diff --git a/.github/workflows/build_deploy_docs.yml b/.github/workflows/documentation.yml similarity index 96% rename from .github/workflows/build_deploy_docs.yml rename to .github/workflows/documentation.yml index 40f9b4dd..97f13272 100644 --- a/.github/workflows/build_deploy_docs.yml +++ b/.github/workflows/documentation.yml @@ -45,8 +45,8 @@ jobs: python-version: 3.8 poetry-version: 1.2.2 - - name: Install docs and notebook dependencies - run: poetry install -E notebook -E docs + - name: Install notebook dependencies + run: poetry install -E notebook --with docs - name: Install pandoc run: | diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 00000000..65c0ab14 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,155 @@ +name: Publish to PyPI + +# Workflow runs prerelease job on every push to main branch +# and a release job on every tag push. +# A publish job is executed on every successful prerelease or release job +# And if publish is successful, the version is also updated in the pyproject.toml file and pushed to main branch + # By default, a workflow run that is triggered by a push event will + # not trigger another push event when it pushes changes to the repository. +# The package is distributed as sed-processor +on: + push: + branches: + - main + tags: + - '*' + +jobs: + prerelease: + if: github.ref == 'refs/heads/main' + runs-on: ubuntu-latest + outputs: + version: ${{ steps.version.outputs.version }} + steps: + - uses: actions/checkout@v3 + with: + lfs: true + path: 'sed-processor' + + - name: "Setup Python, Poetry and Dependencies" + uses: zain-sohail/action-setup-cache-python-poetry@main + with: + python-version: 3.8 + poetry-version: 1.2.2 + working-directory: sed-processor + + - name: Change to distribution name in toml file + run: | + cd sed-processor + sed -i 's/name = "sed"/name = "sed-processor"/' pyproject.toml + + - name: bump pre-release version + id: version + working-directory: sed-processor + run: | + VERSION=$(poetry version -s prerelease) + echo "version=$VERSION" >> $GITHUB_OUTPUT + poetry build + + - name: Upload artifact + uses: actions/upload-artifact@v3 + with: + name: dist + path: sed-processor/dist + + - name: Upload pyproject.toml + uses: actions/upload-artifact@v3 + with: + name: pyproject + path: sed-processor/pyproject.toml + + release: + if: startsWith(github.ref, 'refs/tags/') + runs-on: ubuntu-latest + outputs: + version: ${{ steps.version.outputs.version }} + steps: + - uses: actions/checkout@v3 + with: + lfs: true + path: 'sed-processor' + + - name: "Setup Python, Poetry and Dependencies" + uses: zain-sohail/action-setup-cache-python-poetry@main + with: + python-version: 3.8 + poetry-version: 1.2.2 + working-directory: sed-processor + + - name: Change to distribution name in toml file + run: | + cd sed-processor + sed -i 's/name = "sed"/name = "sed-processor"/' pyproject.toml + + - name: Bump release version and build + id: version + working-directory: sed-processor + run: | + VERSION=$(echo ${GITHUB_REF#refs/tags/v} | sed 's/-.*//') + echo "version=$VERSION" >> $GITHUB_OUTPUT + poetry version $VERSION + poetry build + + - name: Upload artifact + uses: actions/upload-artifact@v3 + with: + name: dist + path: sed-processor/dist + + - name: Upload pyproject.toml + uses: actions/upload-artifact@v3 + with: + name: pyproject + path: sed-processor/pyproject.toml + + publish: + needs: [prerelease, release] + if: always() && (needs.prerelease.result == 'success' || needs.release.result == 'success') + runs-on: ubuntu-latest + outputs: + version: ${{ needs.prerelease.outputs.version || needs.release.outputs.version }} + environment: + name: pypi + url: https://pypi.org/p/sed-processor + permissions: + id-token: write + + steps: + - name: Download a single artifact + uses: actions/download-artifact@v3 + with: + name: dist + + - name: Publish package distributions to PyPI Test + uses: pypa/gh-action-pypi-publish@release/v1 + with: + packages-dir: . + + bump-version: + needs: publish + if: always() && (needs.publish.result == 'success') + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + with: + lfs: true + path: 'sed-processor' + + - name: Download pyproject.toml + uses: actions/download-artifact@v3 + with: + name: pyproject + path: sed-processor + + # new_branch set for cases when tagging a release + - name: Commit changes + uses: EndBug/add-and-commit@v9 + with: + default_author: github_actions + message: 'bump version to ${{ needs.publish.outputs.version }}' + add: pyproject.toml + cwd: sed-processor + new_branch: main + # By default, a workflow run that is triggered by a push event will + # not trigger another push event when it pushes changes to the repository. + # So no problem here. diff --git a/.github/workflows/testing_coverage.yml b/.github/workflows/testing_coverage.yml index 22413d83..e33409a2 100644 --- a/.github/workflows/testing_coverage.yml +++ b/.github/workflows/testing_coverage.yml @@ -25,12 +25,12 @@ jobs: with: python-version: 3.8 poetry-version: 1.2.2 - + # Run pytest with coverage report, saving to xml - name: Run tests on python 3.8 run: | poetry run pytest --cov --cov-report xml:cobertura.xml --full-trace --show-capture=no -sv -n auto tests/ - + # Take report and upload to coveralls - name: Coveralls uses: coverallsapp/github-action@v2 diff --git a/LICENSE b/LICENSE index df28b2c0..74ab188a 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2022 OpenCOMPES +Copyright (c) 2022-2023 OpenCOMPES Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 5ea5c0f6..aa6f08c1 100644 --- a/README.md +++ b/README.md @@ -1,61 +1,94 @@ -# sed -[![Documentation Status](https://github.com/OpenCOMPES/sed/actions/workflows/build_deploy_docs.yml/badge.svg)](https://opencompes.github.io/sed/) +[![Documentation Status](https://github.com/OpenCOMPES/sed/actions/workflows/documentation.yml/badge.svg)](https://opencompes.github.io/sed/) ![](https://github.com/OpenCOMPES/sed/actions/workflows/linting.yml/badge.svg?branch=main) ![](https://github.com/OpenCOMPES/sed/actions/workflows/testing_multiversion.yml/badge.svg?branch=main) -![](https://img.shields.io/pypi/pyversions/sedprocessor) -![](https://img.shields.io/pypi/l/sedprocessor) -![](https://img.shields.io/pypi/v/sedprocessor) +![](https://img.shields.io/pypi/pyversions/sed-processor) +![](https://img.shields.io/pypi/l/sed-processor) +[![](https://img.shields.io/pypi/v/sed-processor)](https://pypi.org/project/sed-processor) [![Coverage Status](https://coveralls.io/repos/github/OpenCOMPES/sed/badge.svg?branch=main&kill_cache=1)](https://coveralls.io/github/OpenCOMPES/sed?branch=main) +# Single Event Data Frame Processor -Single Event Data Frame Processor: Backend to handle photoelectron resolved datastreams +Backend to handle photoelectron resolved datastreams. -# Installation +## Installation -## Conda approach +### Pip (for users) -Clone this repository and cd to its root folder. -Create a new environment by typing: +- Create a new virtual environment using either venv, pyenv, conda, etc. See below for an example. + +```bash +python -m venv .sed-venv ``` -conda env create -f env.yml + +- Activate your environment: + +```bash +source .sed-venv/bin/activate ``` -This should install all the requirements to run `sed` in your environment. -To activate your environment: + +- Install `sed`, distributed as `sed-processor` on PyPI: + +```bash +pip install sed-processor ``` -conda activate sed_conda + +- This should install all the requirements to run `sed` in your environment. + +- If you intend to work with Jupyter notebooks, it is helpful to install a Jupyter kernel for your environment. This can be done, once your environment is activated, by typing: + +```bash +python -m ipykernel install --user --name=sed_kernel ``` -If you intend to work with jupyter notebooks, it is helpfull to install a jupyter kernel of your environment. This can be done, once activating your environment, by typing: +### For Contributors + +To contribute to the development of `sed`, you can follow these steps: + +1. Clone the repository: + +```bash +git clone https://github.com/OpenCOMPES/sed.git +cd sed ``` -python -m ipykernel install --user --name=sed_conda + +2. Install the repository in editable mode: + +```bash +pip install -e . ``` +Now you have the development version of `sed` installed in your local environment. Feel free to make changes and submit pull requests. -## Poetry approach (better, but more complex) +### Poetry (for maintainers) - Prerequisites: - + poetry: https://python-poetry.org/docs/ - + pyenv: https://github.com/pyenv/pyenv + + Poetry: https://python-poetry.org/docs/ -- Clone this repository and check the python version within the `[tool.poetry.dependencies]` section of the `pyproject.toml` file - + If your system is using a different Python version, use `pyenv` to create and activate a Python version compatible with the specifications from the `pyproject.toml`. See [pyenv basic usage](https://github.com/pyenv/pyenv) - Create a virtual environment by typing: -```python + +```bash poetry shell ``` - + A new shell will be spawn with the new environment activated + +- A new shell will be spawned with the new environment activated. - Install the dependencies from the `pyproject.toml` by typing: -```python -poetry install + +```bash +poetry install --with dev, docs ``` -- If you wish to use the virtual environment created by poetry to work in a Jupyter notebook, you first need to install the optional notebook dependencies and then create a Jupyter kernel for that. - + Install the optional dependencies ipykernel and jupyter - ```python +- If you wish to use the virtual environment created by Poetry to work in a Jupyter notebook, you first need to install the optional notebook dependencies and then create a Jupyter kernel for that. + + + Install the optional dependencies `ipykernel` and `jupyter`: + + ```bash poetry install -E notebook ``` - + Make sure to run the command below within your virtual environment ('poetry run' ensures this) by typing: - ```python + + + Make sure to run the command below within your virtual environment (`poetry run` ensures this) by typing: + + ```bash poetry run ipython kernel install --user --name=sed_poetry ``` - + The new kernel will be eligible now from your kernels list in Jupyter + + + The new kernel will now be available in your Jupyter kernels list. diff --git a/docs/conf.py b/docs/conf.py index e1bc1bd0..1d7e3575 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -3,35 +3,35 @@ # This file only contains a selection of the most common options. For a full # list see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html - # -- Path setup -------------------------------------------------------------- - # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # -import tomlkit import os import sys -sys.path.insert(0, os.path.abspath('..')) + +import tomlkit + +sys.path.insert(0, os.path.abspath("..")) # -- Project information ----------------------------------------------------- def _get_project_meta(): - with open('../pyproject.toml') as pyproject: + with open("../pyproject.toml") as pyproject: file_contents = pyproject.read() - return tomlkit.parse(file_contents)['tool']['poetry'] + return tomlkit.parse(file_contents)["tool"]["poetry"] pkg_meta = _get_project_meta() -project = str(pkg_meta['name']) -copyright = '2022, OpenCOMPES team' -author = 'OpenCOMPES team' +project = str(pkg_meta["name"]) +copyright = "2022, OpenCOMPES team" +author = "OpenCOMPES team" # The short X.Y version -version = str(pkg_meta['version']) +version = str(pkg_meta["version"]) # The full version, including alpha/beta/rc tags release = version @@ -40,28 +40,38 @@ def _get_project_meta(): # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. -extensions = ['sphinx_rtd_theme', 'sphinx.ext.autodoc', 'sphinx.ext.napoleon', - 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.autosummary', - 'sphinx.ext.coverage', 'sphinx_autodoc_typehints', "bokeh.sphinxext.bokeh_autodoc", - "bokeh.sphinxext.bokeh_plot", 'nbsphinx'] +extensions = [ + "sphinx_rtd_theme", + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "sphinx.ext.todo", + "sphinx.ext.coverage", + "sphinx.ext.autosummary", + "sphinx.ext.coverage", + "sphinx_autodoc_typehints", + "bokeh.sphinxext.bokeh_autodoc", + "bokeh.sphinxext.bokeh_plot", + "nbsphinx", + "myst_parser", +] -autoclass_content = 'class' -autodoc_member_order = 'bysource' +autoclass_content = "class" +autodoc_member_order = "bysource" autodoc_mock_imports = [ - 'astor', - 'pep8ext_naming', - 'flake8_builtins', - 'flake8_quotes', + "astor", + "pep8ext_naming", + "flake8_builtins", + "flake8_quotes", ] -autodoc_member_order = 'bysource' +autodoc_member_order = "bysource" autodoc_default_options = { - 'members': True, - 'undoc-members': True, - 'exclude-members': '__dict__,__weakref__', - 'show-inheritance': True, + "members": True, + "undoc-members": True, + "exclude-members": "__dict__,__weakref__", + "show-inheritance": True, } @@ -71,16 +81,16 @@ def _get_project_meta(): always_document_param_types = True typehints_use_rtype = False typehints_fully_qualified = True -typehints_defaults = 'comma' +typehints_defaults = "comma" # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] # -- Options for HTML output ------------------------------------------------- @@ -88,9 +98,9 @@ def _get_project_meta(): # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'sphinx_rtd_theme' +html_theme = "sphinx_rtd_theme" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +html_static_path = ["_static"] diff --git a/docs/getting_started.rst b/docs/getting_started.rst new file mode 100644 index 00000000..fba01724 --- /dev/null +++ b/docs/getting_started.rst @@ -0,0 +1,2 @@ +.. include:: ../README.md + :parser: myst_parser.sphinx_ diff --git a/docs/index.rst b/docs/index.rst index 6d8755b6..85e55254 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -3,7 +3,15 @@ Single-Event DataFrame (SED) documentation .. toctree:: :maxdepth: 1 - :numbered: + :caption: Getting Started + + getting_started + tutorial/1_binning_fake_data + tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data + tutorial/3_metadata_collection_and_export_to_NeXus + +.. toctree:: + :maxdepth: 1 :caption: SED Core Modules sed/core @@ -16,18 +24,8 @@ Single-Event DataFrame (SED) documentation sed/metadata sed/config -.. toctree:: - :maxdepth: 1 - :numbered: - :caption: Examples - - tutorial/1_binning_fake_data.ipynb - tutorial/2_conversion_pipeline_for_example_time-resolved_ARPES_data.ipynb - tutorial/3_metadata_collection_and_export_to_NeXus.ipynb - .. toctree:: :maxdepth: 2 - :numbered: :caption: Contributing misc/maintain diff --git a/docs/misc/maintain.rst b/docs/misc/maintain.rst index 0033a27e..91cf2cb5 100644 --- a/docs/misc/maintain.rst +++ b/docs/misc/maintain.rst @@ -1,4 +1,12 @@ How to maintain =================================================== -refer to github wiki as well \ No newline at end of file +refer to github wiki as well + +Building docs +=================================================== + +run +poetry shell +poetry install --with docs +sphinx-build -b html docs _build diff --git a/poetry.lock b/poetry.lock index 5bbafccc..214395c8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. [[package]] name = "alabaster" @@ -343,7 +343,7 @@ tzdata = ["tzdata"] name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" -optional = true +optional = false python-versions = ">=3.6.0" files = [ {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"}, @@ -361,7 +361,7 @@ lxml = ["lxml"] name = "bleach" version = "6.1.0" description = "An easy safelist-based HTML-sanitizing tool." -optional = true +optional = false python-versions = ">=3.8" files = [ {file = "bleach-6.1.0-py3-none-any.whl", hash = "sha256:3225f354cfc436b9789c66c4ee030194bee0568fbf9cbdad3bc8b5c26c5f12b6"}, @@ -966,7 +966,7 @@ files = [ name = "defusedxml" version = "0.7.1" description = "XML bomb protection for Python stdlib modules" -optional = true +optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ {file = "defusedxml-0.7.1-py2.py3-none-any.whl", hash = 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files = [ - {file = "wcwidth-0.2.9-py2.py3-none-any.whl", hash = "sha256:9a929bd8380f6cd9571a968a9c8f4353ca58d7cd812a4822bba831f8d685b223"}, - {file = "wcwidth-0.2.9.tar.gz", hash = "sha256:a675d1a4a2d24ef67096a04b85b02deeecd8e226f57b5e3a72dbb9ed99d27da8"}, + {file = "wcwidth-0.2.10-py2.py3-none-any.whl", hash = "sha256:aec5179002dd0f0d40c456026e74a729661c9d468e1ed64405e3a6c2176ca36f"}, + {file = "wcwidth-0.2.10.tar.gz", hash = "sha256:390c7454101092a6a5e43baad8f83de615463af459201709556b6e4b1c861f97"}, ] [[package]] @@ -5954,7 +5944,7 @@ tests = ["pytest", "pytest-cov"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -optional = true +optional = false python-versions = "*" files = [ {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, @@ -6058,10 +6048,9 @@ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.link testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [extras] -docs = ["nbsphinx", "sphinx", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "tomlkit"] notebook = ["ipykernel", "jupyter", "jupyterlab-h5web"] [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.11" -content-hash = "3924393493e074e135a3fa24fee9d5a0d400d6af09e4cc4602b3beae6b5a2dac" +content-hash = "7459ff0a476900f9668c8ca30e4ea444d603878f179ba92262cd46dfe9da2790" diff --git a/pyproject.toml b/pyproject.toml index 6f1ee400..b5e89bb0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,16 @@ [tool.poetry] -name = "sed" -version = "0.1.0" +name = "sed-processor" +packages = [ + {include = "sed"} +] +version = "0.1.5a2" description = "Single Event Data Frame Processor: Backend to handle photoelectron resolved datastreams" -authors = ["Muhammad Zain Sohail "] +authors = ["OpenCOMPES team "] +readme = "README.md" +repository = "https://github.com/OpenCOMPES/sed" +documentation = "https://opencompes.github.io/sed/" +keywords = ["sed", "mpes", "flash", "arpes"] +license = "MIT" [tool.poetry.dependencies] python = ">=3.8,<3.11" @@ -34,16 +42,10 @@ pyarrow = "^14.0.1" jupyter = {version = "^1.0.0", extras = ["notebook"], optional = true} ipykernel = {version = "^6.9.1", extras = ["notebook"], optional = true} jupyterlab-h5web = {version = ">=7.0.0", extras = ["notebook"], optional = true} -sphinx = {version = ">4.4.0", extras = ["docs"], optional = true} -sphinx-rtd-theme = {version = ">1.0.0", extras = ["docs"], optional = true} -tomlkit = {version = ">0.10.0", extras = ["docs"], optional = true} -sphinx-autodoc-typehints = {version = ">1.17.0", extras = ["docs"], optional = true} -nbsphinx = {version = "^0.9.3", extras = ["docs"], optional = true} [tool.poetry.extras] notebook = ["jupyter", "ipykernel", "jupyterlab-h5web"] -docs = ["Sphinx", "sphinx-rtd-theme", "tomlkit", "sphinx-autodoc-typehints", "nbsphinx"] [tool.poetry.group.dev.dependencies] pytest = "^7.0.1" @@ -56,6 +58,17 @@ pycodestyle = "^2.11.1" types-pyyaml = "^6.0.12.12" types-requests = "^2.31.0.9" +[tool.poetry.group.docs] +optional = true + +[tool.poetry.group.docs.dependencies] +sphinx = "^7.1.2" +sphinx-rtd-theme = "^1.0.0" +tomlkit = "^0.12.0" +sphinx-autodoc-typehints = "^1.17.0" +nbsphinx = "^0.9.3" +myst-parser = "^2.0.0" + [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api"