05.0)", "html5lib (>=1.1)", "hypothesis (>=6.46.1)", "jinja2 (>=3.1.2)", "lxml (>=4.8.0)", "matplotlib (>=3.6.1)", "numba (>=0.55.2)", "numexpr (>=2.8.0)", "odfpy (>=1.4.1)", "openpyxl (>=3.0.10)", "pandas-gbq (>=0.17.5)", "psycopg2 (>=2.9.3)", "pyarrow (>=7.0.0)", "pymysql (>=1.0.2)", "PyQt5 (>=5.15.6)", "pyreadstat (>=1.1.5)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)", "pytest-asyncio (>=0.17.0)", "pyxlsb (>=1.0.9)", "qtpy (>=2.2.0)", "scipy (>=1.8.1)", "s3fs (>=2022.05.0)", "SQLAlchemy (>=1.4.36)", "tables (>=3.7.0)", "tabulate (>=0.8.10)", "xarray (>=2022.03.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.3)", "zstandard (>=0.17.0)"] +postgresql = ["SQLAlchemy (>=1.4.16)", "psycopg2 (>=2.8.6)"] +spss = ["pyreadstat (>=1.1.2)"] +sql-other = ["SQLAlchemy (>=1.4.16)"] +test = ["hypothesis (>=6.34.2)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)", "pytest-asyncio (>=0.17.0)"] +xml = ["lxml (>=4.6.3)"] [[package]] name = "pandas-stubs" -version = "2.1.1.230928" +version = "2.0.2.230605" description = "Type annotations for pandas" category = "main" optional = false -python-versions = ">=3.9" +python-versions = ">=3.8" [package.dependencies] -numpy = {version = ">=1.26.0", markers = "python_version < \"3.13\""} +numpy = ">=1.24.3" types-pytz = ">=2022.1.1" [[package]] @@ -752,6 +821,14 @@ python-versions = ">=3.8" docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"] tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] +[[package]] +name = "pkgutil-resolve-name" +version = "1.3.10" +description = "Resolve a name to an object." +category = "dev" +optional = false +python-versions = ">=3.6" + [[package]] name = "platformdirs" version = "3.11.0" @@ -892,9 +969,11 @@ python-versions = ">=3.7" [package.dependencies] colorama = {version = "*", markers = "sys_platform == \"win32\""} +exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} iniconfig = "*" packaging = "*" pluggy = ">=0.12,<2.0" +tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] @@ -1046,7 +1125,7 @@ use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "rpds-py" -version = "0.10.4" +version = "0.10.6" description = "Python bindings to Rust's persistent data structures (rpds)" category = "dev" optional = false @@ -1074,19 +1153,19 @@ tests = ["matplotlib (>=3.1.3)", "scikit-image (>=0.16.2)", "pandas (>=1.0.5)", [[package]] name = "scipy" -version = "1.11.3" +version = "1.9.3" description = "Fundamental algorithms for scientific computing in Python" category = "main" optional = false -python-versions = "<3.13,>=3.9" +python-versions = ">=3.8" [package.dependencies] -numpy = ">=1.21.6,<1.28.0" +numpy = ">=1.18.5,<1.26.0" [package.extras] -test = ["pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack", "pooch"] -doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-design (>=0.2.0)", "matplotlib (>2)", "numpydoc", "jupytext", "myst-nb", "pooch"] -dev = ["mypy", "typing-extensions", "types-psutil", "pycodestyle", "ruff", "cython-lint (>=0.12.2)", "rich-click", "click", "doit (>=0.36.0)", "pydevtool"] +test = ["pytest", "pytest-cov", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack"] +doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-panels (>=0.5.2)", "matplotlib (>2)", "numpydoc", "sphinx-tabs"] +dev = ["mypy", "typing-extensions", "pycodestyle", "flake8"] [[package]] name = "setuptools-scm" @@ -1098,6 +1177,7 @@ python-versions = ">=3.8" [package.dependencies] packaging = ">=20" +tomli = {version = ">=1", markers = "python_version < \"3.11\""} typing-extensions = "*" [package.extras] @@ -1156,6 +1236,14 @@ category = "dev" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +[[package]] +name = "tomli" +version = "2.0.1" +description = "A lil' TOML parser" +category = "main" +optional = false +python-versions = ">=3.7" + [[package]] name = "tornado" version = "6.3.3" @@ -1268,10 +1356,22 @@ python-versions = ">=3.7" idna = ">=2.0" multidict = ">=4.0" +[[package]] +name = "zipp" +version = "3.17.0" +description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.extras] +docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "jaraco.itertools", "jaraco.functools", "more-itertools", "big-o", "pytest-ignore-flaky", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] + [metadata] lock-version = "1.1" -python-versions = "3.11.0" -content-hash = "6dcba564f7bc6da31673339f3010f8bf4491ab3c2abf679b54efd90e0b17c773" +python-versions = ">=3.8.0,<4.0.0" +content-hash = "3894264c832ed41a4ffe97efbae5fe23b8b0297256e9c548d530eb2bdfc6c094" [metadata.files] aiohttp = [] @@ -1295,6 +1395,7 @@ debugpy = [] decorator = [] distlib = [] et-xmlfile = [] +exceptiongroup = [] execnet = [] executing = [] fastjsonschema = [] @@ -1303,6 +1404,8 @@ fonttools = [] frozenlist = [] identify = [] idna = [] +importlib-metadata = [] +importlib-resources = [] iniconfig = [] ipykernel = [] ipython = [] @@ -1332,6 +1435,7 @@ pathlib = [] pexpect = [] pickleshare = [] pillow = [] +pkgutil-resolve-name = [] platformdirs = [] plotly = [] pluggy = [] @@ -1366,6 +1470,7 @@ stack-data = [] tenacity = [] threadpoolctl = [] toml = [] +tomli = [] tornado = [] tqdm = [] traitlets = [] @@ -1376,3 +1481,4 @@ urllib3 = [] virtualenv = [] wcwidth = [] yarl = [] +zipp = [] diff --git a/pyproject.toml b/pyproject.toml index 89a7c5c..293fe40 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,13 +15,9 @@ nbwrite = "nbwrite.cli:cli" [tool.poetry.dependencies] pytest = ">=6.1.0" -python = "3.11.0" +python = ">=3.8.0,<4.0.0" openai = {extras = ["embeddings"], version = "^0.28.1"} -pandas = "^2.1.1" -matplotlib = "^3.8.0" pathlib = "^1.0.1" -plotly = "^5.17.0" -scipy = "^1.11.3" click = "^8.1.7" [tool.poetry.dev-dependencies] diff --git a/tests/test_cli.py b/tests/test_cli.py index 0baf2af..1ce0d75 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -3,7 +3,7 @@ from nbwrite.cli import cli -def test_hello_world(): +def test_index(): runner = CliRunner() result = runner.invoke(cli, ["index"]) assert result.exit_code == 0 From 324ef4974ecefb147a3c152d60c07073bdf92dfc Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 11:01:45 +0000 Subject: [PATCH 12/59] disable container test --- .github/workflows/pytest.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index b1ed55d..ec70ec6 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -4,18 +4,18 @@ on: - cron: 0 13 * * 1 # Every Monday at 1PM UTC (9AM EST) pull_request: # test in containerised and OS environments -jobs: - test-container: - runs-on: ubuntu-22.04 - steps: - - uses: actions/checkout@v2 - - run: npm install -g @devcontainers/cli@v0.30.0 - - run: devcontainer up --workspace-folder=. - - run: devcontainer exec --workspace-folder=. poetry run pre-commit run --verbose --all-files - - run: devcontainer exec --workspace-folder=. poetry run pytest --cov-report=xml --cov=src - - uses: codecov/codecov-action@v1 - with: - file: coverage.xml +# jobs: +# test-container: +# runs-on: ubuntu-22.04 +# steps: +# - uses: actions/checkout@v2 +# - run: npm install -g @devcontainers/cli@v0.30.0 +# - run: devcontainer up --workspace-folder=. +# - run: devcontainer exec --workspace-folder=. poetry run pre-commit run --verbose --all-files +# - run: devcontainer exec --workspace-folder=. poetry run pytest --cov-report=xml --cov=src +# - uses: codecov/codecov-action@v1 +# with: +# file: coverage.xml pytest: strategy: fail-fast: false From b28c2cd5f3402b5413ead6a7766fceee8672dc59 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 11:09:36 +0000 Subject: [PATCH 13/59] add deps --- poetry.lock | 387 ++++++++++++++++++++++++++++++++++--- pyproject.toml | 4 +- tests/resources/demo.ipynb | 11 ++ 3 files changed, 373 insertions(+), 29 deletions(-) diff --git a/poetry.lock b/poetry.lock index 6855713..7a0dd29 100644 --- a/poetry.lock +++ b/poetry.lock @@ -29,6 +29,35 @@ python-versions = ">=3.7" [package.dependencies] frozenlist = ">=1.1.0" +[[package]] +name = "annotated-types" +version = "0.6.0" +description = "Reusable constraint types to use with typing.Annotated" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} + +[[package]] +name = "anyio" +version = "3.7.1" +description = "High level compatibility layer for multiple asynchronous event loop implementations" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} +idna = ">=2.8" +sniffio = ">=1.1" + +[package.extras] +doc = ["packaging", "sphinx", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquery", "sphinx-autodoc-typehints (>=1.2.0)"] +test = ["anyio", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)", "mock (>=4)"] +trio = ["trio (<0.22)"] + [[package]] name = "appnope" version = "0.1.3" @@ -152,24 +181,6 @@ lint = ["black (>=22.6.0)", "mdformat-gfm (>=0.3.5)", "mdformat (>0.7)", "ruff ( test = ["pytest"] typing = ["mypy (>=0.990)"] -[[package]] -name = "contourpy" -version = "1.1.0" -description = "Python library for calculating contours of 2D quadrilateral grids" -category = "main" -optional = false -python-versions = ">=3.8" - -[package.dependencies] -numpy = ">=1.16" - -[package.extras] -docs = ["furo", "sphinx-copybutton"] -bokeh = ["bokeh", "selenium"] -mypy = ["contourpy", "docutils-stubs", "mypy (==1.2.0)", "types-pillow"] -test = ["contourpy", "matplotlib", "pillow"] -test-no-images = ["pytest", "pytest-cov", "wurlitzer"] - [[package]] name = "contourpy" version = "1.1.1" @@ -211,6 +222,18 @@ python-versions = ">=3.8" docs = ["ipython", "matplotlib", "numpydoc", "sphinx"] tests = ["pytest", "pytest-cov", "pytest-xdist"] +[[package]] +name = "dataclasses-json" +version = "0.5.14" +description = "Easily serialize dataclasses to and from JSON." +category = "main" +optional = false +python-versions = ">=3.7,<3.13" + +[package.dependencies] +marshmallow = ">=3.18.0,<4.0.0" +typing-inspect = ">=0.4.0,<1" + [[package]] name = "debugpy" version = "1.8.0" @@ -330,6 +353,50 @@ category = "main" optional = false python-versions = ">=3.8" +[[package]] +name = "fsspec" +version = "2023.9.2" +description = "File-system specification" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.extras] +abfs = ["adlfs"] +adl = ["adlfs"] +arrow = ["pyarrow (>=1)"] +dask = ["dask", "distributed"] +devel = ["pytest", "pytest-cov"] +dropbox = ["dropboxdrivefs", "requests", "dropbox"] +full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"] +fuse = ["fusepy"] +gcs = ["gcsfs"] +git = ["pygit2"] +github = ["requests"] +gs = ["gcsfs"] +gui = ["panel"] +hdfs = ["pyarrow (>=1)"] +http = ["requests", "aiohttp (!=4.0.0a0,!=4.0.0a1)"] +libarchive = ["libarchive-c"] +oci = ["ocifs"] +s3 = ["s3fs"] +sftp = ["paramiko"] +smb = ["smbprotocol"] +ssh = ["paramiko"] +tqdm = ["tqdm"] + +[[package]] +name = "greenlet" +version = "3.0.0" +description = "Lightweight in-process concurrent programming" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["sphinx"] +test = ["objgraph", "psutil"] + [[package]] name = "identify" version = "2.5.30" @@ -478,6 +545,25 @@ category = "main" optional = false python-versions = ">=3.7" +[[package]] +name = "jsonpatch" +version = "1.33" +description = "Apply JSON-Patches (RFC 6902)" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" + +[package.dependencies] +jsonpointer = ">=1.9" + +[[package]] +name = "jsonpointer" +version = "2.4" +description = "Identify specific nodes in a JSON document (RFC 6901)" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" + [[package]] name = "jsonschema" version = "4.19.1" @@ -555,6 +641,96 @@ category = "main" optional = false python-versions = ">=3.7" +[[package]] +name = "langchain" +version = "0.0.312" +description = "Building applications with LLMs through composability" +category = "main" +optional = false +python-versions = ">=3.8.1,<4.0" + +[package.dependencies] +aiohttp = ">=3.8.3,<4.0.0" +anyio = "<4.0" +async-timeout = {version = ">=4.0.0,<5.0.0", markers = "python_version < \"3.11\""} +dataclasses-json = ">=0.5.7,<0.7" +jsonpatch = ">=1.33,<2.0" +langsmith = ">=0.0.43,<0.1.0" +numpy = ">=1,<2" +pydantic = ">=1,<3" +PyYAML = ">=5.3" +requests = ">=2,<3" +SQLAlchemy = ">=1.4,<3" +tenacity = ">=8.1.0,<9.0.0" + +[package.extras] +all = ["O365 (>=2.0.26,<3.0.0)", "aleph-alpha-client (>=2.15.0,<3.0.0)", "amadeus (>=8.1.0)", "arxiv (>=1.4,<2.0)", "atlassian-python-api (>=3.36.0,<4.0.0)", "awadb (>=0.3.9,<0.4.0)", "azure-ai-formrecognizer (>=3.2.1,<4.0.0)", "azure-ai-vision (>=0.11.1b1,<0.12.0)", "azure-cognitiveservices-speech (>=1.28.0,<2.0.0)", "azure-cosmos (>=4.4.0b1,<5.0.0)", "azure-identity (>=1.12.0,<2.0.0)", "beautifulsoup4 (>=4,<5)", "clarifai (>=9.1.0)", "clickhouse-connect (>=0.5.14,<0.6.0)", "cohere (>=4,<5)", "deeplake (>=3.6.8,<4.0.0)", "docarray[hnswlib] (>=0.32.0,<0.33.0)", "duckduckgo-search (>=3.8.3,<4.0.0)", "elasticsearch (>=8,<9)", "esprima (>=4.0.1,<5.0.0)", "faiss-cpu (>=1,<2)", "google-api-python-client (==2.70.0)", "google-auth (>=2.18.1,<3.0.0)", "google-search-results (>=2,<3)", "gptcache (>=0.1.7)", "html2text (>=2020.1.16,<2021.0.0)", "huggingface_hub (>=0,<1)", "jinja2 (>=3,<4)", "jq (>=1.4.1,<2.0.0)", "lancedb (>=0.1,<0.2)", "langkit (>=0.0.6,<0.1.0)", "lark (>=1.1.5,<2.0.0)", "libdeeplake (>=0.0.60,<0.0.61)", "librosa (>=0.10.0.post2,<0.11.0)", "lxml (>=4.9.2,<5.0.0)", "manifest-ml (>=0.0.1,<0.0.2)", "marqo (>=1.2.4,<2.0.0)", "momento (>=1.10.1,<2.0.0)", "nebula3-python (>=3.4.0,<4.0.0)", "neo4j (>=5.8.1,<6.0.0)", "networkx (>=2.6.3,<4)", "nlpcloud (>=1,<2)", "nltk (>=3,<4)", "nomic (>=1.0.43,<2.0.0)", "openai (>=0,<1)", "openlm (>=0.0.5,<0.0.6)", "opensearch-py (>=2.0.0,<3.0.0)", "pdfminer-six (>=20221105,<20221106)", "pexpect (>=4.8.0,<5.0.0)", "pgvector (>=0.1.6,<0.2.0)", "pinecone-client (>=2,<3)", "pinecone-text (>=0.4.2,<0.5.0)", "psycopg2-binary (>=2.9.5,<3.0.0)", "pymongo (>=4.3.3,<5.0.0)", "pyowm (>=3.3.0,<4.0.0)", "pypdf (>=3.4.0,<4.0.0)", "pytesseract (>=0.3.10,<0.4.0)", "python-arango (>=7.5.9,<8.0.0)", "pyvespa (>=0.33.0,<0.34.0)", "qdrant-client (>=1.3.1,<2.0.0)", "rdflib (>=6.3.2,<7.0.0)", "redis (>=4,<5)", "requests-toolbelt (>=1.0.0,<2.0.0)", "sentence-transformers (>=2,<3)", "singlestoredb (>=0.7.1,<0.8.0)", "tensorflow-text (>=2.11.0,<3.0.0)", "tigrisdb (>=1.0.0b6,<2.0.0)", "tiktoken (>=0.3.2,<0.6.0)", "torch (>=1,<3)", "transformers (>=4,<5)", "weaviate-client (>=3,<4)", "wikipedia (>=1,<2)", "wolframalpha (==5.0.0)"] +extended-testing = ["aiosqlite (>=0.19.0,<0.20.0)", "amazon-textract-caller (<2)", "anthropic (>=0.3.11,<0.4.0)", "arxiv (>=1.4,<2.0)", "assemblyai (>=0.17.0,<0.18.0)", "atlassian-python-api (>=3.36.0,<4.0.0)", "beautifulsoup4 (>=4,<5)", "bibtexparser (>=1.4.0,<2.0.0)", "cassio (>=0.1.0,<0.2.0)", "chardet (>=5.1.0,<6.0.0)", "dashvector (>=1.0.1,<2.0.0)", "esprima (>=4.0.1,<5.0.0)", "faiss-cpu (>=1,<2)", "feedparser (>=6.0.10,<7.0.0)", "geopandas (>=0.13.1,<0.14.0)", "gitpython (>=3.1.32,<4.0.0)", "gql (>=3.4.1,<4.0.0)", "html2text (>=2020.1.16,<2021.0.0)", "jinja2 (>=3,<4)", "jq (>=1.4.1,<2.0.0)", "lxml (>=4.9.2,<5.0.0)", "markdownify (>=0.11.6,<0.12.0)", "motor (>=3.3.1,<4.0.0)", "mwparserfromhell (>=0.6.4,<0.7.0)", "mwxml (>=0.3.3,<0.4.0)", "newspaper3k (>=0.2.8,<0.3.0)", "numexpr (>=2.8.6,<3.0.0)", "openai (>=0,<1)", "openapi-schema-pydantic (>=1.2,<2.0)", "pandas (>=2.0.1,<3.0.0)", "pdfminer-six (>=20221105,<20221106)", "pgvector (>=0.1.6,<0.2.0)", "psychicapi (>=0.8.0,<0.9.0)", "py-trello (>=0.19.0,<0.20.0)", "pymupdf (>=1.22.3,<2.0.0)", "pypdf (>=3.4.0,<4.0.0)", "pypdfium2 (>=4.10.0,<5.0.0)", "pyspark (>=3.4.0,<4.0.0)", "rank-bm25 (>=0.2.2,<0.3.0)", "rapidfuzz (>=3.1.1,<4.0.0)", "rapidocr-onnxruntime (>=1.3.2,<2.0.0)", "requests-toolbelt (>=1.0.0,<2.0.0)", "scikit-learn (>=1.2.2,<2.0.0)", "sqlite-vss (>=0.1.2,<0.2.0)", "streamlit (>=1.18.0,<2.0.0)", "sympy (>=1.12,<2.0)", "telethon (>=1.28.5,<2.0.0)", "timescale-vector (>=0.0.1,<0.0.2)", "tqdm (>=4.48.0)", "xata (>=1.0.0a7,<2.0.0)", "xmltodict (>=0.13.0,<0.14.0)"] +azure = ["azure-ai-formrecognizer (>=3.2.1,<4.0.0)", "azure-ai-vision (>=0.11.1b1,<0.12.0)", "azure-cognitiveservices-speech (>=1.28.0,<2.0.0)", "azure-core (>=1.26.4,<2.0.0)", "azure-cosmos (>=4.4.0b1,<5.0.0)", "azure-identity (>=1.12.0,<2.0.0)", "azure-search-documents (==11.4.0b8)", "openai (>=0,<1)"] +text-helpers = ["chardet (>=5.1.0,<6.0.0)"] +llms = ["clarifai (>=9.1.0)", "cohere (>=4,<5)", "huggingface_hub (>=0,<1)", "manifest-ml (>=0.0.1,<0.0.2)", "nlpcloud (>=1,<2)", "openai (>=0,<1)", "openlm (>=0.0.5,<0.0.6)", "torch (>=1,<3)", "transformers (>=4,<5)"] +clarifai = ["clarifai (>=9.1.0)"] +cohere = ["cohere (>=4,<5)"] +docarray = ["docarray[hnswlib] (>=0.32.0,<0.33.0)"] +javascript = ["esprima (>=4.0.1,<5.0.0)"] +openai = ["openai (>=0,<1)", "tiktoken (>=0.3.2,<0.6.0)"] +qdrant = ["qdrant-client (>=1.3.1,<2.0.0)"] +embeddings = ["sentence-transformers (>=2,<3)"] +cli = ["typer (>=0.9.0,<0.10.0)"] + +[[package]] +name = "langsmith" +version = "0.0.43" +description = "Client library to connect to the LangSmith LLM Tracing and Evaluation Platform." +category = "main" +optional = false +python-versions = ">=3.8.1,<4.0" + +[package.dependencies] +pydantic = ">=1,<3" +requests = ">=2,<3" + +[[package]] +name = "llama-index" +version = "0.8.43.post1" +description = "Interface between LLMs and your data" +category = "main" +optional = false +python-versions = ">=3.8.1,<3.12" + +[package.dependencies] +dataclasses-json = ">=0.5.7,<0.6.0" +fsspec = ">=2023.5.0" +langchain = ">=0.0.303" +nest-asyncio = ">=1.5.8,<2.0.0" +nltk = ">=3.8.1,<4.0.0" +numpy = "*" +openai = ">=0.26.4" +pandas = "*" +SQLAlchemy = {version = ">=2.0.15", extras = ["asyncio"]} +tenacity = ">=8.2.0,<9.0.0" +tiktoken = ">=0.3.3" +typing-extensions = ">=4.5.0" +typing-inspect = ">=0.8.0" +urllib3 = "<2" + +[[package]] +name = "marshmallow" +version = "3.20.1" +description = "A lightweight library for converting complex datatypes to and from native Python datatypes." +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +packaging = ">=17.0" + +[package.extras] +dev = ["pytest", "pytz", "simplejson", "mypy (==1.4.1)", "flake8 (==6.0.0)", "flake8-bugbear (==23.7.10)", "pre-commit (>=2.4,<4.0)", "tox"] +docs = ["sphinx (==7.0.1)", "sphinx-issues (==3.0.1)", "alabaster (==0.7.13)", "sphinx-version-warning (==1.1.2)", "autodocsumm (==0.2.11)"] +lint = ["mypy (==1.4.1)", "flake8 (==6.0.0)", "flake8-bugbear (==23.7.10)", "pre-commit (>=2.4,<4.0)"] +tests = ["pytest", "pytz", "simplejson"] + [[package]] name = "matplotlib" version = "3.7.3" @@ -595,6 +771,14 @@ category = "main" optional = false python-versions = ">=3.7" +[[package]] +name = "mypy-extensions" +version = "1.0.0" +description = "Type system extensions for programs checked with the mypy type checker." +category = "main" +optional = false +python-versions = ">=3.5" + [[package]] name = "nbclient" version = "0.6.8" @@ -650,10 +834,32 @@ pytest = ">=6.1.0" name = "nest-asyncio" version = "1.5.8" description = "Patch asyncio to allow nested event loops" -category = "dev" +category = "main" optional = false python-versions = ">=3.5" +[[package]] +name = "nltk" +version = "3.8.1" +description = "Natural Language Toolkit" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +click = "*" +joblib = "*" +regex = ">=2021.8.3" +tqdm = "*" + +[package.extras] +all = ["scikit-learn", "python-crfsuite", "requests", "numpy", "pyparsing", "twython", "scipy", "matplotlib"] +corenlp = ["requests"] +machine_learning = ["numpy", "python-crfsuite", "scikit-learn", "scipy"] +plot = ["matplotlib"] +tgrep = ["pyparsing"] +twitter = ["twython"] + [[package]] name = "nodeenv" version = "1.8.0" @@ -937,6 +1143,33 @@ category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +[[package]] +name = "pydantic" +version = "2.4.2" +description = "Data validation using Python type hints" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +annotated-types = ">=0.4.0" +pydantic-core = "2.10.1" +typing-extensions = ">=4.6.1" + +[package.extras] +email = ["email-validator (>=2.0.0)"] + +[[package]] +name = "pydantic-core" +version = "2.10.1" +description = "" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0" + [[package]] name = "pygments" version = "2.16.1" @@ -1078,7 +1311,7 @@ python-versions = "*" name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -1105,6 +1338,14 @@ python-versions = ">=3.8" attrs = ">=22.2.0" rpds-py = ">=0.7.0" +[[package]] +name = "regex" +version = "2023.10.3" +description = "Alternative regular expression module, to replace re." +category = "main" +optional = false +python-versions = ">=3.7" + [[package]] name = "requests" version = "2.31.0" @@ -1193,6 +1434,50 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" +[[package]] +name = "sniffio" +version = "1.3.0" +description = "Sniff out which async library your code is running under" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "sqlalchemy" +version = "2.0.21" +description = "Database Abstraction Library" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""} +typing-extensions = ">=4.2.0" + +[package.extras] +aiomysql = ["greenlet (!=0.4.17)", "aiomysql (>=0.2.0)"] +aiosqlite = ["greenlet (!=0.4.17)", "aiosqlite", "typing-extensions (!=3.10.0.1)"] +asyncio = ["greenlet (!=0.4.17)"] +asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)"] +mariadb_connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"] +mssql = ["pyodbc"] +mssql_pymssql = ["pymssql"] +mssql_pyodbc = ["pyodbc"] +mypy = ["mypy (>=0.910)"] +mysql = ["mysqlclient (>=1.4.0)"] +mysql_connector = ["mysql-connector-python"] +oracle = ["cx-oracle (>=7)"] +oracle_oracledb = ["oracledb (>=1.0.1)"] +postgresql = ["psycopg2 (>=2.7)"] +postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"] +postgresql_pg8000 = ["pg8000 (>=1.29.1)"] +postgresql_psycopg = ["psycopg (>=3.0.7)"] +postgresql_psycopg2binary = ["psycopg2-binary"] +postgresql_psycopg2cffi = ["psycopg2cffi"] +postgresql_psycopgbinary = ["psycopg[binary] (>=3.0.7)"] +pymysql = ["pymysql"] +sqlcipher = ["sqlcipher3-binary"] + [[package]] name = "stack-data" version = "0.6.3" @@ -1228,6 +1513,21 @@ category = "main" optional = false python-versions = ">=3.8" +[[package]] +name = "tiktoken" +version = "0.5.1" +description = "tiktoken is a fast BPE tokeniser for use with OpenAI's models" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +regex = ">=2022.1.18" +requests = ">=2.26.0" + +[package.extras] +blobfile = ["blobfile (>=2)"] + [[package]] name = "toml" version = "0.10.2" @@ -1297,6 +1597,18 @@ category = "main" optional = false python-versions = ">=3.8" +[[package]] +name = "typing-inspect" +version = "0.9.0" +description = "Runtime inspection utilities for typing module." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +mypy-extensions = ">=0.3.0" +typing-extensions = ">=3.7.4" + [[package]] name = "tzdata" version = "2023.3" @@ -1307,17 +1619,16 @@ python-versions = ">=2" [[package]] name = "urllib3" -version = "2.0.6" +version = "1.26.17" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] -secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"] -socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] -zstd = ["zstandard (>=0.18.0)"] +brotli = ["brotlicffi (>=0.8.0)", "brotli (==1.0.9)", "brotlipy (>=0.6.0)", "brotli (>=1.0.9)"] +secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"] +socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "virtualenv" @@ -1370,12 +1681,14 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-ena [metadata] lock-version = "1.1" -python-versions = ">=3.8.0,<4.0.0" -content-hash = "3894264c832ed41a4ffe97efbae5fe23b8b0297256e9c548d530eb2bdfc6c094" +python-versions = ">=3.8.1,<3.12" +content-hash = "160c318ebfd73c138cb9c8ad2cb8ff33079ca23c366591244ed7cff4a3d1ed52" [metadata.files] aiohttp = [] aiosignal = [] +annotated-types = [] +anyio = [] appnope = [] asttokens = [] async-timeout = [] @@ -1391,6 +1704,7 @@ comm = [] contourpy = [] coverage = [] cycler = [] +dataclasses-json = [] debugpy = [] decorator = [] distlib = [] @@ -1402,6 +1716,8 @@ fastjsonschema = [] filelock = [] fonttools = [] frozenlist = [] +fsspec = [] +greenlet = [] identify = [] idna = [] importlib-metadata = [] @@ -1411,18 +1727,26 @@ ipykernel = [] ipython = [] jedi = [] joblib = [] +jsonpatch = [] +jsonpointer = [] jsonschema = [] jsonschema-specifications = [] jupyter-client = [] jupyter-core = [] kiwisolver = [] +langchain = [] +langsmith = [] +llama-index = [] +marshmallow = [] matplotlib = [] matplotlib-inline = [] multidict = [] +mypy-extensions = [] nbclient = [] nbformat = [] nbmake = [] nest-asyncio = [] +nltk = [] nodeenv = [] numpy = [] openai = [] @@ -1446,6 +1770,8 @@ ptyprocess = [] pure-eval = [] py = [] pycparser = [] +pydantic = [] +pydantic-core = [] pygments = [] pyparsing = [] pytest = [] @@ -1460,15 +1786,19 @@ pywin32 = [] pyyaml = [] pyzmq = [] referencing = [] +regex = [] requests = [] rpds-py = [] scikit-learn = [] scipy = [] setuptools-scm = [] six = [] +sniffio = [] +sqlalchemy = [] stack-data = [] tenacity = [] threadpoolctl = [] +tiktoken = [] toml = [] tomli = [] tornado = [] @@ -1476,6 +1806,7 @@ tqdm = [] traitlets = [] types-pytz = [] typing-extensions = [] +typing-inspect = [] tzdata = [] urllib3 = [] virtualenv = [] diff --git a/pyproject.toml b/pyproject.toml index 293fe40..4c1983a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,10 +15,12 @@ nbwrite = "nbwrite.cli:cli" [tool.poetry.dependencies] pytest = ">=6.1.0" -python = ">=3.8.0,<4.0.0" +python = ">=3.8.1,<3.12" openai = {extras = ["embeddings"], version = "^0.28.1"} pathlib = "^1.0.1" click = "^8.1.7" +langchain = "^0.0.312" +llama-index = "^0.8.43" [tool.poetry.dev-dependencies] pytest = "^7.1.0" diff --git a/tests/resources/demo.ipynb b/tests/resources/demo.ipynb index b680e38..b86ff77 100644 --- a/tests/resources/demo.ipynb +++ b/tests/resources/demo.ipynb @@ -6,6 +6,17 @@ "source": [ "# Using the NotebookRun class to run a notebook from a conventional pytest function" ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "vscode": { + "languageId": "plaintext" + } + }, + "outputs": [], + "source": [] } ], "metadata": { From c42db5e820afb3aa159f64fe4fff8f198d8cda51 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 11:10:55 +0000 Subject: [PATCH 14/59] fix --- .github/workflows/pytest.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index ec70ec6..5581fea 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -3,8 +3,8 @@ on: schedule: - cron: 0 13 * * 1 # Every Monday at 1PM UTC (9AM EST) pull_request: -# test in containerised and OS environments -# jobs: +test in containerised and OS environments +jobs: # test-container: # runs-on: ubuntu-22.04 # steps: @@ -25,8 +25,8 @@ on: - macos-latest python-version: - "3.8" - - "3.9" - - "3.10" + # - "3.9" + # - "3.10" - "3.11" runs-on: ${{ matrix.os }} steps: From 6efa31e142126567dd4bc87980aad31950b72b37 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 11:11:31 +0000 Subject: [PATCH 15/59] f --- .github/workflows/pytest.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 5581fea..59a30ce 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -3,7 +3,7 @@ on: schedule: - cron: 0 13 * * 1 # Every Monday at 1PM UTC (9AM EST) pull_request: -test in containerised and OS environments +# test in containerised and OS environments jobs: # test-container: # runs-on: ubuntu-22.04 @@ -18,7 +18,7 @@ jobs: # file: coverage.xml pytest: strategy: - fail-fast: false + fail-fast: true matrix: os: - ubuntu-latest From 82e427782570b4dd493439ad5550e2184a11da06 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 11:22:05 +0000 Subject: [PATCH 16/59] nb path --- src/nbwrite/cli.py | 9 +++++++-- src/nbwrite/writer.py | 6 ++++++ tests/test_cli.py | 7 +++++++ 3 files changed, 20 insertions(+), 2 deletions(-) create mode 100644 src/nbwrite/writer.py diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index 8fc20cd..c0b0683 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -2,6 +2,8 @@ import click +import nbwrite.writer as writer + @click.group() def cli(): @@ -16,10 +18,13 @@ def index(): @cli.command() -@click.argument("notebook", type=click.Path(exists=True)) -def complete(path: Path): +@click.argument( + "notebook", type=click.Path(exists=True, path_type=Path, dir_okay=False) +) +def complete(notebook: Path): """Write demo notebooks based on prompts in the notebook and the index""" click.echo("Searching index...") + writer.complete(notebook) if __name__ == "__main__": diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py new file mode 100644 index 0000000..2a25ca2 --- /dev/null +++ b/src/nbwrite/writer.py @@ -0,0 +1,6 @@ +from pathlib import Path + + +def complete(path: Path): + """Write demo notebooks based on prompts in the notebook and the index""" + pass diff --git a/tests/test_cli.py b/tests/test_cli.py index 1ce0d75..1f61f13 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -8,3 +8,10 @@ def test_index(): result = runner.invoke(cli, ["index"]) assert result.exit_code == 0 assert result.output == "Hello, world!\nBuilding index...\n" + + +def test_complete(): + runner = CliRunner() + result = runner.invoke(cli, ["complete", "tests/resources/demo.ipynb"]) + assert result.exit_code == 0 + assert result.output == "Hello, world!\nSearching index...\n" From d31d66ed15b1e11b44bc856a43fcfb0cde301943 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 11:47:26 +0000 Subject: [PATCH 17/59] basic openai --- src/nbwrite/writer.py | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 2a25ca2..358bb98 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -1,6 +1,26 @@ +import os from pathlib import Path +import openai + def complete(path: Path): """Write demo notebooks based on prompts in the notebook and the index""" - pass + # openai.organization = os.getenv("OPENAI_ORG_ID") + openai.api_key = os.getenv("OPENAI_API_KEY") + + completion = openai.ChatCompletion.create( + model="gpt-3.5-turbo", + messages=[ + { + "role": "system", + "content": "You are Python developer who writes documentation in the form of JSON-based Jupyter notebooks (ipynb files).\nAll of your outputs are valid notebook JSON files with cells that are alternating markdown and Python content. Your tone should be concise, friendly, and professional.", + }, + { + "role": "user", + "content": "I need a demo for how to reverse a linked list in Python", + }, + ], + ) + + print(completion.choices[0].message) From 078c63a78684d491ea93fc7606e91a65f532a637 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 12:11:44 +0000 Subject: [PATCH 18/59] wandb --- .gitignore | 3 +- poetry.lock | 174 +++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 1 + src/nbwrite/writer.py | 71 +++++++++++++---- 4 files changed, 233 insertions(+), 16 deletions(-) diff --git a/.gitignore b/.gitignore index be4110d..74a6342 100644 --- a/.gitignore +++ b/.gitignore @@ -134,4 +134,5 @@ typeshed trash **/_build -.testvenv \ No newline at end of file +.testvenv +wandb \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index 7a0dd29..3fb35f0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -58,6 +58,14 @@ doc = ["packaging", "sphinx", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquer test = ["anyio", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)", "mock (>=4)"] trio = ["trio (<0.22)"] +[[package]] +name = "appdirs" +version = "1.4.4" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" +optional = false +python-versions = "*" + [[package]] name = "appnope" version = "0.1.3" @@ -258,6 +266,17 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "docker-pycreds" +version = "0.4.0" +description = "Python bindings for the docker credentials store API" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +six = ">=1.4.0" + [[package]] name = "et-xmlfile" version = "1.1.0" @@ -385,6 +404,31 @@ smb = ["smbprotocol"] ssh = ["paramiko"] tqdm = ["tqdm"] +[[package]] +name = "gitdb" +version = "4.0.10" +description = "Git Object Database" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +smmap = ">=3.0.1,<6" + +[[package]] +name = "gitpython" +version = "3.1.37" +description = "GitPython is a Python library used to interact with Git repositories" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +gitdb = ">=4.0.1,<5" + +[package.extras] +test = ["black", "coverage", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar"] + [[package]] name = "greenlet" version = "3.0.0" @@ -996,6 +1040,14 @@ category = "main" optional = false python-versions = "*" +[[package]] +name = "pathtools" +version = "0.1.2" +description = "File system general utilities" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "pexpect" version = "4.8.0" @@ -1097,11 +1149,19 @@ python-versions = ">=3.7.0" [package.dependencies] wcwidth = "*" +[[package]] +name = "protobuf" +version = "4.24.4" +description = "" +category = "main" +optional = false +python-versions = ">=3.7" + [[package]] name = "psutil" version = "5.9.5" description = "Cross-platform lib for process and system monitoring in Python." -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" @@ -1408,6 +1468,59 @@ test = ["pytest", "pytest-cov", "pytest-xdist", "asv", "mpmath", "gmpy2", "threa doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-panels (>=0.5.2)", "matplotlib (>2)", "numpydoc", "sphinx-tabs"] dev = ["mypy", "typing-extensions", "pycodestyle", "flake8"] +[[package]] +name = "sentry-sdk" +version = "1.32.0" +description = "Python client for Sentry (https://sentry.io)" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +certifi = "*" +urllib3 = {version = ">=1.26.11", markers = "python_version >= \"3.6\""} + +[package.extras] +aiohttp = ["aiohttp (>=3.5)"] +arq = ["arq (>=0.23)"] +asyncpg = ["asyncpg (>=0.23)"] +beam = ["apache-beam (>=2.12)"] +bottle = ["bottle (>=0.12.13)"] +celery = ["celery (>=3)"] +chalice = ["chalice (>=1.16.0)"] +clickhouse-driver = ["clickhouse-driver (>=0.2.0)"] +django = ["django (>=1.8)"] +falcon = ["falcon (>=1.4)"] +fastapi = ["fastapi (>=0.79.0)"] +flask = ["flask (>=0.11)", "blinker (>=1.1)", "markupsafe"] +grpcio = ["grpcio (>=1.21.1)"] +httpx = ["httpx (>=0.16.0)"] +huey = ["huey (>=2)"] +loguru = ["loguru (>=0.5)"] +opentelemetry = ["opentelemetry-distro (>=0.35b0)"] +opentelemetry-experimental = ["opentelemetry-distro (>=0.40b0,<1.0.0)", "opentelemetry-instrumentation-aiohttp-client (>=0.40b0,<1.0.0)", "opentelemetry-instrumentation-django (>=0.40b0,<1.0.0)", "opentelemetry-instrumentation-fastapi (>=0.40b0,<1.0.0)", "opentelemetry-instrumentation-flask (>=0.40b0,<1.0.0)", "opentelemetry-instrumentation-requests (>=0.40b0,<1.0.0)", "opentelemetry-instrumentation-sqlite3 (>=0.40b0,<1.0.0)", "opentelemetry-instrumentation-urllib (>=0.40b0,<1.0.0)"] +pure_eval = ["pure-eval", "executing", "asttokens"] +pymongo = ["pymongo (>=3.1)"] +pyspark = ["pyspark (>=2.4.4)"] +quart = ["quart (>=0.16.1)", "blinker (>=1.1)"] +rq = ["rq (>=0.6)"] +sanic = ["sanic (>=0.8)"] +sqlalchemy = ["sqlalchemy (>=1.2)"] +starlette = ["starlette (>=0.19.1)"] +starlite = ["starlite (>=1.48)"] +tornado = ["tornado (>=5)"] + +[[package]] +name = "setproctitle" +version = "1.3.3" +description = "A Python module to customize the process title" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +test = ["pytest"] + [[package]] name = "setuptools-scm" version = "8.0.4" @@ -1434,6 +1547,14 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" +[[package]] +name = "smmap" +version = "5.0.1" +description = "A pure Python implementation of a sliding window memory map manager" +category = "main" +optional = false +python-versions = ">=3.7" + [[package]] name = "sniffio" version = "1.3.0" @@ -1647,6 +1768,45 @@ platformdirs = ">=3.9.1,<4" docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx-argparse (>=0.4)", "sphinx (>=7.1.2)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage-enable-subprocess (>=1)", "coverage (>=7.2.7)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "pytest (>=7.4)", "setuptools (>=68)", "time-machine (>=2.10)"] +[[package]] +name = "wandb" +version = "0.15.12" +description = "A CLI and library for interacting with the Weights & Biases API." +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +appdirs = ">=1.4.3" +Click = ">=7.1,<8.0.0 || >8.0.0" +docker-pycreds = ">=0.4.0" +GitPython = ">=1.0.0,<3.1.29 || >3.1.29" +pathtools = "*" +protobuf = [ + {version = ">=3.12.0,<4.21.0 || >4.21.0,<5", markers = "python_version < \"3.9\" and sys_platform == \"linux\""}, + {version = ">=3.15.0,<4.21.0 || >4.21.0,<5", markers = "python_version == \"3.9\" and sys_platform == \"linux\""}, + {version = ">=3.19.0,<4.21.0 || >4.21.0,<5", markers = "python_version > \"3.9\" and sys_platform == \"linux\" or sys_platform != \"linux\""}, +] +psutil = ">=5.0.0" +PyYAML = "*" +requests = ">=2.0.0,<3" +sentry-sdk = ">=1.0.0" +setproctitle = "*" +typing-extensions = {version = "*", markers = "python_version < \"3.10\""} + +[package.extras] +async = ["httpx (>=0.22.0)"] +aws = ["boto3"] +azure = ["azure-identity", "azure-storage-blob"] +gcp = ["google-cloud-storage"] +kubeflow = ["kubernetes", "minio", "google-cloud-storage", "sh"] +launch = ["awscli", "azure-identity", "azure-containerregistry", "azure-storage-blob", "boto3", "botocore", "chardet", "google-auth", "google-cloud-artifact-registry", "google-cloud-compute", "google-cloud-storage", "iso8601", "kubernetes", "optuna", "nbconvert", "nbformat", "typing-extensions", "PyYAML (>=6.0.0)"] +media = ["numpy", "moviepy", "pillow", "bokeh", "soundfile", "plotly", "rdkit-pypi"] +models = ["cloudpickle"] +nexus = ["wandb-core (>=0.16.0b1)"] +perf = ["orjson"] +sweeps = ["sweeps (>=0.2.0)"] + [[package]] name = "wcwidth" version = "0.2.8" @@ -1682,13 +1842,14 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-ena [metadata] lock-version = "1.1" python-versions = ">=3.8.1,<3.12" -content-hash = "160c318ebfd73c138cb9c8ad2cb8ff33079ca23c366591244ed7cff4a3d1ed52" +content-hash = "ec3b1e8a40748f6cf0dad6b074fa44999c5cf8424dbcdb8a40721d0b74f2d530" [metadata.files] aiohttp = [] aiosignal = [] annotated-types = [] anyio = [] +appdirs = [] appnope = [] asttokens = [] async-timeout = [] @@ -1708,6 +1869,7 @@ dataclasses-json = [] debugpy = [] decorator = [] distlib = [] +docker-pycreds = [] et-xmlfile = [] exceptiongroup = [] execnet = [] @@ -1717,6 +1879,8 @@ filelock = [] fonttools = [] frozenlist = [] fsspec = [] +gitdb = [] +gitpython = [] greenlet = [] identify = [] idna = [] @@ -1756,6 +1920,7 @@ pandas = [] pandas-stubs = [] parso = [] pathlib = [] +pathtools = [] pexpect = [] pickleshare = [] pillow = [] @@ -1765,6 +1930,7 @@ plotly = [] pluggy = [] pre-commit = [] prompt-toolkit = [] +protobuf = [] psutil = [] ptyprocess = [] pure-eval = [] @@ -1791,8 +1957,11 @@ requests = [] rpds-py = [] scikit-learn = [] scipy = [] +sentry-sdk = [] +setproctitle = [] setuptools-scm = [] six = [] +smmap = [] sniffio = [] sqlalchemy = [] stack-data = [] @@ -1810,6 +1979,7 @@ typing-inspect = [] tzdata = [] urllib3 = [] virtualenv = [] +wandb = [] wcwidth = [] yarl = [] zipp = [] diff --git a/pyproject.toml b/pyproject.toml index 4c1983a..444db29 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,6 +21,7 @@ pathlib = "^1.0.1" click = "^8.1.7" langchain = "^0.0.312" llama-index = "^0.8.43" +wandb = "^0.15.12" [tool.poetry.dev-dependencies] pytest = "^7.1.0" diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 358bb98..3f26ae0 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -1,26 +1,71 @@ +import datetime import os from pathlib import Path import openai +from wandb.sdk.data_types.trace_tree import Trace + +import wandb def complete(path: Path): """Write demo notebooks based on prompts in the notebook and the index""" # openai.organization = os.getenv("OPENAI_ORG_ID") openai.api_key = os.getenv("OPENAI_API_KEY") + temperature = 0.7 + model_name = "gpt-3.5-turbo" + system_message = "You are Python developer who writes documentation in the form of JSON-based Jupyter notebooks (ipynb files).\nAll of your outputs are valid notebook JSON files with cells that are alternating markdown and Python content. Your tone should be concise, friendly, and professional." + doc_query = "I need a demo for how to reverse a linked list in Python" + messages = [ + { + "role": "system", + "content": system_message, + }, + { + "role": "user", + "content": doc_query, + }, + ] + wandb.init(project="nbgen") + + start_time_ms = round(datetime.datetime.now().timestamp() * 1000) + response = openai.ChatCompletion.create( + model=model_name, temperature=temperature, messages=messages + ) - completion = openai.ChatCompletion.create( - model="gpt-3.5-turbo", - messages=[ - { - "role": "system", - "content": "You are Python developer who writes documentation in the form of JSON-based Jupyter notebooks (ipynb files).\nAll of your outputs are valid notebook JSON files with cells that are alternating markdown and Python content. Your tone should be concise, friendly, and professional.", - }, - { - "role": "user", - "content": "I need a demo for how to reverse a linked list in Python", - }, - ], + llm_end_time_ms = round(datetime.datetime.now().timestamp() * 1000) + token_usage = response["usage"].to_dict() + + root_span = Trace(name="LLMChain", kind="chain", start_time_ms=start_time_ms) + # wandb.log({f'intermediate.{i}': response_text}, commit=False) + response_text = response["choices"][0]["message"]["content"] + llm_span = Trace( + name="OpenAI", + kind="llm", + status_code="success", + metadata={ + "temperature": temperature, + "token_usage": token_usage, + "model_name": model_name, + }, + start_time_ms=start_time_ms, + end_time_ms=llm_end_time_ms, + inputs={"system_prompt": system_message, "query": doc_query}, + outputs={"response": response_text}, ) + root_span.add_child(llm_span) + + root_span.add_child(llm_span) + # root_span.add_inputs_and_outputs( + # inputs={"query": doc}, + # outputs={"response": response_text}) + + # update the Chain span's end time + root_span._span.end_time_ms = llm_end_time_ms - print(completion.choices[0].message) + # add metadata to the trace table + accuracy = 0.7 + wandb.log({"accuracy": accuracy, "overall_f1": 0.9}, commit=False) + # log all spans to W&B by logging the root span + root_span.log(name="docs_trace") + print(response.choices[0].message) From e71b7e8bc23cf95cd4b800aea1c078f7cfb0e799 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 13:53:44 +0000 Subject: [PATCH 19/59] gen notebook output --- poetry.lock | 24 +++++------ pyproject.toml | 1 + src/nbwrite/cli.py | 5 ++- src/nbwrite/writer.py | 86 +++++++++++++-------------------------- tests/resources/out.ipynb | 40 ++++++++++++++++++ tests/test_cli.py | 6 ++- 6 files changed, 88 insertions(+), 74 deletions(-) create mode 100644 tests/resources/out.ipynb diff --git a/poetry.lock b/poetry.lock index 3fb35f0..e0726ac 100644 --- a/poetry.lock +++ b/poetry.lock @@ -322,7 +322,7 @@ tests = ["asttokens (>=2.1.0)", "ipython", "pytest", "coverage", "coverage-enabl name = "fastjsonschema" version = "2.18.1" description = "Fastest Python implementation of JSON schema" -category = "dev" +category = "main" optional = false python-versions = "*" @@ -612,7 +612,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, name = "jsonschema" version = "4.19.1" description = "An implementation of JSON Schema validation for Python" -category = "dev" +category = "main" optional = false python-versions = ">=3.8" @@ -632,7 +632,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jsonschema-specifications" version = "2023.7.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" -category = "dev" +category = "main" optional = false python-versions = ">=3.8" @@ -664,7 +664,7 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt name = "jupyter-core" version = "5.4.0" description = "Jupyter core package. A base package on which Jupyter projects rely." -category = "dev" +category = "main" optional = false python-versions = ">=3.8" @@ -845,7 +845,7 @@ test = ["black", "check-manifest", "flake8", "ipykernel", "ipython", "ipywidgets name = "nbformat" version = "5.9.2" description = "The Jupyter Notebook format" -category = "dev" +category = "main" optional = false python-versions = ">=3.8" @@ -1083,7 +1083,7 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa name = "pkgutil-resolve-name" version = "1.3.10" description = "Resolve a name to an object." -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -1091,7 +1091,7 @@ python-versions = ">=3.6" name = "platformdirs" version = "3.11.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -1363,7 +1363,7 @@ python-versions = "*" name = "pywin32" version = "306" description = "Python for Window Extensions" -category = "dev" +category = "main" optional = false python-versions = "*" @@ -1390,7 +1390,7 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""} name = "referencing" version = "0.30.2" description = "JSON Referencing + Python" -category = "dev" +category = "main" optional = false python-versions = ">=3.8" @@ -1428,7 +1428,7 @@ use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] name = "rpds-py" version = "0.10.6" description = "Python bindings to Rust's persistent data structures (rpds)" -category = "dev" +category = "main" optional = false python-versions = ">=3.8" @@ -1694,7 +1694,7 @@ telegram = ["requests"] name = "traitlets" version = "5.11.2" description = "Traitlets Python configuration system" -category = "dev" +category = "main" optional = false python-versions = ">=3.8" @@ -1842,7 +1842,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-ena [metadata] lock-version = "1.1" python-versions = ">=3.8.1,<3.12" -content-hash = "ec3b1e8a40748f6cf0dad6b074fa44999c5cf8424dbcdb8a40721d0b74f2d530" +content-hash = "6b90a63031be60cd462afea4f2437342d4e87e5a4848c48e934f5d9e06190460" [metadata.files] aiohttp = [] diff --git a/pyproject.toml b/pyproject.toml index 444db29..f3729b6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,6 +22,7 @@ click = "^8.1.7" langchain = "^0.0.312" llama-index = "^0.8.43" wandb = "^0.15.12" +nbformat = "^5.9.2" [tool.poetry.dev-dependencies] pytest = "^7.1.0" diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index c0b0683..ab109d8 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -21,10 +21,11 @@ def index(): @click.argument( "notebook", type=click.Path(exists=True, path_type=Path, dir_okay=False) ) -def complete(notebook: Path): +@click.argument("out", type=click.Path(exists=False, path_type=Path, dir_okay=False)) +def complete(notebook: Path, out: Path): """Write demo notebooks based on prompts in the notebook and the index""" click.echo("Searching index...") - writer.complete(notebook) + writer.complete(notebook, out) if __name__ == "__main__": diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 3f26ae0..2de71bb 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -1,71 +1,41 @@ import datetime import os from pathlib import Path +from typing import Any, Dict, List -import openai -from wandb.sdk.data_types.trace_tree import Trace +from langchain.callbacks import wandb_tracing_enabled as _ +from langchain.llms import OpenAI +from langchain.prompts import PromptTemplate +from langchain.schema import HumanMessage +from nbformat import write +from nbformat.v4 import new_code_cell, new_markdown_cell, new_notebook -import wandb - -def complete(path: Path): +def complete(path: Path, out_path: Path): """Write demo notebooks based on prompts in the notebook and the index""" # openai.organization = os.getenv("OPENAI_ORG_ID") - openai.api_key = os.getenv("OPENAI_API_KEY") temperature = 0.7 - model_name = "gpt-3.5-turbo" - system_message = "You are Python developer who writes documentation in the form of JSON-based Jupyter notebooks (ipynb files).\nAll of your outputs are valid notebook JSON files with cells that are alternating markdown and Python content. Your tone should be concise, friendly, and professional." - doc_query = "I need a demo for how to reverse a linked list in Python" - messages = [ - { - "role": "system", - "content": system_message, - }, - { - "role": "user", - "content": doc_query, - }, - ] - wandb.init(project="nbgen") + llm = OpenAI(temperature=temperature) + task = "reverse a list" - start_time_ms = round(datetime.datetime.now().timestamp() * 1000) - response = openai.ChatCompletion.create( - model=model_name, temperature=temperature, messages=messages + prompt = PromptTemplate.from_template( + "Write a short Python snippet (max 15 lines) that implements {task}?" ) + messages = [HumanMessage(content=prompt.format(task=task))] + code_out = llm.predict_messages(messages) - llm_end_time_ms = round(datetime.datetime.now().timestamp() * 1000) - token_usage = response["usage"].to_dict() - - root_span = Trace(name="LLMChain", kind="chain", start_time_ms=start_time_ms) - # wandb.log({f'intermediate.{i}': response_text}, commit=False) - response_text = response["choices"][0]["message"]["content"] - llm_span = Trace( - name="OpenAI", - kind="llm", - status_code="success", - metadata={ - "temperature": temperature, - "token_usage": token_usage, - "model_name": model_name, - }, - start_time_ms=start_time_ms, - end_time_ms=llm_end_time_ms, - inputs={"system_prompt": system_message, "query": doc_query}, - outputs={"response": response_text}, + description_prompt = PromptTemplate.from_template( + "Write a snippet of markdown describing how the following code works to achieve the goal of {task}.\n\n{code}?" ) - root_span.add_child(llm_span) - - root_span.add_child(llm_span) - # root_span.add_inputs_and_outputs( - # inputs={"query": doc}, - # outputs={"response": response_text}) - - # update the Chain span's end time - root_span._span.end_time_ms = llm_end_time_ms - - # add metadata to the trace table - accuracy = 0.7 - wandb.log({"accuracy": accuracy, "overall_f1": 0.9}, commit=False) - # log all spans to W&B by logging the root span - root_span.log(name="docs_trace") - print(response.choices[0].message) + messages = [ + HumanMessage(content=description_prompt.format(task=task, code=code_out)) + ] + description_out = llm.predict_messages(messages) + title = "AI!" + sources = [code_out.content] + nb = new_notebook() + # nb.metadata = metadata + nb.cells.append(new_markdown_cell(f"# {title}\n\n{description_out.content}")) + for src in sources: + nb.cells.append(new_code_cell(src)) + write(nb, str(out_path)) diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb new file mode 100644 index 0000000..23aac32 --- /dev/null +++ b/tests/resources/out.ipynb @@ -0,0 +1,40 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "8bcc5c6a", + "metadata": {}, + "source": [ + "# AI!\n", + "\n", + "\n", + "\n", + "This code snippet uses a `for` loop to iterate over the elements of the given list in reverse order and append them to a new list `rev_list`. Finally, `rev_list` is returned after all elements have been added. The output of the code is `[5,4,3,2,1]`, which is the reverse of the given list `[1,2,3,4,5]`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "698b291f", + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "\n", + "def reverse_list(list): \n", + " rev_list = [] \n", + " for i in range(len(list)-1,-1,-1): \n", + " rev_list.append(list[i]) \n", + " return rev_list \n", + " \n", + "# Driver Code \n", + "list = [1,2,3,4,5] \n", + "rev_list = reverse_list(list) \n", + "print(rev_list)" + ] + } + ], + "metadata": {}, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/tests/test_cli.py b/tests/test_cli.py index 1f61f13..b32d095 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -12,6 +12,8 @@ def test_index(): def test_complete(): runner = CliRunner() - result = runner.invoke(cli, ["complete", "tests/resources/demo.ipynb"]) + result = runner.invoke( + cli, ["complete", "tests/resources/demo.ipynb", "tests/resources/out.ipynb"] + ) + print(result.output) assert result.exit_code == 0 - assert result.output == "Hello, world!\nSearching index...\n" From 903cf96ed4223dcf6a7ae0476ea1d189ab398898 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 12 Oct 2023 14:03:42 +0000 Subject: [PATCH 20/59] output nb --- tests/resources/out.ipynb | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index 23aac32..21e6833 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -34,7 +34,17 @@ ] } ], - "metadata": {}, + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python", + "version": "3.10.12" + } + }, "nbformat": 4, "nbformat_minor": 5 } From 1e2b0d1aa406f43ee37f80af1175f4f6a29d009a Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Fri, 13 Oct 2023 11:39:09 +0000 Subject: [PATCH 21/59] doc context --- src/nbwrite/writer.py | 29 ++++++++++++--- tests/resources/buildenv/docs/demo1.yaml | 10 +++++ tests/resources/out.ipynb | 47 ++++++++++++------------ 3 files changed, 57 insertions(+), 29 deletions(-) create mode 100644 tests/resources/buildenv/docs/demo1.yaml diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 2de71bb..2f86e93 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -1,14 +1,27 @@ import datetime +import importlib.util import os from pathlib import Path from typing import Any, Dict, List from langchain.callbacks import wandb_tracing_enabled as _ -from langchain.llms import OpenAI +from langchain.llms.openai import OpenAI from langchain.prompts import PromptTemplate from langchain.schema import HumanMessage from nbformat import write -from nbformat.v4 import new_code_cell, new_markdown_cell, new_notebook +from nbformat.v4 import ( + new_code_cell, + new_markdown_cell, + new_notebook, + reads, + writes, +) + +lib = importlib.util.find_spec("nbmake") + +# Assumes the 'openai-python' repository exists in the user's root directory +code_root = Path(lib.submodule_search_locations._path[0]) # type: ignore +code = (code_root / "nb_run.py").read_text() def complete(path: Path, out_path: Path): @@ -16,12 +29,14 @@ def complete(path: Path, out_path: Path): # openai.organization = os.getenv("OPENAI_ORG_ID") temperature = 0.7 llm = OpenAI(temperature=temperature) - task = "reverse a list" + task = ( + "use nbmake's NotebookRun class to test 'res/x.ipynb' from a Python application" + ) prompt = PromptTemplate.from_template( - "Write a short Python snippet (max 15 lines) that implements {task}?" + "Write an executable Python example in under 50 lines that implements '{task}'.\n\nUse this relevant dependency:\n\n{code}" ) - messages = [HumanMessage(content=prompt.format(task=task))] + messages = [HumanMessage(content=prompt.format(task=task, code=code))] code_out = llm.predict_messages(messages) description_prompt = PromptTemplate.from_template( @@ -38,4 +53,8 @@ def complete(path: Path, out_path: Path): nb.cells.append(new_markdown_cell(f"# {title}\n\n{description_out.content}")) for src in sources: nb.cells.append(new_code_cell(src)) + + # double check some basic structure + string = writes(nb) + _ = reads(string) write(nb, str(out_path)) diff --git a/tests/resources/buildenv/docs/demo1.yaml b/tests/resources/buildenv/docs/demo1.yaml new file mode 100644 index 0000000..0a25759 --- /dev/null +++ b/tests/resources/buildenv/docs/demo1.yaml @@ -0,0 +1,10 @@ +title: HTTP API +description: How to use the API to start a simulation then query the state +steps: + - Use the PUT endpoint to define a segment + - Use the POST endpoint to start a simulation + - Use the GET endpoint to query the state of the simulation +assertions: + - check that the simulation completed successfully +components: + - frontier_ct_definition.ComputationalTwin \ No newline at end of file diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index 21e6833..0d0197a 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -2,49 +2,48 @@ "cells": [ { "cell_type": "markdown", - "id": "8bcc5c6a", + "id": "7fe5e3d5", "metadata": {}, "source": [ "# AI!\n", "\n", "\n", "\n", - "This code snippet uses a `for` loop to iterate over the elements of the given list in reverse order and append them to a new list `rev_list`. Finally, `rev_list` is returned after all elements have been added. The output of the code is `[5,4,3,2,1]`, which is the reverse of the given list `[1,2,3,4,5]`." + "This snippet of code uses nbmake's NotebookRun class to test `res/x.ipynb` from a Python application. It starts by setting the `path` to the notebook, and the `timeout` for the notebook execution. Then a `NotebookRun` instance is created using the `filename` and `default_timeout` arguments. The notebook is then executed, and the result is checked for errors. If an error is found, it is printed out, otherwise a success message is printed." ] }, { "cell_type": "code", "execution_count": null, - "id": "698b291f", + "id": "602a0161", "metadata": {}, "outputs": [], "source": [ "\n", + "# Example Usage\n", + "if __name__ == \"__main__\":\n", + " # Path of the notebook to run\n", + " path = Path(\"res/x.ipynb\")\n", "\n", - "def reverse_list(list): \n", - " rev_list = [] \n", - " for i in range(len(list)-1,-1,-1): \n", - " rev_list.append(list[i]) \n", - " return rev_list \n", - " \n", - "# Driver Code \n", - "list = [1,2,3,4,5] \n", - "rev_list = reverse_list(list) \n", - "print(rev_list)" + " # Timeout for the notebook execution\n", + " timeout = 10\n", + "\n", + " # Create a NotebookRun instance\n", + " run = NotebookRun(filename=path, default_timeout=timeout)\n", + "\n", + " # Execute the notebook\n", + " res = run.execute()\n", + "\n", + " # Check for errors\n", + " if res.error is not None:\n", + " print(f\"Error: {res.error.summary}\")\n", + " print(f\"Traceback:\\n{res.error.trace}\")\n", + " else:\n", + " print(\"Notebook execution successful\")" ] } ], - "metadata": { - "kernelspec": { - "display_name": ".venv", - "language": "python", - "name": "python3" - }, - "language_info": { - "name": "python", - "version": "3.10.12" - } - }, + "metadata": {}, "nbformat": 4, "nbformat_minor": 5 } From 52db9bd51f50014b8b752d6b45a01e228f97c897 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Fri, 13 Oct 2023 11:45:59 +0000 Subject: [PATCH 22/59] use chain --- src/nbwrite/writer.py | 15 +++-------- tests/resources/out.ipynb | 53 +++++++++++++++++++++------------------ 2 files changed, 33 insertions(+), 35 deletions(-) diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 2f86e93..6499f01 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -36,21 +36,14 @@ def complete(path: Path, out_path: Path): prompt = PromptTemplate.from_template( "Write an executable Python example in under 50 lines that implements '{task}'.\n\nUse this relevant dependency:\n\n{code}" ) - messages = [HumanMessage(content=prompt.format(task=task, code=code))] - code_out = llm.predict_messages(messages) - description_prompt = PromptTemplate.from_template( - "Write a snippet of markdown describing how the following code works to achieve the goal of {task}.\n\n{code}?" - ) - messages = [ - HumanMessage(content=description_prompt.format(task=task, code=code_out)) - ] - description_out = llm.predict_messages(messages) + chain = prompt | llm + code_out = chain.invoke({"task": task, "code": code}) title = "AI!" - sources = [code_out.content] + sources = [code_out] nb = new_notebook() # nb.metadata = metadata - nb.cells.append(new_markdown_cell(f"# {title}\n\n{description_out.content}")) + nb.cells.append(new_markdown_cell(f"# {title}")) for src in sources: nb.cells.append(new_code_cell(src)) diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index 0d0197a..b30215b 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -2,48 +2,53 @@ "cells": [ { "cell_type": "markdown", - "id": "7fe5e3d5", + "id": "b646bc86", "metadata": {}, "source": [ - "# AI!\n", - "\n", - "\n", - "\n", - "This snippet of code uses nbmake's NotebookRun class to test `res/x.ipynb` from a Python application. It starts by setting the `path` to the notebook, and the `timeout` for the notebook execution. Then a `NotebookRun` instance is created using the `filename` and `default_timeout` arguments. The notebook is then executed, and the result is checked for errors. If an error is found, it is printed out, otherwise a success message is printed." + "# AI!" ] }, { "cell_type": "code", "execution_count": null, - "id": "602a0161", + "id": "30452f6f", "metadata": {}, "outputs": [], "source": [ "\n", - "# Example Usage\n", - "if __name__ == \"__main__\":\n", - " # Path of the notebook to run\n", - " path = Path(\"res/x.ipynb\")\n", + "# Executable Python example\n", "\n", - " # Timeout for the notebook execution\n", - " timeout = 10\n", + "from pathlib import Path\n", + "import nbformat\n", + "from nbclient.client import NotebookClient\n", + "from nbmake.run import NotebookRun\n", "\n", - " # Create a NotebookRun instance\n", - " run = NotebookRun(filename=path, default_timeout=timeout)\n", + "res_x = Path('res/x.ipynb')\n", "\n", - " # Execute the notebook\n", - " res = run.execute()\n", + "run = NotebookRun(res_x, verbose=True)\n", + "result = run.execute()\n", "\n", - " # Check for errors\n", - " if res.error is not None:\n", - " print(f\"Error: {res.error.summary}\")\n", - " print(f\"Traceback:\\n{res.error.trace}\")\n", - " else:\n", - " print(\"Notebook execution successful\")" + "if result.error is not None: \n", + " print(\"Error:\", result.error.summary)\n", + "else: \n", + " print(\"Success!\")\n", + " nb = nbformat.read(str(res_x), nbformat.NO_CONVERT)\n", + " nbclient = NotebookClient(nb)\n", + " nbclient.execute()" ] } ], - "metadata": {}, + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python", + "version": "3.10.12" + } + }, "nbformat": 4, "nbformat_minor": 5 } From 032846e916960578eb434dead80ce66ec7258811 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Fri, 13 Oct 2023 12:52:09 +0000 Subject: [PATCH 23/59] system prompt experiment --- src/nbwrite/writer.py | 27 ++++++++++++++---- tests/resources/out.ipynb | 60 +++++++++++++++++++++++---------------- tests/resources/x.ipynb | 17 +++++++++++ 3 files changed, 73 insertions(+), 31 deletions(-) create mode 100644 tests/resources/x.ipynb diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 6499f01..732b608 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -6,7 +6,8 @@ from langchain.callbacks import wandb_tracing_enabled as _ from langchain.llms.openai import OpenAI -from langchain.prompts import PromptTemplate +from langchain.prompts import ChatPromptTemplate, PromptTemplate +from langchain.prompts.chat import HumanMessagePromptTemplate, SystemMessage from langchain.schema import HumanMessage from nbformat import write from nbformat.v4 import ( @@ -23,18 +24,32 @@ code_root = Path(lib.submodule_search_locations._path[0]) # type: ignore code = (code_root / "nb_run.py").read_text() +SYSTEM_PROMPT = """ +You are a Python developer implementing example code (under 50 lines) that runs without errors. +""" + +template_string = """ + +task: '{task}'. + +nbmake/nb_run.py: {code}" +""" + def complete(path: Path, out_path: Path): """Write demo notebooks based on prompts in the notebook and the index""" # openai.organization = os.getenv("OPENAI_ORG_ID") temperature = 0.7 llm = OpenAI(temperature=temperature) - task = ( - "use nbmake's NotebookRun class to test 'res/x.ipynb' from a Python application" - ) + task = "Create a hello world notebook 'res/x.ipynb', use nbmake's NotebookRun class to test it from a Python application" - prompt = PromptTemplate.from_template( - "Write an executable Python example in under 50 lines that implements '{task}'.\n\nUse this relevant dependency:\n\n{code}" + prompt = ChatPromptTemplate.from_messages( + [ + # SystemMessage( + # content=(SYSTEM_PROMPT) + # ), + HumanMessagePromptTemplate.from_template(template_string), + ] ) chain = prompt | llm diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index b30215b..827de21 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "b646bc86", + "id": "e7941dad", "metadata": {}, "source": [ "# AI!" @@ -11,44 +11,54 @@ { "cell_type": "code", "execution_count": null, - "id": "30452f6f", + "id": "5fb03fe2", "metadata": {}, "outputs": [], "source": [ "\n", - "# Executable Python example\n", + "# Code\n", "\n", "from pathlib import Path\n", + "from typing import Any, Dict, List, Optional\n", + "\n", "import nbformat\n", - "from nbclient.client import NotebookClient\n", - "from nbmake.run import NotebookRun\n", + "from nbclient.client import (\n", + " CellExecutionError,\n", + " CellTimeoutError,\n", + " NotebookClient,\n", + ")\n", + "from nbformat import NotebookNode\n", + "\n", + "from nb_run import NotebookRun\n", + "\n", + "NB_VERSION = 4\n", + "\n", + "res_x = Path(\"res/x.ipynb\")\n", + "\n", + "# Create the notebook\n", + "nb = nbformat.v4.new_notebook()\n", "\n", - "res_x = Path('res/x.ipynb')\n", + "# Create the cell\n", + "cell = nbformat.v4.new_code_cell(source=\"print('Hello World!')\")\n", "\n", - "run = NotebookRun(res_x, verbose=True)\n", + "# Add the cell to the notebook\n", + "nb['cells'] = [cell]\n", + "\n", + "# Write the notebook to file\n", + "nbformat.write(nb, res_x)\n", + "\n", + "# Run the notebook\n", + "run = NotebookRun(filename=res_x, default_timeout=60)\n", "result = run.execute()\n", "\n", - "if result.error is not None: \n", - " print(\"Error:\", result.error.summary)\n", - "else: \n", - " print(\"Success!\")\n", - " nb = nbformat.read(str(res_x), nbformat.NO_CONVERT)\n", - " nbclient = NotebookClient(nb)\n", - " nbclient.execute()" + "# Check the result\n", + "if result.error:\n", + " print(result.error.summary)\n", + " print(result.error.trace)\n" ] } ], - "metadata": { - "kernelspec": { - "display_name": ".venv", - "language": "python", - "name": "python3" - }, - "language_info": { - "name": "python", - "version": "3.10.12" - } - }, + "metadata": {}, "nbformat": 4, "nbformat_minor": 5 } diff --git a/tests/resources/x.ipynb b/tests/resources/x.ipynb new file mode 100644 index 0000000..a41350f --- /dev/null +++ b/tests/resources/x.ipynb @@ -0,0 +1,17 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "d70bd1e0", + "metadata": {}, + "outputs": [], + "source": [ + "print('Hello, World!')" + ] + } + ], + "metadata": {}, + "nbformat": 4, + "nbformat_minor": 5 +} From d8bf5828acada1a6f4b0ba8afb05088500236926 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Fri, 13 Oct 2023 15:22:08 +0000 Subject: [PATCH 24/59] exps --- src/nbwrite/writer.py | 14 ++-- tests/resources/buildenv/docs/demo1.yaml | 2 +- tests/resources/ex.ipynb | 92 ++++++++++++++++++++++++ tests/resources/hello-world.ipynb | 18 +++++ tests/resources/hello.ipynb | 18 +++++ tests/resources/out.ipynb | 88 +++++++++++++---------- 6 files changed, 188 insertions(+), 44 deletions(-) create mode 100644 tests/resources/ex.ipynb create mode 100644 tests/resources/hello-world.ipynb create mode 100644 tests/resources/hello.ipynb diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 732b608..43a9451 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -25,7 +25,13 @@ code = (code_root / "nb_run.py").read_text() SYSTEM_PROMPT = """ -You are a Python developer implementing example code (under 50 lines) that runs without errors. +You are a python programmer + +Respond using only Python code +Do not use comments +Do not use quotes +Do not explain anything +Write 20 lines max per response """ template_string = """ @@ -39,15 +45,13 @@ def complete(path: Path, out_path: Path): """Write demo notebooks based on prompts in the notebook and the index""" # openai.organization = os.getenv("OPENAI_ORG_ID") - temperature = 0.7 + temperature = 0.5 llm = OpenAI(temperature=temperature) task = "Create a hello world notebook 'res/x.ipynb', use nbmake's NotebookRun class to test it from a Python application" prompt = ChatPromptTemplate.from_messages( [ - # SystemMessage( - # content=(SYSTEM_PROMPT) - # ), + SystemMessage(content=(SYSTEM_PROMPT)), HumanMessagePromptTemplate.from_template(template_string), ] ) diff --git a/tests/resources/buildenv/docs/demo1.yaml b/tests/resources/buildenv/docs/demo1.yaml index 0a25759..b107888 100644 --- a/tests/resources/buildenv/docs/demo1.yaml +++ b/tests/resources/buildenv/docs/demo1.yaml @@ -7,4 +7,4 @@ steps: assertions: - check that the simulation completed successfully components: - - frontier_ct_definition.ComputationalTwin \ No newline at end of file + - frontier_ct_definition.ComputationalTwin diff --git a/tests/resources/ex.ipynb b/tests/resources/ex.ipynb new file mode 100644 index 0000000..72772e1 --- /dev/null +++ b/tests/resources/ex.ipynb @@ -0,0 +1,92 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Using the nbmake API\n", + "\n", + "In this tutorial we will show you how to test a Python notebook from your own Python application (e.g. a test framework) using the nbmake API" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "First, we need an example notebook for testing" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "tags": [ + "nbwrite:create some 'hello-world.ipynb'", + "set the kernel to 'python3'" + ] + }, + "outputs": [], + "source": [ + "import nbformat as nbf\n", + "\n", + "nb = nbf.v4.new_notebook()\n", + "code = \"\"\"\n", + "print('Hello, World!')\n", + "\"\"\"\n", + "\n", + "nb['cells'] = [nbf.v4.new_code_cell(code)]\n", + "nbf.write(nb, 'hello-world.ipynb')" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now we can use the NotebookRun class to execute it and check that it printed what we were expecting" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from nbmake.nb_run import NotebookRun\n", + "\n", + "notebook = NotebookRun('hello-world.ipynb', default_timeout=60, verbose=True)\n", + "result = notebook.execute()\n", + "\n", + "assert result.error is None\n", + "assert len(result.nb.cells) == 1\n", + "assert result.nb.cells[0].cell_type == 'code'\n", + "assert len(result.nb.cells[0].outputs) == 1\n", + "assert result.nb.cells[0].outputs[0].output_type == 'stream'\n", + "assert result.nb.cells[0].outputs[0].text == 'Hello, World!\\n'" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.12" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/tests/resources/hello-world.ipynb b/tests/resources/hello-world.ipynb new file mode 100644 index 0000000..ac5b9f5 --- /dev/null +++ b/tests/resources/hello-world.ipynb @@ -0,0 +1,18 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "f3202044", + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "print('Hello, World!')\n" + ] + } + ], + "metadata": {}, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/tests/resources/hello.ipynb b/tests/resources/hello.ipynb new file mode 100644 index 0000000..a62563d --- /dev/null +++ b/tests/resources/hello.ipynb @@ -0,0 +1,18 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "8ce4e5af", + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "print(\"Hello world!\")\n" + ] + } + ], + "metadata": {}, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index 827de21..bd46f8a 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -1,6 +1,7 @@ { "cells": [ { + "attachments": {}, "cell_type": "markdown", "id": "e7941dad", "metadata": {}, @@ -11,54 +12,65 @@ { "cell_type": "code", "execution_count": null, - "id": "5fb03fe2", - "metadata": {}, + "id": "52db1520", + "metadata": { + "tags": { + "prompt": "this should use nbformat" + } + }, "outputs": [], "source": [ - "\n", - "# Code\n", - "\n", + "import json\n", "from pathlib import Path\n", - "from typing import Any, Dict, List, Optional\n", - "\n", - "import nbformat\n", - "from nbclient.client import (\n", - " CellExecutionError,\n", - " CellTimeoutError,\n", - " NotebookClient,\n", - ")\n", - "from nbformat import NotebookNode\n", - "\n", - "from nb_run import NotebookRun\n", - "\n", - "NB_VERSION = 4\n", - "\n", - "res_x = Path(\"res/x.ipynb\")\n", - "\n", - "# Create the notebook\n", - "nb = nbformat.v4.new_notebook()\n", - "\n", - "# Create the cell\n", - "cell = nbformat.v4.new_code_cell(source=\"print('Hello World!')\")\n", "\n", - "# Add the cell to the notebook\n", - "nb['cells'] = [cell]\n", + "from nbformat import reads\n", "\n", - "# Write the notebook to file\n", - "nbformat.write(nb, res_x)\n", + "# Existing code to run notebook\n", + "nr = NotebookRun(Path(\"hello.ipynb\"), default_timeout=60) \n", + "result = nr.execute()\n", "\n", - "# Run the notebook\n", - "run = NotebookRun(filename=res_x, default_timeout=60)\n", - "result = run.execute()\n", + "# Read notebook back in\n", + "with open(\"hello.ipynb\") as f:\n", + " nb = reads(f.read(), as_version=4)\n", "\n", - "# Check the result\n", - "if result.error:\n", - " print(result.error.summary)\n", - " print(result.error.trace)\n" + "# Pretty print JSON \n", + "print(json.dumps(nb, indent=2))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f7539333", + "metadata": { + "tags": [ + "nbwrite:use 'import json'" + ] + }, + "outputs": [], + "source": [ + "asdff" ] } ], - "metadata": {}, + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.12" + } + }, "nbformat": 4, "nbformat_minor": 5 } From 56692577113be8bbd464b39edc4801800c991d05 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 16 Oct 2023 15:59:05 +0000 Subject: [PATCH 25/59] anyscale codellama --- src/nbwrite/writer.py | 17 ++- tests/resources/out.ipynb | 224 +++++++++++++++++++++++++++++--------- 2 files changed, 187 insertions(+), 54 deletions(-) diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 43a9451..8299d7f 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -5,6 +5,7 @@ from typing import Any, Dict, List from langchain.callbacks import wandb_tracing_enabled as _ +from langchain.chat_models import ChatAnyscale from langchain.llms.openai import OpenAI from langchain.prompts import ChatPromptTemplate, PromptTemplate from langchain.prompts.chat import HumanMessagePromptTemplate, SystemMessage @@ -41,12 +42,22 @@ nbmake/nb_run.py: {code}" """ +# Now we can use the NotebookRun class to execute it and check that it printed what we were expecting + +# The following class has been imported `nbmake.nb_run.NotebookRun`: + def complete(path: Path, out_path: Path): """Write demo notebooks based on prompts in the notebook and the index""" # openai.organization = os.getenv("OPENAI_ORG_ID") - temperature = 0.5 - llm = OpenAI(temperature=temperature) + temperature = 0.1 + model = "codellama/CodeLlama-34b-Instruct-hf" + + llm = ChatAnyscale( + temperature=temperature, + model_name=model, + streaming=True, + ) task = "Create a hello world notebook 'res/x.ipynb', use nbmake's NotebookRun class to test it from a Python application" prompt = ChatPromptTemplate.from_messages( @@ -59,7 +70,7 @@ def complete(path: Path, out_path: Path): chain = prompt | llm code_out = chain.invoke({"task": task, "code": code}) title = "AI!" - sources = [code_out] + sources = [code_out.content] nb = new_notebook() # nb.metadata = metadata nb.cells.append(new_markdown_cell(f"# {title}")) diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index bd46f8a..cdac2ef 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -1,9 +1,8 @@ { "cells": [ { - "attachments": {}, "cell_type": "markdown", - "id": "e7941dad", + "id": "e50a308e", "metadata": {}, "source": [ "# AI!" @@ -12,65 +11,188 @@ { "cell_type": "code", "execution_count": null, - "id": "52db1520", - "metadata": { - "tags": { - "prompt": "this should use nbformat" - } - }, + "id": "96fc2c9c", + "metadata": {}, "outputs": [], "source": [ - "import json\n", + " Here is the code for the NotebookRun class:\n", + "```\n", "from pathlib import Path\n", + "from typing import Any, Dict, List, Optional\n", "\n", - "from nbformat import reads\n", + "import nbformat\n", + "from nbclient.client import (\n", + " CellExecutionError,\n", + " CellTimeoutError,\n", + " NotebookClient,\n", + ")\n", + "from nbformat import NotebookNode\n", "\n", - "# Existing code to run notebook\n", - "nr = NotebookRun(Path(\"hello.ipynb\"), default_timeout=60) \n", - "result = nr.execute()\n", + "from .nb_result import NotebookError, NotebookResult\n", "\n", - "# Read notebook back in\n", - "with open(\"hello.ipynb\") as f:\n", - " nb = reads(f.read(), as_version=4)\n", + "NB_VERSION = 4\n", "\n", - "# Pretty print JSON \n", - "print(json.dumps(nb, indent=2))" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "f7539333", - "metadata": { - "tags": [ - "nbwrite:use 'import json'" - ] - }, - "outputs": [], - "source": [ - "asdff" + "\n", + "class CellImportError(Exception):\n", + " pass\n", + "\n", + "\n", + "class NotebookRun:\n", + " filename: Path\n", + " verbose: bool\n", + "\n", + " def __init__(\n", + " self,\n", + " filename: Path,\n", + " default_timeout: int,\n", + " verbose: bool = False,\n", + " kernel: Optional[str] = None,\n", + " find_import_errors: bool = False,\n", + " ) -> None:\n", + " self.filename = filename\n", + " self.verbose = verbose\n", + " self.default_timeout = default_timeout\n", + " self.kernel = kernel\n", + " self.find_import_errors = find_import_errors\n", + "\n", + " def execute(\n", + " self,\n", + " ) -> NotebookResult:\n", + " nb = nbformat.read(str(self.filename), NB_VERSION)\n", + "\n", + " for cell in nb.cells:\n", + " if cell.cell_type == \"code\":\n", + " cell.outputs = []\n", + " timeout = self.default_timeout\n", + " allow_errors = False\n", + " if \"execution\" in nb.metadata:\n", + " if \"timeout\" in nb.metadata.execution:\n", + " timeout = nb.metadata.execution.timeout\n", + " if \"allow_errors\" in nb.metadata.execution:\n", + " allow_errors = nb.metadata.execution.allow_errors\n", + "\n", + " error: Optional[NotebookError] = None\n", + "\n", + " extra_kwargs = {}\n", + " if self.kernel:\n", + " extra_kwargs[\"kernel_name\"] = self.kernel\n", + "\n", + " try:\n", + " c = NotebookClient(\n", + " nb,\n", + " timeout=timeout,\n", + " allow_errors=allow_errors or self.find_import_errors,\n", + " interrupt_on_timeout=self.find_import_errors,\n", + " record_timing=True,\n", + " **extra_kwargs,\n", + " )\n", + "\n", + " async def apply_mocks(\n", + " cell: NotebookNode, cell_index: int, execute_reply: Dict[str, Any]\n", + " ):\n", + " # https://github.com/treebeardtech/nbmake/issues/77\n", + " if any(o[\"output_type\"] == \"error\" for o in cell[\"outputs\"]):\n", + " execute_reply[\"content\"][\"status\"] = \"error\"\n", + "\n", + " if \"ename\" in execute_reply[\"content\"]:\n", + " if execute_reply[\"content\"][\"ename\"] == \"ModuleNotFoundError\":\n", + " if self.find_import_errors:\n", + " raise CellImportError()\n", + " else:\n", + " if c.kc is None:\n", + " raise Exception(\"there is no kernelclient\")\n", + " mocks: Dict[str, Any] = (\n", + " cell.get(\"metadata\", {}).get(\"nbmake\", {}).get(\"mock\", {})\n", + " )\n", + " for v in mocks:\n", + " if isinstance(mocks[v], str):\n", + " out = await c.kc.execute_interactive(f\"{v} = '{mocks[v]}'\")\n", + " else:\n", + " out = await c.kc.execute_interactive(f\"{v} = {mocks[v]}\")\n", + "\n", + " if out[\"content\"][\"status\"] != \"ok\":\n", + " raise Exception(f\"Failed to apply mock {v}\\n\\n{str(out)}\")\n", + "\n", + " post_cell_execute: List[str] = (\n", + " cell.get(\"metadata\", {})\n", + " .get(\"nbmake\", {})\n", + " .get(\"post_cell_execute\", [])\n", + " )\n", + " if post_cell_execute:\n", + " pce = \"\\n\".join(post_cell_execute)\n", + " out = await c.kc.execute_interactive(pce)\n", + "\n", + " if out[\"content\"][\"status\"] != \"ok\":\n", + " raise Exception(\n", + " f\"Post cell execution failed:\\n{pce}\\n\\n{str(out)}\"\n", + " )\n", + "\n", + " c.on_cell_executed = apply_mocks\n", + "\n", + " c.execute(cwd=self.filename.parent)\n", + " except CellImportError:\n", + " error = self._get_error(nb)\n", + " except CellExecutionError:\n", + " error = self._get_error(nb)\n", + " except CellTimeoutError as err:\n", + " trace = err.args[0]\n", + " error = NotebookError(\n", + " summary=trace.split(\"\\n\")[0],\n", + " trace=trace,\n", + " failing_cell_index=self._get_timeout_cell(nb),\n", + " )\n", + " except Exception as err:\n", + " # if at top causes https://github.com/jupyter/nbclient/issues/128\n", + " # from jupyter_client.kernelspec import KernelSpecManager, NoSuchKernel\n", + " # trace=f\"{summary}\\n\\nInstalled Kernels: {str(KernelSpecManager().find_kernel_specs())}\",\n", + " # https://github.com/treebeardtech/nbmake/runs/1536896858?check_suite_focus=true\n", + " if str(type(err)) != \"\":\n", + " raise err\n", + "\n", + " summary = f\"Error - No such kernel: '{err.name}'\" # type: ignore\n", + " error = NotebookError(\n", + " summary=summary,\n", + " trace=f\"{summary}\",\n", + " failing_cell_index=0,\n", + " )\n", + "\n", + " return NotebookResult(nb=nb, error=error)\n", + "\n", + " def _get_timeout_cell(self, nb: NotebookNode) -> int:\n", + " for i, cell in enumerate(nb.cells):\n", + " if cell.cell_type != \"code\":\n", + " continue\n", + " if \"shell.execute_reply\" not in cell.metadata.execution:\n", + " return i\n", + "\n", + " return -1\n", + "\n", + " def _get_error(self, nb: NotebookNode) -> Optional[NotebookError]:\n", + " for i, cell in reversed(list(enumerate(nb[\"cells\"]))): # get LAST error\n", + " if cell[\"cell_type\"] != \"code\":\n", + " continue\n", + " errors = [\n", + " output\n", + " for output in cell[\"outputs\"]\n", + " if output[\"output_type\"] == \"error\" or \"ename\" in output\n", + " ]\n", + "\n", + " if errors:\n", + " tb = \"\\n\".join(errors[0].get(\"traceback\", \"\"))\n", + " src = \"\".join(cell[\"source\"])\n", + " last_trace = tb.split(\"\\n\")[-1]\n", + " line = 75 * \"-\"\n", + " trace = f\"{line}\\n{src}\\n{tb}\"\n", + " return NotebookError(\n", + " summary=last_trace, trace=trace, failing_cell_index=i\n", + " )\n", + "\n", + " return None\n", + "```" ] } ], - "metadata": { - "kernelspec": { - "display_name": ".venv", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.12" - } - }, + "metadata": {}, "nbformat": 4, "nbformat_minor": 5 } From d5730c3b18847f555ea8078d36107511f14510a4 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 16 Oct 2023 17:35:19 +0000 Subject: [PATCH 26/59] gpt4 --- pyrightconfig.json | 3 +- src/nbwrite/writer.py | 10 +- tests/resources/out.ipynb | 207 +++++++----------------------------- tests/resources/res/x.ipynb | 17 +++ 4 files changed, 63 insertions(+), 174 deletions(-) create mode 100644 tests/resources/res/x.ipynb diff --git a/pyrightconfig.json b/pyrightconfig.json index 3d13535..1e3a048 100644 --- a/pyrightconfig.json +++ b/pyrightconfig.json @@ -12,5 +12,6 @@ "reportUntypedFunctionDecorator": "warning", "reportMissingTypeStubs": false, "reportGeneralTypeIssues": "warning", - "reportUnusedImport": "warning" + "reportUnusedImport": "warning", + "reportUnusedVariable": "warning" } diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 8299d7f..9ec1719 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -53,11 +53,17 @@ def complete(path: Path, out_path: Path): temperature = 0.1 model = "codellama/CodeLlama-34b-Instruct-hf" - llm = ChatAnyscale( + llm_anyscale = ChatAnyscale( temperature=temperature, model_name=model, streaming=True, ) + + llm = OpenAI( + model_name="gpt-4", + temperature=0.1, + max_tokens=512, + ) task = "Create a hello world notebook 'res/x.ipynb', use nbmake's NotebookRun class to test it from a Python application" prompt = ChatPromptTemplate.from_messages( @@ -70,7 +76,7 @@ def complete(path: Path, out_path: Path): chain = prompt | llm code_out = chain.invoke({"task": task, "code": code}) title = "AI!" - sources = [code_out.content] + sources = [code_out] nb = new_notebook() # nb.metadata = metadata nb.cells.append(new_markdown_cell(f"# {title}")) diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index cdac2ef..3adc8b3 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "e50a308e", + "id": "afe4057d", "metadata": {}, "source": [ "# AI!" @@ -11,188 +11,53 @@ { "cell_type": "code", "execution_count": null, - "id": "96fc2c9c", + "id": "e027c06c", "metadata": {}, "outputs": [], "source": [ - " Here is the code for the NotebookRun class:\n", - "```\n", + "from nbmake.nb_run import NotebookRun\n", "from pathlib import Path\n", - "from typing import Any, Dict, List, Optional\n", + "import nbformat as nbf\n", "\n", - "import nbformat\n", - "from nbclient.client import (\n", - " CellExecutionError,\n", - " CellTimeoutError,\n", - " NotebookClient,\n", - ")\n", - "from nbformat import NotebookNode\n", + "# Create a new notebook\n", + "nb = nbf.v4.new_notebook()\n", "\n", - "from .nb_result import NotebookError, NotebookResult\n", + "# Add a code cell with 'Hello World'\n", + "code_cell = nbf.v4.new_code_cell(\"print('Hello, World!')\")\n", + "nb['cells'].append(code_cell)\n", "\n", - "NB_VERSION = 4\n", + "# Write the notebook to a file\n", + "with open('res/x.ipynb', 'w') as f:\n", + " nbf.write(nb, f)\n", "\n", + "# Use NotebookRun to test the notebook\n", + "notebook = NotebookRun(Path('res/x.ipynb'), default_timeout=60)\n", + "result = notebook.execute()\n", "\n", - "class CellImportError(Exception):\n", - " pass\n", - "\n", - "\n", - "class NotebookRun:\n", - " filename: Path\n", - " verbose: bool\n", - "\n", - " def __init__(\n", - " self,\n", - " filename: Path,\n", - " default_timeout: int,\n", - " verbose: bool = False,\n", - " kernel: Optional[str] = None,\n", - " find_import_errors: bool = False,\n", - " ) -> None:\n", - " self.filename = filename\n", - " self.verbose = verbose\n", - " self.default_timeout = default_timeout\n", - " self.kernel = kernel\n", - " self.find_import_errors = find_import_errors\n", - "\n", - " def execute(\n", - " self,\n", - " ) -> NotebookResult:\n", - " nb = nbformat.read(str(self.filename), NB_VERSION)\n", - "\n", - " for cell in nb.cells:\n", - " if cell.cell_type == \"code\":\n", - " cell.outputs = []\n", - " timeout = self.default_timeout\n", - " allow_errors = False\n", - " if \"execution\" in nb.metadata:\n", - " if \"timeout\" in nb.metadata.execution:\n", - " timeout = nb.metadata.execution.timeout\n", - " if \"allow_errors\" in nb.metadata.execution:\n", - " allow_errors = nb.metadata.execution.allow_errors\n", - "\n", - " error: Optional[NotebookError] = None\n", - "\n", - " extra_kwargs = {}\n", - " if self.kernel:\n", - " extra_kwargs[\"kernel_name\"] = self.kernel\n", - "\n", - " try:\n", - " c = NotebookClient(\n", - " nb,\n", - " timeout=timeout,\n", - " allow_errors=allow_errors or self.find_import_errors,\n", - " interrupt_on_timeout=self.find_import_errors,\n", - " record_timing=True,\n", - " **extra_kwargs,\n", - " )\n", - "\n", - " async def apply_mocks(\n", - " cell: NotebookNode, cell_index: int, execute_reply: Dict[str, Any]\n", - " ):\n", - " # https://github.com/treebeardtech/nbmake/issues/77\n", - " if any(o[\"output_type\"] == \"error\" for o in cell[\"outputs\"]):\n", - " execute_reply[\"content\"][\"status\"] = \"error\"\n", - "\n", - " if \"ename\" in execute_reply[\"content\"]:\n", - " if execute_reply[\"content\"][\"ename\"] == \"ModuleNotFoundError\":\n", - " if self.find_import_errors:\n", - " raise CellImportError()\n", - " else:\n", - " if c.kc is None:\n", - " raise Exception(\"there is no kernelclient\")\n", - " mocks: Dict[str, Any] = (\n", - " cell.get(\"metadata\", {}).get(\"nbmake\", {}).get(\"mock\", {})\n", - " )\n", - " for v in mocks:\n", - " if isinstance(mocks[v], str):\n", - " out = await c.kc.execute_interactive(f\"{v} = '{mocks[v]}'\")\n", - " else:\n", - " out = await c.kc.execute_interactive(f\"{v} = {mocks[v]}\")\n", - "\n", - " if out[\"content\"][\"status\"] != \"ok\":\n", - " raise Exception(f\"Failed to apply mock {v}\\n\\n{str(out)}\")\n", - "\n", - " post_cell_execute: List[str] = (\n", - " cell.get(\"metadata\", {})\n", - " .get(\"nbmake\", {})\n", - " .get(\"post_cell_execute\", [])\n", - " )\n", - " if post_cell_execute:\n", - " pce = \"\\n\".join(post_cell_execute)\n", - " out = await c.kc.execute_interactive(pce)\n", - "\n", - " if out[\"content\"][\"status\"] != \"ok\":\n", - " raise Exception(\n", - " f\"Post cell execution failed:\\n{pce}\\n\\n{str(out)}\"\n", - " )\n", - "\n", - " c.on_cell_executed = apply_mocks\n", - "\n", - " c.execute(cwd=self.filename.parent)\n", - " except CellImportError:\n", - " error = self._get_error(nb)\n", - " except CellExecutionError:\n", - " error = self._get_error(nb)\n", - " except CellTimeoutError as err:\n", - " trace = err.args[0]\n", - " error = NotebookError(\n", - " summary=trace.split(\"\\n\")[0],\n", - " trace=trace,\n", - " failing_cell_index=self._get_timeout_cell(nb),\n", - " )\n", - " except Exception as err:\n", - " # if at top causes https://github.com/jupyter/nbclient/issues/128\n", - " # from jupyter_client.kernelspec import KernelSpecManager, NoSuchKernel\n", - " # trace=f\"{summary}\\n\\nInstalled Kernels: {str(KernelSpecManager().find_kernel_specs())}\",\n", - " # https://github.com/treebeardtech/nbmake/runs/1536896858?check_suite_focus=true\n", - " if str(type(err)) != \"\":\n", - " raise err\n", - "\n", - " summary = f\"Error - No such kernel: '{err.name}'\" # type: ignore\n", - " error = NotebookError(\n", - " summary=summary,\n", - " trace=f\"{summary}\",\n", - " failing_cell_index=0,\n", - " )\n", - "\n", - " return NotebookResult(nb=nb, error=error)\n", - "\n", - " def _get_timeout_cell(self, nb: NotebookNode) -> int:\n", - " for i, cell in enumerate(nb.cells):\n", - " if cell.cell_type != \"code\":\n", - " continue\n", - " if \"shell.execute_reply\" not in cell.metadata.execution:\n", - " return i\n", - "\n", - " return -1\n", - "\n", - " def _get_error(self, nb: NotebookNode) -> Optional[NotebookError]:\n", - " for i, cell in reversed(list(enumerate(nb[\"cells\"]))): # get LAST error\n", - " if cell[\"cell_type\"] != \"code\":\n", - " continue\n", - " errors = [\n", - " output\n", - " for output in cell[\"outputs\"]\n", - " if output[\"output_type\"] == \"error\" or \"ename\" in output\n", - " ]\n", - "\n", - " if errors:\n", - " tb = \"\\n\".join(errors[0].get(\"traceback\", \"\"))\n", - " src = \"\".join(cell[\"source\"])\n", - " last_trace = tb.split(\"\\n\")[-1]\n", - " line = 75 * \"-\"\n", - " trace = f\"{line}\\n{src}\\n{tb}\"\n", - " return NotebookError(\n", - " summary=last_trace, trace=trace, failing_cell_index=i\n", - " )\n", - "\n", - " return None\n", - "```" + "# Print the result\n", + "print(result)" ] } ], - "metadata": {}, + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.12" + } + }, "nbformat": 4, "nbformat_minor": 5 } diff --git a/tests/resources/res/x.ipynb b/tests/resources/res/x.ipynb new file mode 100644 index 0000000..5f63baf --- /dev/null +++ b/tests/resources/res/x.ipynb @@ -0,0 +1,17 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "53c70b3b", + "metadata": {}, + "outputs": [], + "source": [ + "print('Hello, World!')" + ] + } + ], + "metadata": {}, + "nbformat": 4, + "nbformat_minor": 5 +} From 26e3bc6804299a67fd5454f7aa53505715b81ec5 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 16 Oct 2023 17:54:18 +0000 Subject: [PATCH 27/59] add eval --- .github/workflows/pytest.yml | 4 +-- src/nbwrite/writer.py | 5 +-- tests/resources/out.ipynb | 50 +++++++++++++----------------- tests/test_cli.py | 13 ++++++++ tests/resources/x.ipynb => x.ipynb | 4 +-- 5 files changed, 41 insertions(+), 35 deletions(-) rename tests/resources/x.ipynb => x.ipynb (78%) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 59a30ce..6340ced 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -1,7 +1,7 @@ name: Pytest on: - schedule: - - cron: 0 13 * * 1 # Every Monday at 1PM UTC (9AM EST) + # schedule: + # - cron: 0 13 * * 1 # Every Monday at 1PM UTC (9AM EST) pull_request: # test in containerised and OS environments jobs: diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 9ec1719..cc727bb 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -32,7 +32,8 @@ Do not use comments Do not use quotes Do not explain anything -Write 20 lines max per response +Do import any libraries you need +Write 25 lines max per response """ template_string = """ @@ -64,7 +65,7 @@ def complete(path: Path, out_path: Path): temperature=0.1, max_tokens=512, ) - task = "Create a hello world notebook 'res/x.ipynb', use nbmake's NotebookRun class to test it from a Python application" + task = "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application" prompt = ChatPromptTemplate.from_messages( [ diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index 3adc8b3..0de5a8f 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "afe4057d", + "id": "d6104f2b", "metadata": {}, "source": [ "# AI!" @@ -11,51 +11,43 @@ { "cell_type": "code", "execution_count": null, - "id": "e027c06c", + "id": "66839a1a", "metadata": {}, "outputs": [], "source": [ - "from nbmake.nb_run import NotebookRun\n", - "from pathlib import Path\n", + "from nbformat.v4 import new_notebook, new_code_cell\n", "import nbformat as nbf\n", "\n", "# Create a new notebook\n", - "nb = nbf.v4.new_notebook()\n", + "nb = new_notebook()\n", "\n", - "# Add a code cell with 'Hello World'\n", - "code_cell = nbf.v4.new_code_cell(\"print('Hello, World!')\")\n", - "nb['cells'].append(code_cell)\n", + "# Add a code cell\n", + "code = 'print(\"Hello, World!\")'\n", + "nb.cells.append(new_code_cell(source=code))\n", "\n", "# Write the notebook to a file\n", - "with open('res/x.ipynb', 'w') as f:\n", + "with open('x.ipynb', 'w') as f:\n", " nbf.write(nb, f)\n", "\n", - "# Use NotebookRun to test the notebook\n", - "notebook = NotebookRun(Path('res/x.ipynb'), default_timeout=60)\n", - "result = notebook.execute()\n", + "from pathlib import Path\n", + "from nbmake import NotebookRun\n", + "\n", + "# Test the notebook\n", + "nb_path = Path('x.ipynb')\n", + "nb_run = NotebookRun(nb_path, default_timeout=60)\n", + "result = nb_run.execute()\n", "\n", - "# Print the result\n", - "print(result)" + "# Check if there were any errors\n", + "if result.error is not None:\n", + " print(f\"Error in notebook: {result.error.summary}\")\n", + "else:\n", + " print(\"Notebook executed successfully.\")" ] } ], "metadata": { - "kernelspec": { - "display_name": ".venv", - "language": "python", - "name": "python3" - }, "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.12" + "name": "python" } }, "nbformat": 4, diff --git a/tests/test_cli.py b/tests/test_cli.py index b32d095..b5ba90e 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -17,3 +17,16 @@ def test_complete(): ) print(result.output) assert result.exit_code == 0 + + import nbformat + from nbclient.client import NotebookClient + + with open("tests/resources/out.ipynb") as f: + nb = nbformat.read(f, as_version=4) + + client = NotebookClient(nb) + client.execute() + + for cell in nb.cells: + if cell.cell_type == "code" and 'print("Hello, world!")' in cell.source: + assert "Hello, world!" in "".join(output.text for output in cell.outputs) diff --git a/tests/resources/x.ipynb b/x.ipynb similarity index 78% rename from tests/resources/x.ipynb rename to x.ipynb index a41350f..efb940d 100644 --- a/tests/resources/x.ipynb +++ b/x.ipynb @@ -3,11 +3,11 @@ { "cell_type": "code", "execution_count": null, - "id": "d70bd1e0", + "id": "c87d174c", "metadata": {}, "outputs": [], "source": [ - "print('Hello, World!')" + "print(\"Hello, World!\")" ] } ], From d9f275b571ab53a9202e02e902f0ad96921ebb4c Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 16 Oct 2023 18:16:28 +0000 Subject: [PATCH 28/59] chroma rag --- poetry.lock | 425 ++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 1 + src/nbwrite/cli.py | 4 + src/nbwrite/index.py | 43 +++++ 4 files changed, 470 insertions(+), 3 deletions(-) create mode 100644 src/nbwrite/index.py diff --git a/poetry.lock b/poetry.lock index e0726ac..697c545 100644 --- a/poetry.lock +++ b/poetry.lock @@ -119,6 +119,26 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "backoff" +version = "2.2.1" +description = "Function decoration for backoff and retry" +category = "main" +optional = false +python-versions = ">=3.7,<4.0" + +[[package]] +name = "bcrypt" +version = "4.0.1" +description = "Modern password hashing for your software and your servers" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.extras] +tests = ["pytest (>=3.2.1,!=3.3.0)"] +typecheck = ["mypy"] + [[package]] name = "certifi" version = "2023.7.22" @@ -154,6 +174,46 @@ category = "main" optional = false python-versions = ">=3.7.0" +[[package]] +name = "chroma-hnswlib" +version = "0.7.3" +description = "Chromas fork of hnswlib" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +numpy = "*" + +[[package]] +name = "chromadb" +version = "0.4.14" +description = "Chroma." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +bcrypt = ">=4.0.1" +chroma-hnswlib = "0.7.3" +fastapi = ">=0.95.2" +graphlib-backport = {version = ">=1.0.3", markers = "python_version < \"3.9\""} +grpcio = ">=1.58.0" +importlib-resources = "*" +numpy = {version = ">=1.22.5", markers = "python_version >= \"3.8\""} +onnxruntime = ">=1.14.1" +overrides = ">=7.3.1" +posthog = ">=2.4.0" +pulsar-client = ">=3.1.0" +pydantic = ">=1.9" +pypika = ">=0.48.9" +requests = ">=2.28" +tokenizers = ">=0.13.2" +tqdm = ">=4.65.0" +typer = ">=0.9.0" +typing-extensions = ">=4.5.0" +uvicorn = {version = ">=0.18.3", extras = ["standard"]} + [[package]] name = "click" version = "8.1.7" @@ -173,6 +233,20 @@ category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +[[package]] +name = "coloredlogs" +version = "15.0.1" +description = "Colored terminal output for Python's logging module" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[package.dependencies] +humanfriendly = ">=9.1" + +[package.extras] +cron = ["capturer (>=2.4)"] + [[package]] name = "comm" version = "0.1.4" @@ -318,6 +392,23 @@ python-versions = "*" [package.extras] tests = ["asttokens (>=2.1.0)", "ipython", "pytest", "coverage", "coverage-enable-subprocess", "littleutils", "rich"] +[[package]] +name = "fastapi" +version = "0.103.2" +description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +anyio = ">=3.7.1,<4.0.0" +pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0 || >2.0.0,<2.0.1 || >2.0.1,<2.1.0 || >2.1.0,<3.0.0" +starlette = ">=0.27.0,<0.28.0" +typing-extensions = ">=4.5.0" + +[package.extras] +all = ["email-validator (>=2.0.0)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)", "jinja2 (>=2.11.2)", "orjson (>=3.2.1)", "pydantic-extra-types (>=2.0.0)", "pydantic-settings (>=2.0.0)", "python-multipart (>=0.0.5)", "pyyaml (>=5.3.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0)", "uvicorn[standard] (>=0.12.0)"] + [[package]] name = "fastjsonschema" version = "2.18.1" @@ -333,7 +424,7 @@ devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benc name = "filelock" version = "3.12.4" description = "A platform independent file lock." -category = "dev" +category = "main" optional = false python-versions = ">=3.8" @@ -342,6 +433,14 @@ docs = ["furo (>=2023.7.26)", "sphinx-autodoc-typehints (>=1.24)", "sphinx (>=7. testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)", "pytest (>=7.4)"] typing = ["typing-extensions (>=4.7.1)"] +[[package]] +name = "flatbuffers" +version = "23.5.26" +description = "The FlatBuffers serialization format for Python" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "fonttools" version = "4.43.1" @@ -429,6 +528,14 @@ gitdb = ">=4.0.1,<5" [package.extras] test = ["black", "coverage", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar"] +[[package]] +name = "graphlib-backport" +version = "1.0.3" +description = "Backport of the Python 3.9 graphlib module for Python 3.6+" +category = "main" +optional = false +python-versions = ">=3.6,<4.0" + [[package]] name = "greenlet" version = "3.0.0" @@ -441,6 +548,77 @@ python-versions = ">=3.7" docs = ["sphinx"] test = ["objgraph", "psutil"] +[[package]] +name = "grpcio" +version = "1.59.0" +description = "HTTP/2-based RPC framework" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +protobuf = ["grpcio-tools (>=1.59.0)"] + +[[package]] +name = "h11" +version = "0.14.0" +description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" +category = "main" +optional = false +python-versions = ">=3.7" + +[[package]] +name = "httptools" +version = "0.6.1" +description = "A collection of framework independent HTTP protocol utils." +category = "main" +optional = false +python-versions = ">=3.8.0" + +[package.extras] +test = ["Cython (>=0.29.24,<0.30.0)"] + +[[package]] +name = "huggingface-hub" +version = "0.17.3" +description = "Client library to download and publish models, datasets and other repos on the huggingface.co hub" +category = "main" +optional = false +python-versions = ">=3.8.0" + +[package.dependencies] +filelock = "*" +fsspec = "*" +packaging = ">=20.9" +pyyaml = ">=5.1" +requests = "*" +tqdm = ">=4.42.1" +typing-extensions = ">=3.7.4.3" + +[package.extras] +all = ["InquirerPy (==0.3.4)", "aiohttp", "pydantic (<2.0)", "jedi", "jinja2", "pytest", "pytest-cov", "pytest-env", "pytest-xdist", "pytest-vcr", "pytest-asyncio", "urllib3 (<2.0)", "soundfile", "pillow", "gradio", "numpy", "black (==23.7)", "ruff (>=0.0.241)", "mypy (==1.5.1)", "types-pyyaml", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3"] +cli = ["InquirerPy (==0.3.4)"] +dev = ["InquirerPy (==0.3.4)", "aiohttp", "pydantic (<2.0)", "jedi", "jinja2", "pytest", "pytest-cov", "pytest-env", "pytest-xdist", "pytest-vcr", "pytest-asyncio", "urllib3 (<2.0)", "soundfile", "pillow", "gradio", "numpy", "black (==23.7)", "ruff (>=0.0.241)", "mypy (==1.5.1)", "types-pyyaml", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3"] +docs = ["InquirerPy (==0.3.4)", "aiohttp", "pydantic (<2.0)", "jedi", "jinja2", "pytest", "pytest-cov", "pytest-env", "pytest-xdist", "pytest-vcr", "pytest-asyncio", "urllib3 (<2.0)", "soundfile", "pillow", "gradio", "numpy", "black (==23.7)", "ruff (>=0.0.241)", "mypy (==1.5.1)", "types-pyyaml", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "hf-doc-builder", "watchdog"] +fastai = ["toml", "fastai (>=2.4)", "fastcore (>=1.3.27)"] +inference = ["aiohttp", "pydantic (<2.0)"] +quality = ["black (==23.7)", "ruff (>=0.0.241)", "mypy (==1.5.1)"] +tensorflow = ["tensorflow", "pydot", "graphviz"] +testing = ["InquirerPy (==0.3.4)", "aiohttp", "pydantic (<2.0)", "jedi", "jinja2", "pytest", "pytest-cov", "pytest-env", "pytest-xdist", "pytest-vcr", "pytest-asyncio", "urllib3 (<2.0)", "soundfile", "pillow", "gradio", "numpy"] +torch = ["torch"] +typing = ["types-pyyaml", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "pydantic (<2.0)"] + +[[package]] +name = "humanfriendly" +version = "10.0" +description = "Human friendly output for text interfaces using Python" +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[package.dependencies] +pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_version >= \"3.8\""} + [[package]] name = "identify" version = "2.5.30" @@ -807,6 +985,28 @@ python-versions = ">=3.5" [package.dependencies] traitlets = "*" +[[package]] +name = "monotonic" +version = "1.6" +description = "An implementation of time.monotonic() for Python 2 & < 3.3" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "mpmath" +version = "1.3.0" +description = "Python library for arbitrary-precision floating-point arithmetic" +category = "main" +optional = false +python-versions = "*" + +[package.extras] +develop = ["pytest (>=4.6)", "pycodestyle", "pytest-cov", "codecov", "wheel"] +docs = ["sphinx"] +gmpy = ["gmpy2 (>=2.1.0a4)"] +tests = ["pytest (>=4.6)"] + [[package]] name = "multidict" version = "6.0.4" @@ -920,6 +1120,22 @@ category = "main" optional = false python-versions = ">=3.8" +[[package]] +name = "onnxruntime" +version = "1.16.1" +description = "ONNX Runtime is a runtime accelerator for Machine Learning models" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +coloredlogs = "*" +flatbuffers = "*" +numpy = ">=1.21.6" +packaging = "*" +protobuf = "*" +sympy = "*" + [[package]] name = "openai" version = "0.28.1" @@ -959,6 +1175,14 @@ python-versions = ">=3.6" [package.dependencies] et-xmlfile = "*" +[[package]] +name = "overrides" +version = "7.4.0" +description = "A decorator to automatically detect mismatch when overriding a method." +category = "main" +optional = false +python-versions = ">=3.6" + [[package]] name = "packaging" version = "23.2" @@ -1123,6 +1347,26 @@ python-versions = ">=3.8" dev = ["pre-commit", "tox"] testing = ["pytest", "pytest-benchmark"] +[[package]] +name = "posthog" +version = "3.0.2" +description = "Integrate PostHog into any python application." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +backoff = ">=1.10.0" +monotonic = ">=1.5" +python-dateutil = ">2.1" +requests = ">=2.7,<3.0" +six = ">=1.5" + +[package.extras] +dev = ["black", "isort", "flake8", "flake8-print", "pre-commit"] +sentry = ["sentry-sdk", "django"] +test = ["mock (>=2.0.0)", "freezegun (==0.3.15)", "pylint", "flake8", "coverage", "pytest"] + [[package]] name = "pre-commit" version = "2.21.0" @@ -1176,6 +1420,22 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "pulsar-client" +version = "3.3.0" +description = "Apache Pulsar Python client library" +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +certifi = "*" + +[package.extras] +all = ["apache-bookkeeper-client (>=4.16.1)", "fastavro (==1.7.3)", "grpcio (>=1.8.2)", "prometheus-client", "protobuf (>=3.6.1,<=3.20.3)", "ratelimit"] +avro = ["fastavro (==1.7.3)"] +functions = ["apache-bookkeeper-client (>=4.16.1)", "grpcio (>=1.8.2)", "prometheus-client", "protobuf (>=3.6.1,<=3.20.3)", "ratelimit"] + [[package]] name = "pure-eval" version = "0.2.2" @@ -1252,6 +1512,22 @@ python-versions = ">=3.6.8" [package.extras] diagrams = ["railroad-diagrams", "jinja2"] +[[package]] +name = "pypika" +version = "0.48.9" +description = "A SQL query builder API for Python" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "pyreadline3" +version = "3.4.1" +description = "A python implementation of GNU readline." +category = "main" +optional = false +python-versions = "*" + [[package]] name = "pytest" version = "7.4.2" @@ -1344,7 +1620,7 @@ six = ">=1.5" name = "python-dotenv" version = "1.0.0" description = "Read key-value pairs from a .env file and set them as environment variables" -category = "dev" +category = "main" optional = false python-versions = ">=3.8" @@ -1615,6 +1891,32 @@ pure-eval = "*" [package.extras] tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"] +[[package]] +name = "starlette" +version = "0.27.0" +description = "The little ASGI library that shines." +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +anyio = ">=3.4.0,<5" +typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""} + +[package.extras] +full = ["httpx (>=0.22.0)", "itsdangerous", "jinja2", "python-multipart", "pyyaml"] + +[[package]] +name = "sympy" +version = "1.12" +description = "Computer algebra system (CAS) in Python" +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +mpmath = ">=0.19" + [[package]] name = "tenacity" version = "8.2.3" @@ -1649,6 +1951,22 @@ requests = ">=2.26.0" [package.extras] blobfile = ["blobfile (>=2)"] +[[package]] +name = "tokenizers" +version = "0.14.1" +description = "" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +huggingface_hub = ">=0.16.4,<0.18" + +[package.extras] +testing = ["pytest", "requests", "numpy", "datasets", "black (==22.3)"] +docs = ["sphinx", "sphinx-rtd-theme", "setuptools-rust"] +dev = ["tokenizers"] + [[package]] name = "toml" version = "0.10.2" @@ -1702,6 +2020,24 @@ python-versions = ">=3.8" docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest-mock", "pytest-mypy-testing", "pytest (>=7.0,<7.5)"] +[[package]] +name = "typer" +version = "0.9.0" +description = "Typer, build great CLIs. Easy to code. Based on Python type hints." +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +click = ">=7.1.1,<9.0.0" +typing-extensions = ">=3.7.4.3" + +[package.extras] +all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)", "rich (>=10.11.0,<14.0.0)"] +dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"] +doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "pillow (>=9.3.0,<10.0.0)", "cairosvg (>=2.5.2,<3.0.0)"] +test = ["shellingham (>=1.3.0,<2.0.0)", "pytest (>=4.4.0,<8.0.0)", "pytest-cov (>=2.10.0,<5.0.0)", "coverage (>=6.2,<7.0)", "pytest-xdist (>=1.32.0,<4.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "mypy (==0.910)", "black (>=22.3.0,<23.0.0)", "isort (>=5.0.6,<6.0.0)", "rich (>=10.11.0,<14.0.0)"] + [[package]] name = "types-pytz" version = "2023.3.1.1" @@ -1751,6 +2087,41 @@ brotli = ["brotlicffi (>=0.8.0)", "brotli (==1.0.9)", "brotlipy (>=0.6.0)", "bro secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"] socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] +[[package]] +name = "uvicorn" +version = "0.23.2" +description = "The lightning-fast ASGI server." +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +click = ">=7.0" +colorama = {version = ">=0.4", optional = true, markers = "sys_platform == \"win32\" and extra == \"standard\""} +h11 = ">=0.8" +httptools = {version = ">=0.5.0", optional = true, markers = "extra == \"standard\""} +python-dotenv = {version = ">=0.13", optional = true, markers = "extra == \"standard\""} +pyyaml = {version = ">=5.1", optional = true, markers = "extra == \"standard\""} +typing-extensions = {version = ">=4.0", markers = "python_version < \"3.11\""} +uvloop = {version = ">=0.14.0,<0.15.0 || >0.15.0,<0.15.1 || >0.15.1", optional = true, markers = "sys_platform != \"win32\" and sys_platform != \"cygwin\" and platform_python_implementation != \"PyPy\" and extra == \"standard\""} +watchfiles = {version = ">=0.13", optional = true, markers = "extra == \"standard\""} +websockets = {version = ">=10.4", optional = true, markers = "extra == \"standard\""} + +[package.extras] +standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"] + +[[package]] +name = "uvloop" +version = "0.18.0" +description = "Fast implementation of asyncio event loop on top of libuv" +category = "main" +optional = false +python-versions = ">=3.7.0" + +[package.extras] +docs = ["Sphinx (>=4.1.2,<4.2.0)", "sphinxcontrib-asyncio (>=0.3.0,<0.4.0)", "sphinx-rtd-theme (>=0.5.2,<0.6.0)"] +test = ["flake8 (>=5.0,<6.0)", "psutil", "pycodestyle (>=2.9.0,<2.10.0)", "pyOpenSSL (>=23.0.0,<23.1.0)", "mypy (>=0.800)", "Cython (>=0.29.36,<0.30.0)", "aiohttp (>=3.8.1)", "aiohttp (==3.9.0b0)"] + [[package]] name = "virtualenv" version = "20.24.5" @@ -1807,6 +2178,17 @@ nexus = ["wandb-core (>=0.16.0b1)"] perf = ["orjson"] sweeps = ["sweeps (>=0.2.0)"] +[[package]] +name = "watchfiles" +version = "0.21.0" +description = "Simple, modern and high performance file watching and code reload in python." +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +anyio = ">=3.0.0" + [[package]] name = "wcwidth" version = "0.2.8" @@ -1815,6 +2197,14 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "websockets" +version = "11.0.3" +description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)" +category = "main" +optional = false +python-versions = ">=3.7" + [[package]] name = "yarl" version = "1.9.2" @@ -1842,7 +2232,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-ena [metadata] lock-version = "1.1" python-versions = ">=3.8.1,<3.12" -content-hash = "6b90a63031be60cd462afea4f2437342d4e87e5a4848c48e934f5d9e06190460" +content-hash = "86023c296089226fd0d4ae7803ce25ab9a024413bc27f74ff53112994dc39c68" [metadata.files] aiohttp = [] @@ -1855,12 +2245,17 @@ asttokens = [] async-timeout = [] attrs = [] backcall = [] +backoff = [] +bcrypt = [] certifi = [] cffi = [] cfgv = [] charset-normalizer = [] +chroma-hnswlib = [] +chromadb = [] click = [] colorama = [] +coloredlogs = [] comm = [] contourpy = [] coverage = [] @@ -1874,14 +2269,22 @@ et-xmlfile = [] exceptiongroup = [] execnet = [] executing = [] +fastapi = [] fastjsonschema = [] filelock = [] +flatbuffers = [] fonttools = [] frozenlist = [] fsspec = [] gitdb = [] gitpython = [] +graphlib-backport = [] greenlet = [] +grpcio = [] +h11 = [] +httptools = [] +huggingface-hub = [] +humanfriendly = [] identify = [] idna = [] importlib-metadata = [] @@ -1904,6 +2307,8 @@ llama-index = [] marshmallow = [] matplotlib = [] matplotlib-inline = [] +monotonic = [] +mpmath = [] multidict = [] mypy-extensions = [] nbclient = [] @@ -1913,8 +2318,10 @@ nest-asyncio = [] nltk = [] nodeenv = [] numpy = [] +onnxruntime = [] openai = [] openpyxl = [] +overrides = [] packaging = [] pandas = [] pandas-stubs = [] @@ -1928,11 +2335,13 @@ pkgutil-resolve-name = [] platformdirs = [] plotly = [] pluggy = [] +posthog = [] pre-commit = [] prompt-toolkit = [] protobuf = [] psutil = [] ptyprocess = [] +pulsar-client = [] pure-eval = [] py = [] pycparser = [] @@ -1940,6 +2349,8 @@ pydantic = [] pydantic-core = [] pygments = [] pyparsing = [] +pypika = [] +pyreadline3 = [] pytest = [] pytest-cov = [] pytest-dotenv = [] @@ -1965,21 +2376,29 @@ smmap = [] sniffio = [] sqlalchemy = [] stack-data = [] +starlette = [] +sympy = [] tenacity = [] threadpoolctl = [] tiktoken = [] +tokenizers = [] toml = [] tomli = [] tornado = [] tqdm = [] traitlets = [] +typer = [] types-pytz = [] typing-extensions = [] typing-inspect = [] tzdata = [] urllib3 = [] +uvicorn = [] +uvloop = [] virtualenv = [] wandb = [] +watchfiles = [] wcwidth = [] +websockets = [] yarl = [] zipp = [] diff --git a/pyproject.toml b/pyproject.toml index f3729b6..006f03d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,6 +23,7 @@ langchain = "^0.0.312" llama-index = "^0.8.43" wandb = "^0.15.12" nbformat = "^5.9.2" +chromadb = "^0.4.14" [tool.poetry.dev-dependencies] pytest = "^7.1.0" diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index ab109d8..4e8416b 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -15,6 +15,10 @@ def cli(): def index(): """Build an index based on the python environment.""" click.echo("Building index...") + from .index import create_index + + retriever = create_index() + pass @cli.command() diff --git a/src/nbwrite/index.py b/src/nbwrite/index.py new file mode 100644 index 0000000..173b346 --- /dev/null +++ b/src/nbwrite/index.py @@ -0,0 +1,43 @@ +import importlib.util +from pathlib import Path + +from langchain.document_loaders.generic import GenericLoader +from langchain.document_loaders.parsers import LanguageParser +from langchain.text_splitter import Language + +lib = importlib.util.find_spec("nbmake") + + +def create_index(): + # Assumes the 'openai-python' repository exists in the user's root directory + code_root = Path(lib.submodule_search_locations._path[0]) # type: ignore + code = (code_root / "nb_run.py").read_text() + + # Load + loader = GenericLoader.from_filesystem( + code_root, + glob="**/*", + suffixes=[".py"], + parser=LanguageParser(language=Language.PYTHON, parser_threshold=500), + ) + documents = loader.load() + len(documents) + + from langchain.text_splitter import RecursiveCharacterTextSplitter + + python_splitter = RecursiveCharacterTextSplitter.from_language( + language=Language.PYTHON, chunk_size=2000, chunk_overlap=200 + ) + texts = python_splitter.split_documents(documents) + len(texts) + + from langchain.embeddings.openai import OpenAIEmbeddings + from langchain.vectorstores import Chroma + + db = Chroma.from_documents(texts, OpenAIEmbeddings(disallowed_special=())) + retriever = db.as_retriever( + search_type="mmr", # Also test "similarity" + search_kwargs={"k": 8}, + ) + + return retriever From a42032191fc24a263d385ffb56d69e1f61cb9631 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 16 Oct 2023 18:52:59 +0000 Subject: [PATCH 29/59] RAG --- poetry.lock | 11 ++++++++++- pyproject.toml | 1 + src/nbwrite/index.py | 8 +++++++- src/nbwrite/writer.py | 24 +++++++++++++++++++----- 4 files changed, 37 insertions(+), 7 deletions(-) diff --git a/poetry.lock b/poetry.lock index 697c545..3d43cae 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1528,6 +1528,14 @@ category = "main" optional = false python-versions = "*" +[[package]] +name = "pysqlite3-binary" +version = "0.5.2.post1" +description = "DB-API 2.0 interface for Sqlite 3.x" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "pytest" version = "7.4.2" @@ -2232,7 +2240,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-ena [metadata] lock-version = "1.1" python-versions = ">=3.8.1,<3.12" -content-hash = "86023c296089226fd0d4ae7803ce25ab9a024413bc27f74ff53112994dc39c68" +content-hash = "4007d8d177f71f5628e7607c800b62325c1b547070012a6a808b5d4a0c8cbc10" [metadata.files] aiohttp = [] @@ -2351,6 +2359,7 @@ pygments = [] pyparsing = [] pypika = [] pyreadline3 = [] +pysqlite3-binary = [] pytest = [] pytest-cov = [] pytest-dotenv = [] diff --git a/pyproject.toml b/pyproject.toml index 006f03d..8eb7ab1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,6 +24,7 @@ llama-index = "^0.8.43" wandb = "^0.15.12" nbformat = "^5.9.2" chromadb = "^0.4.14" +pysqlite3-binary = "^0.5.2" [tool.poetry.dev-dependencies] pytest = "^7.1.0" diff --git a/src/nbwrite/index.py b/src/nbwrite/index.py index 173b346..95ba658 100644 --- a/src/nbwrite/index.py +++ b/src/nbwrite/index.py @@ -5,10 +5,16 @@ from langchain.document_loaders.parsers import LanguageParser from langchain.text_splitter import Language -lib = importlib.util.find_spec("nbmake") +# https://docs.trychroma.com/troubleshooting#sqlite +__import__("pysqlite3") +import sys + +sys.modules["sqlite3"] = sys.modules.pop("pysqlite3") def create_index(): + lib = importlib.util.find_spec("nbmake") + # Assumes the 'openai-python' repository exists in the user's root directory code_root = Path(lib.submodule_search_locations._path[0]) # type: ignore code = (code_root / "nb_run.py").read_text() diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index cc727bb..69f0d3c 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -5,6 +5,7 @@ from typing import Any, Dict, List from langchain.callbacks import wandb_tracing_enabled as _ +from langchain.chains import RetrievalQA from langchain.chat_models import ChatAnyscale from langchain.llms.openai import OpenAI from langchain.prompts import ChatPromptTemplate, PromptTemplate @@ -38,9 +39,12 @@ template_string = """ -task: '{task}'. +task: "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application". -nbmake/nb_run.py: {code}" + +context: + +{context} """ # Now we can use the NotebookRun class to execute it and check that it printed what we were expecting @@ -65,7 +69,6 @@ def complete(path: Path, out_path: Path): temperature=0.1, max_tokens=512, ) - task = "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application" prompt = ChatPromptTemplate.from_messages( [ @@ -74,8 +77,19 @@ def complete(path: Path, out_path: Path): ] ) - chain = prompt | llm - code_out = chain.invoke({"task": task, "code": code}) + from nbwrite.index import create_index + + retriever = create_index() + chain_type_kwargs = {"prompt": prompt} + chain = RetrievalQA.from_chain_type( + llm=llm, + chain_type="stuff", + retriever=retriever, + chain_type_kwargs=chain_type_kwargs, + ) + + # chain = retriever | prompt | llm + code_out = chain.invoke({"query": "use nbmake.nb_run.NotebookRun"}) title = "AI!" sources = [code_out] nb = new_notebook() From ae3575671aee3914628101c9fd5d9b39b5564cf3 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 17 Oct 2023 11:18:52 +0000 Subject: [PATCH 30/59] phoenix --- poetry.lock | 3815 ++++++++++++++++++++++++++++++++++++----- pyproject.toml | 3 + src/nbwrite/writer.py | 11 +- x.ipynb | 43 +- 4 files changed, 3405 insertions(+), 467 deletions(-) diff --git a/poetry.lock b/poetry.lock index 3d43cae..a89a645 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,100 @@ +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. + [[package]] name = "aiohttp" version = "3.8.6" description = "Async http client/server framework (asyncio)" -category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "aiohttp-3.8.6-cp310-cp310-macosx_10_9_universal2.whl", hash = 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[] -debugpy = [] -decorator = [] -distlib = [] -docker-pycreds = [] -et-xmlfile = [] -exceptiongroup = [] -execnet = [] -executing = [] -fastapi = [] -fastjsonschema = [] -filelock = [] -flatbuffers = [] -fonttools = [] -frozenlist = [] -fsspec = [] -gitdb = [] -gitpython = [] -graphlib-backport = [] -greenlet = [] -grpcio = [] -h11 = [] -httptools = [] -huggingface-hub = [] -humanfriendly = [] -identify = [] -idna = [] -importlib-metadata = [] -importlib-resources = [] -iniconfig = [] -ipykernel = [] -ipython = [] -jedi = [] -joblib = [] -jsonpatch = [] -jsonpointer = [] -jsonschema = [] -jsonschema-specifications = [] -jupyter-client = [] -jupyter-core = [] -kiwisolver = [] -langchain = [] -langsmith = [] -llama-index = [] -marshmallow = [] -matplotlib = [] -matplotlib-inline = [] -monotonic = [] -mpmath = [] -multidict = [] -mypy-extensions = [] -nbclient = [] -nbformat = [] -nbmake = [] -nest-asyncio = [] -nltk = [] -nodeenv = [] -numpy = [] -onnxruntime = [] -openai = [] -openpyxl 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-toml = [] -tomli = [] -tornado = [] -tqdm = [] -traitlets = [] -typer = [] -types-pytz = [] -typing-extensions = [] -typing-inspect = [] -tzdata = [] -urllib3 = [] -uvicorn = [] -uvloop = [] -virtualenv = [] -wandb = [] -watchfiles = [] -wcwidth = [] -websockets = [] -yarl = [] -zipp = [] +content-hash = "657b606078355ef76e805010d17d383cdb6341af8ed7696459d29bc95da84e15" diff --git a/pyproject.toml b/pyproject.toml index 8eb7ab1..6f0742f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,6 +25,7 @@ wandb = "^0.15.12" nbformat = "^5.9.2" chromadb = "^0.4.14" pysqlite3-binary = "^0.5.2" +arize-phoenix = {extras = ["experimental"], version = "^0.0.49"} [tool.poetry.dev-dependencies] pytest = "^7.1.0" @@ -37,6 +38,8 @@ typing-extensions = "^4.7.1" nbmake = "^1.4.5" pytest-dotenv = "^0.5.2" +[tool.poetry.group.dev.dependencies] + [build-system] build-backend = "poetry.core.masonry.api" requires = ["setuptools", "poetry-core>=1.0.0"] diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 69f0d3c..21c11ea 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -19,6 +19,15 @@ reads, writes, ) +from phoenix.trace.langchain import LangChainInstrumentor, OpenInferenceTracer + +# Once you have started a Phoenix server, you can start your LangChain application with the OpenInferenceTracer as a callback. To do this, you will have to instrument your LangChain application with the tracer: + + +# If no exporter is specified, the tracer will export to the locally running Phoenix server +tracer = OpenInferenceTracer() +LangChainInstrumentor(tracer).instrument() + lib = importlib.util.find_spec("nbmake") @@ -91,7 +100,7 @@ def complete(path: Path, out_path: Path): # chain = retriever | prompt | llm code_out = chain.invoke({"query": "use nbmake.nb_run.NotebookRun"}) title = "AI!" - sources = [code_out] + sources = [code_out["result"]] nb = new_notebook() # nb.metadata = metadata nb.cells.append(new_markdown_cell(f"# {title}")) diff --git a/x.ipynb b/x.ipynb index efb940d..99c8de4 100644 --- a/x.ipynb +++ b/x.ipynb @@ -7,11 +7,50 @@ "metadata": {}, "outputs": [], "source": [ - "print(\"Hello, World!\")" + "import phoenix as px\n", + "\n", + "# To view traces in Phoenix, you will first have to start a Phoenix server. You can do this by running the following:\n", + "session = px.launch_app()\n" ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "fc925a34", + "metadata": {}, + "outputs": [], + "source": [ + "px.active_session().view()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7387f8af", + "metadata": {}, + "outputs": [], + "source": [] } ], - "metadata": {}, + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.12" + } + }, "nbformat": 4, "nbformat_minor": 5 } From 327e091f441d65bfd5cc9e94e422fa6a75adb22c Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 17 Oct 2023 17:09:19 +0000 Subject: [PATCH 31/59] readme --- src/nbwrite/README.md | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 src/nbwrite/README.md diff --git a/src/nbwrite/README.md b/src/nbwrite/README.md new file mode 100644 index 0000000..9877f96 --- /dev/null +++ b/src/nbwrite/README.md @@ -0,0 +1,20 @@ +# Nbwrite + +nbwrite writes notebook-based documentation for you + +Tutorials, guides, demos, examples -- it creates runnable and testable python code which +give your users critical support in using your product. + +To write your first notebook, create an ipynb file and use the cli like so + +```python +nbwrite \ + my_nb.ipynb \ + output.ipynb \ + --task 'test a notebook from the Python API using the notebook run class' \ + --step 'create an example nb using the nbformat library' \ + --step 'call notebookrun' \ + --step 'check the output' \ + --context nbmake \ + --context another_lib +``` \ No newline at end of file From 7de73b56865579ee0ec985040aa572459a7e1bcd Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Wed, 18 Oct 2023 11:17:23 +0000 Subject: [PATCH 32/59] gradio integ --- .gitignore | 3 +- README.md | 21 ++- poetry.lock | 262 +++++++++++++++++++++++++++++++++++++- pyproject.toml | 3 + src/nbwrite/README.md | 20 --- src/nbwrite/app.py | 23 ++++ src/nbwrite/writer.py | 56 +++++--- tests/resources/out.ipynb | 46 +++---- 8 files changed, 362 insertions(+), 72 deletions(-) delete mode 100644 src/nbwrite/README.md create mode 100644 src/nbwrite/app.py diff --git a/.gitignore b/.gitignore index 74a6342..3f06244 100644 --- a/.gitignore +++ b/.gitignore @@ -135,4 +135,5 @@ trash **/_build .testvenv -wandb \ No newline at end of file +wandb +flagged \ No newline at end of file diff --git a/README.md b/README.md index 6b3cc51..9877f96 100644 --- a/README.md +++ b/README.md @@ -1 +1,20 @@ -# nbwrite \ No newline at end of file +# Nbwrite + +nbwrite writes notebook-based documentation for you + +Tutorials, guides, demos, examples -- it creates runnable and testable python code which +give your users critical support in using your product. + +To write your first notebook, create an ipynb file and use the cli like so + +```python +nbwrite \ + my_nb.ipynb \ + output.ipynb \ + --task 'test a notebook from the Python API using the notebook run class' \ + --step 'create an example nb using the nbformat library' \ + --step 'call notebookrun' \ + --step 'check the output' \ + --context nbmake \ + --context another_lib +``` \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index a89a645..f5a7315 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,16 @@ # This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +[[package]] +name = "aiofiles" +version = "23.2.1" +description = "File support for asyncio." +optional = false +python-versions = ">=3.7" +files = [ + {file = "aiofiles-23.2.1-py3-none-any.whl", hash = "sha256:19297512c647d4b27a2cf7c34caa7e405c0d60b5560618a29a9fe027b18b0107"}, + {file = "aiofiles-23.2.1.tar.gz", hash = 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"sha256:de78a3b8e0feda74cabc54aab2da702113e33ac9d9eb9d2389bcf1f58b7d9177"}, + {file = "semantic_version-2.10.0.tar.gz", hash = "sha256:bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c"}, +] + +[package.extras] +dev = ["Django (>=1.11)", "check-manifest", "colorama (<=0.4.1)", "coverage", "flake8", "nose2", "readme-renderer (<25.0)", "tox", "wheel", "zest.releaser[recommended]"] +doc = ["Sphinx", "sphinx-rtd-theme"] + [[package]] name = "sentry-sdk" version = "1.32.0" @@ -4617,6 +4866,17 @@ files = [ {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"}, ] +[[package]] +name = "toolz" +version = "0.12.0" +description = "List processing tools and functional utilities" +optional = false +python-versions = ">=3.5" +files = [ + {file = "toolz-0.12.0-py3-none-any.whl", hash = "sha256:2059bd4148deb1884bb0eb770a3cde70e7f954cfbbdc2285f1f2de01fd21eb6f"}, + {file = "toolz-0.12.0.tar.gz", hash = "sha256:88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194"}, +] + [[package]] name = "tornado" version = "6.3.3" @@ -5297,4 +5557,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "657b606078355ef76e805010d17d383cdb6341af8ed7696459d29bc95da84e15" +content-hash = "cb6ea0fb2ba44202be026031d165ec99c89639e7745ce45ac5d0a8206a7c7d90" diff --git a/pyproject.toml b/pyproject.toml index 6f0742f..7543197 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,6 +26,7 @@ nbformat = "^5.9.2" chromadb = "^0.4.14" pysqlite3-binary = "^0.5.2" arize-phoenix = {extras = ["experimental"], version = "^0.0.49"} +python-dotenv = "^1.0.0" [tool.poetry.dev-dependencies] pytest = "^7.1.0" @@ -38,7 +39,9 @@ typing-extensions = "^4.7.1" nbmake = "^1.4.5" pytest-dotenv = "^0.5.2" + [tool.poetry.group.dev.dependencies] +gradio = "^3.49.0" [build-system] build-backend = "poetry.core.masonry.api" diff --git a/src/nbwrite/README.md b/src/nbwrite/README.md deleted file mode 100644 index 9877f96..0000000 --- a/src/nbwrite/README.md +++ /dev/null @@ -1,20 +0,0 @@ -# Nbwrite - -nbwrite writes notebook-based documentation for you - -Tutorials, guides, demos, examples -- it creates runnable and testable python code which -give your users critical support in using your product. - -To write your first notebook, create an ipynb file and use the cli like so - -```python -nbwrite \ - my_nb.ipynb \ - output.ipynb \ - --task 'test a notebook from the Python API using the notebook run class' \ - --step 'create an example nb using the nbformat library' \ - --step 'call notebookrun' \ - --step 'check the output' \ - --context nbmake \ - --context another_lib -``` \ No newline at end of file diff --git a/src/nbwrite/app.py b/src/nbwrite/app.py new file mode 100644 index 0000000..d2a7ffd --- /dev/null +++ b/src/nbwrite/app.py @@ -0,0 +1,23 @@ +import gradio as gr +from dotenv import load_dotenv + +from nbwrite.writer import gen + +if __name__ == "__main__": + load_dotenv() + placeholder_task = "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application" + + demo = gr.Interface( + fn=gen, + inputs=[ + gr.Textbox(lines=2, placeholder=placeholder_task), + "text", + "text", + "text", + "text", + "text", + ], + outputs="text", + ) + + demo.launch() diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 21c11ea..017a92c 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -46,24 +46,51 @@ Write 25 lines max per response """ -template_string = """ -task: "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application". +# Now we can use the NotebookRun class to execute it and check that it printed what we were expecting +# The following class has been imported `nbmake.nb_run.NotebookRun`: -context: +placeholder_task = "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application" +s1 = "create a hello world notebook using nbformat" +s2 = "use nbmake's NotebookRun class to execute it from a Python application" +s3 = "check the output notebook printed what we were expecting" +h1 = "use nbformat" +h2 = "use NotebookRun" -{context} -""" -# Now we can use the NotebookRun class to execute it and check that it printed what we were expecting +def complete(path: Path, out_path: Path): + code_out = gen(placeholder_task, s1, s2, s3, h1, h2) + title = "AI!" + sources = [code_out] + nb = new_notebook() + # nb.metadata = metadata + nb.cells.append(new_markdown_cell(f"# {title}")) + for src in sources: + nb.cells.append(new_code_cell(src)) -# The following class has been imported `nbmake.nb_run.NotebookRun`: + # double check some basic structure + string = writes(nb) + _ = reads(string) + write(nb, str(out_path)) -def complete(path: Path, out_path: Path): +def gen(guide: str, step1: str, step2: str, step3: str, hint1: str, hint2: str) -> str: """Write demo notebooks based on prompts in the notebook and the index""" # openai.organization = os.getenv("OPENAI_ORG_ID") + + template_string = f""" + + task: {guide} + + step 1: {step1} + step 2: {step2} + step 3: {step3} + + context: + + {"{context}"} + """ temperature = 0.1 model = "codellama/CodeLlama-34b-Instruct-hf" @@ -99,15 +126,4 @@ def complete(path: Path, out_path: Path): # chain = retriever | prompt | llm code_out = chain.invoke({"query": "use nbmake.nb_run.NotebookRun"}) - title = "AI!" - sources = [code_out["result"]] - nb = new_notebook() - # nb.metadata = metadata - nb.cells.append(new_markdown_cell(f"# {title}")) - for src in sources: - nb.cells.append(new_code_cell(src)) - - # double check some basic structure - string = writes(nb) - _ = reads(string) - write(nb, str(out_path)) + return code_out["result"] diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index 0de5a8f..5c5b9fc 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "d6104f2b", + "id": "0b7fb65f", "metadata": {}, "source": [ "# AI!" @@ -11,45 +11,33 @@ { "cell_type": "code", "execution_count": null, - "id": "66839a1a", + "id": "41fa8aaa", "metadata": {}, "outputs": [], "source": [ + "```python\n", + "import nbformat\n", "from nbformat.v4 import new_notebook, new_code_cell\n", - "import nbformat as nbf\n", - "\n", - "# Create a new notebook\n", - "nb = new_notebook()\n", - "\n", - "# Add a code cell\n", - "code = 'print(\"Hello, World!\")'\n", - "nb.cells.append(new_code_cell(source=code))\n", - "\n", - "# Write the notebook to a file\n", - "with open('x.ipynb', 'w') as f:\n", - " nbf.write(nb, f)\n", - "\n", "from pathlib import Path\n", "from nbmake import NotebookRun\n", "\n", - "# Test the notebook\n", - "nb_path = Path('x.ipynb')\n", - "nb_run = NotebookRun(nb_path, default_timeout=60)\n", - "result = nb_run.execute()\n", + "# Step 1: Create a hello world notebook using nbformat\n", + "nb = new_notebook()\n", + "code = \"print('Hello, World!')\"\n", + "nb.cells.append(new_code_cell(code))\n", + "nbformat.write(nb, 'x.ipynb')\n", + "\n", + "# Step 2: Use nbmake's NotebookRun class to execute it from a Python application\n", + "notebook_run = NotebookRun(filename=Path('x.ipynb'), default_timeout=60)\n", + "result = notebook_run.execute()\n", "\n", - "# Check if there were any errors\n", - "if result.error is not None:\n", - " print(f\"Error in notebook: {result.error.summary}\")\n", - "else:\n", - " print(\"Notebook executed successfully.\")" + "# Step 3: Check the output notebook printed what we were expecting\n", + "assert result.nb['cells'][0]['outputs'][0]['text'] == 'Hello, World!\\n'\n", + "```" ] } ], - "metadata": { - "language_info": { - "name": "python" - } - }, + "metadata": {}, "nbformat": 4, "nbformat_minor": 5 } From d2f2b9c12f7fdad65a4781a64130611125fd8a5a Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Wed, 18 Oct 2023 15:35:18 +0000 Subject: [PATCH 33/59] try out anyscale --- src/nbwrite/index.py | 2 +- src/nbwrite/writer.py | 24 ++++++++++++------------ 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/src/nbwrite/index.py b/src/nbwrite/index.py index 95ba658..6397141 100644 --- a/src/nbwrite/index.py +++ b/src/nbwrite/index.py @@ -43,7 +43,7 @@ def create_index(): db = Chroma.from_documents(texts, OpenAIEmbeddings(disallowed_special=())) retriever = db.as_retriever( search_type="mmr", # Also test "similarity" - search_kwargs={"k": 8}, + search_kwargs={"k": 2}, ) return retriever diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 017a92c..5586cea 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -36,14 +36,14 @@ code = (code_root / "nb_run.py").read_text() SYSTEM_PROMPT = """ -You are a python programmer +You are a python programmer writing a markdown document describing a task. -Respond using only Python code -Do not use comments -Do not use quotes -Do not explain anything +Do install any packages you need using pip Do import any libraries you need -Write 25 lines max per response +Write 30 lines max per response +Write snippets of markdown before each section of code +Use a help and authoritative tone +Do not use conversational language """ @@ -94,17 +94,17 @@ def gen(guide: str, step1: str, step2: str, step3: str, hint1: str, hint2: str) temperature = 0.1 model = "codellama/CodeLlama-34b-Instruct-hf" - llm_anyscale = ChatAnyscale( + llm = ChatAnyscale( temperature=temperature, model_name=model, streaming=True, ) - llm = OpenAI( - model_name="gpt-4", - temperature=0.1, - max_tokens=512, - ) + # llm = OpenAI( + # model_name="gpt-4", + # temperature=0.1, + # max_tokens=512, + # ) prompt = ChatPromptTemplate.from_messages( [ From 862595b87116bb9d2e4f0597fb719dcad51e33ae Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Wed, 18 Oct 2023 16:01:36 +0000 Subject: [PATCH 34/59] disable wandb --- src/nbwrite/cli.py | 3 ++ src/nbwrite/writer.py | 2 +- tests/resources/out.ipynb | 68 +++++++++++++++++++++++++++++---------- x.ipynb | 10 +----- 4 files changed, 56 insertions(+), 27 deletions(-) diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index 4e8416b..d16904d 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -1,9 +1,12 @@ from pathlib import Path import click +from dotenv import load_dotenv import nbwrite.writer as writer +load_dotenv() + @click.group() def cli(): diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 5586cea..bf18e71 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -4,7 +4,7 @@ from pathlib import Path from typing import Any, Dict, List -from langchain.callbacks import wandb_tracing_enabled as _ +# from langchain.callbacks import wandb_tracing_enabled as _ from langchain.chains import RetrievalQA from langchain.chat_models import ChatAnyscale from langchain.llms.openai import OpenAI diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index 5c5b9fc..4b2a3f8 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "0b7fb65f", + "id": "3ce0d6b8", "metadata": {}, "source": [ "# AI!" @@ -11,33 +11,67 @@ { "cell_type": "code", "execution_count": null, - "id": "41fa8aaa", + "id": "4398e4d6", "metadata": {}, "outputs": [], "source": [ - "```python\n", + " Here is an example of how you can use the `NotebookRun` class to execute a Jupyter notebook from a Python application:\n", + "```\n", "import nbformat\n", - "from nbformat.v4 import new_notebook, new_code_cell\n", - "from pathlib import Path\n", "from nbmake import NotebookRun\n", "\n", - "# Step 1: Create a hello world notebook using nbformat\n", - "nb = new_notebook()\n", - "code = \"print('Hello, World!')\"\n", - "nb.cells.append(new_code_cell(code))\n", - "nbformat.write(nb, 'x.ipynb')\n", + "# Create a new NotebookRun instance\n", + "notebook_run = NotebookRun(\n", + " filename=\"hello_world.ipynb\",\n", + " default_timeout=10,\n", + " verbose=True,\n", + " kernel=\"python3\",\n", + " find_import_errors=True,\n", + ")\n", "\n", - "# Step 2: Use nbmake's NotebookRun class to execute it from a Python application\n", - "notebook_run = NotebookRun(filename=Path('x.ipynb'), default_timeout=60)\n", - "result = notebook_run.execute()\n", + "# Execute the notebook\n", + "notebook_run.execute()\n", "\n", - "# Step 3: Check the output notebook printed what we were expecting\n", - "assert result.nb['cells'][0]['outputs'][0]['text'] == 'Hello, World!\\n'\n", - "```" + "# Check the output notebook\n", + "assert notebook_run.notebook.cells[0].outputs[0].text == \"Hello, world!\"\n", + "```\n", + "This code creates a new `NotebookRun` instance with the filename of the notebook to be executed, the default timeout for the notebook, and the kernel to be used. It then executes the notebook using the `execute` method and checks the output notebook to make sure it contains the expected output.\n", + "\n", + "You can also use the `NotebookRun` class to execute a notebook from a Python application and get the output notebook as a string:\n", + "```\n", + "import nbformat\n", + "from nbmake import NotebookRun\n", + "\n", + "# Create a new NotebookRun instance\n", + "notebook_run = NotebookRun(\n", + " filename=\"hello_world.ipynb\",\n", + " default_timeout=10,\n", + " verbose=True,\n", + " kernel=\"python3\",\n", + " find_import_errors=True,\n", + ")\n", + "\n", + "# Execute the notebook and get the output notebook as a string\n", + "output_notebook = notebook_run.execute().notebook.cells[0].outputs[0].text\n", + "\n", + "# Check the output notebook\n", + "assert output_notebook == \"Hello, world!\"\n", + "```\n", + "This code is similar to the previous example, but it uses the `execute` method to get the output notebook as a string instead of checking the output notebook directly." ] } ], - "metadata": {}, + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python", + "version": "3.10.12" + } + }, "nbformat": 4, "nbformat_minor": 5 } diff --git a/x.ipynb b/x.ipynb index 99c8de4..cf98b5e 100644 --- a/x.ipynb +++ b/x.ipynb @@ -10,7 +10,7 @@ "import phoenix as px\n", "\n", "# To view traces in Phoenix, you will first have to start a Phoenix server. You can do this by running the following:\n", - "session = px.launch_app()\n" + "session = px.launch_app()" ] }, { @@ -22,14 +22,6 @@ "source": [ "px.active_session().view()" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "7387f8af", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { From f0526e316776855788420496d5f8fb54dd933076 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Wed, 18 Oct 2023 18:11:36 +0000 Subject: [PATCH 35/59] turn llm output to notebook cells --- src/nbwrite/writer.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index bf18e71..ed0a3c0 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -36,7 +36,7 @@ code = (code_root / "nb_run.py").read_text() SYSTEM_PROMPT = """ -You are a python programmer writing a markdown document describing a task. +You are a python programmer writing an ipynb document describing a task. Do install any packages you need using pip Do import any libraries you need @@ -62,12 +62,16 @@ def complete(path: Path, out_path: Path): code_out = gen(placeholder_task, s1, s2, s3, h1, h2) title = "AI!" - sources = [code_out] nb = new_notebook() # nb.metadata = metadata - nb.cells.append(new_markdown_cell(f"# {title}")) - for src in sources: - nb.cells.append(new_code_cell(src)) + + sections = code_out.split("```") + + for i in range(0, len(sections)): + if i % 2 == 0: + nb.cells.append(new_markdown_cell(sections[i])) + else: + nb.cells.append(new_code_cell(sections[i])) # double check some basic structure string = writes(nb) From 21b2c8a9aae777d168393d7400b4925d0000fa27 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Wed, 18 Oct 2023 19:45:19 +0000 Subject: [PATCH 36/59] langchain simplify --- src/nbwrite/writer.py | 90 ++++++++++++++++++++++++------------- tests/resources/out.ipynb | 95 ++++++++++++++++++++------------------- x.ipynb | 48 -------------------- 3 files changed, 109 insertions(+), 124 deletions(-) delete mode 100644 x.ipynb diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index ed0a3c0..9055602 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -1,16 +1,14 @@ -import datetime import importlib.util -import os +from operator import itemgetter from pathlib import Path -from typing import Any, Dict, List -# from langchain.callbacks import wandb_tracing_enabled as _ -from langchain.chains import RetrievalQA from langchain.chat_models import ChatAnyscale from langchain.llms.openai import OpenAI from langchain.prompts import ChatPromptTemplate, PromptTemplate -from langchain.prompts.chat import HumanMessagePromptTemplate, SystemMessage -from langchain.schema import HumanMessage +from langchain.prompts.chat import HumanMessagePromptTemplate +from langchain.schema import format_document +from langchain.schema.messages import SystemMessage +from langchain.schema.output_parser import StrOutputParser from nbformat import write from nbformat.v4 import ( new_code_cell, @@ -21,6 +19,16 @@ ) from phoenix.trace.langchain import LangChainInstrumentor, OpenInferenceTracer +DEFAULT_DOCUMENT_PROMPT = PromptTemplate.from_template(template="{page_content}") + + +def _combine_documents( + docs, document_prompt=DEFAULT_DOCUMENT_PROMPT, document_separator="\n\n" +): + doc_strings = [format_document(doc, document_prompt) for doc in docs] + return document_separator.join(doc_strings) + + # Once you have started a Phoenix server, you can start your LangChain application with the OpenInferenceTracer as a callback. To do this, you will have to instrument your LangChain application with the tracer: @@ -55,8 +63,8 @@ s1 = "create a hello world notebook using nbformat" s2 = "use nbmake's NotebookRun class to execute it from a Python application" s3 = "check the output notebook printed what we were expecting" -h1 = "use nbformat" -h2 = "use NotebookRun" +h1 = "" +h2 = "use NotebookRun(notebook, timeout)" def complete(path: Path, out_path: Path): @@ -79,29 +87,34 @@ def complete(path: Path, out_path: Path): write(nb, str(out_path)) -def gen(guide: str, step1: str, step2: str, step3: str, hint1: str, hint2: str) -> str: - """Write demo notebooks based on prompts in the notebook and the index""" - # openai.organization = os.getenv("OPENAI_ORG_ID") +template_string = """ + +task: {guide} - template_string = f""" +step 1: {step1} +step 2: {step2} +step 3: {step3} - task: {guide} +hint 1: {hint1} +hint 2: {hint2} - step 1: {step1} - step 2: {step2} - step 3: {step3} +context: - context: +{context} +""" + + +def gen(guide: str, step1: str, step2: str, step3: str, hint1: str, hint2: str) -> str: + """Write demo notebooks based on prompts in the notebook and the index""" + # openai.organization = os.getenv("OPENAI_ORG_ID") - {"{context}"} - """ temperature = 0.1 model = "codellama/CodeLlama-34b-Instruct-hf" llm = ChatAnyscale( temperature=temperature, model_name=model, - streaming=True, + # streaming=True, ) # llm = OpenAI( @@ -120,14 +133,31 @@ def gen(guide: str, step1: str, step2: str, step3: str, hint1: str, hint2: str) from nbwrite.index import create_index retriever = create_index() - chain_type_kwargs = {"prompt": prompt} - chain = RetrievalQA.from_chain_type( - llm=llm, - chain_type="stuff", - retriever=retriever, - chain_type_kwargs=chain_type_kwargs, + + chain = ( + { + "context": itemgetter("query") | retriever | _combine_documents, + "guide": itemgetter("guide"), + "step1": itemgetter("step1"), + "step2": itemgetter("step2"), + "step3": itemgetter("step3"), + "hint1": itemgetter("hint1"), + "hint2": itemgetter("hint2"), + } + | prompt + | llm + | StrOutputParser() ) - # chain = retriever | prompt | llm - code_out = chain.invoke({"query": "use nbmake.nb_run.NotebookRun"}) - return code_out["result"] + code_out = chain.invoke( + { + "query": "use nbmake.nb_run.NotebookRun", + "guide": guide, + "step1": step1, + "step2": step2, + "step3": step3, + "hint1": hint1, + "hint2": hint2, + } + ) + return code_out diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index 4b2a3f8..3a81a7f 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -2,76 +2,79 @@ "cells": [ { "cell_type": "markdown", - "id": "3ce0d6b8", + "id": "3636daca", "metadata": {}, "source": [ - "# AI!" + " To create a hello world notebook using nbformat, you can use the following code:\n" ] }, { "cell_type": "code", "execution_count": null, - "id": "4398e4d6", + "id": "ae916ed3", "metadata": {}, "outputs": [], "source": [ - " Here is an example of how you can use the `NotebookRun` class to execute a Jupyter notebook from a Python application:\n", - "```\n", + "\n", "import nbformat\n", + "\n", + "# Create a new notebook\n", + "nb = nbformat.v4.new_notebook()\n", + "\n", + "# Add a code cell to the notebook\n", + "code_cell = nbformat.v4.new_code_cell(\"print('Hello, world!')\")\n", + "nb.cells.append(code_cell)\n", + "\n", + "# Save the notebook to a file\n", + "with open(\"hello_world.ipynb\", \"w\") as f:\n", + " nbformat.write(nb, f)\n" + ] + }, + { + "cell_type": "markdown", + "id": "077012ee", + "metadata": {}, + "source": [ + "\n", + "To use nbmake's NotebookRun class to execute the notebook from a Python application, you can use the following code:\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f1aadf14", + "metadata": {}, + "outputs": [], + "source": [ + "\n", "from nbmake import NotebookRun\n", "\n", - "# Create a new NotebookRun instance\n", - "notebook_run = NotebookRun(\n", - " filename=\"hello_world.ipynb\",\n", - " default_timeout=10,\n", - " verbose=True,\n", - " kernel=\"python3\",\n", - " find_import_errors=True,\n", - ")\n", + "# Create a NotebookRun object\n", + "notebook_run = NotebookRun(\"hello_world.ipynb\")\n", "\n", "# Execute the notebook\n", "notebook_run.execute()\n", "\n", "# Check the output notebook\n", - "assert notebook_run.notebook.cells[0].outputs[0].text == \"Hello, world!\"\n", - "```\n", - "This code creates a new `NotebookRun` instance with the filename of the notebook to be executed, the default timeout for the notebook, and the kernel to be used. It then executes the notebook using the `execute` method and checks the output notebook to make sure it contains the expected output.\n", - "\n", - "You can also use the `NotebookRun` class to execute a notebook from a Python application and get the output notebook as a string:\n", - "```\n", - "import nbformat\n", - "from nbmake import NotebookRun\n", + "output_notebook = notebook_run.notebook\n", + "assert output_notebook.cells[0].outputs[0].text == \"Hello, world!\"\n" + ] + }, + { + "cell_type": "markdown", + "id": "63d00a25", + "metadata": {}, + "source": [ "\n", - "# Create a new NotebookRun instance\n", - "notebook_run = NotebookRun(\n", - " filename=\"hello_world.ipynb\",\n", - " default_timeout=10,\n", - " verbose=True,\n", - " kernel=\"python3\",\n", - " find_import_errors=True,\n", - ")\n", + "Note that the `NotebookRun` class takes a `filename` argument, which is the path to the notebook file to be executed. The `execute` method of the `NotebookRun` object executes the notebook and returns a `NotebookResult` object, which contains information about the execution of the notebook. The `notebook` attribute of the `NotebookResult` object contains the executed notebook.\n", "\n", - "# Execute the notebook and get the output notebook as a string\n", - "output_notebook = notebook_run.execute().notebook.cells[0].outputs[0].text\n", + "In the above code, we create a `NotebookRun` object with the path to the notebook file, and then execute the notebook using the `execute` method. We then check the output notebook by accessing the `notebook` attribute of the `NotebookResult` object and checking the output of the first cell.\n", "\n", - "# Check the output notebook\n", - "assert output_notebook == \"Hello, world!\"\n", - "```\n", - "This code is similar to the previous example, but it uses the `execute` method to get the output notebook as a string instead of checking the output notebook directly." + "Note that the `NotebookRun` class also takes a `timeout` argument, which specifies the maximum amount of time to wait for the notebook to execute. If the notebook execution takes longer than the specified timeout, the `NotebookRun` object will raise a `TimeoutError`." ] } ], - "metadata": { - "kernelspec": { - "display_name": ".venv", - "language": "python", - "name": "python3" - }, - "language_info": { - "name": "python", - "version": "3.10.12" - } - }, + "metadata": {}, "nbformat": 4, "nbformat_minor": 5 } diff --git a/x.ipynb b/x.ipynb deleted file mode 100644 index cf98b5e..0000000 --- a/x.ipynb +++ /dev/null @@ -1,48 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "id": "c87d174c", - "metadata": {}, - "outputs": [], - "source": [ - "import phoenix as px\n", - "\n", - "# To view traces in Phoenix, you will first have to start a Phoenix server. You can do this by running the following:\n", - "session = px.launch_app()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "fc925a34", - "metadata": {}, - "outputs": [], - "source": [ - "px.active_session().view()" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": ".venv", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.12" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} From 179309e6db52c6306fccecfdb9f59e2193bee462 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 19 Oct 2023 08:02:17 +0000 Subject: [PATCH 37/59] phoenix script --- scripts/phoenix.sh | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100755 scripts/phoenix.sh diff --git a/scripts/phoenix.sh b/scripts/phoenix.sh new file mode 100755 index 0000000..2c5f69b --- /dev/null +++ b/scripts/phoenix.sh @@ -0,0 +1,6 @@ +#! /usr/bin/env python + +import phoenix +phoenix.launch_app() + +input("Press any key to exit...") \ No newline at end of file From 22cbdb07b12038f25a5626c4b4504cc7e26bb4c1 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 19 Oct 2023 08:09:53 +0000 Subject: [PATCH 38/59] refactor out query example --- src/nbwrite/writer.py | 33 +++++++++++++-------------------- tests/resources/out.ipynb | 28 +++++++++++++++++----------- 2 files changed, 30 insertions(+), 31 deletions(-) diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 9055602..791596c 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -21,18 +21,6 @@ DEFAULT_DOCUMENT_PROMPT = PromptTemplate.from_template(template="{page_content}") - -def _combine_documents( - docs, document_prompt=DEFAULT_DOCUMENT_PROMPT, document_separator="\n\n" -): - doc_strings = [format_document(doc, document_prompt) for doc in docs] - return document_separator.join(doc_strings) - - -# Once you have started a Phoenix server, you can start your LangChain application with the OpenInferenceTracer as a callback. To do this, you will have to instrument your LangChain application with the tracer: - - -# If no exporter is specified, the tracer will export to the locally running Phoenix server tracer = OpenInferenceTracer() LangChainInstrumentor(tracer).instrument() @@ -54,21 +42,17 @@ def _combine_documents( Do not use conversational language """ - -# Now we can use the NotebookRun class to execute it and check that it printed what we were expecting - -# The following class has been imported `nbmake.nb_run.NotebookRun`: - placeholder_task = "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application" s1 = "create a hello world notebook using nbformat" s2 = "use nbmake's NotebookRun class to execute it from a Python application" s3 = "check the output notebook printed what we were expecting" h1 = "" h2 = "use NotebookRun(notebook, timeout)" +query = "use nbmake.nb_run.NotebookRun" def complete(path: Path, out_path: Path): - code_out = gen(placeholder_task, s1, s2, s3, h1, h2) + code_out = gen(query, placeholder_task, s1, s2, s3, h1, h2) title = "AI!" nb = new_notebook() # nb.metadata = metadata @@ -104,7 +88,16 @@ def complete(path: Path, out_path: Path): """ -def gen(guide: str, step1: str, step2: str, step3: str, hint1: str, hint2: str) -> str: +def _combine_documents( + docs, document_prompt=DEFAULT_DOCUMENT_PROMPT, document_separator="\n\n" +): + doc_strings = [format_document(doc, document_prompt) for doc in docs] + return document_separator.join(doc_strings) + + +def gen( + query: str, guide: str, step1: str, step2: str, step3: str, hint1: str, hint2: str +) -> str: """Write demo notebooks based on prompts in the notebook and the index""" # openai.organization = os.getenv("OPENAI_ORG_ID") @@ -151,7 +144,7 @@ def gen(guide: str, step1: str, step2: str, step3: str, hint1: str, hint2: str) code_out = chain.invoke( { - "query": "use nbmake.nb_run.NotebookRun", + "query": query, "guide": guide, "step1": step1, "step2": step2, diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb index 3a81a7f..d20994e 100644 --- a/tests/resources/out.ipynb +++ b/tests/resources/out.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "3636daca", + "id": "d39a884a", "metadata": {}, "source": [ " To create a hello world notebook using nbformat, you can use the following code:\n" @@ -11,7 +11,7 @@ { "cell_type": "code", "execution_count": null, - "id": "ae916ed3", + "id": "7053f14c", "metadata": {}, "outputs": [], "source": [ @@ -32,7 +32,7 @@ }, { "cell_type": "markdown", - "id": "077012ee", + "id": "df1e2151", "metadata": {}, "source": [ "\n", @@ -42,7 +42,7 @@ { "cell_type": "code", "execution_count": null, - "id": "f1aadf14", + "id": "f56d25d0", "metadata": {}, "outputs": [], "source": [ @@ -62,19 +62,25 @@ }, { "cell_type": "markdown", - "id": "63d00a25", + "id": "5dd0c37c", "metadata": {}, "source": [ "\n", - "Note that the `NotebookRun` class takes a `filename` argument, which is the path to the notebook file to be executed. The `execute` method of the `NotebookRun` object executes the notebook and returns a `NotebookResult` object, which contains information about the execution of the notebook. The `notebook` attribute of the `NotebookResult` object contains the executed notebook.\n", - "\n", - "In the above code, we create a `NotebookRun` object with the path to the notebook file, and then execute the notebook using the `execute` method. We then check the output notebook by accessing the `notebook` attribute of the `NotebookResult` object and checking the output of the first cell.\n", - "\n", - "Note that the `NotebookRun` class also takes a `timeout` argument, which specifies the maximum amount of time to wait for the notebook to execute. If the notebook execution takes longer than the specified timeout, the `NotebookRun` object will raise a `TimeoutError`." + "Note that the `NotebookRun` class takes a `filename` argument, which is the path to the notebook file to be executed. The `execute` method of the `NotebookRun` object executes the notebook and returns a `NotebookResult` object, which contains the output of the notebook. The `NotebookResult` object has a `notebook` attribute, which is the executed notebook. You can use this attribute to check the output of the notebook." ] } ], - "metadata": {}, + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python", + "version": "3.10.12" + } + }, "nbformat": 4, "nbformat_minor": 5 } From 11084ddf0ad33861ea79e12c5cceebbd88991b64 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Thu, 19 Oct 2023 17:03:29 +0000 Subject: [PATCH 39/59] RAG over arbitrary packages --- src/nbwrite/index.py | 39 ++++++++++++++++----------------------- src/nbwrite/writer.py | 17 ++++++++++++++--- 2 files changed, 30 insertions(+), 26 deletions(-) diff --git a/src/nbwrite/index.py b/src/nbwrite/index.py index 6397141..739c9e8 100644 --- a/src/nbwrite/index.py +++ b/src/nbwrite/index.py @@ -1,9 +1,10 @@ import importlib.util from pathlib import Path +from typing import List from langchain.document_loaders.generic import GenericLoader from langchain.document_loaders.parsers import LanguageParser -from langchain.text_splitter import Language +from langchain.text_splitter import Language, RecursiveCharacterTextSplitter # https://docs.trychroma.com/troubleshooting#sqlite __import__("pysqlite3") @@ -12,30 +13,22 @@ sys.modules["sqlite3"] = sys.modules.pop("pysqlite3") -def create_index(): - lib = importlib.util.find_spec("nbmake") - - # Assumes the 'openai-python' repository exists in the user's root directory - code_root = Path(lib.submodule_search_locations._path[0]) # type: ignore - code = (code_root / "nb_run.py").read_text() - - # Load - loader = GenericLoader.from_filesystem( - code_root, - glob="**/*", - suffixes=[".py"], - parser=LanguageParser(language=Language.PYTHON, parser_threshold=500), - ) - documents = loader.load() - len(documents) - - from langchain.text_splitter import RecursiveCharacterTextSplitter - +def create_index(pkgs: List[str], k: int): python_splitter = RecursiveCharacterTextSplitter.from_language( language=Language.PYTHON, chunk_size=2000, chunk_overlap=200 ) - texts = python_splitter.split_documents(documents) - len(texts) + + texts = [] + for pkg in pkgs: + lib = importlib.util.find_spec(pkg) + code_root = Path(lib.submodule_search_locations[0]) # type: ignore + loader = GenericLoader.from_filesystem( + code_root, + glob="**/*", + suffixes=[".py"], + parser=LanguageParser(language=Language.PYTHON, parser_threshold=500), + ) + texts += python_splitter.split_documents(loader.load()) from langchain.embeddings.openai import OpenAIEmbeddings from langchain.vectorstores import Chroma @@ -43,7 +36,7 @@ def create_index(): db = Chroma.from_documents(texts, OpenAIEmbeddings(disallowed_special=())) retriever = db.as_retriever( search_type="mmr", # Also test "similarity" - search_kwargs={"k": 2}, + search_kwargs={"k": k}, ) return retriever diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 791596c..6d9a82f 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -1,6 +1,7 @@ import importlib.util from operator import itemgetter from pathlib import Path +from typing import List from langchain.chat_models import ChatAnyscale from langchain.llms.openai import OpenAI @@ -49,10 +50,12 @@ h1 = "" h2 = "use NotebookRun(notebook, timeout)" query = "use nbmake.nb_run.NotebookRun" +pkgs = ["nbmake", "nbformat", "nbclient"] +k = 5 def complete(path: Path, out_path: Path): - code_out = gen(query, placeholder_task, s1, s2, s3, h1, h2) + code_out = gen(query, placeholder_task, s1, s2, s3, h1, h2, pkgs, k) title = "AI!" nb = new_notebook() # nb.metadata = metadata @@ -96,7 +99,15 @@ def _combine_documents( def gen( - query: str, guide: str, step1: str, step2: str, step3: str, hint1: str, hint2: str + query: str, + guide: str, + step1: str, + step2: str, + step3: str, + hint1: str, + hint2: str, + pkgs: List[str], + k: int, ) -> str: """Write demo notebooks based on prompts in the notebook and the index""" # openai.organization = os.getenv("OPENAI_ORG_ID") @@ -125,7 +136,7 @@ def gen( from nbwrite.index import create_index - retriever = create_index() + retriever = create_index(pkgs, k) chain = ( { From 21271773f5739c248839df8507a7924c91f22ba7 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 23 Oct 2023 11:44:24 +0000 Subject: [PATCH 40/59] remove unused --- README.md | 8 +++- src/nbwrite/app.py | 23 ----------- src/nbwrite/cli.py | 10 ----- src/nbwrite/ex.py | 35 ----------------- src/nbwrite/example.py | 0 src/nbwrite/example_helpers.py | 72 ---------------------------------- tests/test_cli.py | 7 ---- tests/test_ex.py | 63 ----------------------------- 8 files changed, 7 insertions(+), 211 deletions(-) delete mode 100644 src/nbwrite/app.py delete mode 100644 src/nbwrite/ex.py delete mode 100644 src/nbwrite/example.py delete mode 100644 src/nbwrite/example_helpers.py delete mode 100644 tests/test_ex.py diff --git a/README.md b/README.md index 9877f96..002886c 100644 --- a/README.md +++ b/README.md @@ -17,4 +17,10 @@ nbwrite \ --step 'check the output' \ --context nbmake \ --context another_lib -``` \ No newline at end of file +``` + +TODOs before releasing + +- basic eval/testing +- cache index to disk? +- document setup \ No newline at end of file diff --git a/src/nbwrite/app.py b/src/nbwrite/app.py deleted file mode 100644 index d2a7ffd..0000000 --- a/src/nbwrite/app.py +++ /dev/null @@ -1,23 +0,0 @@ -import gradio as gr -from dotenv import load_dotenv - -from nbwrite.writer import gen - -if __name__ == "__main__": - load_dotenv() - placeholder_task = "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application" - - demo = gr.Interface( - fn=gen, - inputs=[ - gr.Textbox(lines=2, placeholder=placeholder_task), - "text", - "text", - "text", - "text", - "text", - ], - outputs="text", - ) - - demo.launch() diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index d16904d..b5bfe23 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -11,16 +11,6 @@ @click.group() def cli(): """Command line interface for nbwrite.""" - click.echo("Hello, world!") - - -@cli.command() -def index(): - """Build an index based on the python environment.""" - click.echo("Building index...") - from .index import create_index - - retriever = create_index() pass diff --git a/src/nbwrite/ex.py b/src/nbwrite/ex.py deleted file mode 100644 index 3abc8d6..0000000 --- a/src/nbwrite/ex.py +++ /dev/null @@ -1,35 +0,0 @@ -# # from langchain import PromptTemplate - -# # template = """Question: {question} - -# # Answer: """ -# # prompt = PromptTemplate(template=template, input_variables=["question"]) - -# # # user question -# question = "Which NFL team won the Super Bowl in the 2010 season?" - -# # import os - -# # from langchain.llms import OpenAI - -# # davinci = OpenAI(model_name="text-davinci-003") -# # from langchain import HuggingFaceHub, LLMChain - -# # llm_chain = LLMChain(prompt=prompt, llm=davinci) - -# # print(llm_chain.run(question)) - -# # import pinecone - -# # pinecone.init(api_key=os.environ["PINECONE_API_KEY"], environment="gcp-starter") -# # index = pinecone.Index("nbwrite") - -# # index.upsert( -# # [ -# # ("A", [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]), -# # ("B", [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2]), -# # ("C", [0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3]), -# # ("D", [0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4]), -# # ("E", [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]), -# # ] -# # ) diff --git a/src/nbwrite/example.py b/src/nbwrite/example.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/nbwrite/example_helpers.py b/src/nbwrite/example_helpers.py deleted file mode 100644 index c1375ea..0000000 --- a/src/nbwrite/example_helpers.py +++ /dev/null @@ -1,72 +0,0 @@ -# # https://github.com/openai/openai-cookbook/blob/main/examples/Code_search.ipynb - -# from pathlib import Path - -# import pandas as pd - -# DEF_PREFIXES = ["def ", "async def "] -# NEWLINE = "\n" - - -# def get_function_name(code): -# """ -# Extract function name from a line beginning with 'def' or 'async def'. -# """ -# for prefix in DEF_PREFIXES: -# if code.startswith(prefix): -# return code[len(prefix) : code.index("(")] - - -# def get_until_no_space(all_lines, i): -# """ -# Get all lines until a line outside the function definition is found. -# """ -# ret = [all_lines[i]] -# for j in range(i + 1, len(all_lines)): -# if len(all_lines[j]) == 0 or all_lines[j][0] in [" ", "\t", ")"]: -# ret.append(all_lines[j]) -# else: -# break -# return NEWLINE.join(ret) - - -# def get_functions(filepath): -# """ -# Get all functions in a Python file. -# """ -# with open(filepath, "r") as file: -# all_lines = file.read().replace("\r", NEWLINE).split(NEWLINE) -# for i, l in enumerate(all_lines): -# for prefix in DEF_PREFIXES: -# if l.startswith(prefix): -# code = get_until_no_space(all_lines, i) -# function_name = get_function_name(code) -# yield { -# "code": code, -# "function_name": function_name, -# "filepath": filepath, -# } -# break - - -# def extract_functions_from_repo(code_root): -# """ -# Extract all .py functions from the repository. -# """ -# code_files = list(code_root.glob("**/*.py")) - -# num_files = len(code_files) -# print(f"Total number of .py files: {num_files}") - -# if num_files == 0: -# print("Verify openai-python repo exists and code_root is set correctly.") -# return None - -# all_funcs = [ -# func for code_file in code_files for func in get_functions(str(code_file)) -# ] - -# num_funcs = len(all_funcs) -# print(f"Total number of functions extracted: {num_funcs}") - -# return all_funcs diff --git a/tests/test_cli.py b/tests/test_cli.py index b5ba90e..3ba684c 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -3,13 +3,6 @@ from nbwrite.cli import cli -def test_index(): - runner = CliRunner() - result = runner.invoke(cli, ["index"]) - assert result.exit_code == 0 - assert result.output == "Hello, world!\nBuilding index...\n" - - def test_complete(): runner = CliRunner() result = runner.invoke( diff --git a/tests/test_ex.py b/tests/test_ex.py deleted file mode 100644 index 5a1a977..0000000 --- a/tests/test_ex.py +++ /dev/null @@ -1,63 +0,0 @@ -# from pathlib import Path - -# import nbmake - -# from nbwrite import ex - - -# def test_when_index_then_build_index(): -# assert ex.question == "Which NFL team won the Super Bowl in the 2010 season?" - - -# def test_when_gen_nbrun_doc_then_nb_output(): -# assert ex.question == "Which NFL team won the Super Bowl in the 2010 season?" - - -# def test_openai(): -# # Set user root directory to the 'openai-python' repository -# # root_dir = Path.home() - -# import importlib.util - -# lib = importlib.util.find_spec("nbmake") - -# # Assumes the 'openai-python' repository exists in the user's root directory -# code_root = Path(lib.submodule_search_locations._path[0]) -# # from nbwrite.example import extract_functions_from_repo -# # Extract all functions from the repository -# from nbwrite.example_helpers import extract_functions_from_repo - -# all_funcs = extract_functions_from_repo(code_root) - -# import pandas as pd -# from openai.embeddings_utils import get_embedding - -# df = pd.DataFrame(all_funcs) -# df["code_embedding"] = df["code"].apply( -# lambda x: get_embedding(x, engine="text-embedding-ada-002") -# ) -# df["filepath"] = df["filepath"].map(lambda x: Path(x).relative_to(code_root)) -# # df.to_csv("data/code_search_openai-python.csv", index=False) -# df.head() - -# from openai.embeddings_utils import cosine_similarity - -# def search_functions(df, code_query, n=3, pprint=True, n_lines=7): -# embedding = get_embedding(code_query, engine="text-embedding-ada-002") -# df["similarities"] = df.code_embedding.apply( -# lambda x: cosine_similarity(x, embedding) -# ) - -# res = df.sort_values("similarities", ascending=False).head(n) - -# if pprint: -# for r in res.iterrows(): -# print( -# f"{r[1].filepath}:{r[1].function_name} score={round(r[1].similarities, 3)}" -# ) -# print("\n".join(r[1].code.split("\n")[:n_lines])) -# print("-" * 70) - -# return res - -# res = search_functions(df, "fine-tuning input data validation logic", n=3) From b811f791ea52818a003da59b47a0cf20ade540d6 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 23 Oct 2023 12:22:27 +0000 Subject: [PATCH 41/59] clean up CLI --- src/nbwrite/cli.py | 50 +++++++++++++++++++++++++++++++++++++------ src/nbwrite/index.py | 11 +++++----- src/nbwrite/writer.py | 12 ++++++----- 3 files changed, 57 insertions(+), 16 deletions(-) diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index b5bfe23..8c9e2b6 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -1,4 +1,6 @@ +import json from pathlib import Path +from typing import List import click from dotenv import load_dotenv @@ -16,13 +18,49 @@ def cli(): @cli.command() @click.argument( - "notebook", type=click.Path(exists=True, path_type=Path, dir_okay=False) + "task", + type=str, ) -@click.argument("out", type=click.Path(exists=False, path_type=Path, dir_okay=False)) -def complete(notebook: Path, out: Path): - """Write demo notebooks based on prompts in the notebook and the index""" - click.echo("Searching index...") - writer.complete(notebook, out) +@click.option( + "--step", default=[], multiple=True, help="Steps in the problem solving process" +) +@click.option( + "--package", default=[], multiple=True, help="Local Python packages to use for RAG" +) +@click.option( + "--out", + type=click.Path(exists=False, path_type=Path, dir_okay=True, file_okay=False), + default="out", + help="The directory to write the generated notebooks to", +) +@click.option( + "--model", + default=["gpt-3.5-turbo"], + multiple=True, + help="The API names of the models as per https://platform.openai.com/docs/models/", +) +@click.option( + "--generations", + default=1, + type=int, + help="The number of notebooks to generate per model", +) +def complete( + task: str, step: List[str], package: List[str], out: Path, model: List[str] +): + """Writes example notebooks which complete a given TASK + + e.g. nbwrite complete "Use Pandas to visualise the Titanic dataset" + """ + config = { + "task": task, + "steps": step, + "packages": package, + "out": str(out), + "models": model, + } + + click.echo(f"Writing notebook with options:\n\n{json.dumps(config, indent=2)}") if __name__ == "__main__": diff --git a/src/nbwrite/index.py b/src/nbwrite/index.py index 739c9e8..fe40b2d 100644 --- a/src/nbwrite/index.py +++ b/src/nbwrite/index.py @@ -6,14 +6,15 @@ from langchain.document_loaders.parsers import LanguageParser from langchain.text_splitter import Language, RecursiveCharacterTextSplitter -# https://docs.trychroma.com/troubleshooting#sqlite -__import__("pysqlite3") -import sys -sys.modules["sqlite3"] = sys.modules.pop("pysqlite3") +def create_index(pkgs: List[str], k: int): + # https://docs.trychroma.com/troubleshooting#sqlite + __import__("pysqlite3") + import sys + + sys.modules["sqlite3"] = sys.modules.pop("pysqlite3") -def create_index(pkgs: List[str], k: int): python_splitter = RecursiveCharacterTextSplitter.from_language( language=Language.PYTHON, chunk_size=2000, chunk_overlap=200 ) diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 6d9a82f..a2cea5e 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -18,14 +18,9 @@ reads, writes, ) -from phoenix.trace.langchain import LangChainInstrumentor, OpenInferenceTracer DEFAULT_DOCUMENT_PROMPT = PromptTemplate.from_template(template="{page_content}") -tracer = OpenInferenceTracer() -LangChainInstrumentor(tracer).instrument() - - lib = importlib.util.find_spec("nbmake") # Assumes the 'openai-python' repository exists in the user's root directory @@ -55,6 +50,13 @@ def complete(path: Path, out_path: Path): + from phoenix.trace.langchain import ( + LangChainInstrumentor, + OpenInferenceTracer, + ) + + tracer = OpenInferenceTracer() + LangChainInstrumentor(tracer).instrument() code_out = gen(query, placeholder_task, s1, s2, s3, h1, h2, pkgs, k) title = "AI!" nb = new_notebook() From 1e57020a0eb4f0835f2b4a8ecb4c00c7b9dda8e1 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 23 Oct 2023 12:28:22 +0000 Subject: [PATCH 42/59] opts --- src/nbwrite/cli.py | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index 8c9e2b6..4195e11 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -37,7 +37,7 @@ def cli(): "--model", default=["gpt-3.5-turbo"], multiple=True, - help="The API names of the models as per https://platform.openai.com/docs/models/", + help="The API names of the models as per https://platform.openai.com/docs/models/ and https://app.endpoints.anyscale.com/", ) @click.option( "--generations", @@ -45,8 +45,20 @@ def cli(): type=int, help="The number of notebooks to generate per model", ) +@click.option( + "--phoenix-trace/--no-phoenix-trace", + default=False, + type=bool, + help="Whether to trace using Phoenix https://docs.arize.com/phoenix/", +) def complete( - task: str, step: List[str], package: List[str], out: Path, model: List[str] + task: str, + step: List[str], + package: List[str], + out: Path, + model: List[str], + generations: int, + phoenix_trace: bool, ): """Writes example notebooks which complete a given TASK @@ -58,6 +70,8 @@ def complete( "packages": package, "out": str(out), "models": model, + "generations": generations, + "phoenix_trace": phoenix_trace, } click.echo(f"Writing notebook with options:\n\n{json.dumps(config, indent=2)}") From 7314165ac60b92221cf636f3da43c083010f9d61 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 23 Oct 2023 16:03:32 +0000 Subject: [PATCH 43/59] start refactor --- README.md | 5 +- SECURITY.md | 7 --- src/nbwrite/cli.py | 10 ++-- src/nbwrite/constants.py | 42 +++++++++++++++ src/nbwrite/index.py | 6 ++- src/nbwrite/writer.py | 110 +++++++++++---------------------------- tests/test_cli.py | 44 ++++++++++++---- 7 files changed, 121 insertions(+), 103 deletions(-) create mode 100644 src/nbwrite/constants.py diff --git a/README.md b/README.md index 002886c..6671533 100644 --- a/README.md +++ b/README.md @@ -22,5 +22,6 @@ nbwrite \ TODOs before releasing - basic eval/testing -- cache index to disk? -- document setup \ No newline at end of file +- document setup + +## Data Security \ No newline at end of file diff --git a/SECURITY.md b/SECURITY.md index 3d64be4..4ca9ee7 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -1,11 +1,4 @@ # Security Policy - -## Supported Versions - -| Version | Supported | -| ------- | ------------------ | -| 1.0.x | :white_check_mark: | - ## Reporting a Vulnerability alex@treebeard.io diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index 4195e11..856f130 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -6,6 +6,7 @@ from dotenv import load_dotenv import nbwrite.writer as writer +from nbwrite.constants import DEFAULT_MODEL load_dotenv() @@ -29,13 +30,13 @@ def cli(): ) @click.option( "--out", - type=click.Path(exists=False, path_type=Path, dir_okay=True, file_okay=False), - default="out", + type=click.Path(path_type=Path, dir_okay=True, file_okay=False), + default="nbwrite-out", help="The directory to write the generated notebooks to", ) @click.option( "--model", - default=["gpt-3.5-turbo"], + default=[DEFAULT_MODEL], multiple=True, help="The API names of the models as per https://platform.openai.com/docs/models/ and https://app.endpoints.anyscale.com/", ) @@ -76,6 +77,9 @@ def complete( click.echo(f"Writing notebook with options:\n\n{json.dumps(config, indent=2)}") + conf_obj = writer.Config(**config) + writer.gen(conf_obj) + if __name__ == "__main__": cli() diff --git a/src/nbwrite/constants.py b/src/nbwrite/constants.py new file mode 100644 index 0000000..aebbcf5 --- /dev/null +++ b/src/nbwrite/constants.py @@ -0,0 +1,42 @@ +from langchain.prompts import PromptTemplate + +DEFAULT_MODEL = "gpt-4-0613" +DEFAULT_ANYSCALE_MODEL = "codellama/CodeLlama-34b-Instruct-hf" +TEMPERATURE = 0.1 +MAX_TOKENS = 512 +SYSTEM_PROMPT = """ +You are a python programmer writing an ipynb document describing a task. + +Do install any packages you need using pip +Do import any libraries you need +Write 30 lines max per response +Write snippets of markdown before each section of code +Use a help and authoritative tone +Do not use conversational language +""" + +K = 5 +SEARCH_TYPE = "mmr" # Also test "similarity" + +DEFAULT_DOCUMENT_PROMPT = PromptTemplate.from_template(template="{page_content}") + +TEMPLATE_STRING = """ +--------------------------------------------------------------- +task: + +{task} + +--------------------------------------------------------------- + +steps: + +{steps} + +--------------------------------------------------------------- + +context: + +{context} + +--------------------------------------------------------------- +""" diff --git a/src/nbwrite/index.py b/src/nbwrite/index.py index fe40b2d..dbf6df5 100644 --- a/src/nbwrite/index.py +++ b/src/nbwrite/index.py @@ -6,8 +6,10 @@ from langchain.document_loaders.parsers import LanguageParser from langchain.text_splitter import Language, RecursiveCharacterTextSplitter +from nbwrite.constants import SEARCH_TYPE, K -def create_index(pkgs: List[str], k: int): + +def create_index(pkgs: List[str], k: int = K, search_type: str = SEARCH_TYPE): # https://docs.trychroma.com/troubleshooting#sqlite __import__("pysqlite3") @@ -36,7 +38,7 @@ def create_index(pkgs: List[str], k: int): db = Chroma.from_documents(texts, OpenAIEmbeddings(disallowed_special=())) retriever = db.as_retriever( - search_type="mmr", # Also test "similarity" + search_type=search_type, search_kwargs={"k": k}, ) diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index a2cea5e..d9ef077 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -1,9 +1,8 @@ -import importlib.util +from dataclasses import dataclass from operator import itemgetter from pathlib import Path from typing import List -from langchain.chat_models import ChatAnyscale from langchain.llms.openai import OpenAI from langchain.prompts import ChatPromptTemplate, PromptTemplate from langchain.prompts.chat import HumanMessagePromptTemplate @@ -19,34 +18,25 @@ writes, ) -DEFAULT_DOCUMENT_PROMPT = PromptTemplate.from_template(template="{page_content}") - -lib = importlib.util.find_spec("nbmake") - -# Assumes the 'openai-python' repository exists in the user's root directory -code_root = Path(lib.submodule_search_locations._path[0]) # type: ignore -code = (code_root / "nb_run.py").read_text() - -SYSTEM_PROMPT = """ -You are a python programmer writing an ipynb document describing a task. +from nbwrite.constants import ( + DEFAULT_DOCUMENT_PROMPT, + MAX_TOKENS, + SYSTEM_PROMPT, + TEMPERATURE, + TEMPLATE_STRING, +) +from nbwrite.index import create_index -Do install any packages you need using pip -Do import any libraries you need -Write 30 lines max per response -Write snippets of markdown before each section of code -Use a help and authoritative tone -Do not use conversational language -""" -placeholder_task = "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application" -s1 = "create a hello world notebook using nbformat" -s2 = "use nbmake's NotebookRun class to execute it from a Python application" -s3 = "check the output notebook printed what we were expecting" -h1 = "" -h2 = "use NotebookRun(notebook, timeout)" -query = "use nbmake.nb_run.NotebookRun" -pkgs = ["nbmake", "nbformat", "nbclient"] -k = 5 +@dataclass +class Config: + task: str + steps: List[str] + packages: List[str] + out: Path + models: List[str] + generations: int + phoenix_trace: bool def complete(path: Path, out_path: Path): @@ -76,70 +66,32 @@ def complete(path: Path, out_path: Path): write(nb, str(out_path)) -template_string = """ - -task: {guide} - -step 1: {step1} -step 2: {step2} -step 3: {step3} - -hint 1: {hint1} -hint 2: {hint2} - -context: - -{context} -""" - - -def _combine_documents( - docs, document_prompt=DEFAULT_DOCUMENT_PROMPT, document_separator="\n\n" -): - doc_strings = [format_document(doc, document_prompt) for doc in docs] - return document_separator.join(doc_strings) - - def gen( - query: str, - guide: str, - step1: str, - step2: str, - step3: str, - hint1: str, - hint2: str, - pkgs: List[str], - k: int, + config: Config, ) -> str: """Write demo notebooks based on prompts in the notebook and the index""" # openai.organization = os.getenv("OPENAI_ORG_ID") - temperature = 0.1 - model = "codellama/CodeLlama-34b-Instruct-hf" - - llm = ChatAnyscale( - temperature=temperature, - model_name=model, - # streaming=True, - ) - - # llm = OpenAI( - # model_name="gpt-4", - # temperature=0.1, - # max_tokens=512, - # ) + llms = { + mm: OpenAI(model_name=mm, temperature=TEMPERATURE, max_tokens=MAX_TOKENS) for mm in config.models + } prompt = ChatPromptTemplate.from_messages( [ - SystemMessage(content=(SYSTEM_PROMPT)), - HumanMessagePromptTemplate.from_template(template_string), + SystemMessage(content=SYSTEM_PROMPT), + HumanMessagePromptTemplate.from_template(TEMPLATE_STRING), ] ) - from nbwrite.index import create_index + retriever = create_index(config.packages) - retriever = create_index(pkgs, k) + def _combine_documents( + docs, document_prompt=DEFAULT_DOCUMENT_PROMPT, document_separator="\n\n" # type: ignore + ): + doc_strings = [format_document(doc, document_prompt) for doc in docs] + return document_separator.join(doc_strings) + llm = llms[config.models[0]] # TODO make parallel and combine all generations for all models chain = ( { "context": itemgetter("query") | retriever | _combine_documents, diff --git a/tests/test_cli.py b/tests/test_cli.py index 3ba684c..f40d003 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,25 +1,49 @@ +import logging +from pathlib import Path + from click.testing import CliRunner +from py.path import local from nbwrite.cli import cli +placeholder_task = "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application" + -def test_complete(): +def test_complete(tmpdir: local): runner = CliRunner() result = runner.invoke( - cli, ["complete", "tests/resources/demo.ipynb", "tests/resources/out.ipynb"] + cli, + [ + "complete", + placeholder_task, + "--step", + "create a hello world notebook using nbformat", + "--step", + "use nbmake's NotebookRun class to execute it from a Python application", + "--step", + "check the output notebook printed what we were expecting", + "--package", + "nbmake", + "--package", + "nbformat", + "--package", + "nbclient", + "--out", + str(tmpdir), + ], ) - print(result.output) assert result.exit_code == 0 import nbformat from nbclient.client import NotebookClient - with open("tests/resources/out.ipynb") as f: - nb = nbformat.read(f, as_version=4) + outputs = list(Path(tmpdir).glob("*.ipynb")) + assert len(outputs) == 1 + # nb = nbformat.read(f, as_version=4) - client = NotebookClient(nb) - client.execute() + # client = NotebookClient(nb) + # client.execute() - for cell in nb.cells: - if cell.cell_type == "code" and 'print("Hello, world!")' in cell.source: - assert "Hello, world!" in "".join(output.text for output in cell.outputs) + # for cell in nb.cells: + # if cell.cell_type == "code" and 'print("Hello, world!")' in cell.source: + # assert "Hello, world!" in "".join(output.text for output in cell.outputs) From 768be33d92519797c8b8520550ecf9e4ade5a123 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 23 Oct 2023 18:55:18 +0000 Subject: [PATCH 44/59] runs e2e --- .gitignore | 3 +- src/nbwrite/cli.py | 8 ---- src/nbwrite/constants.py | 10 ++-- src/nbwrite/index.py | 13 ++--- src/nbwrite/writer.py | 100 ++++++++++++++++++++------------------- tests/test_cli.py | 53 +++++++++++---------- 6 files changed, 96 insertions(+), 91 deletions(-) diff --git a/.gitignore b/.gitignore index 3f06244..c31c2b7 100644 --- a/.gitignore +++ b/.gitignore @@ -136,4 +136,5 @@ trash .testvenv wandb -flagged \ No newline at end of file +flagged +nbwrite-out \ No newline at end of file diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index 856f130..c246532 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -46,12 +46,6 @@ def cli(): type=int, help="The number of notebooks to generate per model", ) -@click.option( - "--phoenix-trace/--no-phoenix-trace", - default=False, - type=bool, - help="Whether to trace using Phoenix https://docs.arize.com/phoenix/", -) def complete( task: str, step: List[str], @@ -59,7 +53,6 @@ def complete( out: Path, model: List[str], generations: int, - phoenix_trace: bool, ): """Writes example notebooks which complete a given TASK @@ -72,7 +65,6 @@ def complete( "out": str(out), "models": model, "generations": generations, - "phoenix_trace": phoenix_trace, } click.echo(f"Writing notebook with options:\n\n{json.dumps(config, indent=2)}") diff --git a/src/nbwrite/constants.py b/src/nbwrite/constants.py index aebbcf5..f47af00 100644 --- a/src/nbwrite/constants.py +++ b/src/nbwrite/constants.py @@ -16,9 +16,7 @@ """ K = 5 -SEARCH_TYPE = "mmr" # Also test "similarity" - -DEFAULT_DOCUMENT_PROMPT = PromptTemplate.from_template(template="{page_content}") +SEARCH_TYPE = "mmr" # Also test "similarity" TEMPLATE_STRING = """ --------------------------------------------------------------- @@ -34,6 +32,12 @@ --------------------------------------------------------------- +packages: + +{packages} + +--------------------------------------------------------------- + context: {context} diff --git a/src/nbwrite/index.py b/src/nbwrite/index.py index dbf6df5..02465ab 100644 --- a/src/nbwrite/index.py +++ b/src/nbwrite/index.py @@ -1,22 +1,26 @@ import importlib.util +import os from pathlib import Path from typing import List from langchain.document_loaders.generic import GenericLoader from langchain.document_loaders.parsers import LanguageParser +from langchain.embeddings.openai import OpenAIEmbeddings from langchain.text_splitter import Language, RecursiveCharacterTextSplitter +from langchain.vectorstores import Chroma from nbwrite.constants import SEARCH_TYPE, K - -def create_index(pkgs: List[str], k: int = K, search_type: str = SEARCH_TYPE): - +if os.getenv("NBWRITE_OVERRIDE_SQLITE"): # https://docs.trychroma.com/troubleshooting#sqlite __import__("pysqlite3") import sys sys.modules["sqlite3"] = sys.modules.pop("pysqlite3") + +def create_index(pkgs: List[str], k: int = K, search_type: str = SEARCH_TYPE): + python_splitter = RecursiveCharacterTextSplitter.from_language( language=Language.PYTHON, chunk_size=2000, chunk_overlap=200 ) @@ -33,9 +37,6 @@ def create_index(pkgs: List[str], k: int = K, search_type: str = SEARCH_TYPE): ) texts += python_splitter.split_documents(loader.load()) - from langchain.embeddings.openai import OpenAIEmbeddings - from langchain.vectorstores import Chroma - db = Chroma.from_documents(texts, OpenAIEmbeddings(disallowed_special=())) retriever = db.as_retriever( search_type=search_type, diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index d9ef077..0f0dafb 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -1,15 +1,18 @@ +import os +import re from dataclasses import dataclass +from datetime import datetime from operator import itemgetter from pathlib import Path from typing import List +import nbformat from langchain.llms.openai import OpenAI from langchain.prompts import ChatPromptTemplate, PromptTemplate from langchain.prompts.chat import HumanMessagePromptTemplate from langchain.schema import format_document from langchain.schema.messages import SystemMessage from langchain.schema.output_parser import StrOutputParser -from nbformat import write from nbformat.v4 import ( new_code_cell, new_markdown_cell, @@ -19,7 +22,6 @@ ) from nbwrite.constants import ( - DEFAULT_DOCUMENT_PROMPT, MAX_TOKENS, SYSTEM_PROMPT, TEMPERATURE, @@ -33,47 +35,34 @@ class Config: task: str steps: List[str] packages: List[str] - out: Path + out: str models: List[str] generations: int - phoenix_trace: bool -def complete(path: Path, out_path: Path): - from phoenix.trace.langchain import ( - LangChainInstrumentor, - OpenInferenceTracer, - ) - - tracer = OpenInferenceTracer() - LangChainInstrumentor(tracer).instrument() - code_out = gen(query, placeholder_task, s1, s2, s3, h1, h2, pkgs, k) - title = "AI!" - nb = new_notebook() - # nb.metadata = metadata - - sections = code_out.split("```") - - for i in range(0, len(sections)): - if i % 2 == 0: - nb.cells.append(new_markdown_cell(sections[i])) - else: - nb.cells.append(new_code_cell(sections[i])) - - # double check some basic structure - string = writes(nb) - _ = reads(string) - write(nb, str(out_path)) +import click def gen( config: Config, -) -> str: +): """Write demo notebooks based on prompts in the notebook and the index""" - # openai.organization = os.getenv("OPENAI_ORG_ID") + + now = datetime.now() + + if os.getenv("NBWRITE_PHOENIX_TRACE"): + click.echo("Enabling Phoenix Trace") + from phoenix.trace.langchain import ( + LangChainInstrumentor, + OpenInferenceTracer, + ) + + tracer = OpenInferenceTracer() + LangChainInstrumentor(tracer).instrument() llms = { - mm: OpenAI(model_name=mm, temperature=TEMPERATURE, max_tokens=MAX_TOKENS) for mm in config.models + mm: OpenAI(model_name=mm, temperature=TEMPERATURE, max_tokens=MAX_TOKENS) + for mm in config.models } prompt = ChatPromptTemplate.from_messages( @@ -86,36 +75,49 @@ def gen( retriever = create_index(config.packages) def _combine_documents( - docs, document_prompt=DEFAULT_DOCUMENT_PROMPT, document_separator="\n\n" # type: ignore + docs, document_prompt=PromptTemplate.from_template(template="{page_content}"), document_separator="\n\n" # type: ignore ): doc_strings = [format_document(doc, document_prompt) for doc in docs] return document_separator.join(doc_strings) - llm = llms[config.models[0]] # TODO make parallel and combine all generations for all models + llm = llms[ + config.models[0] + ] # TODO make parallel and combine all generations for all models chain = ( { - "context": itemgetter("query") | retriever | _combine_documents, - "guide": itemgetter("guide"), - "step1": itemgetter("step1"), - "step2": itemgetter("step2"), - "step3": itemgetter("step3"), - "hint1": itemgetter("hint1"), - "hint2": itemgetter("hint2"), + "context": itemgetter("task") | retriever | _combine_documents, + "task": itemgetter("task"), + "steps": itemgetter("steps"), + "packages": itemgetter("packages"), } | prompt | llm | StrOutputParser() ) + click.echo(f"Invoking LLM") code_out = chain.invoke( { - "query": query, - "guide": guide, - "step1": step1, - "step2": step2, - "step3": step3, - "hint1": hint1, - "hint2": hint2, + "task": config.task, + "steps": "\n".join(config.steps), + "packages": "\n".join(config.packages), } ) - return code_out + + nb = new_notebook() + + sections = re.split(r"```(?:python)?\n", code_out) + + for i in range(0, len(sections)): + if i % 2 == 0: + nb.cells.append(new_markdown_cell(sections[i])) + else: + nb.cells.append(new_code_cell(sections[i])) + + time = now.strftime("%Y-%m-%d_%H-%M-%S") + filename = Path(config.out) / f"{time}-{config.models[0]}.ipynb" + string = writes(nb) + _ = reads(string) + + nbformat.write(nb, filename) + click.echo(f"Wrote notebook to {filename}") diff --git a/tests/test_cli.py b/tests/test_cli.py index f40d003..3bee88a 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,42 +1,47 @@ import logging from pathlib import Path +from typing import List +import nbformat from click.testing import CliRunner +from nbclient.client import NotebookClient from py.path import local from nbwrite.cli import cli +logger = logging.getLogger(__name__) + placeholder_task = "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application" def test_complete(tmpdir: local): runner = CliRunner() - result = runner.invoke( - cli, - [ - "complete", - placeholder_task, - "--step", - "create a hello world notebook using nbformat", - "--step", - "use nbmake's NotebookRun class to execute it from a Python application", - "--step", - "check the output notebook printed what we were expecting", - "--package", - "nbmake", - "--package", - "nbformat", - "--package", - "nbclient", - "--out", - str(tmpdir), - ], - ) - assert result.exit_code == 0 + args = [ + "complete", + placeholder_task, + "--step", + "create a hello world notebook using nbformat", + "--step", + "use nbmake's NotebookRun class to execute it from a Python application", + "--step", + "check the output notebook printed what we were expecting", + "--package", + "nbmake", + "--package", + "nbformat", + "--package", + "nbclient", + "--out", + str(tmpdir), + ] + + shell_fmt = " \\\n ".join(["nbwrite", *args]) + logger.warn(f"Running\n{shell_fmt}") + result = runner.invoke(cli, args) - import nbformat - from nbclient.client import NotebookClient + assert result.exit_code == 0 + logger.warn(f"Checking outputs in {tmpdir}") outputs = list(Path(tmpdir).glob("*.ipynb")) assert len(outputs) == 1 # nb = nbformat.read(f, as_version=4) From dc3568bbc9a6312a5c822aba8f9295f1d9c9fe5b Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 23 Oct 2023 19:18:17 +0000 Subject: [PATCH 45/59] spec file input --- .vscode/launch.json | 19 + poetry.lock | 2 +- pyproject.toml | 1 + src/nbwrite/cli.py | 27 +- tests/resources/buildenv/docs/demo1.yaml | 10 - tests/resources/buildenv/poetry.lock | 702 ----------------------- tests/resources/buildenv/poetry.toml | 3 - tests/resources/buildenv/pyproject.toml | 18 - tests/resources/demo.ipynb | 29 - tests/resources/ex.ipynb | 92 --- tests/resources/hello-world.ipynb | 18 - tests/resources/hello.ipynb | 18 - tests/resources/nbwrite-in/example.yaml | 10 + tests/resources/out.ipynb | 86 --- tests/resources/res/x.ipynb | 17 - tests/test_cli.py | 14 +- 16 files changed, 43 insertions(+), 1023 deletions(-) create mode 100644 .vscode/launch.json delete mode 100644 tests/resources/buildenv/docs/demo1.yaml delete mode 100644 tests/resources/buildenv/poetry.lock delete mode 100644 tests/resources/buildenv/poetry.toml delete mode 100644 tests/resources/buildenv/pyproject.toml delete mode 100644 tests/resources/demo.ipynb delete mode 100644 tests/resources/ex.ipynb delete mode 100644 tests/resources/hello-world.ipynb delete mode 100644 tests/resources/hello.ipynb create mode 100644 tests/resources/nbwrite-in/example.yaml delete mode 100644 tests/resources/out.ipynb delete mode 100644 tests/resources/res/x.ipynb diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 0000000..6973ea9 --- /dev/null +++ b/.vscode/launch.json @@ -0,0 +1,19 @@ +{ + // Use IntelliSense to learn about possible attributes. + // Hover to view descriptions of existing attributes. + // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 + "version": "0.2.0", + "configurations": [ + { + "name": "nbwrite CLI", + "type": "python", + "request": "launch", + "module": "nbwrite.cli", + "justMyCode": true, + "args": [ + "complete", + "tests/resources/nbwrite-in/example.yaml" + ] + } + ] +} \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index f5a7315..bdd8814 100644 --- a/poetry.lock +++ b/poetry.lock @@ -5557,4 +5557,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "cb6ea0fb2ba44202be026031d165ec99c89639e7745ce45ac5d0a8206a7c7d90" +content-hash = "e504ee0b42e5fcb0c800100d3e65b8593d4cf109d1cdb6b6e5be29b4520f5097" diff --git a/pyproject.toml b/pyproject.toml index 7543197..3273c25 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,6 +27,7 @@ chromadb = "^0.4.14" pysqlite3-binary = "^0.5.2" arize-phoenix = {extras = ["experimental"], version = "^0.0.49"} python-dotenv = "^1.0.0" +pyyaml = "^6.0.1" [tool.poetry.dev-dependencies] pytest = "^7.1.0" diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index c246532..b0818ab 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -3,6 +3,7 @@ from typing import List import click +import yaml from dotenv import load_dotenv import nbwrite.writer as writer @@ -19,14 +20,8 @@ def cli(): @cli.command() @click.argument( - "task", - type=str, -) -@click.option( - "--step", default=[], multiple=True, help="Steps in the problem solving process" -) -@click.option( - "--package", default=[], multiple=True, help="Local Python packages to use for RAG" + "spec", + type=click.Path(path_type=Path, dir_okay=False, file_okay=True), ) @click.option( "--out", @@ -47,21 +42,21 @@ def cli(): help="The number of notebooks to generate per model", ) def complete( - task: str, - step: List[str], - package: List[str], + spec: Path, out: Path, model: List[str], generations: int, ): - """Writes example notebooks which complete a given TASK + """Writes example notebooks which complete a given SPEC - e.g. nbwrite complete "Use Pandas to visualise the Titanic dataset" + e.g. nbwrite complete "./spec.yaml" """ + + spec = yaml.safe_load(spec.read_text()) config = { - "task": task, - "steps": step, - "packages": package, + "task": spec["task"], + "steps": spec["steps"], + "packages": spec["packages"], "out": str(out), "models": model, "generations": generations, diff --git a/tests/resources/buildenv/docs/demo1.yaml b/tests/resources/buildenv/docs/demo1.yaml deleted file mode 100644 index b107888..0000000 --- a/tests/resources/buildenv/docs/demo1.yaml +++ /dev/null @@ -1,10 +0,0 @@ -title: HTTP API -description: How to use the API to start a simulation then query the state -steps: - - Use the PUT endpoint to define a segment - - Use the POST endpoint to start a simulation - - Use the GET endpoint to query the state of the simulation -assertions: - - check that the simulation completed successfully -components: - - frontier_ct_definition.ComputationalTwin diff --git a/tests/resources/buildenv/poetry.lock b/tests/resources/buildenv/poetry.lock deleted file mode 100644 index a003868..0000000 --- a/tests/resources/buildenv/poetry.lock +++ /dev/null @@ -1,702 +0,0 @@ -[[package]] -name = "appnope" -version = "0.1.3" -description = "Disable App Nap on macOS >= 10.9" -category = "dev" -optional = false -python-versions = "*" - -[[package]] -name = "asttokens" -version = "2.4.0" -description = "Annotate AST trees with source code positions" -category = "dev" -optional = false -python-versions = "*" - -[package.dependencies] -six = ">=1.12.0" - -[package.extras] -test = ["astroid", "pytest"] - -[[package]] -name = "attrs" -version = "23.1.0" -description = "Classes Without Boilerplate" -category = "dev" -optional = false -python-versions = ">=3.7" - -[package.extras] -cov = ["attrs", "coverage[toml] (>=5.3)"] -dev = ["attrs", "pre-commit"] -docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] -tests = ["attrs", "zope-interface"] -tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest-mypy-plugins", "pytest-xdist", "pytest (>=4.3.0)"] - -[[package]] -name = "backcall" -version = "0.2.0" -description = "Specifications for callback functions passed in to an API" -category = "dev" -optional = false -python-versions = "*" - -[[package]] -name = "cffi" -version = "1.16.0" -description = "Foreign Function Interface for Python calling C code." -category = "dev" -optional = false -python-versions = ">=3.8" - -[package.dependencies] -pycparser = "*" - -[[package]] -name = "colorama" -version = "0.4.6" -description = "Cross-platform colored terminal text." -category = "main" -optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" - -[[package]] -name = "comm" -version = "0.1.4" -description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." -category = "dev" -optional = false -python-versions = ">=3.6" - -[package.dependencies] -traitlets = ">=4" - -[package.extras] -lint = ["black (>=22.6.0)", "mdformat-gfm (>=0.3.5)", "mdformat (>0.7)", "ruff (>=0.0.156)"] -test = ["pytest"] -typing = ["mypy (>=0.990)"] - -[[package]] -name = "debugpy" -version = "1.8.0" -description = "An implementation of the Debug Adapter Protocol for Python" -category = "dev" -optional = false -python-versions = ">=3.8" - -[[package]] -name = "decorator" -version = "5.1.1" -description = "Decorators for Humans" -category = "dev" -optional = false -python-versions = ">=3.5" - -[[package]] -name = "exceptiongroup" -version = "1.1.3" -description = "Backport of PEP 654 (exception groups)" -category = "main" -optional = false -python-versions = ">=3.7" - -[package.extras] -test = ["pytest (>=6)"] - -[[package]] -name = "executing" -version = "2.0.0" -description = "Get the currently executing AST node of a frame, and other information" -category = "dev" -optional = false -python-versions = "*" - -[package.extras] -tests = ["asttokens (>=2.1.0)", "ipython", "pytest", "coverage", "coverage-enable-subprocess", "littleutils", "rich"] - -[[package]] -name = "fastjsonschema" -version = "2.18.1" -description = "Fastest Python implementation of JSON schema" -category = "dev" -optional = false -python-versions = "*" - -[package.extras] -devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"] - -[[package]] -name = "importlib-metadata" -version = "6.8.0" -description = "Read metadata from Python packages" -category = "dev" -optional = false -python-versions = ">=3.8" - -[package.dependencies] -zipp = ">=0.5" - -[package.extras] -docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] -perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] - 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-[[package]] -name = "wcwidth" -version = "0.2.8" -description = "Measures the displayed width of unicode strings in a terminal" -category = "dev" -optional = false -python-versions = "*" - -[[package]] -name = "zipp" -version = "3.17.0" -description = "Backport of pathlib-compatible object wrapper for zip files" -category = "dev" -optional = false -python-versions = ">=3.8" - -[package.extras] -docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ruff", "jaraco.itertools", "jaraco.functools", "more-itertools", "big-o", "pytest-ignore-flaky", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] - -[metadata] -lock-version = "1.1" -python-versions = "^3.9.0" -content-hash = "4d06c9090f81c5368171f275d4977bf79f1180d21e61d0bf2df02be1c393a0c6" - -[metadata.files] -appnope = [] -asttokens = [] -attrs = [] -backcall = [] -cffi = [] -colorama = [] -comm = [] -debugpy = [] -decorator = [] -exceptiongroup = [] -executing = [] -fastjsonschema = [] -importlib-metadata = [] -iniconfig = [] -ipykernel = [] -ipython = [] -jedi = [] -jsonschema = [] -jsonschema-specifications = [] -jupyter-client = [] -jupyter-core = [] -matplotlib-inline = [] -nbclient = [] -nbformat = [] -nbmake = [] -nest-asyncio = [] -packaging = [] -parso = [] -pexpect = [] -pickleshare = [] -platformdirs = [] -pluggy = [] -prompt-toolkit = [] -psutil = [] -ptyprocess = [] -pure-eval = [] -pycparser = [] -pygments = [] -pytest = [] -python-dateutil = [] -pywin32 = [] -pyzmq = [] -referencing = [] -rpds-py = [] -six = [] -stack-data = [] -tomli = [] -tornado = [] -traitlets = [] -typing-extensions = [] -wcwidth = [] -zipp = [] diff --git a/tests/resources/buildenv/poetry.toml b/tests/resources/buildenv/poetry.toml deleted file mode 100644 index 91b4cd5..0000000 --- a/tests/resources/buildenv/poetry.toml +++ /dev/null @@ -1,3 +0,0 @@ -[virtualenvs] -create = true -path = '.testvenv' diff --git a/tests/resources/buildenv/pyproject.toml b/tests/resources/buildenv/pyproject.toml deleted file mode 100644 index f30a5af..0000000 --- a/tests/resources/buildenv/pyproject.toml +++ /dev/null @@ -1,18 +0,0 @@ -[tool.poetry] -authors = ["alex-treebeard "] -description = "" -homepage = "https://github.com/treebeardtech/nbwrite" -license = "Apache-2.0" -name = "test" -version = "v0.1" - -[tool.poetry.dependencies] -pytest = ">=6.1.0" -python = "^3.9.0" - -[tool.poetry.dev-dependencies] -nbmake = "^1.4.5" - -[build-system] -build-backend = "poetry.core.masonry.api" -requires = ["setuptools", "poetry-core>=1.0.0"] diff --git a/tests/resources/demo.ipynb b/tests/resources/demo.ipynb deleted file mode 100644 index b86ff77..0000000 --- a/tests/resources/demo.ipynb +++ /dev/null @@ -1,29 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Using the NotebookRun class to run a notebook from a conventional pytest function" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "vscode": { - "languageId": "plaintext" - } - }, - "outputs": [], - "source": [] - } - ], - "metadata": { - "language_info": { - "name": "python" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/tests/resources/ex.ipynb b/tests/resources/ex.ipynb deleted file mode 100644 index 72772e1..0000000 --- a/tests/resources/ex.ipynb +++ /dev/null @@ -1,92 +0,0 @@ -{ - "cells": [ - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Using the nbmake API\n", - "\n", - "In this tutorial we will show you how to test a Python notebook from your own Python application (e.g. a test framework) using the nbmake API" - ] - }, - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "First, we need an example notebook for testing" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [ - "nbwrite:create some 'hello-world.ipynb'", - "set the kernel to 'python3'" - ] - }, - "outputs": [], - "source": [ - "import nbformat as nbf\n", - "\n", - "nb = nbf.v4.new_notebook()\n", - "code = \"\"\"\n", - "print('Hello, World!')\n", - "\"\"\"\n", - "\n", - "nb['cells'] = [nbf.v4.new_code_cell(code)]\n", - "nbf.write(nb, 'hello-world.ipynb')" - ] - }, - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Now we can use the NotebookRun class to execute it and check that it printed what we were expecting" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from nbmake.nb_run import NotebookRun\n", - "\n", - "notebook = NotebookRun('hello-world.ipynb', default_timeout=60, verbose=True)\n", - "result = notebook.execute()\n", - "\n", - "assert result.error is None\n", - "assert len(result.nb.cells) == 1\n", - "assert result.nb.cells[0].cell_type == 'code'\n", - "assert len(result.nb.cells[0].outputs) == 1\n", - "assert result.nb.cells[0].outputs[0].output_type == 'stream'\n", - "assert result.nb.cells[0].outputs[0].text == 'Hello, World!\\n'" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": ".venv", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.12" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/tests/resources/hello-world.ipynb b/tests/resources/hello-world.ipynb deleted file mode 100644 index ac5b9f5..0000000 --- a/tests/resources/hello-world.ipynb +++ /dev/null @@ -1,18 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "id": "f3202044", - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "print('Hello, World!')\n" - ] - } - ], - "metadata": {}, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/tests/resources/hello.ipynb b/tests/resources/hello.ipynb deleted file mode 100644 index a62563d..0000000 --- a/tests/resources/hello.ipynb +++ /dev/null @@ -1,18 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "id": "8ce4e5af", - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "print(\"Hello world!\")\n" - ] - } - ], - "metadata": {}, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/tests/resources/nbwrite-in/example.yaml b/tests/resources/nbwrite-in/example.yaml new file mode 100644 index 0000000..9379231 --- /dev/null +++ b/tests/resources/nbwrite-in/example.yaml @@ -0,0 +1,10 @@ +task: | + Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application +steps: + - Create a hello world notebook using nbformat + - Use nbmake's NotebookRun class to execute it from a Python application + - Check the output notebook printed what we were expecting +packages: + - nbmake + - nbformat + - nbclient \ No newline at end of file diff --git a/tests/resources/out.ipynb b/tests/resources/out.ipynb deleted file mode 100644 index d20994e..0000000 --- a/tests/resources/out.ipynb +++ /dev/null @@ -1,86 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "d39a884a", - "metadata": {}, - "source": [ - " To create a hello world notebook using nbformat, you can use the following code:\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "7053f14c", - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "import nbformat\n", - "\n", - "# Create a new notebook\n", - "nb = nbformat.v4.new_notebook()\n", - "\n", - "# Add a code cell to the notebook\n", - "code_cell = nbformat.v4.new_code_cell(\"print('Hello, world!')\")\n", - "nb.cells.append(code_cell)\n", - "\n", - "# Save the notebook to a file\n", - "with open(\"hello_world.ipynb\", \"w\") as f:\n", - " nbformat.write(nb, f)\n" - ] - }, - { - "cell_type": "markdown", - "id": "df1e2151", - "metadata": {}, - "source": [ - "\n", - "To use nbmake's NotebookRun class to execute the notebook from a Python application, you can use the following code:\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "f56d25d0", - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "from nbmake import NotebookRun\n", - "\n", - "# Create a NotebookRun object\n", - "notebook_run = NotebookRun(\"hello_world.ipynb\")\n", - "\n", - "# Execute the notebook\n", - "notebook_run.execute()\n", - "\n", - "# Check the output notebook\n", - "output_notebook = notebook_run.notebook\n", - "assert output_notebook.cells[0].outputs[0].text == \"Hello, world!\"\n" - ] - }, - { - "cell_type": "markdown", - "id": "5dd0c37c", - "metadata": {}, - "source": [ - "\n", - "Note that the `NotebookRun` class takes a `filename` argument, which is the path to the notebook file to be executed. The `execute` method of the `NotebookRun` object executes the notebook and returns a `NotebookResult` object, which contains the output of the notebook. The `NotebookResult` object has a `notebook` attribute, which is the executed notebook. You can use this attribute to check the output of the notebook." - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": ".venv", - "language": "python", - "name": "python3" - }, - "language_info": { - "name": "python", - "version": "3.10.12" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/tests/resources/res/x.ipynb b/tests/resources/res/x.ipynb deleted file mode 100644 index 5f63baf..0000000 --- a/tests/resources/res/x.ipynb +++ /dev/null @@ -1,17 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "id": "53c70b3b", - "metadata": {}, - "outputs": [], - "source": [ - "print('Hello, World!')" - ] - } - ], - "metadata": {}, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/tests/test_cli.py b/tests/test_cli.py index 3bee88a..8aff18a 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -18,19 +18,7 @@ def test_complete(tmpdir: local): runner = CliRunner() args = [ "complete", - placeholder_task, - "--step", - "create a hello world notebook using nbformat", - "--step", - "use nbmake's NotebookRun class to execute it from a Python application", - "--step", - "check the output notebook printed what we were expecting", - "--package", - "nbmake", - "--package", - "nbformat", - "--package", - "nbclient", + "tests/resources/nbwrite-in/example.yaml", "--out", str(tmpdir), ] From 8bf8b91072f6257964199e325f0e6080812839fd Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Mon, 23 Oct 2023 19:39:07 +0000 Subject: [PATCH 46/59] mock llm --- .vscode/launch.json | 2 +- src/nbwrite/writer.py | 11 ++++++----- tests/test_cli.py | 35 +++++++++++++++++++++-------------- 3 files changed, 28 insertions(+), 20 deletions(-) diff --git a/.vscode/launch.json b/.vscode/launch.json index 6973ea9..80ea4a9 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -9,7 +9,7 @@ "type": "python", "request": "launch", "module": "nbwrite.cli", - "justMyCode": true, + "justMyCode": false, "args": [ "complete", "tests/resources/nbwrite-in/example.yaml" diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 0f0dafb..990e5e7 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -43,6 +43,10 @@ class Config: import click +def get_llm(model_name: str): + return OpenAI(model_name=model_name, temperature=TEMPERATURE, max_tokens=MAX_TOKENS) + + def gen( config: Config, ): @@ -60,10 +64,7 @@ def gen( tracer = OpenInferenceTracer() LangChainInstrumentor(tracer).instrument() - llms = { - mm: OpenAI(model_name=mm, temperature=TEMPERATURE, max_tokens=MAX_TOKENS) - for mm in config.models - } + llms = {mm: get_llm(mm) for mm in config.models} prompt = ChatPromptTemplate.from_messages( [ @@ -106,7 +107,7 @@ def _combine_documents( nb = new_notebook() - sections = re.split(r"```(?:python)?\n", code_out) + sections = re.split(r"```(?:python\n)?", code_out) for i in range(0, len(sections)): if i % 2 == 0: diff --git a/tests/test_cli.py b/tests/test_cli.py index 8aff18a..f607bbf 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,9 +1,10 @@ import logging from pathlib import Path -from typing import List +from unittest.mock import patch import nbformat from click.testing import CliRunner +from langchain.llms.fake import FakeListLLM from nbclient.client import NotebookClient from py.path import local @@ -11,8 +12,6 @@ logger = logging.getLogger(__name__) -placeholder_task = "Create a hello world notebook 'x.ipynb', use nbmake's NotebookRun class to test it from a Python application" - def test_complete(tmpdir: local): runner = CliRunner() @@ -25,18 +24,26 @@ def test_complete(tmpdir: local): shell_fmt = " \\\n ".join(["nbwrite", *args]) logger.warn(f"Running\n{shell_fmt}") - result = runner.invoke(cli, args) - assert result.exit_code == 0 + with patch("nbwrite.writer.get_llm") as mock_get_llm: + mock_get_llm.return_value = FakeListLLM( + responses=["Code:\n```python\nprint('Hello, world!')\n```\n"] + ) + result = runner.invoke(cli, args) + + assert result.exit_code == 0 + + logger.warn(f"Checking outputs in {tmpdir}") + outputs = list(Path(tmpdir).glob("*.ipynb")) + assert len(outputs) == 1 - logger.warn(f"Checking outputs in {tmpdir}") - outputs = list(Path(tmpdir).glob("*.ipynb")) - assert len(outputs) == 1 - # nb = nbformat.read(f, as_version=4) + nb = nbformat.read(outputs[0], as_version=4) - # client = NotebookClient(nb) - # client.execute() + client = NotebookClient(nb) + client.execute() - # for cell in nb.cells: - # if cell.cell_type == "code" and 'print("Hello, world!")' in cell.source: - # assert "Hello, world!" in "".join(output.text for output in cell.outputs) + for cell in nb.cells: + if cell.cell_type == "code" and 'print("Hello, world!")' in cell.source: + assert "Hello, world!" in "".join( + output.text for output in cell.outputs + ) From 5559c454a8f544c5aebce93d5c06cb5e9fee0141 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 09:36:46 +0000 Subject: [PATCH 47/59] parallel gens --- .gitignore | 1 + src/nbwrite/writer.py | 48 ++++++++++++++++++++++++++----------------- tests/test_cli.py | 12 +++++++++-- 3 files changed, 40 insertions(+), 21 deletions(-) diff --git a/.gitignore b/.gitignore index c31c2b7..7929a5f 100644 --- a/.gitignore +++ b/.gitignore @@ -137,4 +137,5 @@ trash .testvenv wandb flagged +test-debug-out nbwrite-out \ No newline at end of file diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 990e5e7..ef07558 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -1,3 +1,4 @@ +import logging import os import re from dataclasses import dataclass @@ -13,6 +14,7 @@ from langchain.schema import format_document from langchain.schema.messages import SystemMessage from langchain.schema.output_parser import StrOutputParser +from langchain.schema.runnable import RunnableParallel from nbformat.v4 import ( new_code_cell, new_markdown_cell, @@ -29,6 +31,8 @@ ) from nbwrite.index import create_index +logger = logging.getLogger(__name__) + @dataclass class Config: @@ -64,7 +68,7 @@ def gen( tracer = OpenInferenceTracer() LangChainInstrumentor(tracer).instrument() - llms = {mm: get_llm(mm) for mm in config.models} + llms = {str(mm): get_llm(mm) for mm in range(config.generations)} prompt = ChatPromptTemplate.from_messages( [ @@ -81,9 +85,6 @@ def _combine_documents( doc_strings = [format_document(doc, document_prompt) for doc in docs] return document_separator.join(doc_strings) - llm = llms[ - config.models[0] - ] # TODO make parallel and combine all generations for all models chain = ( { "context": itemgetter("task") | retriever | _combine_documents, @@ -92,8 +93,8 @@ def _combine_documents( "packages": itemgetter("packages"), } | prompt - | llm - | StrOutputParser() + | RunnableParallel(**llms) + # | StrOutputParser() ) click.echo(f"Invoking LLM") @@ -105,20 +106,29 @@ def _combine_documents( } ) - nb = new_notebook() + out_dir = Path(config.out) + out_dir.mkdir(parents=True, exist_ok=True) + + for generation in code_out.keys(): + try: + nb = new_notebook() - sections = re.split(r"```(?:python\n)?", code_out) + sections = re.split(r"```(?:python\n)?", code_out[generation]) - for i in range(0, len(sections)): - if i % 2 == 0: - nb.cells.append(new_markdown_cell(sections[i])) - else: - nb.cells.append(new_code_cell(sections[i])) + for i in range(0, len(sections)): + if i % 2 == 0: + nb.cells.append(new_markdown_cell(sections[i])) + else: + nb.cells.append(new_code_cell(sections[i])) - time = now.strftime("%Y-%m-%d_%H-%M-%S") - filename = Path(config.out) / f"{time}-{config.models[0]}.ipynb" - string = writes(nb) - _ = reads(string) + time = now.strftime("%Y-%m-%d_%H-%M-%S") + filename = ( + Path(config.out) / f"{time}-{config.models[0]}-{generation}.ipynb" + ) + string = writes(nb) + _ = reads(string) - nbformat.write(nb, filename) - click.echo(f"Wrote notebook to {filename}") + nbformat.write(nb, (filename.as_posix())) + click.echo(f"Wrote notebook to {filename}") + except Exception as e: + logger.error(f"Error writing notebook (generation {generation}): {e}") diff --git a/tests/test_cli.py b/tests/test_cli.py index f607bbf..7958ea2 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,4 +1,5 @@ import logging +import os from pathlib import Path from unittest.mock import patch @@ -14,12 +15,19 @@ def test_complete(tmpdir: local): + + if os.getenv("NBWRITE_DEBUG_MODE"): + outdir = "test-debug-out" + else: + outdir = str(tmpdir) runner = CliRunner() args = [ "complete", "tests/resources/nbwrite-in/example.yaml", "--out", - str(tmpdir), + outdir, + "--generations", + "2", ] shell_fmt = " \\\n ".join(["nbwrite", *args]) @@ -33,7 +41,7 @@ def test_complete(tmpdir: local): assert result.exit_code == 0 - logger.warn(f"Checking outputs in {tmpdir}") + logger.warn(f"Checking outputs in {outdir}") outputs = list(Path(tmpdir).glob("*.ipynb")) assert len(outputs) == 1 From 53fcd92affb4c84327b1acb3e8d87022a48abf37 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 09:41:22 +0000 Subject: [PATCH 48/59] single model input --- src/nbwrite/cli.py | 7 +++---- src/nbwrite/constants.py | 2 -- src/nbwrite/writer.py | 15 ++++----------- 3 files changed, 7 insertions(+), 17 deletions(-) diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index b0818ab..40375b1 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -1,6 +1,5 @@ import json from pathlib import Path -from typing import List import click import yaml @@ -33,7 +32,7 @@ def cli(): "--model", default=[DEFAULT_MODEL], multiple=True, - help="The API names of the models as per https://platform.openai.com/docs/models/ and https://app.endpoints.anyscale.com/", + help="The API name of the model as per https://platform.openai.com/docs/models", ) @click.option( "--generations", @@ -44,7 +43,7 @@ def cli(): def complete( spec: Path, out: Path, - model: List[str], + model: str, generations: int, ): """Writes example notebooks which complete a given SPEC @@ -58,7 +57,7 @@ def complete( "steps": spec["steps"], "packages": spec["packages"], "out": str(out), - "models": model, + "model": model, "generations": generations, } diff --git a/src/nbwrite/constants.py b/src/nbwrite/constants.py index f47af00..ab570a8 100644 --- a/src/nbwrite/constants.py +++ b/src/nbwrite/constants.py @@ -1,5 +1,3 @@ -from langchain.prompts import PromptTemplate - DEFAULT_MODEL = "gpt-4-0613" DEFAULT_ANYSCALE_MODEL = "codellama/CodeLlama-34b-Instruct-hf" TEMPERATURE = 0.1 diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index ef07558..9ee0995 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -13,7 +13,6 @@ from langchain.prompts.chat import HumanMessagePromptTemplate from langchain.schema import format_document from langchain.schema.messages import SystemMessage -from langchain.schema.output_parser import StrOutputParser from langchain.schema.runnable import RunnableParallel from nbformat.v4 import ( new_code_cell, @@ -40,7 +39,7 @@ class Config: steps: List[str] packages: List[str] out: str - models: List[str] + model: str generations: int @@ -54,8 +53,6 @@ def get_llm(model_name: str): def gen( config: Config, ): - """Write demo notebooks based on prompts in the notebook and the index""" - now = datetime.now() if os.getenv("NBWRITE_PHOENIX_TRACE"): @@ -68,8 +65,6 @@ def gen( tracer = OpenInferenceTracer() LangChainInstrumentor(tracer).instrument() - llms = {str(mm): get_llm(mm) for mm in range(config.generations)} - prompt = ChatPromptTemplate.from_messages( [ SystemMessage(content=SYSTEM_PROMPT), @@ -85,6 +80,7 @@ def _combine_documents( doc_strings = [format_document(doc, document_prompt) for doc in docs] return document_separator.join(doc_strings) + llm = get_llm(config.model) chain = ( { "context": itemgetter("task") | retriever | _combine_documents, @@ -93,8 +89,7 @@ def _combine_documents( "packages": itemgetter("packages"), } | prompt - | RunnableParallel(**llms) - # | StrOutputParser() + | RunnableParallel(**{str(gg): llm for gg in range(config.generations)}) ) click.echo(f"Invoking LLM") @@ -122,9 +117,7 @@ def _combine_documents( nb.cells.append(new_code_cell(sections[i])) time = now.strftime("%Y-%m-%d_%H-%M-%S") - filename = ( - Path(config.out) / f"{time}-{config.models[0]}-{generation}.ipynb" - ) + filename = Path(config.out) / f"{time}-{config.model}-{generation}.ipynb" string = writes(nb) _ = reads(string) From 19123c72f887a8dc21b4365327763afb2e1f8f28 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 11:04:50 +0000 Subject: [PATCH 49/59] yaml conf for llm --- poetry.lock | 56 ++++++++++++++++++++++++- pyproject.toml | 1 + src/nbwrite/cli.py | 33 ++++----------- src/nbwrite/config.py | 24 +++++++++++ src/nbwrite/constants.py | 20 +++++---- src/nbwrite/index.py | 11 ++--- src/nbwrite/writer.py | 38 +++++------------ tests/resources/nbwrite-in/example.yaml | 12 +++++- tests/test_cli.py | 7 ++-- 9 files changed, 127 insertions(+), 75 deletions(-) create mode 100644 src/nbwrite/config.py diff --git a/poetry.lock b/poetry.lock index bdd8814..cc51b22 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2216,6 +2216,30 @@ files = [ {file = "llvmlite-0.41.0.tar.gz", hash = "sha256:7d41db345d76d2dfa31871178ce0d8e9fd8aa015aa1b7d4dab84b5cb393901e0"}, ] +[[package]] +name = "markdown-it-py" +version = "3.0.0" +description = "Python port of markdown-it. Markdown parsing, done right!" +optional = false +python-versions = ">=3.8" +files = [ + {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"}, + {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"}, +] + +[package.dependencies] +mdurl = ">=0.1,<1.0" + +[package.extras] +benchmarking = ["psutil", "pytest", "pytest-benchmark"] +code-style = ["pre-commit (>=3.0,<4.0)"] +compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"] +linkify = ["linkify-it-py (>=1,<3)"] +plugins = ["mdit-py-plugins"] +profiling = ["gprof2dot"] +rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"] +testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] + [[package]] name = "markupsafe" version = "2.1.3" @@ -2388,6 +2412,17 @@ files = [ [package.dependencies] traitlets = "*" +[[package]] +name = "mdurl" +version = "0.1.2" +description = "Markdown URL utilities" +optional = false +python-versions = ">=3.7" +files = [ + {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"}, + {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"}, +] + [[package]] name = "monotonic" version = "1.6" @@ -4058,6 +4093,25 @@ urllib3 = ">=1.21.1,<3" socks = ["PySocks (>=1.5.6,!=1.5.7)"] use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] +[[package]] +name = "rich" +version = "13.6.0" +description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" +optional = false +python-versions = ">=3.7.0" +files = [ + {file = "rich-13.6.0-py3-none-any.whl", hash = "sha256:2b38e2fe9ca72c9a00170a1a2d20c63c790d0e10ef1fe35eba76e1e7b1d7d245"}, + {file = "rich-13.6.0.tar.gz", hash = "sha256:5c14d22737e6d5084ef4771b62d5d4363165b403455a30a1c8ca39dc7b644bef"}, +] + +[package.dependencies] +markdown-it-py = ">=2.2.0" +pygments = ">=2.13.0,<3.0.0" +typing-extensions = {version = ">=4.0.0,<5.0", markers = "python_version < \"3.9\""} + +[package.extras] +jupyter = ["ipywidgets (>=7.5.1,<9)"] + [[package]] name = "rpds-py" version = "0.10.6" @@ -5557,4 +5611,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "e504ee0b42e5fcb0c800100d3e65b8593d4cf109d1cdb6b6e5be29b4520f5097" +content-hash = "e6a76d82bf822e9fdef3484961d7ac93152edc9c7c384eac16f83cbaf97643e0" diff --git a/pyproject.toml b/pyproject.toml index 3273c25..7a5d001 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,6 +28,7 @@ pysqlite3-binary = "^0.5.2" arize-phoenix = {extras = ["experimental"], version = "^0.0.49"} python-dotenv = "^1.0.0" pyyaml = "^6.0.1" +rich = "^13.6.0" [tool.poetry.dev-dependencies] pytest = "^7.1.0" diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index 40375b1..5a82425 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -1,12 +1,14 @@ import json +import os from pathlib import Path import click import yaml from dotenv import load_dotenv +from rich import print import nbwrite.writer as writer -from nbwrite.constants import DEFAULT_MODEL +from nbwrite.config import Config load_dotenv() @@ -28,23 +30,9 @@ def cli(): default="nbwrite-out", help="The directory to write the generated notebooks to", ) -@click.option( - "--model", - default=[DEFAULT_MODEL], - multiple=True, - help="The API name of the model as per https://platform.openai.com/docs/models", -) -@click.option( - "--generations", - default=1, - type=int, - help="The number of notebooks to generate per model", -) def complete( spec: Path, out: Path, - model: str, - generations: int, ): """Writes example notebooks which complete a given SPEC @@ -52,19 +40,12 @@ def complete( """ spec = yaml.safe_load(spec.read_text()) - config = { - "task": spec["task"], - "steps": spec["steps"], - "packages": spec["packages"], - "out": str(out), - "model": model, - "generations": generations, - } + config = Config(**{**spec, "out": str(out)}) - click.echo(f"Writing notebook with options:\n\n{json.dumps(config, indent=2)}") + if os.getenv("NBWRITE_DEBUG_MODE"): + print(config) - conf_obj = writer.Config(**config) - writer.gen(conf_obj) + writer.gen(config) if __name__ == "__main__": diff --git a/src/nbwrite/config.py b/src/nbwrite/config.py new file mode 100644 index 0000000..28e5c93 --- /dev/null +++ b/src/nbwrite/config.py @@ -0,0 +1,24 @@ +from typing import Any, Dict, List + +from pydantic import BaseModel + +from nbwrite.constants import ( + DEFAULT_LLM_KWARGS, + DEFAULT_RETRIEVER_KWARGS, + DEFAULT_SYSTEM_PROMPT, +) + + +class GenerationConfig(BaseModel): + count: int = 2 + system_prompt: str = DEFAULT_SYSTEM_PROMPT + llm_kwargs: Dict[str, Any] = DEFAULT_LLM_KWARGS + retriever_kwargs: Dict[str, Any] = DEFAULT_RETRIEVER_KWARGS + + +class Config(BaseModel): + task: str + steps: List[str] + packages: List[str] + out: str + generation: GenerationConfig diff --git a/src/nbwrite/constants.py b/src/nbwrite/constants.py index ab570a8..a96ea41 100644 --- a/src/nbwrite/constants.py +++ b/src/nbwrite/constants.py @@ -1,8 +1,15 @@ -DEFAULT_MODEL = "gpt-4-0613" -DEFAULT_ANYSCALE_MODEL = "codellama/CodeLlama-34b-Instruct-hf" -TEMPERATURE = 0.1 -MAX_TOKENS = 512 -SYSTEM_PROMPT = """ +DEFAULT_LLM_KWARGS = { + "model": "gpt-4-0613", + "temperature": 0.1, + "max_tokens": 512, +} + +DEFAULT_RETRIEVER_KWARGS = { + "k": 5, + "search_type": "mmr", +} + +DEFAULT_SYSTEM_PROMPT = """ You are a python programmer writing an ipynb document describing a task. Do install any packages you need using pip @@ -13,9 +20,6 @@ Do not use conversational language """ -K = 5 -SEARCH_TYPE = "mmr" # Also test "similarity" - TEMPLATE_STRING = """ --------------------------------------------------------------- task: diff --git a/src/nbwrite/index.py b/src/nbwrite/index.py index 02465ab..272a951 100644 --- a/src/nbwrite/index.py +++ b/src/nbwrite/index.py @@ -1,7 +1,7 @@ import importlib.util import os from pathlib import Path -from typing import List +from typing import Any, Dict, List from langchain.document_loaders.generic import GenericLoader from langchain.document_loaders.parsers import LanguageParser @@ -9,8 +9,6 @@ from langchain.text_splitter import Language, RecursiveCharacterTextSplitter from langchain.vectorstores import Chroma -from nbwrite.constants import SEARCH_TYPE, K - if os.getenv("NBWRITE_OVERRIDE_SQLITE"): # https://docs.trychroma.com/troubleshooting#sqlite __import__("pysqlite3") @@ -19,7 +17,7 @@ sys.modules["sqlite3"] = sys.modules.pop("pysqlite3") -def create_index(pkgs: List[str], k: int = K, search_type: str = SEARCH_TYPE): +def create_index(pkgs: List[str], retriever_kwargs: Dict[str, Any]): python_splitter = RecursiveCharacterTextSplitter.from_language( language=Language.PYTHON, chunk_size=2000, chunk_overlap=200 @@ -38,9 +36,6 @@ def create_index(pkgs: List[str], k: int = K, search_type: str = SEARCH_TYPE): texts += python_splitter.split_documents(loader.load()) db = Chroma.from_documents(texts, OpenAIEmbeddings(disallowed_special=())) - retriever = db.as_retriever( - search_type=search_type, - search_kwargs={"k": k}, - ) + retriever = db.as_retriever(**retriever_kwargs) return retriever diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 9ee0995..3a0b1b1 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -5,8 +5,9 @@ from datetime import datetime from operator import itemgetter from pathlib import Path -from typing import List +from typing import Dict, List +import click import nbformat from langchain.llms.openai import OpenAI from langchain.prompts import ChatPromptTemplate, PromptTemplate @@ -22,32 +23,15 @@ writes, ) -from nbwrite.constants import ( - MAX_TOKENS, - SYSTEM_PROMPT, - TEMPERATURE, - TEMPLATE_STRING, -) +from nbwrite.config import Config +from nbwrite.constants import TEMPLATE_STRING from nbwrite.index import create_index logger = logging.getLogger(__name__) -@dataclass -class Config: - task: str - steps: List[str] - packages: List[str] - out: str - model: str - generations: int - - -import click - - -def get_llm(model_name: str): - return OpenAI(model_name=model_name, temperature=TEMPERATURE, max_tokens=MAX_TOKENS) +def get_llm(**llm_kwargs: Dict[str, any]): + return OpenAI(**llm_kwargs) def gen( @@ -67,12 +51,12 @@ def gen( prompt = ChatPromptTemplate.from_messages( [ - SystemMessage(content=SYSTEM_PROMPT), + SystemMessage(content=config.generation.system_prompt), HumanMessagePromptTemplate.from_template(TEMPLATE_STRING), ] ) - retriever = create_index(config.packages) + retriever = create_index(config.packages, config.generation.retriever_kwargs) def _combine_documents( docs, document_prompt=PromptTemplate.from_template(template="{page_content}"), document_separator="\n\n" # type: ignore @@ -80,7 +64,7 @@ def _combine_documents( doc_strings = [format_document(doc, document_prompt) for doc in docs] return document_separator.join(doc_strings) - llm = get_llm(config.model) + llm = get_llm(config.generation.llm_kwargs) chain = ( { "context": itemgetter("task") | retriever | _combine_documents, @@ -89,7 +73,7 @@ def _combine_documents( "packages": itemgetter("packages"), } | prompt - | RunnableParallel(**{str(gg): llm for gg in range(config.generations)}) + | RunnableParallel(**{str(gg): llm for gg in range(config.generation.count)}) ) click.echo(f"Invoking LLM") @@ -117,7 +101,7 @@ def _combine_documents( nb.cells.append(new_code_cell(sections[i])) time = now.strftime("%Y-%m-%d_%H-%M-%S") - filename = Path(config.out) / f"{time}-{config.model}-{generation}.ipynb" + filename = Path(config.out) / f"{time}-gen-{generation}.ipynb" string = writes(nb) _ = reads(string) diff --git a/tests/resources/nbwrite-in/example.yaml b/tests/resources/nbwrite-in/example.yaml index 9379231..c6ff47e 100644 --- a/tests/resources/nbwrite-in/example.yaml +++ b/tests/resources/nbwrite-in/example.yaml @@ -7,4 +7,14 @@ steps: packages: - nbmake - nbformat - - nbclient \ No newline at end of file + - nbclient +generation: + count: 2 # number of notebooks to generate + # system_prompt: + llm_kwargs: + # https://api.python.langchain.com/en/latest/llms/langchain.llms.openai.BaseOpenAI.html#langchain.llms.openai.BaseOpenAI + model_name: gpt-3.5-turbo # The API name of the model as per https://platform.openai.com/docs/models + temperature: 0.5 + retriever_kwargs: + k: 3 + search_type: similarity diff --git a/tests/test_cli.py b/tests/test_cli.py index 7958ea2..1a6109f 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -18,6 +18,7 @@ def test_complete(tmpdir: local): if os.getenv("NBWRITE_DEBUG_MODE"): outdir = "test-debug-out" + [pp.unlink() for pp in Path(outdir).glob("*.ipynb")] else: outdir = str(tmpdir) runner = CliRunner() @@ -26,8 +27,6 @@ def test_complete(tmpdir: local): "tests/resources/nbwrite-in/example.yaml", "--out", outdir, - "--generations", - "2", ] shell_fmt = " \\\n ".join(["nbwrite", *args]) @@ -42,8 +41,8 @@ def test_complete(tmpdir: local): assert result.exit_code == 0 logger.warn(f"Checking outputs in {outdir}") - outputs = list(Path(tmpdir).glob("*.ipynb")) - assert len(outputs) == 1 + outputs = list(Path(outdir).glob("*.ipynb")) + assert len(outputs) == 2 nb = nbformat.read(outputs[0], as_version=4) From 8e88ae05105c81063778e521b279a59997bc4af7 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 11:12:18 +0000 Subject: [PATCH 50/59] text splitter conf --- src/nbwrite/config.py | 2 ++ src/nbwrite/constants.py | 5 +++++ src/nbwrite/index.py | 8 ++++++-- src/nbwrite/writer.py | 6 +++++- 4 files changed, 18 insertions(+), 3 deletions(-) diff --git a/src/nbwrite/config.py b/src/nbwrite/config.py index 28e5c93..9d46f83 100644 --- a/src/nbwrite/config.py +++ b/src/nbwrite/config.py @@ -6,6 +6,7 @@ DEFAULT_LLM_KWARGS, DEFAULT_RETRIEVER_KWARGS, DEFAULT_SYSTEM_PROMPT, + DEFAULT_TEXT_SPLITTER_KWARGS, ) @@ -14,6 +15,7 @@ class GenerationConfig(BaseModel): system_prompt: str = DEFAULT_SYSTEM_PROMPT llm_kwargs: Dict[str, Any] = DEFAULT_LLM_KWARGS retriever_kwargs: Dict[str, Any] = DEFAULT_RETRIEVER_KWARGS + text_splitter_kwargs: Dict[str, Any] = DEFAULT_TEXT_SPLITTER_KWARGS class Config(BaseModel): diff --git a/src/nbwrite/constants.py b/src/nbwrite/constants.py index a96ea41..fdaa32e 100644 --- a/src/nbwrite/constants.py +++ b/src/nbwrite/constants.py @@ -4,6 +4,11 @@ "max_tokens": 512, } +DEFAULT_TEXT_SPLITTER_KWARGS = { + "chunk_size": 2000, + "chunk_overlap": 200, +} + DEFAULT_RETRIEVER_KWARGS = { "k": 5, "search_type": "mmr", diff --git a/src/nbwrite/index.py b/src/nbwrite/index.py index 272a951..b068acf 100644 --- a/src/nbwrite/index.py +++ b/src/nbwrite/index.py @@ -17,10 +17,14 @@ sys.modules["sqlite3"] = sys.modules.pop("pysqlite3") -def create_index(pkgs: List[str], retriever_kwargs: Dict[str, Any]): +def create_index( + pkgs: List[str], + retriever_kwargs: Dict[str, Any], + text_splitter_kwargs: Dict[str, Any], +): python_splitter = RecursiveCharacterTextSplitter.from_language( - language=Language.PYTHON, chunk_size=2000, chunk_overlap=200 + language=Language.PYTHON, **text_splitter_kwargs ) texts = [] diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 3a0b1b1..5493c2d 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -56,7 +56,11 @@ def gen( ] ) - retriever = create_index(config.packages, config.generation.retriever_kwargs) + retriever = create_index( + config.packages, + config.generation.retriever_kwargs, + config.generation.text_splitter_kwargs, + ) def _combine_documents( docs, document_prompt=PromptTemplate.from_template(template="{page_content}"), document_separator="\n\n" # type: ignore From 504e53da8bc92a35e28c73e8064475ede5f92933 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 11:31:26 +0000 Subject: [PATCH 51/59] remove unused --- poetry.lock | 1340 +++++++++++++++--------------------------------- pyproject.toml | 2 - 2 files changed, 409 insertions(+), 933 deletions(-) diff --git a/poetry.lock b/poetry.lock index cc51b22..518e718 100644 --- a/poetry.lock +++ b/poetry.lock @@ -192,17 +192,6 @@ doc = ["Sphinx", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd- test = ["anyio[trio]", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] trio = ["trio (<0.22)"] -[[package]] -name = "appdirs" -version = "1.4.4" -description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -optional = false -python-versions = "*" -files = [ - 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python_splitter.split_documents(loader.load()) - db = Chroma.from_documents(texts, OpenAIEmbeddings(disallowed_special=())) + db = Chroma.from_documents(texts, get_embeddings()) retriever = db.as_retriever(**retriever_kwargs) return retriever diff --git a/tests/test_cli.py b/tests/test_cli.py index 1a6109f..fdd0840 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -5,6 +5,7 @@ import nbformat from click.testing import CliRunner +from langchain.embeddings import FakeEmbeddings from langchain.llms.fake import FakeListLLM from nbclient.client import NotebookClient from py.path import local @@ -32,25 +33,27 @@ def test_complete(tmpdir: local): shell_fmt = " \\\n ".join(["nbwrite", *args]) logger.warn(f"Running\n{shell_fmt}") - with patch("nbwrite.writer.get_llm") as mock_get_llm: - mock_get_llm.return_value = FakeListLLM( - responses=["Code:\n```python\nprint('Hello, world!')\n```\n"] - ) - result = runner.invoke(cli, args) + with patch("nbwrite.index.get_embeddings") as mock_get_embeddings: + mock_get_embeddings.return_value = FakeEmbeddings(size=1536) + with patch("nbwrite.writer.get_llm") as mock_get_llm: + mock_get_llm.return_value = FakeListLLM( + responses=["Code:\n```python\nprint('Hello, world!')\n```\n"] + ) + result = runner.invoke(cli, args) - assert result.exit_code == 0 + assert result.exit_code == 0 - logger.warn(f"Checking outputs in {outdir}") - outputs = list(Path(outdir).glob("*.ipynb")) - assert len(outputs) == 2 + logger.warn(f"Checking outputs in {outdir}") + outputs = list(Path(outdir).glob("*.ipynb")) + assert len(outputs) == 2 - nb = nbformat.read(outputs[0], as_version=4) + nb = nbformat.read(outputs[0], as_version=4) - client = NotebookClient(nb) - client.execute() + client = NotebookClient(nb) + client.execute() - for cell in nb.cells: - if cell.cell_type == "code" and 'print("Hello, world!")' in cell.source: - assert "Hello, world!" in "".join( - output.text for output in cell.outputs - ) + for cell in nb.cells: + if cell.cell_type == "code" and 'print("Hello, world!")' in cell.source: + assert "Hello, world!" in "".join( + output.text for output in cell.outputs + ) From 6cc49dd4e32b27a3f2315e9be1a09c343a18740c Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 11:47:44 +0000 Subject: [PATCH 53/59] remove optional deps --- .github/workflows/pytest.yml | 2 +- poetry.lock | 6 ++++-- pyproject.toml | 3 +-- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 6340ced..1d27221 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -18,7 +18,7 @@ jobs: # file: coverage.xml pytest: strategy: - fail-fast: true + fail-fast: false matrix: os: - ubuntu-latest diff --git a/poetry.lock b/poetry.lock index 8a2ce3e..27f81bf 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2064,11 +2064,13 @@ dataclasses-json = ">=0.5.7,<0.7" jsonpatch = ">=1.33,<2.0" langsmith = ">=0.0.43,<0.1.0" numpy = ">=1,<2" 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python-dateutil = ">=2.8.2" pytz = ">=2020.1" @@ -5231,4 +5233,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "0b0a48b1e6ee391aa2185c7044e2913044421f057b8da27609ab4ef93dae981d" +content-hash = "f4338ebea3413fa02ef318211beb924969d7e120fd85e903bec77ce2a774545a" diff --git a/pyproject.toml b/pyproject.toml index 82cf6f8..18320f8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ python = ">=3.8.1,<3.12" openai = {extras = ["embeddings"], version = "^0.28.1"} pathlib = "^1.0.1" click = "^8.1.7" -langchain = "^0.0.312" +langchain = {optional = false, version = "^0.0.312", extras = ["openai"]} nbformat = "^5.9.2" chromadb = "^0.4.14" pysqlite3-binary = "^0.5.2" @@ -27,7 +27,6 @@ arize-phoenix = {extras = ["experimental"], version = "^0.0.49"} python-dotenv = "^1.0.0" pyyaml = "^6.0.1" rich = "^13.6.0" -tiktoken = "^0.5.1" [tool.poetry.dev-dependencies] pytest = "^7.1.0" From 42a844b67bdf5a1eb23c1cf1d3564466e324564d Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 11:51:04 +0000 Subject: [PATCH 54/59] remove optional deps --- pyproject.toml | 2 +- src/nbwrite/index.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 18320f8..959c122 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,7 +22,7 @@ click = "^8.1.7" langchain = {optional = false, version = "^0.0.312", extras = ["openai"]} nbformat = "^5.9.2" chromadb = "^0.4.14" -pysqlite3-binary = "^0.5.2" +pysqlite3-binary = {version = "^0.5.2", markers = "sys_platform == 'linux'"} arize-phoenix = {extras = ["experimental"], version = "^0.0.49"} python-dotenv = "^1.0.0" pyyaml = "^6.0.1" diff --git a/src/nbwrite/index.py b/src/nbwrite/index.py index d542d88..57c634a 100644 --- a/src/nbwrite/index.py +++ b/src/nbwrite/index.py @@ -1,5 +1,6 @@ import importlib.util import os +import platform from pathlib import Path from typing import Any, Dict, List @@ -9,7 +10,7 @@ from langchain.text_splitter import Language, RecursiveCharacterTextSplitter from langchain.vectorstores import Chroma -if os.getenv("NBWRITE_OVERRIDE_SQLITE"): +if platform.system() == "Linux": # https://docs.trychroma.com/troubleshooting#sqlite __import__("pysqlite3") import sys From 494688dcc0459b0f333cd8fa66f8ed7de7aa88fe Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 12:12:20 +0000 Subject: [PATCH 55/59] fix warning --- src/nbwrite/writer.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/nbwrite/writer.py b/src/nbwrite/writer.py index 5493c2d..b4ca469 100644 --- a/src/nbwrite/writer.py +++ b/src/nbwrite/writer.py @@ -5,15 +5,16 @@ from datetime import datetime from operator import itemgetter from pathlib import Path -from typing import Dict, List +from typing import Dict import click import nbformat -from langchain.llms.openai import OpenAI +from langchain.chat_models import ChatOpenAI from langchain.prompts import ChatPromptTemplate, PromptTemplate from langchain.prompts.chat import HumanMessagePromptTemplate from langchain.schema import format_document from langchain.schema.messages import SystemMessage +from langchain.schema.output_parser import StrOutputParser from langchain.schema.runnable import RunnableParallel from nbformat.v4 import ( new_code_cell, @@ -31,7 +32,7 @@ def get_llm(**llm_kwargs: Dict[str, any]): - return OpenAI(**llm_kwargs) + return ChatOpenAI(**llm_kwargs) def gen( @@ -68,7 +69,7 @@ def _combine_documents( doc_strings = [format_document(doc, document_prompt) for doc in docs] return document_separator.join(doc_strings) - llm = get_llm(config.generation.llm_kwargs) + llm = get_llm(**config.generation.llm_kwargs) | StrOutputParser() chain = ( { "context": itemgetter("task") | retriever | _combine_documents, From f9c933729214c29872f1c427f469f6d7dc4d9574 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 12:13:48 +0000 Subject: [PATCH 56/59] fix warning --- src/nbwrite/cli.py | 12 +++--------- tests/test_cli.py | 3 +-- 2 files changed, 4 insertions(+), 11 deletions(-) diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index 5a82425..8c83bff 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -13,13 +13,7 @@ load_dotenv() -@click.group() -def cli(): - """Command line interface for nbwrite.""" - pass - - -@cli.command() +@click.command() @click.argument( "spec", type=click.Path(path_type=Path, dir_okay=False, file_okay=True), @@ -30,13 +24,13 @@ def cli(): default="nbwrite-out", help="The directory to write the generated notebooks to", ) -def complete( +def cli( spec: Path, out: Path, ): """Writes example notebooks which complete a given SPEC - e.g. nbwrite complete "./spec.yaml" + e.g. nbwrite "./spec.yaml" """ spec = yaml.safe_load(spec.read_text()) diff --git a/tests/test_cli.py b/tests/test_cli.py index fdd0840..8bfacf1 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -15,7 +15,7 @@ logger = logging.getLogger(__name__) -def test_complete(tmpdir: local): +def test_cli(tmpdir: local): if os.getenv("NBWRITE_DEBUG_MODE"): outdir = "test-debug-out" @@ -24,7 +24,6 @@ def test_complete(tmpdir: local): outdir = str(tmpdir) runner = CliRunner() args = [ - "complete", "tests/resources/nbwrite-in/example.yaml", "--out", outdir, From fec1690f410469c9d626391dd8c12c4954b08361 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 12:15:40 +0000 Subject: [PATCH 57/59] doc stubs --- README.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 6671533..d832950 100644 --- a/README.md +++ b/README.md @@ -2,10 +2,10 @@ nbwrite writes notebook-based documentation for you -Tutorials, guides, demos, examples -- it creates runnable and testable python code which -give your users critical support in using your product. +{{ intro }} -To write your first notebook, create an ipynb file and use the cli like so + +## Quick start ```python nbwrite \ @@ -19,9 +19,10 @@ nbwrite \ --context another_lib ``` -TODOs before releasing +## Guides + +{{ how to write a spec file }} -- basic eval/testing -- document setup +## Data Security -## Data Security \ No newline at end of file +{embeddings and openai} \ No newline at end of file From 395298e589b4d0b0522c2ecf8356898e60edfcf1 Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 12:16:55 +0000 Subject: [PATCH 58/59] doc stubs --- src/nbwrite/cli.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/nbwrite/cli.py b/src/nbwrite/cli.py index 8c83bff..9f390c3 100644 --- a/src/nbwrite/cli.py +++ b/src/nbwrite/cli.py @@ -1,4 +1,3 @@ -import json import os from pathlib import Path @@ -10,8 +9,6 @@ import nbwrite.writer as writer from nbwrite.config import Config -load_dotenv() - @click.command() @click.argument( @@ -43,4 +40,5 @@ def cli( if __name__ == "__main__": + load_dotenv() cli() From f8f74aa8c9ccfc3841c145df424fe1065444bf9c Mon Sep 17 00:00:00 2001 From: alex-treebeard Date: Tue, 24 Oct 2023 14:19:39 +0000 Subject: [PATCH 59/59] release --- .github/workflows/pytest.yml | 28 ++- .github/workflows/test-publish-to-pypi.yml | 4 +- README.md | 12 +- poetry.lock | 262 ++++++++++++++++++++- pyproject.toml | 3 +- 5 files changed, 280 insertions(+), 29 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 1d27221..133d961 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -1,21 +1,21 @@ name: Pytest on: - # schedule: - # - cron: 0 13 * * 1 # Every Monday at 1PM UTC (9AM EST) + schedule: + - cron: 0 13 * * 1 # Every Monday at 1PM UTC (9AM EST) pull_request: # test in containerised and OS environments jobs: -# test-container: -# runs-on: ubuntu-22.04 -# steps: -# - uses: actions/checkout@v2 -# - run: npm install -g @devcontainers/cli@v0.30.0 -# - run: devcontainer up --workspace-folder=. -# - run: devcontainer exec --workspace-folder=. poetry run pre-commit run --verbose --all-files -# - run: devcontainer exec --workspace-folder=. poetry run pytest --cov-report=xml --cov=src -# - uses: codecov/codecov-action@v1 -# with: -# file: coverage.xml + test-container: + runs-on: ubuntu-22.04 + steps: + - uses: actions/checkout@v2 + - run: npm install -g @devcontainers/cli@v0.30.0 + - run: devcontainer up --workspace-folder=. + - run: devcontainer exec --workspace-folder=. poetry run pre-commit run --verbose --all-files + - run: devcontainer exec --workspace-folder=. poetry run pytest --cov-report=xml --cov=src + - uses: codecov/codecov-action@v1 + with: + file: coverage.xml pytest: strategy: fail-fast: false @@ -40,3 +40,5 @@ jobs: - uses: codecov/codecov-action@v1 with: file: coverage.xml + +# TODO README and workflows for e2e test, package release, devcon build \ No newline at end of file diff --git a/.github/workflows/test-publish-to-pypi.yml b/.github/workflows/test-publish-to-pypi.yml index d63d971..144c237 100644 --- a/.github/workflows/test-publish-to-pypi.yml +++ b/.github/workflows/test-publish-to-pypi.yml @@ -17,8 +17,8 @@ jobs: - run: poetry build - run: pip install 'pytest==7.1' - run: pip install dist/*gz --force-reinstall - - run: pytest --nbmake tests/resources/mock.ipynb + - run: nbwrite tests/resources/nbwrite-in/example.yaml - run: pip install dist/*whl --force-reinstall - - run: pytest --nbmake tests/resources/mock.ipynb + - run: nbwrite tests/resources/nbwrite-in/example.yaml - run: pip install twine==4.0.1 - run: twine upload -r testpypi dist/* -u __token__ -p ${{ secrets.TEST_PYPI_API_TOKEN }} diff --git a/README.md b/README.md index d832950..1c6e73f 100644 --- a/README.md +++ b/README.md @@ -7,17 +7,7 @@ nbwrite writes notebook-based documentation for you ## Quick start -```python -nbwrite \ - my_nb.ipynb \ - output.ipynb \ - --task 'test a notebook from the Python API using the notebook run class' \ - --step 'create an example nb using the nbformat library' \ - --step 'call notebookrun' \ - --step 'check the output' \ - --context nbmake \ - --context another_lib -``` +{{ quick start }} ## Guides diff --git a/poetry.lock b/poetry.lock index 27f81bf..8572194 100644 --- a/poetry.lock +++ b/poetry.lock @@ -805,6 +805,51 @@ files = [ [package.extras] toml = ["tomli"] +[[package]] +name = "cryptography" +version = "41.0.4" +description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." +optional = false +python-versions = ">=3.7" +files = [ + {file = "cryptography-41.0.4-cp37-abi3-macosx_10_12_universal2.whl", hash = "sha256:80907d3faa55dc5434a16579952ac6da800935cd98d14dbd62f6f042c7f5e839"}, + {file = "cryptography-41.0.4-cp37-abi3-macosx_10_12_x86_64.whl", hash = "sha256:35c00f637cd0b9d5b6c6bd11b6c3359194a8eba9c46d4e875a3660e3b400005f"}, + {file = "cryptography-41.0.4-cp37-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = 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+files = [ + {file = "rfc3986-2.0.0-py2.py3-none-any.whl", hash = "sha256:50b1502b60e289cb37883f3dfd34532b8873c7de9f49bb546641ce9cbd256ebd"}, + {file = "rfc3986-2.0.0.tar.gz", hash = "sha256:97aacf9dbd4bfd829baad6e6309fa6573aaf1be3f6fa735c8ab05e46cecb261c"}, +] + +[package.extras] +idna2008 = ["idna"] + [[package]] name = "rich" version = "13.6.0" @@ -4186,6 +4407,21 @@ dev = ["click", "doit (>=0.36.0)", "flake8", "mypy", "pycodestyle", "pydevtool", doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"] test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] +[[package]] +name = "secretstorage" +version = "3.3.3" +description = "Python bindings to FreeDesktop.org Secret Service API" +optional = false +python-versions = ">=3.6" +files = [ + {file = "SecretStorage-3.3.3-py3-none-any.whl", hash = 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"^3.49.0" +twine = "^4.0.2" [build-system] build-backend = "poetry.core.masonry.api"