diff --git a/.copier-answers.yml b/.copier-answers.yml new file mode 100644 index 00000000..ebdc0740 --- /dev/null +++ b/.copier-answers.yml @@ -0,0 +1,13 @@ +# This file is managed by Copier; DO NOT EDIT OR REMOVE. +_commit: v0.2.1 +_src_path: https://github.com/quantco/copier-template-python-open-source +add_autobump_workflow: true +author_email: plateau@uwekorn.com +author_name: Data Engineering Collective +github_url: https://github.com/data-engineering-collective/plateau +github_user: xhochy +minimal_python_version: py311 +project_short_description: A Python library to manage (create, read, update, delete) + large amounts of tabular data in a blob store. +project_slug: plateau +use_devcontainer: false diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..18f6c7e9 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +pixi.lock linguist-language=YAML linguist-generated=true diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml new file mode 100644 index 00000000..fda59d29 --- /dev/null +++ b/.github/workflows/benchmarks.yml @@ -0,0 +1,25 @@ +name: Benchmarks + +on: + schedule: + - cron: "0 0 * * 0" # weekly on Sunday + +jobs: + benchmarks: + timeout-minutes: 30 + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0 + - name: Set up pixi + uses: prefix-dev/setup-pixi@ba3bb36eb2066252b2363392b7739741bb777659 # v0.8.1 + with: + environments: benchmark + - name: Install package + run: pixi run -e benchmark postinstall + - name: Running benchmarks + run: | + pixi run -e benchmark asv --config ./asv_bench/asv.conf.json machine --machine github --os unknown --arch unknown --cpu unknown --ram unknown + pixi run -e benchmark asv --config ./asv_bench/asv.conf.json run -E existing:same | sed "/failed$/ s/^/##[error]/" | tee benchmarks.log + if grep "failed" benchmarks.log > /dev/null ; then + exit 1 + fi diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 00000000..c852f394 --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,52 @@ +name: Build +on: + pull_request: + push: + branches: + - main + tags: + - "*" + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0 + - name: Set up pixi + uses: prefix-dev/setup-pixi@ba3bb36eb2066252b2363392b7739741bb777659 # v0.8.1 + with: + environments: build + - name: Build project + run: pixi run -e build build-wheel + - name: Check package + run: pixi run -e build check-wheel + - name: Upload package + uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0 + with: + name: artifact + path: dist/* + + release: + name: Publish package + if: startsWith(github.ref, 'refs/tags/') + needs: [build] + runs-on: ubuntu-latest + permissions: + id-token: write + environment: pypi + steps: + - uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8 + with: + name: artifact + path: dist + - name: Publish package on TestPyPi + uses: pypa/gh-action-pypi-publish@f7600683efdcb7656dec5b29656edb7bc586e597 # v1.10.3 + with: + repository-url: https://test.pypi.org/legacy/ + user: __token__ + password: ${{ secrets.PYPI_PASSWORD }} + - name: Publish package on PyPi + uses: pypa/gh-action-pypi-publish@f7600683efdcb7656dec5b29656edb7bc586e597 # v1.10.3 + with: + user: __token__ + password: ${{ secrets.PYPI_PASSWORD }} diff --git a/.github/workflows/ci-pre-commit.yml b/.github/workflows/ci-pre-commit.yml deleted file mode 100644 index 43bfa42c..00000000 --- a/.github/workflows/ci-pre-commit.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: pre-commit - -on: [push, pull_request] - -jobs: - build: - name: "Linux - pre-commit checks - Python 3.10" - timeout-minutes: 30 - runs-on: ubuntu-latest - env: - PRE_COMMIT_USE_MICROMAMBA: 1 - steps: - - name: Checkout branch - uses: actions/checkout@v4 - - name: Set up micromamba - uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 - - name: Add micromamba to GITHUB_PATH - run: echo "${HOME}/micromamba-bin" >> "$GITHUB_PATH" - - name: Install Python 3.10 - uses: actions/setup-python@v5 - with: - python-version: "3.10" - - name: Run pre-commit checks - uses: pre-commit/action@v3.0.1 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c0c27f52..cc691eaa 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -6,6 +6,7 @@ on: branches: - "main" - "pre-commit-autoupdate" + - "update-pixi" tags: - "*" schedule: @@ -17,167 +18,56 @@ on: - cron: "0 0 * * *" jobs: - build: + pre-commit: + timeout-minutes: 30 + runs-on: ubuntu-latest + steps: + - name: Checkout branch + uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0 + - name: Set up pixi + uses: prefix-dev/setup-pixi@ba3bb36eb2066252b2363392b7739741bb777659 # v0.8.1 + with: + environments: default lint + - name: pre-commit + run: pixi run pre-commit-run --color=always --show-diff-on-failure + + tests: strategy: fail-fast: false matrix: - numfocus_nightly: [false] - os: ["ubuntu-latest"] - pandas: [""] - pyarrow: ["4.0.1", "nightly"] - python: ["3.10"] - include: - - numfocus_nightly: true - os: "ubuntu-latest" - pandas: "" - pyarrow: "nightly" - python: "3.10" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "1.5.3" - pyarrow: "13.0.0" - python: "3.11" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "7.0.0" - python: "3.10" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "8.0.1" - python: "3.10" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "9.0.0" - python: "3.10" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "10.0.1" - python: "3.11" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "11.0.0" - python: "3.11" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "12.0.0" - python: "3.11" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "13.0.0" - python: "3.11" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "13.0.0" - python: "3.12" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "14.0.1" - python: "3.12" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "15.0.0" - python: "3.12" - - numfocus_nightly: false - os: "ubuntu-latest" - pandas: "" - pyarrow: "18.1.0" - python: "3.12" - continue-on-error: ${{ matrix.numfocus_nightly || matrix.pyarrow == 'nightly' }} - - runs-on: ${{ matrix.os }} - - defaults: - run: - # see https://github.com/conda-incubator/setup-miniconda/#important - shell: bash -l {0} + environment: + [ + "py310-pyarrow15-0-2", + "py310-pyarrow16-1", + "py310-pyarrow17-0", + "py310-pyarrow18-1", + "py311-pyarrow15-0-2", + "py311-pyarrow16-1", + "py311-pyarrow17-0", + "py311-pyarrow18-1", + "py312-pyarrow15-0-2", + "py312-pyarrow16-1", + "py312-pyarrow17-0", + "py312-pyarrow18-1", + ] - env: - IS_MASTER_BUILD: ${{ !matrix.numfocus_nightly && matrix.os == 'ubuntu-latest' && matrix.pyarrow == '4.0.1' && matrix.python == '3.8' }} - IS_TAG: ${{ github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')}} + runs-on: "ubuntu-latest" steps: - # CI setup - - name: Is Master Build? - run: echo $IS_MASTER_BUILD - - name: Checkout - uses: actions/checkout@v4 - - name: Set up Conda env - uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 + - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0 + - name: Set up pixi + uses: prefix-dev/setup-pixi@ba3bb36eb2066252b2363392b7739741bb777659 # v0.8.1 with: - environment-file: environment.yml - cache-environment: true - create-args: >- - python=${{ matrix.python }} - - name: Install Pyarrow (non-nightly) - run: micromamba install -y pyarrow==${{ matrix.pyarrow }} - if: matrix.pyarrow != 'nightly' && matrix.pandas == '' - - name: Install Pyarrow (nightly) - # Install both arrow-cpp and pyarrow to make sure that we have the - # latest nightly of both packages. It is sadly not guaranteed that the - # nightlies and the latest release would otherwise work together. - run: micromamba update -c arrow-nightlies -c conda-forge arrow-cpp pyarrow - if: matrix.pyarrow == 'nightly' - - name: Install Pyarrow (downgrade pandas) - run: micromamba install -y --no-py-pin pyarrow==${{ matrix.pyarrow }} pandas==${{ matrix.pandas }} - if: matrix.pyarrow != 'nightly' && matrix.pandas != '' - - name: Pip Install NumFOCUS nightly - # NumFOCUS nightly wheels, contains numpy and pandas - # TODO(gh-45): Re-add numpy - run: python -m pip install --pre --upgrade --timeout=60 --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/ pandas - if: matrix.numfocus_nightly + environments: ${{ matrix.environment }} # References the environments defined in pixi.toml - name: Install repository - run: python -m pip install --no-build-isolation --no-deps --disable-pip-version-check -e . - - name: Test import - run: | - python -c "import plateau" - python -c "import plateau.api" - python -c "import plateau.api.dataset" - python -c "import plateau.api.serialization" - python -c "import plateau.core" - python -c "import plateau.io" - python -c "import plateau.io_components" - python -c "import plateau.serialization" - python -c "import plateau.utils" + run: pixi run postinstall - # Tests - name: Pytest - # FIXME: Add `-n auto` again to allow for parallelism here. - run: pytest --cov --cov-report xml - - - name: Running benchmarks - run: | - asv --config ./asv_bench/asv.conf.json machine --machine github --os unknown --arch unknown --cpu unknown --ram unknown - asv --config ./asv_bench/asv.conf.json run -E existing:same | sed "/failed$/ s/^/##[error]/" | tee benchmarks.log - if grep "failed" benchmarks.log > /dev/null ; then - exit 1 - fi - if: env.IS_MASTER_BUILD == 'true' - - # Builds - - name: Build Wheel and sdist - run: python -m build --no-isolation + run: pixi run test-coverage -n auto - name: Codecov uses: codecov/codecov-action@v5.1.1 with: file: ./coverage.xml token: ${{ secrets.CODECOV_TOKEN }} - name: pytest-numfocus_nightly_${{ matrix.numfocus_nightly }}-os_${{ matrix.os }}-pyarrow_${{ matrix.pyarrow }}-python_${{ matrix.python }} - - # Release - - name: Publish to PyPI - if: env.IS_MASTER_BUILD == 'true' && env.IS_TAG == 'true' - uses: pypa/gh-action-pypi-publish@master - with: - user: __token__ - password: ${{ secrets.PYPI_PASSWORD }} + name: pytest-${{ matrix.environment }} diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index c60c371d..6bbdf4f4 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -14,13 +14,13 @@ name: "CodeQL" on: push: branches: - - "main" - - "pre-commit-autoupdate" + - "main" + - "pre-commit-autoupdate" pull_request: # The branches below must be a subset of the branches above - branches: [ "main" ] + branches: ["main"] schedule: - - cron: '38 17 * * 5' + - cron: "38 17 * * 5" jobs: analyze: @@ -34,43 +34,42 @@ jobs: strategy: fail-fast: false matrix: - language: [ 'python' ] + language: ["python"] # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ] # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support steps: - - name: Checkout repository - uses: actions/checkout@v4 + - name: Checkout repository + uses: actions/checkout@v4 - # Initializes the CodeQL tools for scanning. - - name: Initialize CodeQL - uses: github/codeql-action/init@v3 - with: - languages: ${{ matrix.language }} - # If you wish to specify custom queries, you can do so here or in a config file. - # By default, queries listed here will override any specified in a config file. - # Prefix the list here with "+" to use these queries and those in the config file. + # Initializes the CodeQL tools for scanning. + - name: Initialize CodeQL + uses: github/codeql-action/init@v3 + with: + languages: ${{ matrix.language }} + # If you wish to specify custom queries, you can do so here or in a config file. + # By default, queries listed here will override any specified in a config file. + # Prefix the list here with "+" to use these queries and those in the config file. - # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs - # queries: security-extended,security-and-quality + # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs + # queries: security-extended,security-and-quality + # Autobuild attempts to build any compiled languages (C/C++, C#, Go, or Java). + # If this step fails, then you should remove it and run the build manually (see below) + - name: Autobuild + uses: github/codeql-action/autobuild@v3 - # Autobuild attempts to build any compiled languages (C/C++, C#, Go, or Java). - # If this step fails, then you should remove it and run the build manually (see below) - - name: Autobuild - uses: github/codeql-action/autobuild@v3 + # ℹī¸ Command-line programs to run using the OS shell. + # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun - # ℹī¸ Command-line programs to run using the OS shell. - # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun + # If the Autobuild fails above, remove it and uncomment the following three lines. + # modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance. - # If the Autobuild fails above, remove it and uncomment the following three lines. - # modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance. + # - run: | + # echo "Run, Build Application using script" + # ./location_of_script_within_repo/buildscript.sh - # - run: | - # echo "Run, Build Application using script" - # ./location_of_script_within_repo/buildscript.sh - - - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v3 - with: - category: "/language:${{matrix.language}}" + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v3 + with: + category: "/language:${{matrix.language}}" diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml deleted file mode 100644 index 76d2b0cb..00000000 --- a/.github/workflows/docs.yml +++ /dev/null @@ -1,37 +0,0 @@ -name: Documentation CI - -on: - pull_request: - push: - branches: - - "main" - - "pre-commit-autoupdate" - tags: - - "*" - -jobs: - build: - runs-on: ubuntu-latest - steps: - - name: Checkout source - uses: actions/checkout@v4 - - - name: Setup Conda Environment - uses: conda-incubator/setup-miniconda@v3 - with: - miniforge-variant: Miniforge3 - miniforge-version: 24.9.2-0 - use-mamba: true - environment-file: docs/environment-docs.yml - activate-environment: plateau-docs - python-version: 3.12 - - - name: List conda - shell: bash -l {0} - run: conda list - - - name: Build docs - shell: bash -l {0} - run: | - python -m pip install --no-build-isolation --no-deps -e . - sphinx-build -b html docs docs/_build diff --git a/.github/workflows/nighlies.yml b/.github/workflows/nighlies.yml new file mode 100644 index 00000000..3893c8fb --- /dev/null +++ b/.github/workflows/nighlies.yml @@ -0,0 +1,51 @@ +name: Nightlies +on: + schedule: + - cron: "0 5 * * *" + workflow_dispatch: + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +permissions: + id-token: write + contents: read + issues: write + +jobs: + nightlies: + name: Nightlies + timeout-minutes: 30 + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + environment: [ + # nightlies (e.g. pyarrow) will be installed in the following steps + "py310-pyarrow18-1", + "py311-pyarrow18-1", + "py312-pyarrow18-1", + ] + + steps: + - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0 + - name: Set up pixi + uses: prefix-dev/setup-pixi@ba3bb36eb2066252b2363392b7739741bb777659 # v0.8.1 + with: + environments: ${{ matrix.environment }} + + - name: Install Pyarrow nightly + # The nightlies channel for conda is currently empty: https://github.com/apache/arrow/issues/41856 + # We therefore rely on the pip nightlies: https://github.com/data-engineering-collective/plateau/pull/184#discussion_r1888429974 + run: pixi run pip install --extra-index-url https://pypi.fury.io/arrow-nightlies/ --prefer-binary --pre pyarrow + - name: Pip Install NumFOCUS nightly + # NumFOCUS nightly wheels, contains numpy and pandas + # TODO(gh-45): Re-add numpy + run: pixi run python -m pip install --pre --upgrade --timeout=60 --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/ pandas + + - name: Install repository + run: pixi run postinstall + + - name: Pytest + run: pixi run test-coverage -n auto diff --git a/.github/workflows/pre-commit-autoupdate.yml b/.github/workflows/pre-commit-autoupdate.yml index 0db0ef20..57807baf 100644 --- a/.github/workflows/pre-commit-autoupdate.yml +++ b/.github/workflows/pre-commit-autoupdate.yml @@ -1,13 +1,12 @@ name: pre-commit autoupdate on: - workflow_dispatch: - schedule: - - cron: "0 6 4 * *" + workflow_dispatch: + schedule: + - cron: "0 6 4 * *" defaults: run: - shell: - bash -el {0} + shell: bash -el {0} jobs: check_update: @@ -19,22 +18,15 @@ jobs: # We need to checkout with SSH here to have actions run on the PR. with: ssh-key: ${{ secrets.SSH_PRIVATE_KEY }} - - name: Set up Conda env - uses: mamba-org/setup-micromamba@068f1ab4b37ed9b3d9f73da7db90a0cda0a48d29 + - name: Set up pixi + uses: prefix-dev/setup-pixi@ba3bb36eb2066252b2363392b7739741bb777659 # v0.8.1 with: - environment-name: pre-commit - create-args: >- - -c - conda-forge - pre-commit - mamba + environments: default lint - name: Update pre-commit hooks and run id: versions - env: - PRE_COMMIT_USE_MAMBA: 1 run: | - pre-commit autoupdate - pre-commit run -a || true + pixi run pre-commit-update + pixi run pre-commit-run --color=always --show-diff-on-failure || true - uses: peter-evans/create-pull-request@5e914681df9dc83aa4e4905692ca88beb2f9e91f with: commit-message: "Auto-update pre-commit hooks" @@ -44,4 +36,3 @@ jobs: This PR updates them to the latest and already ran `pre-commit run -a` for you to fix any changes in formatting. branch: pre-commit-autoupdate delete-branch: true - sign-commits: true diff --git a/.github/workflows/update-lockfiles.yml b/.github/workflows/update-lockfiles.yml new file mode 100644 index 00000000..a2d04c56 --- /dev/null +++ b/.github/workflows/update-lockfiles.yml @@ -0,0 +1,34 @@ +name: Update lockfiles +permissions: + contents: write + pull-requests: write + +on: + workflow_dispatch: + schedule: + - cron: 0 5 1 * * + +jobs: + pixi-update: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0 + - name: Set up pixi + uses: prefix-dev/setup-pixi@ba3bb36eb2066252b2363392b7739741bb777659 # v0.8.1 + with: + run-install: false + - name: Update lockfiles + run: | + pixi update --json --no-install | pixi exec pixi-diff-to-markdown >> diff.md + - name: Create pull request + uses: peter-evans/create-pull-request@5e914681df9dc83aa4e4905692ca88beb2f9e91f # v7.0.5 + with: + token: ${{ secrets.GITHUB_TOKEN }} + commit-message: Update pixi lockfile + title: Update pixi lockfile + body-path: diff.md + branch: update-pixi + base: main + labels: pixi + delete-branch: true + add-paths: pixi.lock diff --git a/.gitignore b/.gitignore index 95d9aafc..84ecb12d 100644 --- a/.gitignore +++ b/.gitignore @@ -29,3 +29,5 @@ _test_worker-* build/ dist/ venv/ + +.pixi diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index bfa51733..7700dcae 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,41 +1,71 @@ +exclude: ^(\.copier-answers\.yml)|.pixi$ repos: - # Run ruff first because autofix behaviour is enabled - - repo: https://github.com/Quantco/pre-commit-mirrors-ruff - rev: "0.8.0" + - repo: local hooks: - - id: ruff-conda - - id: ruff-format-conda - - repo: https://github.com/Quantco/pre-commit-mirrors-mypy - rev: "1.13.0" - hooks: - - id: mypy-conda - files: plateau - additional_dependencies: - - -c - - conda-forge - - types-setuptools - - types-decorator - - types-simplejson - - hypothesis - - numpy=2.1.3 - - minimalkv=1.4.2 - - repo: https://github.com/Quantco/pre-commit-mirrors-pyupgrade - rev: 3.19.0 - hooks: - - id: pyupgrade-conda - args: - - --py310-plus - - repo: https://github.com/Quantco/pre-commit-mirrors-prettier - rev: 3.4.1 - hooks: - - id: prettier-conda - files: "\\.md$" - - repo: https://github.com/Quantco/pre-commit-mirrors-docformatter - rev: 1.7.5 - hooks: - - id: docformatter-conda - - repo: https://github.com/Quantco/pre-commit-mirrors-pre-commit-hooks - rev: 5.0.0 - hooks: - - id: trailing-whitespace-conda - - id: end-of-file-fixer-conda + # ensure pixi environments are up to date + # workaround for https://github.com/prefix-dev/pixi/issues/1482 + - id: pixi-install + name: pixi-install + entry: pixi install -e default -e lint + language: system + always_run: true + require_serial: true + pass_filenames: false + # ruff + - id: ruff + name: ruff + entry: pixi run -e lint ruff check --fix --exit-non-zero-on-fix --force-exclude + language: system + types_or: [python, pyi] + require_serial: true + - id: ruff-format + name: ruff-format + entry: pixi run -e lint ruff format --force-exclude + language: system + types_or: [python, pyi] + require_serial: true + # mypy + # Address this in a separate PR: https://github.com/data-engineering-collective/plateau/issues/181 + # - id: mypy + # name: mypy + # entry: pixi run -e default mypy + # language: system + # types: [python] + # require_serial: true + # prettier + - id: prettier + name: prettier + entry: pixi run -e lint prettier --write --list-different --ignore-unknown + language: system + types: [text] + files: \.(md|yml|yaml)$ + # taplo + - id: taplo + name: taplo + entry: pixi run -e lint taplo format + language: system + types: [toml] + # pre-commit-hooks + - id: trailing-whitespace-fixer + name: trailing-whitespace-fixer + entry: pixi run -e lint trailing-whitespace-fixer + language: system + types: [text] + - id: end-of-file-fixer + name: end-of-file-fixer + entry: pixi run -e lint end-of-file-fixer + language: system + types: [text] + - id: check-merge-conflict + name: check-merge-conflict + entry: pixi run -e lint check-merge-conflict --assume-in-merge + language: system + exclude_types: + - rst + # typos + - id: typos + name: typos + entry: pixi run -e lint typos --force-exclude + language: system + types: [text] + require_serial: true diff --git a/.prettierrc b/.prettierrc new file mode 100644 index 00000000..478cc536 --- /dev/null +++ b/.prettierrc @@ -0,0 +1,7 @@ +{ + "singleQuote": false, + "bracketSpacing": true, + "printWidth": 200, + "endOfLine": "auto", + "tabWidth": 2 +} diff --git a/.readthedocs.yml b/.readthedocs.yml index 549d5e19..70c56087 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,20 +1,12 @@ -# .readthedocs.yml -# Read the Docs configuration file -# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details - -# Required version: 2 - build: - os: "ubuntu-20.04" + os: ubuntu-20.04 tools: - python: "mambaforge-4.10" - -# Optionally set the version of Python and requirements required to build your docs -conda: - environment: docs/environment-docs.yml - -python: - install: - - method: pip - path: . + python: mambaforge-latest + commands: + - mamba install -c conda-forge -c nodefaults pixi + - pixi run -e docs postinstall + - pixi run -e docs docs + - pixi run -e docs readthedocs +formats: + - pdf diff --git a/CHANGES.rst b/CHANGES.rst index 74cc489b..1b024097 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -2,6 +2,12 @@ Changelog ========= +Plateau 4.4.1 (2024-12-17) +========================== + +* Port project to use the OSS QuantCo copier template (`copier template https://github.com/Quantco/copier-template-python-open-source`_) and (`pixi https://pixi.sh`_) as environment manager. + + Plateau 4.4.0 (2024-05-23) ========================== @@ -162,7 +168,7 @@ Version 3.19.1 (2021-02-24) Version 3.19.0 (2021-02-12) =========================== -* Fix an issue where updates on cubes or updates on datatsets using +* Fix an issue where updates on cubes or updates on datasets using dask.dataframe might not update all secondary indices, resulting in a corrupt state after the update * Expose compression type and row group chunk size in Cube interface via optional @@ -528,7 +534,7 @@ Version 3.3.0 (2019-08-15) Version 3.2.0 (2019-07-25) ========================== -- Fix gh:66 where predicate pushdown may evalute false results if evaluated +- Fix gh:66 where predicate pushdown may evaluate false results if evaluated using improper types. The behavior now is to raise in these situations. - Predicate pushdown and ``kartothek.serialization.filter_array_like`` will now properly handle pandas Categoricals. - Add ``kartothek.io.dask.bag.read_dataset_as_dataframe_bag`` diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 505034aa..18bf9ee5 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -12,13 +12,12 @@ If you've found a bug, please report it to the issue tracker and #### Installation using pip -To get started, set up a new virtual environment and install all requirements +To get started, set up a a new environment using [pixi](https://pixi.sh) and install all requirements: ```bash -virtualenv plateau-dev --python=python3.9 -source plateau-dev/bin/activate -pip install -e . -pip install -r test-requirements.txt +pixi run pre-commit-install +pixi run postinstall +pixi run test ``` #### Running tests @@ -29,37 +28,36 @@ We're using [pytest](https://pytest.org) as a testing framework and make heavy u To run the tests simply run ```bash -pytest +pixi run test ``` #### Running benchmarks -For performance critical code paths we have [asv](https://pre-commit.com) benchmarks in place in -the subfolder `asv_bench`. +For performance critical code paths we have [asv](https://asv.readthedocs.io/en/latest/) benchmarks in place in the subfolder `asv_bench`. To run the benchmarks a single time and receive immediate feedback run ```bash -asv run --python=same --show-stderr +pixi run -e benchmark postinstall +pixi run -e benchmark asv run --python=same --show-stderr --config ./asv_bench/asv.conf.json ``` #### Building documentation ```bash -python setup.py docs +pixi run -e docs postinstall +pixi run docs ``` #### Code style -To ensure a consistent code style across the code base we're using `black`, `flake8`, -and `isort` for formatting and linting. +To ensure a consistent code style across the code base we're using `prettier` and `ruff` for formatting and linting. -We have pre-commit hooks for all of these tools which take care of formatting -and checking the code. To set up these hooks, please follow the installation -instructions on the [pre-commit](https://pre-commit.com) homepage. +We have [pre-commit](https://pre-commit.com) hooks for all of these tools which take care of formatting +and checking the code. If you prefer to perform manual formatting and linting, you can run the necessary toolchain like this ```bash -pre-commit run -a +pixi run pre-commit-run ``` diff --git a/README.md b/README.md index 0640176f..8cb22c0e 100644 --- a/README.md +++ b/README.md @@ -3,10 +3,12 @@ _flat files, flat land_ [![Build Status](https://github.com/data-engineering-collective/plateau/workflows/CI/badge.svg)](https://github.com/data-engineering-collective/plateau/actions?query=branch%3Amain) +[![conda-forge](https://img.shields.io/conda/vn/conda-forge/minimalkv?logoColor=white&logo=conda-forge)](https://prefix.dev/channels/conda-forge/packages/minimalkv) +[![pypi-version](https://img.shields.io/pypi/v/minimalkv.svg?logo=pypi&logoColor=white)](https://pypi.org/project/minimalkv) +[![python-version](https://img.shields.io/pypi/pyversions/minimalkv?logoColor=white&logo=python)](https://pypi.org/project/minimalkv) [![Documentation Status](https://readthedocs.org/projects/plateau/badge/?version=stable)](https://plateau.readthedocs.io/en/stable/?badge=stable) [![codecov.io](https://codecov.io/github/data-engineering-collective/plateau/coverage.svg?branch=master)](https://codecov.io/github/data-engineering-collective/plateau) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/data-engineering-collective/plateau/blob/master/LICENSE.txt) -[![Anaconda-Server Badge](https://anaconda.org/conda-forge/plateau/badges/installer/conda.svg)](https://conda.anaconda.org/conda-forge) [![Anaconda-Server Badge](https://anaconda.org/conda-forge/plateau/badges/downloads.svg)](https://anaconda.org/conda-forge/plateau) `plateau` is a Python library to manage (create, read, update, delete) large @@ -30,17 +32,25 @@ and selects subsets of data transparently. ## Installation -Installers for the latest released version are availabe at the [Python -package index](https://pypi.org/project/plateau) and on conda-forge. +This project is managed by [pixi](https://pixi.sh). +You can install the package in development mode using: -```sh -# Install with pip -pip install plateau +```bash +git clone https://github.com/data-engineering-collective/plateau +cd plateau + +pixi run pre-commit-install +pixi run postinstall +pixi run test ``` -```sh -# Install with conda/micromamba, optionally add conda-forge as a source -# conda config --add channels conda-forge -conda install plateau -micromamba install plateau +Plateau is also [available on PyPI](http://pypi.python.org/pypi/plateau/) and +can be installed through `pip`: + +```bash +pip install plateau ``` + +## Contributing + +Find details on how to contribute [here](CONTRIBUTING.md). diff --git a/asv_bench/asv.conf.json b/asv_bench/asv.conf.json index 33a8eeac..536c807e 100644 --- a/asv_bench/asv.conf.json +++ b/asv_bench/asv.conf.json @@ -7,5 +7,5 @@ "environment_type": "virtualenv", "env_dir": ".asv/env", "results_dir": ".asv/results", - "html_dir": ".asv/html", + "html_dir": ".asv/html" } diff --git a/asv_bench/benchmarks/config.py b/asv_bench/benchmarks/config.py index 3ce4431c..da9267b4 100644 --- a/asv_bench/benchmarks/config.py +++ b/asv_bench/benchmarks/config.py @@ -4,5 +4,5 @@ class AsvBenchmarkConfig: """A mixin class to define default configurations for our benchmarks.""" - # Use a timer which meassured Wall time (asv default meassures CPU time) + # Use a timer which measured Wall time (asv default measures CPU time) timer = timeit.default_timer diff --git a/asv_bench/benchmarks/write.py b/asv_bench/benchmarks/write.py index 6b8a6c76..c9b6021f 100644 --- a/asv_bench/benchmarks/write.py +++ b/asv_bench/benchmarks/write.py @@ -22,34 +22,34 @@ def generate_mp(): ) -def _partition_metadata(depth, num_leafs): +def _partition_metadata(depth, num_leaves): if depth == 0: return "the_end" - part_meta = _partition_metadata(depth - 1, num_leafs) - return {str(k): part_meta for k in range(num_leafs)} + part_meta = _partition_metadata(depth - 1, num_leaves) + return {str(k): part_meta for k in range(num_leaves)} -def generate_metadata(max_depth=7, num_leafs=5): +def generate_metadata(max_depth=7, num_leaves=5): """Generate a metadata dictionary which holds many `partition_metadata` keys.""" return { "creation_time": "2018-05-05 12:00:00", - "partition_metadata": _partition_metadata(max_depth, num_leafs), + "partition_metadata": _partition_metadata(max_depth, num_leaves), } class TimeStoreDataset(AsvBenchmarkConfig): timeout = 120 params = ([10, 10**2, 10**3], [4], [2, 4]) - param_names = ["num_partitions", "max_depth", "num_leafs"] + param_names = ["num_partitions", "max_depth", "num_leaves"] - def setup(self, num_partitions, max_depth, num_leafs): + def setup(self, num_partitions, max_depth, num_leaves): self.store = get_store_from_url(f"hfs://{tempfile.mkdtemp()}") self.partitions = [generate_mp() for _ in range(num_partitions)] self.dataset_uuid = "dataset_uuid" self.user_dataset_metadata = {} - def time_store_dataset_from_partitions(self, num_partitions, max_depth, num_leafs): + def time_store_dataset_from_partitions(self, num_partitions, max_depth, num_leaves): store_dataset_from_partitions( partition_list=self.partitions, store=self.store, diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..c99e013a --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,89 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = -n +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/minimalkv.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/minimalkv.qhc" + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \ + "run these through (pdf)latex." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff --git a/docs/conf.py b/docs/conf.py index 1bb95910..a0d3ee93 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -113,7 +113,7 @@ # In particular type annotations are rendered as its full path to the class but # the sphinx docs usually expose the high level API path. This renames the -# sphinx targets appropriately. The replacments are all applied, therefore mind +# sphinx targets appropriately. The replacements are all applied, therefore mind # overlapping replacements. reftarget_replace = { "pyarrow.lib.": "pyarrow.", diff --git a/docs/guide/mutating_datasets.rst b/docs/guide/mutating_datasets.rst index c14ceb0b..ffd5ba77 100644 --- a/docs/guide/mutating_datasets.rst +++ b/docs/guide/mutating_datasets.rst @@ -55,7 +55,7 @@ some data there with plateau. Appending Data -------------- -Now, we create ``another_df`` with the same schema as our intial dataframe +Now, we create ``another_df`` with the same schema as our initial dataframe ``df`` and update it using the ``eager`` backend by calling :func:`~plateau.io.eager.update_dataset_from_dataframes`: .. ipython:: python @@ -220,7 +220,7 @@ Garbage collection ------------------ When plateau is executing an operation, it makes sure to not -commit changes to the dataset until the operation has been succesfully completed. If a +commit changes to the dataset until the operation has been successfully completed. If a write operation does not succeed for any reason, although there may be new files written to storage, those files will not be used by the dataset as they will not be referenced in the plateau metadata. Thus, when the user reads the dataset, no new data will diff --git a/docs/guide/partitioning.rst b/docs/guide/partitioning.rst index c44a67c3..4f47cf42 100644 --- a/docs/guide/partitioning.rst +++ b/docs/guide/partitioning.rst @@ -68,7 +68,7 @@ column all get written to the same partition. To do this, we use the store_url, "partitioned_dataset", [df], partition_on="B" ) -Partitioning based on a date column ussually makes sense for timeseries data. +Partitioning based on a date column usually makes sense for timeseries data. Of interest here is ``dm.partitions``: @@ -195,7 +195,7 @@ If you need more control over the size of files and the distribution within the Bucketing uses the values of the requested columns and assigns every unique tuple to one of `num_buckets` files. This not only helps to control output file -sizes but also allows for very efficient querying in combination with seconday +sizes but also allows for very efficient querying in combination with secondary indices, see also :ref:`efficient_querying`. In the below example you can see the same data being used as above but this time we will bucket by column `B` which will no longer create a single file per value in `B` but rather `num_buckets` files. diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 00000000..e287eba2 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,113 @@ +@ECHO OFF + +REM Command file for Sphinx documentation + +set SPHINXBUILD=sphinx-build +set BUILDDIR=_build +set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . +if NOT "%PAPER%" == "" ( + set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% +) + +if "%1" == "" goto help + +if "%1" == "help" ( + :help + echo.Please use `make ^` where ^ is one of + echo. html to make standalone HTML files + echo. dirhtml to make HTML files named index.html in directories + echo. pickle to make pickle files + echo. json to make JSON files + echo. htmlhelp to make HTML files and a HTML help project + echo. qthelp to make HTML files and a qthelp project + echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + echo. changes to make an overview over all changed/added/deprecated items + echo. linkcheck to check all external links for integrity + echo. doctest to run all doctests embedded in the documentation if enabled + goto end +) + +if "%1" == "clean" ( + for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i + del /q /s %BUILDDIR%\* + goto end +) + +if "%1" == "html" ( + %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/html. + goto end +) + +if "%1" == "dirhtml" ( + %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. + goto end +) + +if "%1" == "pickle" ( + %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle + echo. + echo.Build finished; now you can process the pickle files. + goto end +) + +if "%1" == "json" ( + %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json + echo. + echo.Build finished; now you can process the JSON files. + goto end +) + +if "%1" == "htmlhelp" ( + %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp + echo. + echo.Build finished; now you can run HTML Help Workshop with the ^ +.hhp project file in %BUILDDIR%/htmlhelp. + goto end +) + +if "%1" == "qthelp" ( + %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp + echo. + echo.Build finished; now you can run "qcollectiongenerator" with the ^ +.qhcp project file in %BUILDDIR%/qthelp, like this: + echo.^> qcollectiongenerator %BUILDDIR%\qthelp\minimalkv.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\minimalkv.ghc + goto end +) + +if "%1" == "latex" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + echo. + echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "changes" ( + %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes + echo. + echo.The overview file is in %BUILDDIR%/changes. + goto end +) + +if "%1" == "linkcheck" ( + %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck + echo. + echo.Link check complete; look for any errors in the above output ^ +or in %BUILDDIR%/linkcheck/output.txt. + goto end +) + +if "%1" == "doctest" ( + %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest + echo. + echo.Testing of doctests in the sources finished, look at the ^ +results in %BUILDDIR%/doctest/output.txt. + goto end +) + +:end diff --git a/docs/spec/format_specification.rst b/docs/spec/format_specification.rst index 545e3357..efe0d3ac 100644 --- a/docs/spec/format_specification.rst +++ b/docs/spec/format_specification.rst @@ -26,7 +26,7 @@ Goals * Inverted indices for fast query planing * Read access without any locking mechanism * Portable across frameworks and languages - * Seemless integration to OSS community software + * Seamless integration to OSS community software (Apache Arrow, Apache Parquet, pandas, etc.) * Lifecycle management (garbage collection, retention, etc.) * No external service required for state tracking diff --git a/docs/spec/indexing.rst b/docs/spec/indexing.rst index 3686c8be..f3e973ec 100644 --- a/docs/spec/indexing.rst +++ b/docs/spec/indexing.rst @@ -128,7 +128,7 @@ Supported data types for indices include See also -------- -* :doc:`efficient_querying` for some general hints for faster quering +* :doc:`efficient_querying` for some general hints for faster querying * :doc:`storage_layout` * :doc:`../guide/partitioning` for some guidance on how to partition a dataset * :doc:`../guide/dask_indexing` diff --git a/docs/versioning.rst b/docs/versioning.rst index 8011846c..8f11190e 100644 --- a/docs/versioning.rst +++ b/docs/versioning.rst @@ -18,8 +18,7 @@ trigger an increase of the *major* version number. Library API ----------- -plateau exposes a dedicated module to highlight which functions, classes, etc. are considered stable API and are publicly available. We intend to apply [semantic -versioning](https://semver.org) to the best of our ability for the API exposed in :mod:`plateau.api`. See also :doc:`api`. +plateau exposes a dedicated module to highlight which functions, classes, etc. are considered stable API and are publicly available. We intend to apply `semantic versioning `_ to the best of our ability for the API exposed in :mod:`plateau.api`. See also :doc:`api`. We are aware that the API not only consists of the signatures of functions and types of objects exposed by a library but as well by its behaviour. Many changes diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 2b11d09c..00000000 --- a/environment.yml +++ /dev/null @@ -1,43 +0,0 @@ -name: plateau -channels: - - conda-forge - - nodefaults -dependencies: - - python>=3.10 - - pip - - dask>=2022.5.1 # First version with dask.dataframe.from_map. - - decorator - - msgpack-python>=0.5.2 - # Currently dask and numpy==1.16.0 clash - # TODO: add support for numpy>=1.23 - - numpy!=1.15.0,!=1.16.0,<2 - - pandas>=0.23.0,!=1.0.0 - - pyarrow>=4 - - simplejson - - minimalkv>=1.4.2 - - toolz - - urlquote>=1.1.3 - - zstandard - - attrs - - click - - prompt-toolkit - - pyyaml - # Test Code Dependencies - - distributed>=2022.5.1 - - pytz - - cloudpickle - - freezegun - # Test Framework - - hypothesis - - pytest>=4.5.0 - - pytest-cov - - pytest-mock - - setuptools_scm>=8.1 - # GitHub CI - - pandoc - # CLI - - ipython - # ASV // Benchmark - - asv - # Packaging infrastructure - - python-build diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 00000000..cab8e158 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,39558 @@ +version: 5 +environments: + benchmark: + channels: + - 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__osx >=11.0 + - libzlib >=1.2.13,<2.0.0a0 + license: BSD-3-Clause + license_family: BSD + size: 405089 + timestamp: 1714723101397 diff --git a/pixi.toml b/pixi.toml new file mode 100644 index 00000000..77584311 --- /dev/null +++ b/pixi.toml @@ -0,0 +1,123 @@ +[project] +name = "plateau" +channels = ["conda-forge"] +platforms = ["osx-arm64", "osx-64", "linux-64", "linux-aarch64", "win-64"] + +[tasks] +postinstall = "pip install --no-build-isolation --no-deps --disable-pip-version-check -e ." + +[dependencies] +python = ">=3.10" +dask = ">=2022.5.1" +decorator = "*" +msgpack-python = ">=0.5.2" +numpy = ">1.23,<2" +pandas = ">=2" +pyarrow = ">=15" +simplejson = "*" +minimalkv = ">=1.4.2" +toolz = "*" +urlquote = ">=1.1.3" +zstandard = "*" +attrs = "*" +click = "*" +prompt-toolkit = "*" +pyyaml = "*" + + +[host-dependencies] +pip = "*" +setuptools = ">=61" +setuptools-scm = "*" +wheel = "*" + +[feature.test.dependencies] +pytest = ">=6" +pytest-cov = "*" +pytest-mock = "*" +pytest-xdist = ">=3.6.1,<4" +freezegun = "*" +mypy = "*" +distributed = ">=2022.5.1" +pytz = "*" +cloudpickle = "*" +hypothesis = "*" +[feature.test.tasks] +test = "pytest" +test-coverage = "pytest --cov=plateau --cov-report=xml --cov-report=term-missing" + +[feature.build.dependencies] +python-build = "*" +twine = "*" +[feature.build.tasks] +build-wheel = "python -m build --no-isolation ." +check-wheel = "twine check dist/*" + +[feature.lint.dependencies] +pre-commit = "*" +insert-license-header = "*" +docformatter = "*" +ruff = "*" +prettier = "*" +taplo = "*" +pre-commit-hooks = "*" +typos = "*" +[feature.lint.tasks] +pre-commit-install = "pre-commit install" +pre-commit-run = "pre-commit run -a" + +[feature.benchmark.dependencies] +asv = "*" +libmambapy = "*" +conda = "*" + +[feature.docs.dependencies] +sphinx = "*" +jinja2 = "<3.1" +sphinx_rtd_theme = "*" +IPython = "*" +[feature.docs.tasks] +# Run task `postinstall` before building docs in docs environment +docs = "cd docs && make html" +readthedocs = "rm -rf $READTHEDOCS_OUTPUT/html && cp -r docs/_build/html $READTHEDOCS_OUTPUT/html" + + +[feature.py310.dependencies] +python = "3.10.*" +[feature.py311.dependencies] +python = "3.11.*" +[feature.py312.dependencies] +python = "3.12.*" + +# We only support the four most recent versions of pyarrow +[feature.pyarrow15_0_2.dependencies] +pyarrow = "=15.0.2" +[feature.pyarrow16_1.dependencies] +pyarrow = "=16.1.0" +[feature.pyarrow17_0.dependencies] +pyarrow = "=17.0.0" +[feature.pyarrow18_1.dependencies] +pyarrow = "=18.1.0" + +[environments] +default = ["test"] + +py310-pyarrow15-0-2 = ["py310", "pyarrow15_0_2", "test"] +py310-pyarrow16-1 = ["py310", "pyarrow16_1", "test"] +py310-pyarrow17-0 = ["py310", "pyarrow17_0", "test"] +py310-pyarrow18-1 = ["py310", "pyarrow18_1", "test"] + +py311-pyarrow15-0-2 = ["py311", "pyarrow15_0_2", "test"] +py311-pyarrow16-1 = ["py311", "pyarrow16_1", "test"] +py311-pyarrow17-0 = ["py311", "pyarrow17_0", "test"] +py311-pyarrow18-1 = ["py311", "pyarrow18_1", "test"] + +py312-pyarrow15-0-2 = ["py312", "pyarrow15_0_2", "test"] +py312-pyarrow16-1 = ["py312", "pyarrow16_1", "test"] +py312-pyarrow17-0 = ["py312", "pyarrow17_0", "test"] +py312-pyarrow18-1 = ["py312", "pyarrow18_1", "test"] + +build = ["build"] +benchmark = ["benchmark", "test"] +docs = ["docs", "test"] +lint = { features = ["lint"], no-default-feature = true } diff --git a/plateau/core/_deprecation.py b/plateau/core/_deprecation.py index fd138745..ea9f0db9 100644 --- a/plateau/core/_deprecation.py +++ b/plateau/core/_deprecation.py @@ -105,10 +105,10 @@ def wrapper(*args, **kwargs): if new_arg_name is None and old_arg_value is not None: msg = ( - "the '{old_name}' keyword is deprecated and will be " + f"the '{old_arg_name}' keyword is deprecated and will be " "removed in a future version. " - "Please take steps to stop the use of '{old_name}'" - ).format(old_name=old_arg_name) + f"Please take steps to stop the use of '{old_arg_name}'" + ) warnings.warn(msg, FutureWarning, stacklevel=stacklevel) kwargs[old_arg_name] = old_arg_value return func(*args, **kwargs) @@ -120,26 +120,22 @@ def wrapper(*args, **kwargs): else: new_arg_value = mapping(old_arg_value) msg = ( - "the {old_name}={old_val!r} keyword is deprecated, " - "use {new_name}={new_val!r} instead" - ).format( - old_name=old_arg_name, - old_val=old_arg_value, - new_name=new_arg_name, - new_val=new_arg_value, + f"the {old_arg_name}={old_arg_value!r} keyword is deprecated, " + f"use {new_arg_name}={new_arg_value!r} instead" ) else: new_arg_value = old_arg_value msg = ( - "the '{old_name}' keyword is deprecated, " - "use '{new_name}' instead" - ).format(old_name=old_arg_name, new_name=new_arg_name) + f"the '{old_arg_name}' keyword is deprecated, " + f"use '{new_arg_name}' instead" + ) warnings.warn(msg, FutureWarning, stacklevel=stacklevel) if kwargs.get(new_arg_name, None) is not None: msg = ( - "Can only specify '{old_name}' or '{new_name}', " "not both" - ).format(old_name=old_arg_name, new_name=new_arg_name) + f"Can only specify '{old_arg_name}' or '{new_arg_name}', " + "not both" + ) raise TypeError(msg) else: kwargs[new_arg_name] = new_arg_value diff --git a/plateau/core/common_metadata.py b/plateau/core/common_metadata.py index 07d7cc21..c03ea40e 100644 --- a/plateau/core/common_metadata.py +++ b/plateau/core/common_metadata.py @@ -11,7 +11,6 @@ import pyarrow.parquet as pq import simplejson from minimalkv import KeyValueStore -from packaging import version from plateau.core import naming from plateau.core._compat import load_json @@ -31,8 +30,6 @@ "normalize_column_order", ) -PYARROW_LT_13 = version.parse(pa.__version__) < version.parse("13") - class SchemaWrapper: """Wrapper object for pyarrow.Schema to handle forwards and backwards @@ -67,7 +64,7 @@ def _schema_compat(self): pandas_metadata = schema.pandas_metadata index_cols = pandas_metadata["index_columns"] if len(index_cols) > 1: - raise NotImplementedError("Treatement of MultiIndex not implemented.") + raise NotImplementedError("Treatment of MultiIndex not implemented.") for _, col in enumerate(index_cols): # Range index is now serialized using start/end information. This special treatment @@ -531,8 +528,8 @@ def _strip_columns_from_schema(schema, field_names): # This is most likely an indicator for incompatible schemas and we refuse to strip the schema # to not obfurscate the validation result _logger.warning( - "Unexpected field `%s` encountered while trying to strip `null` columns.\n" - "Schema was:\n\n`%s`" % (name, schema) + f"Unexpected field `{name}` encountered while trying to strip `null` columns.\n" + f"Schema was:\n\n`{schema}`" ) return schema return stripped_schema @@ -635,21 +632,16 @@ def _fmt_origin(origin): if reference_to_compare != current_to_compare: schema_diff = _diff_schemas(reference, current) - exception_message = """Schema violation + exception_message = f"""Schema violation -Origin schema: {origin_schema} -Origin reference: {origin_reference} +Origin schema: {_fmt_origin(current.origin)} +Origin reference: {_fmt_origin(reference.origin)} Diff: {schema_diff} Reference schema: -{reference}""".format( - schema_diff=schema_diff, - reference=str(reference), - origin_schema=_fmt_origin(current.origin), - origin_reference=_fmt_origin(reference.origin), - ) +{str(reference)}""" raise ValueError(exception_message) # add all origins to result AFTER error checking, otherwise the error message would be pretty misleading due to the @@ -729,9 +721,7 @@ def validate_shared_columns(schemas, ignore_pandas=False): continue if ref != obj: raise ValueError( - 'Found incompatible entries for column "{}"\n{}\n{}'.format( - col, ref, obj - ) + f'Found incompatible entries for column "{col}"\n{ref}\n{obj}' ) else: seen[col] = obj @@ -767,11 +757,7 @@ def empty_dataframe_from_schema( # HACK: Cast bytes to object in metadata until Pandas bug is fixed: https://github.com/pandas-dev/pandas/issues/50127 schema = schema_metadata_bytes_to_object(schema.internal()) - # Prior to pyarrow 13.0.0 coerce_temporal_nanoseconds didn't exist - # as it was introduced for backwards compatibility with pandas 1.x - _coerce = {} - if not PYARROW_LT_13: - _coerce["coerce_temporal_nanoseconds"] = coerce_temporal_nanoseconds + _coerce = {"coerce_temporal_nanoseconds": coerce_temporal_nanoseconds} df = schema.empty_table().to_pandas(date_as_object=date_as_object, **_coerce) df.columns = df.columns.map(ensure_string_type) diff --git a/plateau/core/dataset.py b/plateau/core/dataset.py index 7c73b3f0..5d2ddf1d 100644 --- a/plateau/core/dataset.py +++ b/plateau/core/dataset.py @@ -484,7 +484,7 @@ def _evaluate_conjunction( df_result = df_result.merge( df, left_index=True, right_index=True, copy=False ) - # Backward-compatability: Set dtype to empty if df is empty. + # Backward-compatibility: Set dtype to empty if df is empty. # With pandas 2.3, the dtype of the numpy is correctly propagated but changes our API. if len(df_result) == 0: df_result.index = df_result.index.astype("object") @@ -496,19 +496,12 @@ class DatasetMetadata(DatasetMetadataBase): def __repr__(self): return ( - "DatasetMetadata(uuid={uuid}, " - "table_name={table_name}, " - "partition_keys={partition_keys}, " - "metadata_version={metadata_version}, " - "indices={indices}, " - "explicit_partitions={explicit_partitions})" - ).format( - uuid=self.uuid, - table_name=self.table_name, - partition_keys=self.partition_keys, - metadata_version=self.metadata_version, - indices=list(self.indices.keys()), - explicit_partitions=self.explicit_partitions, + f"DatasetMetadata(uuid={self.uuid}, " + f"table_name={self.table_name}, " + f"partition_keys={self.partition_keys}, " + f"metadata_version={self.metadata_version}, " + f"indices={list(self.indices.keys())}, " + f"explicit_partitions={self.explicit_partitions})" ) @staticmethod @@ -854,7 +847,7 @@ def create_partition_key( class DatasetMetadataBuilder(CopyMixin): """Incrementally build up a dataset. - In constrast to a :class:`plateau.core.dataset.DatasetMetadata` + In contrast to a :class:`plateau.core.dataset.DatasetMetadata` instance, this object is mutable and may not be a full dataset (e.g. partitions don't need to be fully materialised). """ diff --git a/plateau/core/factory.py b/plateau/core/factory.py index 2b5b477e..af463839 100644 --- a/plateau/core/factory.py +++ b/plateau/core/factory.py @@ -67,9 +67,7 @@ def __init__( self.load_all_indices_flag = load_all_indices def __repr__(self): - return "".format( - self.dataset_uuid, self.is_loaded - ) + return f"" @property def store(self) -> "KeyValueStore": diff --git a/plateau/core/index.py b/plateau/core/index.py index 1d12a5b7..f95ad8fd 100644 --- a/plateau/core/index.py +++ b/plateau/core/index.py @@ -7,7 +7,6 @@ import pandas as pd import pyarrow as pa import pyarrow.parquet as pq -from packaging import version from toolz.itertoolz import partition_all import plateau.core._time @@ -39,8 +38,6 @@ "PartitionIndex", ) -PYARROW_LT_13 = version.parse(pa.__version__) < version.parse("13") - class IndexBase(CopyMixin): """Initialize an IndexBase. @@ -69,10 +66,8 @@ def __init__( ): if column == _PARTITION_COLUMN_NAME: raise ValueError( - "Cannot create an index for column {} due to an internal implementation conflict. " - "Please contact a plateau maintainer if you receive this error message".format( - column - ) + f"Cannot create an index for column {column} due to an internal implementation conflict. " + "Please contact a plateau maintainer if you receive this error message" ) if (dtype is None) and index_dct: # do dtype given but index_dct is present => auto-derive dtype @@ -114,10 +109,8 @@ def __init__( if n_collisions: _logger.warning( - ( - "Value normalization for index column {} resulted in {} collision(s). plateau merged " - "the affected partition lists, but you may want to check if this was desired." - ).format(column, n_collisions) + f"Value normalization for index column {column} resulted in {n_collisions} collision(s). plateau merged " + "the affected partition lists, but you may want to check if this was desired." ) else: # data comes from a trusted source (e.g. an index that we've already preserved and are now reading), so @@ -147,11 +140,7 @@ def observed_values( keys = np.array(list(self.index_dct.keys())) labeled_array = pa.array(keys, type=self.dtype) - # Prior to pyarrow 13.0.0 coerce_temporal_nanoseconds didn't exist - # as it was introduced for backwards compatibility with pandas 1.x - _coerce = {} - if not PYARROW_LT_13: - _coerce["coerce_temporal_nanoseconds"] = coerce_temporal_nanoseconds + _coerce = {"coerce_temporal_nanoseconds": coerce_temporal_nanoseconds} return np.array( labeled_array.to_pandas(date_as_object=date_as_object, **_coerce) ) @@ -300,25 +289,19 @@ def update(self, index: "IndexBase", inplace: bool = False) -> "IndexBase": """ if not isinstance(index, IndexBase): raise TypeError( - "Need to input an plateau.core.index.IndexBase object, instead got `{}`".format( - type(index) - ) + f"Need to input an plateau.core.index.IndexBase object, instead got `{type(index)}`" ) # Assume that if one of the indices dtypes is None, they are compatible. In future versions we should make # dtype a non-optional parameter if self.dtype is not None and index.dtype is not None: if self.dtype != index.dtype: raise TypeError( - "Trying to update an index with different types. Expected `{}` but got `{}`".format( - self.dtype, index.dtype - ) + f"Trying to update an index with different types. Expected `{self.dtype}` but got `{index.dtype}`" ) if self.column != index.column: raise ValueError( - "Trying to update an index with the wrong column. Got `{}` but expected `{}`".format( - index.column, self.column - ) + f"Trying to update an index with the wrong column. Got `{index.column}` but expected `{self.column}`" ) if index.index_dct is None or len(index.index_dct) == 0: @@ -490,9 +473,7 @@ def as_flat_series( table = _index_dct_to_table( self.index_dct, column=self.column, dtype=self.dtype ) - # Prior to pyarrow 13.0.0 coerce_temporal_nanoseconds didn't exist - # as it was introduced for backwards compatibility with pandas 1.x - _coerce = {} if PYARROW_LT_13 else {"coerce_temporal_nanoseconds": True} + _coerce = {"coerce_temporal_nanoseconds": True} df = table.to_pandas(date_as_object=date_as_object, **_coerce) if predicates is not None: @@ -687,12 +668,7 @@ def store(self, store: StoreInput, dataset_uuid: str) -> str: ): storage_key = self.index_storage_key if storage_key is None: - storage_key = "{dataset_uuid}/indices/{column}/{timestamp}{suffix}".format( - dataset_uuid=dataset_uuid, - suffix=naming.EXTERNAL_INDEX_SUFFIX, - column=quote(self.column), - timestamp=quote(self.creation_time.isoformat()), - ) + storage_key = f"{dataset_uuid}/indices/{quote(self.column)}/{quote(self.creation_time.isoformat())}{naming.EXTERNAL_INDEX_SUFFIX}" # The arrow representation of index_dct requires a large amount of memory because strings are duplicated and # flattened into the buffer. To avoid a high peak memory usage, split the index_dct into chunks and only convert @@ -879,9 +855,7 @@ def _parquet_bytes_to_dict(column: str, index_buffer: bytes): if column_type == pa.timestamp("us"): column_type = pa.timestamp("ns") - # Prior to pyarrow 13.0.0 coerce_temporal_nanoseconds didn't exist - # as it was introduced for backwards compatibility with pandas 1.x - _coerce = {} if PYARROW_LT_13 else {"coerce_temporal_nanoseconds": True} + _coerce = {"coerce_temporal_nanoseconds": True} df = table.to_pandas(**_coerce) index_dct = dict( @@ -915,7 +889,7 @@ def _index_dct_to_table(index_dct: IndexDictType, column: str, dtype: pa.DataTyp dtype = pa.timestamp( "ns" ) # workaround pyarrow type inference bug (ARROW-2554) - elif isinstance(probe, (np.bool_, bool)): + elif isinstance(probe, np.bool_ | bool): dtype = pa.bool_() # fix pyarrow input diff --git a/plateau/core/naming.py b/plateau/core/naming.py index 5b2c6c79..2bc13d14 100644 --- a/plateau/core/naming.py +++ b/plateau/core/naming.py @@ -38,9 +38,7 @@ def get_partition_file_prefix( dataset_uuid, partition_label, table, metadata_version=DEFAULT_METADATA_VERSION ): if metadata_version == 4: - file_prefix = "{dataset_uuid}/{table}/{partition_label}".format( - dataset_uuid=dataset_uuid, table=table, partition_label=partition_label - ) + file_prefix = f"{dataset_uuid}/{table}/{partition_label}" else: raise NotImplementedError(f"Metadata version {metadata_version} not supported") return file_prefix diff --git a/plateau/core/testing.py b/plateau/core/testing.py index 8ccd22da..1e22ae1a 100644 --- a/plateau/core/testing.py +++ b/plateau/core/testing.py @@ -86,9 +86,7 @@ def get_scalar_dtype_strategy(exclude=None): del possible_strategies[ex] else: raise ValueError( - "Strategy {} unknown. Possible values are {}".format( - ex, possible_strategies.keys() - ) + f"Strategy {ex} unknown. Possible values are {possible_strategies.keys()}" ) return hyp_st.one_of(*list(possible_strategies.values())) diff --git a/plateau/core/typing.py b/plateau/core/typing.py index b2f69058..725c9a59 100644 --- a/plateau/core/typing.py +++ b/plateau/core/typing.py @@ -1,7 +1,6 @@ from collections.abc import Callable -from typing import Union from minimalkv import KeyValueStore StoreFactory = Callable[[], KeyValueStore] -StoreInput = Union[str, KeyValueStore, StoreFactory] +StoreInput = str | KeyValueStore | StoreFactory diff --git a/plateau/core/utils.py b/plateau/core/utils.py index a5b5388e..e7a37453 100644 --- a/plateau/core/utils.py +++ b/plateau/core/utils.py @@ -14,9 +14,7 @@ def _verify_metadata_version(metadata_version: int) -> None: """This is factored out to be an easier target for mocking.""" if metadata_version < MIN_METADATA_VERSION: raise NotImplementedError( - "Minimal supported metadata version is 4. You requested {metadata_version} instead.".format( - metadata_version=metadata_version - ) + f"Minimal supported metadata version is 4. You requested {metadata_version} instead." ) elif metadata_version > MAX_METADATA_VERSION: raise NotImplementedError( diff --git a/plateau/io/dask/dataframe.py b/plateau/io/dask/dataframe.py index 9c683b5d..f13842e9 100644 --- a/plateau/io/dask/dataframe.py +++ b/plateau/io/dask/dataframe.py @@ -112,7 +112,7 @@ def read_dataset_as_ddf( """ if dask_index_on is not None and not isinstance(dask_index_on, str): raise TypeError( - f"The paramter `dask_index_on` must be a string but got {type(dask_index_on)}" + f"The parameter `dask_index_on` must be a string but got {type(dask_index_on)}" ) if dask_index_on is not None and dispatch_by is not None and len(dispatch_by) > 0: @@ -633,7 +633,7 @@ def hash_dataset( .. note:: - We do not guarantee the hash values to remain constant accross versions. + We do not guarantee the hash values to remain constant across versions. Example output:: diff --git a/plateau/io/eager.py b/plateau/io/eager.py index 7aed25d9..1e0c7f01 100644 --- a/plateau/io/eager.py +++ b/plateau/io/eager.py @@ -535,9 +535,7 @@ def create_empty_dataset_header( store.put(*dataset_builder.to_msgpack()) else: raise ValueError( - "Unknown metadata storage format encountered: {}".format( - metadata_storage_format - ) + f"Unknown metadata storage format encountered: {metadata_storage_format}" ) return dataset_builder.to_dataset() diff --git a/plateau/io/testing/read.py b/plateau/io/testing/read.py index 44afe3c9..9b8afe03 100644 --- a/plateau/io/testing/read.py +++ b/plateau/io/testing/read.py @@ -643,7 +643,7 @@ def test_binary_column_metadata(store_factory, bound_load_dataframes): assert set(df.columns.map(type)) == {str} -def test_extensiondtype_rountrip(store_factory, bound_load_dataframes): +def test_extensiondtype_roundtrip(store_factory, bound_load_dataframes): df = pd.DataFrame({"str": pd.Series(["a", "b"], dtype="string")}) store_dataframes_as_dataset( diff --git a/plateau/io_components/gc.py b/plateau/io_components/gc.py index 4d4f95e0..454d9401 100644 --- a/plateau/io_components/gc.py +++ b/plateau/io_components/gc.py @@ -31,9 +31,7 @@ def dispatch_files_to_gc(dataset_uuid, store_factory, chunk_size, factory): table_files.add(name) for table in ds_factory.tables: - table_path = "{dataset_uuid}/{table}/".format( - dataset_uuid=dataset_uuid, table=table - ) + table_path = f"{dataset_uuid}/{table}/" table_files.add(table_path + TABLE_METADATA_FILE) for key in ds_factory.store.iter_keys(prefix=table_path): remove_table_files.add(key) diff --git a/plateau/io_components/metapartition.py b/plateau/io_components/metapartition.py index 6a193db9..866af27b 100644 --- a/plateau/io_components/metapartition.py +++ b/plateau/io_components/metapartition.py @@ -10,7 +10,6 @@ from typing import ( TYPE_CHECKING, Any, - Optional, Union, cast, ) @@ -73,7 +72,7 @@ "number_rows_per_row_group": np.dtype(int), } -MetaPartitionInput = Optional[Union[pd.DataFrame, Sequence, "MetaPartition"]] +MetaPartitionInput = Union[pd.DataFrame, Sequence, "MetaPartition"] | None def _predicates_to_named(predicates): @@ -136,7 +135,7 @@ def _impl(self, *method_args, **method_kwargs): if len(self) == 0: raise RuntimeError("Invalid MetaPartition. No sub-partitions to act upon.") - # Look whether there is a `store` in the arguments and instatiate it + # Look whether there is a `store` in the arguments and instantiate it # this way we avoid multiple HTTP pools method_args, method_kwargs = _initialize_store_for_metapartition( method, method_args, method_kwargs @@ -149,9 +148,7 @@ def _impl(self, *method_args, **method_kwargs): method_return = method(mp, *method_args, **method_kwargs) if not isinstance(method_return, MetaPartition): raise ValueError( - "Method {} did not return a MetaPartition but {}".format( - method.__name__, type(method_return) - ) + f"Method {method.__name__} did not return a MetaPartition but {type(method_return)}" ) if method_return.is_sentinel: result = method_return @@ -160,9 +157,7 @@ def _impl(self, *method_args, **method_kwargs): result = result.add_metapartition(mp, schema_validation=False) if not isinstance(result, MetaPartition): raise ValueError( - "Result for method {} is not a `MetaPartition` but {}".format( - method.__name__, type(method_return) - ) + f"Result for method {method.__name__} is not a `MetaPartition` but {type(method_return)}" ) return result @@ -286,9 +281,7 @@ def __repr__(self): label = f"NESTED ({len(self.metapartitions)})" else: label = self.label - return "<{_class} v{version} | {label} >".format( - version=self.metadata_version, _class=self.__class__.__name__, label=label - ) + return f"<{self.__class__.__name__} v{self.metadata_version} | {label} >" def __len__(self): return len(self.metapartitions) @@ -744,12 +737,12 @@ def _reconstruct_index_columns( return df original_columns = list(df.columns) - zeros: "npt.NDArray[np.int_]" = np.zeros(len(df), dtype=int) + zeros: npt.NDArray[np.int_] = np.zeros(len(df), dtype=int) schema = self.schema if schema is None: raise ValueError("Cannot reconstruct indices before the schema is loaded.") - # One of the few places `inplace=True` makes a signifcant difference + # One of the few places `inplace=True` makes a significant difference df.reset_index(drop=True, inplace=True) index_names = [primary_key for primary_key, _ in key_indices] @@ -790,9 +783,7 @@ def _reconstruct_index_columns( value = dtype.type(value) else: raise RuntimeError( - "Unexepected object encountered: ({}, {})".format( - dtype, type(dtype) - ) + f"Unexpected object encountered: ({dtype}, {type(dtype)})" ) if categories and primary_key in categories: if convert_to_date: @@ -846,7 +837,7 @@ def store_dataframes( df_serializer: DataFrameSerializer | None = None, ) -> "MetaPartition": """Stores all dataframes of the MetaPartitions and registers the saved - files under the `files` atrribute. The dataframe itself is deleted from + files under the `files` attribute. The dataframe itself is deleted from memory. Parameters @@ -1004,7 +995,7 @@ def _renormalize_meta(meta): @_apply_to_list def build_indices(self, columns: Iterable[str]): """This builds the indices for this metapartition for the given - columns. The indices for the passed columns are rebuilt, so exisiting + columns. The indices for the passed columns are rebuilt, so existing index entries in the metapartition are overwritten. :param columns: A list of columns from which the indices over @@ -1021,9 +1012,7 @@ def build_indices(self, columns: Iterable[str]): df = self.data if not self.is_sentinel and col not in df: raise RuntimeError( - "Column `{corrupt_col}` could not be found in the partition `{partition_label}` Please check for any typos and validate your dataset.".format( - corrupt_col=col, partition_label=self.label - ) + f"Column `{col}` could not be found in the partition `{self.label}` Please check for any typos and validate your dataset." ) possible_values = possible_values | set(df[col].dropna().unique()) @@ -1134,10 +1123,8 @@ def _ensure_compatible_partitioning(self, partition_on): raise ValueError( "Incompatible partitioning encountered. `partition_on` needs to include the already " "existing partition keys and must preserve their order.\n" - "Current partition keys: `{}`\n" - "Partition on called with: `{}`".format( - self.partition_keys, partition_on - ) + f"Current partition keys: `{self.partition_keys}`\n" + f"Partition on called with: `{partition_on}`" ) def _partition_data(self, partition_on): diff --git a/plateau/io_components/read.py b/plateau/io_components/read.py index e8746b4a..46cf81c3 100644 --- a/plateau/io_components/read.py +++ b/plateau/io_components/read.py @@ -69,7 +69,7 @@ def dispatch_metapartitions_from_factory( if len(dispatch_by) == 0: merged_partitions = [((""), base_df)] else: - # Group the resulting MetaParitions by partition keys or a subset of those keys + # Group the resulting MetaPartitions by partition keys or a subset of those keys merged_partitions = base_df.groupby( by=list(dispatch_by), sort=True, as_index=False, observed=True ) diff --git a/plateau/io_components/utils.py b/plateau/io_components/utils.py index 79df34de..b449468d 100644 --- a/plateau/io_components/utils.py +++ b/plateau/io_components/utils.py @@ -142,9 +142,7 @@ def validate_partition_keys( if partition_on != ds_factory.partition_keys: raise ValueError( "Incompatible set of partition keys encountered. " - "Input partitioning was `{}` while actual dataset was `{}`".format( - partition_on, ds_factory.partition_keys - ) + f"Input partitioning was `{partition_on}` while actual dataset was `{ds_factory.partition_keys}`" ) else: partition_on = ds_factory.partition_keys @@ -229,11 +227,11 @@ def normalize_arg(arg_name, old_value): """ def _make_list(_args): - if isinstance(_args, (str, bytes, int, float)): + if isinstance(_args, str | bytes | int | float): return [_args] if _args is None: return [] - if isinstance(_args, (set, frozenset, dict)): + if isinstance(_args, set | frozenset | dict): raise ValueError(f"{type(_args)} is incompatible for normalisation.") return list(_args) @@ -326,8 +324,8 @@ def align_categories(dfs, categoricals): cats = ser.dropna().unique() LOGGER.info( "Encountered non-categorical type where categorical was expected\n" - "Found at index position {ix} for column {col}\n" - "Dtypes: {dtypes}".format(ix=ix, col=column, dtypes=df.dtypes) + f"Found at index position {ix} for column {column}\n" + f"Dtypes: {df.dtypes}" ) else: cats = ser.cat.categories @@ -371,9 +369,9 @@ def sort_values_categorical(df: pd.DataFrame, columns: list[str] | str) -> pd.Da columns = [columns] for col in columns: if isinstance(df[col].dtype, pd.CategoricalDtype): - cat_accesor = df[col].cat - df[col] = cat_accesor.reorder_categories( - sorted(cat_accesor.categories), ordered=True + cat_accessor = df[col].cat + df[col] = cat_accessor.reorder_categories( + sorted(cat_accessor.categories), ordered=True ) return df.sort_values(by=columns).reset_index(drop=True) diff --git a/plateau/io_components/write.py b/plateau/io_components/write.py index d95d3252..88648e30 100644 --- a/plateau/io_components/write.py +++ b/plateau/io_components/write.py @@ -77,10 +77,8 @@ def persist_indices( for column, index in indices.items(): # backwards compat if isinstance(index, dict): - legacy_storage_key = "{dataset_uuid}.{column}{suffix}".format( - dataset_uuid=dataset_uuid, - column=column, - suffix=naming.EXTERNAL_INDEX_SUFFIX, + legacy_storage_key = ( + f"{dataset_uuid}.{column}{naming.EXTERNAL_INDEX_SUFFIX}" ) index = ExplicitSecondaryIndex( column=column, index_dct=index, index_storage_key=legacy_storage_key @@ -117,9 +115,7 @@ def persist_common_metadata( result = validate_compatible(schemas_sorted) except ValueError as e: raise ValueError( - "Schemas for dataset '{dataset_uuid}' are not compatible!\n\n{e}".format( - dataset_uuid=dataset_uuid, e=e - ) + f"Schemas for dataset '{dataset_uuid}' are not compatible!\n\n{e}" ) from e if result: store_schema_metadata( @@ -221,9 +217,7 @@ def store_dataset_from_partitions( store.put(*dataset_builder.to_msgpack()) else: raise ValueError( - "Unknown metadata storage format encountered: {}".format( - metadata_storage_format - ) + f"Unknown metadata storage format encountered: {metadata_storage_format}" ) dataset = dataset_builder.to_dataset() return dataset diff --git a/plateau/serialization/_csv.py b/plateau/serialization/_csv.py index e0a577f3..1810abe4 100644 --- a/plateau/serialization/_csv.py +++ b/plateau/serialization/_csv.py @@ -9,7 +9,6 @@ import pandas as pd import pyarrow as pa from minimalkv import KeyValueStore -from packaging import version from pandas.errors import EmptyDataError from ._generic import ( @@ -20,8 +19,6 @@ filter_df_from_predicates, ) -PYARROW_LT_13 = version.parse(pa.__version__) < version.parse("13") - class CsvSerializer(DataFrameSerializer): def __init__(self, compress=True): @@ -91,7 +88,7 @@ def store(self, store, key_prefix, df): if isinstance(df, pa.Table): # Prior to pyarrow 13.0.0 coerce_temporal_nanoseconds didn't exist # as it was introduced for backwards compatibility with pandas 1.x - _coerce = {} if PYARROW_LT_13 else {"coerce_temporal_nanoseconds": True} + _coerce = {"coerce_temporal_nanoseconds": True} df = df.to_pandas(**_coerce) key = f"{key_prefix}.csv" diff --git a/plateau/serialization/_generic.py b/plateau/serialization/_generic.py index 90ececfd..d1143019 100644 --- a/plateau/serialization/_generic.py +++ b/plateau/serialization/_generic.py @@ -3,7 +3,7 @@ Available constants -**PredicatesType** - A type describing the format of predicates which is a list of ConjuntionType +**PredicatesType** - A type describing the format of predicates which is a list of ConjunctionType **ConjunctionType** - A type describing a single Conjunction which is a list of literals **LiteralType** - A type for a single literal @@ -15,7 +15,7 @@ import warnings from collections.abc import Iterable -from typing import TYPE_CHECKING, Optional, TypeVar +from typing import TYPE_CHECKING, TypeVar import numpy as np import pandas as pd @@ -34,7 +34,7 @@ ConjunctionType = list[LiteralType] # Optional is part of the actual type since predicate=None # is a sential for: All values -PredicatesType = Optional[list[ConjunctionType]] +PredicatesType = list[ConjunctionType] | None class DataFrameSerializer: @@ -252,7 +252,7 @@ def columns_in_predicates(predicates: PredicatesType) -> set[str]: Parameters ---------- predicates: - The predicates to be scaned. + The predicates to be scanned. """ if predicates is None: return set() @@ -290,9 +290,9 @@ def filter_df_from_predicates( """ if predicates is None: return df - indexer: "npt.NDArray[np.bool_]" = np.zeros(len(df), dtype=bool) + indexer: npt.NDArray[np.bool_] = np.zeros(len(df), dtype=bool) for conjunction in predicates: - inner_indexer: "npt.NDArray[np.bool_]" = np.ones(len(df), dtype=bool) + inner_indexer: npt.NDArray[np.bool_] = np.ones(len(df), dtype=bool) for column, op, value in conjunction: column_name = ensure_unicode_string_type(column) filter_array_like( @@ -458,7 +458,7 @@ def filter_array_like( # In the case of an empty list, don't bother with evaluating types, etc. if is_list_like(value) and len(value) == 0: - false_arr: "npt.NDArray[np.bool_]" = np.zeros(len(array_like), dtype=bool) + false_arr: npt.NDArray[np.bool_] = np.zeros(len(array_like), dtype=bool) np.logical_and(false_arr, mask, out=out) return out diff --git a/plateau/serialization/_io_buffer.py b/plateau/serialization/_io_buffer.py index 47f568d0..821a097d 100644 --- a/plateau/serialization/_io_buffer.py +++ b/plateau/serialization/_io_buffer.py @@ -1,7 +1,7 @@ """Improved IO buffering compared to ``io.BufferedReader``. The main issues w/ ``io.BufferedReader`` is that it is only meant of -sequencial reads and that it resets the buffer on ``.seek(...)``. This +sequential reads and that it resets the buffer on ``.seek(...)``. This happens quite often in pyarrow and basically renders the buffereing inefficient. """ @@ -69,7 +69,7 @@ def _raw_seekable(self): def _setup_cache(self): """Set up cache data structure and inspect underlying IO object. - If the cache is already inialized, this is a no-op. + If the cache is already initialized, this is a no-op. """ if self._cached_blocks is not None: # cache initialized, nothing to do diff --git a/plateau/serialization/_parquet.py b/plateau/serialization/_parquet.py index f7ab5db1..149916d8 100644 --- a/plateau/serialization/_parquet.py +++ b/plateau/serialization/_parquet.py @@ -11,7 +11,6 @@ import pyarrow as pa import pyarrow.parquet as pq from minimalkv import KeyValueStore -from packaging import version from pyarrow.parquet import ParquetFile from ._generic import ( @@ -39,16 +38,7 @@ EPOCH_ORDINAL = datetime.date(1970, 1, 1).toordinal() MAX_NB_RETRIES = 6 # longest retry backoff = BACKOFF_TIME * 2**(MAX_NB_RETRIES - 2) BACKOFF_TIME = 0.01 # 10 ms -PYARROW_LT_6 = version.parse(pa.__version__) < version.parse("6") -PYARROW_LT_8 = version.parse(pa.__version__) < version.parse("8") -PYARROW_LT_13 = version.parse(pa.__version__) < version.parse("13") - -# Since pyarrow 6, the Parquet version/features can be selected more granular. -# Version 2.0 is equal to 2.4 but 2.4 doesn't trigger deprecation warnings. -if PYARROW_LT_6: - PARQUET_VERSION = "2.0" -else: - PARQUET_VERSION = "2.4" +PARQUET_VERSION = "2.4" def _empty_table_from_schema(parquet_file): @@ -188,9 +178,7 @@ def __eq__(self, other): ) def __repr__(self): - return "ParquetSerializer(compression={compression!r}, chunk_size={chunk_size!r})".format( - compression=self.compression, chunk_size=self.chunk_size - ) + return f"ParquetSerializer(compression={self.compression!r}, chunk_size={self.chunk_size!r})" @staticmethod def _restore_dataframe( @@ -256,11 +244,7 @@ def _restore_dataframe( else: # ARROW-5139 Column projection with empty columns returns a table w/out index if columns == []: - # Prior to pyarrow 13.0.0 coerce_temporal_nanoseconds didn't exist - # as it was introduced for backwards compatibility with pandas 1.x - _coerce = {} - if not PYARROW_LT_13: - _coerce["coerce_temporal_nanoseconds"] = True + _coerce = {"coerce_temporal_nanoseconds": True} # Create an arrow table with expected index length. df = ( parquet_file.schema.to_arrow_schema() @@ -293,9 +277,7 @@ def _restore_dataframe( # HACK: Cast bytes to object in metadata until Pandas bug is fixed: https://github.com/pandas-dev/pandas/issues/50127 table = table.cast(schema_metadata_bytes_to_object(table.schema)) - # Prior to pyarrow 13.0.0 coerce_temporal_nanoseconds didn't exist - # as it was introduced for backwards compatibility with pandas 1.x - _coerce = {} if PYARROW_LT_13 else {"coerce_temporal_nanoseconds": True} + _coerce = {"coerce_temporal_nanoseconds": True} df = table.to_pandas(date_as_object=date_as_object, **_coerce) # XXX: Patch until Pyarrow bug is resolved: https://issues.apache.org/jira/browse/ARROW-18099?filter=-2 @@ -452,24 +434,14 @@ def _normalize_predicates( break if op == "in": - values = [ + normalized_value = [ _normalize_value(lit, pa_type, column_name=column_name) for lit in literal[2] ] - if for_pushdown and values: - normalized_value = [ - _timelike_to_arrow_encoding(value, pa_type) for value in values - ] - else: - normalized_value = values else: normalized_value = _normalize_value( literal[2], pa_type, column_name=column_name ) - if for_pushdown: - normalized_value = _timelike_to_arrow_encoding( - normalized_value, pa_type - ) new_literal = (literal[0], literal[1], normalized_value) new_conjunction.append(new_literal) @@ -478,15 +450,6 @@ def _normalize_predicates( return normalized_predicates -def _timelike_to_arrow_encoding(value, pa_type): - # Date32 columns are encoded as days since 1970 prior to pyarrow 8 - if PYARROW_LT_8 and pa.types.is_date32(pa_type): - if isinstance(value, datetime.date): - return value.toordinal() - EPOCH_ORDINAL - else: - return value - - def _normalize_value(value, pa_type, column_name=None): if pa.types.is_dictionary(pa_type): pa_type = pa_type.value_type @@ -511,7 +474,7 @@ def _normalize_value(value, pa_type, column_name=None): or pa.types.is_boolean(pa_type) and pd.api.types.is_bool(value) or pa.types.is_timestamp(pa_type) - and not isinstance(value, (bytes, str)) + and not isinstance(value, bytes | str) and ( pd.api.types.is_datetime64_dtype(value) or isinstance(value, datetime.datetime) diff --git a/plateau/utils/converters.py b/plateau/utils/converters.py index 8dc25b0a..62396007 100644 --- a/plateau/utils/converters.py +++ b/plateau/utils/converters.py @@ -80,11 +80,9 @@ def converter_str_tupleset(obj: Iterable[str] | str | None) -> tuple[str, ...]: ValueError If passed set contains duplicates. """ - if isinstance(obj, (dict, frozenset, set)): + if isinstance(obj, dict | frozenset | set): raise TypeError( - "{obj} which has type {tname} has an unstable iteration order".format( - obj=obj, tname=type(obj).__name__ - ) + f"{obj} which has type {type(obj).__name__} has an unstable iteration order" ) result = converter_tuple(obj) result = tuple(converter_str(x) for x in result) @@ -108,7 +106,7 @@ def converter_tuple(obj) -> tuple: """ if obj is None: return () - elif hasattr(obj, "__iter__") and not isinstance(obj, (str, bytes)): + elif hasattr(obj, "__iter__") and not isinstance(obj, str | bytes): return tuple(x for x in obj) else: return (obj,) @@ -137,11 +135,7 @@ def converter_str(obj) -> str: elif isinstance(obj, bytes): return obj.decode("utf-8") else: - raise TypeError( - "Object of type {type} is not a string: {obj}".format( - obj=obj, type=type(obj).__name__ - ) - ) + raise TypeError(f"Object of type {type(obj).__name__} is not a string: {obj}") def get_str_to_python_converter(pa_type): diff --git a/plateau/utils/pandas.py b/plateau/utils/pandas.py index ad5e1bec..822d1d87 100644 --- a/plateau/utils/pandas.py +++ b/plateau/utils/pandas.py @@ -102,7 +102,7 @@ def is_dataframe_sorted(df, columns): ---------- df: pd.DataFrame DataFrame to check. - colums: Iterable[str] + columns: Iterable[str] Column that the DataFrame should be sorted by. Returns @@ -163,7 +163,7 @@ def sort_dataframe(df, columns): Returns ------- df: pandas.DataFrame - Sorted DataFrame w/ reseted index. + Sorted DataFrame w/ reset index. """ columns = list(columns) if is_dataframe_sorted(df, columns): @@ -176,7 +176,7 @@ def sort_dataframe(df, columns): def mask_sorted_duplicates_keep_last(df, columns): - """Mask duplicates on sorted data, keep last occurance as unique entry. + """Mask duplicates on sorted data, keep last occurrence as unique entry. Roughly equivalent to:: @@ -202,10 +202,10 @@ def mask_sorted_duplicates_keep_last(df, columns): """ columns = list(columns) rows = len(df) - mask: "npt.NDArray[np.bool_]" = np.zeros(rows, dtype=bool) + mask: npt.NDArray[np.bool_] = np.zeros(rows, dtype=bool) if (rows > 1) and columns: - sub: "npt.NDArray[np.bool_]" = np.ones(rows - 1, dtype=bool) + sub: npt.NDArray[np.bool_] = np.ones(rows - 1, dtype=bool) for col in columns: data = df[col].values sub &= data[:-1] == data[1:] @@ -215,7 +215,7 @@ def mask_sorted_duplicates_keep_last(df, columns): def drop_sorted_duplicates_keep_last(df, columns): - """Drop duplicates on sorted data, keep last occurance as unique entry. + """Drop duplicates on sorted data, keep last occurrence as unique entry. Roughly equivalent to:: diff --git a/plateau/utils/store.py b/plateau/utils/store.py index afa88ab5..24e0c40f 100644 --- a/plateau/utils/store.py +++ b/plateau/utils/store.py @@ -105,9 +105,7 @@ def _copy_azure_bbs(keys, src_store, tgt_store): break # break from while, continue in for-loop else: raise RuntimeError( - "Error while copying: status is {}: {}".format( - cprop_current.status, cprop_current.status_description - ) + f"Error while copying: status is {cprop_current.status}: {cprop_current.status_description}" ) @@ -166,9 +164,7 @@ def _copy_azure_cc(keys, src_store, tgt_store): break # break from while, continue in for-loop else: raise RuntimeError( - "Error while copying: status is {}: {}".format( - cprop_current.status, cprop_current.status_description - ) + f"Error while copying: status is {cprop_current.status}: {cprop_current.status_description}" ) diff --git a/pyproject.toml b/pyproject.toml index 381381a7..b6c786c8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,45 +1,48 @@ [build-system] -requires = ['setuptools', 'setuptools-scm', 'wheel'] +requires = ["setuptools", "setuptools-scm", "wheel"] [tool.setuptools_scm] # Do not use version_scheme = "post-release", to be consistent with previous versioning [project] name = "plateau" -authors = [{ name = "data engineering collective" }] +description = "A Python library to manage (create, read, update, delete) large amounts of tabular data in a blob store." +authors = [ + { name = "Data Engineering Collective", email = "plateau@uwekorn.com" }, +] dynamic = ["version"] readme = "README.md" license = { file = "LICENSE.txt" } classifiers = [ - "License :: OSI Approved :: MIT License", # According to LICENSE.txt - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", ] dependencies = [ - 'dask[dataframe]!=2021.5.1,!=2021.6.0', # gh475 - 2021.5.1 and 2021.6.0 broke ci, omit those versions - 'decorator', - 'msgpack>=0.5.2', - 'numpy!=1.15.0,!=1.16.0', - 'pandas>=0.23.0,!=1.0.0', - 'pyarrow>=4', - 'simplejson', - 'minimalkv>=1.4.2', - 'toolz', - 'urlquote>=1.1.3', - 'zstandard', - 'attrs', - 'click', - 'prompt-toolkit', - 'pyyaml' + "dask[dataframe]!=2021.5.1,!=2021.6.0", # gh475 - 2021.5.1 and 2021.6.0 broke ci, omit those versions + "decorator", + "msgpack>=0.5.2", + "numpy>1.23,<2", + "pandas>=2", + "pyarrow>=14", + "simplejson", + "minimalkv>=1.4.2", + "toolz", + "urlquote>=1.1.3", + "zstandard", + "attrs", + "click", + "prompt-toolkit", + "pyyaml", ] requires-python = ">=3.10" -urls = {Repository = "https://github.com/data-engineering-collective/plateau"} +urls = { Repository = "https://github.com/data-engineering-collective/plateau" } [tool.setuptools.packages.find] -include = ["plateau"] +include = ["plateau*"] # include all (sub-)packages starting with "plateau" [tool.mypy] python_version = "3.10" @@ -49,14 +52,15 @@ check_untyped_defs = true plugins = "numpy.typing.mypy_plugin" [tool.pytest.ini_options] +testpaths = ["tests"] addopts = "--strict-markers" filterwarnings = [ - "once::DeprecationWarning", - "once::PendingDeprecationWarning", - "ignore:.*(Generated\\sarray\\selement).*:FutureWarning:hypothesis.extra.numpy" + "once::DeprecationWarning", + "once::PendingDeprecationWarning", + "ignore:.*(Generated\\sarray\\selement).*:FutureWarning:hypothesis.extra.numpy", ] markers = [ - "min_metadata_version(version): specify minimum metadata version this test applies to" + "min_metadata_version(version): specify minimum metadata version this test applies to", ] [tool.ruff] @@ -64,8 +68,8 @@ line-length = 88 target-version = "py310" [tool.ruff.lint] -ignore = ["E203", "E266", "E501", "C901"] -select = ["B", "C", "E", "F", "W", "B9", "I001"] +ignore = ["E203", "E266", "E501", "C901", "N806"] +select = ["B", "C", "E", "F", "W", "B9", "I001", "I", "UP", "N"] [tool.ruff.lint.isort] force-wrap-aliases = true @@ -84,3 +88,11 @@ convention = "numpy" [tool.ruff.format] quote-style = "double" indent-style = "space" + + +[tool.typos] +#files.extend-exclude = ["tests/storefact"] +[tool.typos.default.extend-words] +ser = "ser" +fo = "fo" +missings = "missings" diff --git a/tests/conftest.py b/tests/conftest.py index b47fb4e4..eab0d68b 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -225,9 +225,7 @@ def patched__parse_input_to_metapartition( raise AssertionError(f"Traversed through mock. Original error: {e}") from e mocker.patch( - "plateau.io.{backend_identifier}.parse_input_to_metapartition".format( - backend_identifier=backend_identifier - ), + f"plateau.io.{backend_identifier}.parse_input_to_metapartition", patched__parse_input_to_metapartition, ) diff --git a/tests/core/test_common_metadata.py b/tests/core/test_common_metadata.py index 93c693a2..1dff23f4 100644 --- a/tests/core/test_common_metadata.py +++ b/tests/core/test_common_metadata.py @@ -161,7 +161,7 @@ def test_compat_old_rw_path(df_all_types, store): for c in df_all_types.columns if ( not c.startswith("array_") # array types (always null) - and c != "unicode" # unicode type (alway null) + and c != "unicode" # unicode type (always null) and "8" not in c # 8 bit types are casted to 64 bit and "16" not in c # 16 bit types are casted to 64 bit and "32" not in c # 32 bit types are casted to 64 bit @@ -393,7 +393,7 @@ def test_validate_different_cats_different_type(): @pytest.mark.parametrize( "index", [pd.Index([0], dtype="int64"), pd.RangeIndex(start=0, stop=1)] ) -def test_schema_dataframe_rountrip(index, df_all_types): +def test_schema_dataframe_roundtrip(index, df_all_types): df = pd.DataFrame(df_all_types, index=index) schema = make_meta(df, origin="1") diff --git a/tests/core/test_dataset_dyn_part.py b/tests/core/test_dataset_dyn_part.py index 687e851b..20ad6ddb 100644 --- a/tests/core/test_dataset_dyn_part.py +++ b/tests/core/test_dataset_dyn_part.py @@ -380,9 +380,7 @@ def test_overlap_keyspace(store, metadata_version): for dataset_uuid in (dataset_uuid1, dataset_uuid2): partition0_label = "location=L-0/data" - partition0_key = "{}/{}/{}.parquet".format( - dataset_uuid, table, partition0_label - ) + partition0_key = f"{dataset_uuid}/{table}/{partition0_label}.parquet" expected_partitions = {"location=L-0/data": {"files": {"core": partition0_key}}} expected_indices = {"location": {"L-0": ["location=L-0/data"]}} assert DatasetMetadata.storage_keys(dataset_uuid, store) == [ diff --git a/tests/core/test_dataset_explicit_part.py b/tests/core/test_dataset_explicit_part.py index a0500681..61d67142 100644 --- a/tests/core/test_dataset_explicit_part.py +++ b/tests/core/test_dataset_explicit_part.py @@ -279,14 +279,8 @@ def test_load_partition_indices_types(store): "dataset_metadata_version": 4, "dataset_uuid": dataset_uuid, "partitions": { - "{index_name}={index_value}/part_1".format( - index_name=index_name, index_value=index_value - ): { - "files": { - table: "{dataset_uuid}/{table}/location_id=1/part_1.parquet".format( - dataset_uuid=dataset_uuid, table=table - ) - } + f"{index_name}={index_value}/part_1": { + "files": {table: f"{dataset_uuid}/{table}/location_id=1/part_1.parquet"} } }, } diff --git a/tests/io/dask/dataframe/test_read.py b/tests/io/dask/dataframe/test_read.py index 4a13f23b..996b2906 100644 --- a/tests/io/dask/dataframe/test_read.py +++ b/tests/io/dask/dataframe/test_read.py @@ -302,7 +302,7 @@ def test_dask_index_on_non_string_raises(store_factory): ) with pytest.raises( TypeError, - match=f"The paramter `dask_index_on` must be a string but got {type(colA)}", + match=f"The parameter `dask_index_on` must be a string but got {type(colA)}", ): read_dataset_as_ddf( dataset_uuid=dataset_uuid, diff --git a/tests/io/dask/dataframe/test_stats.py b/tests/io/dask/dataframe/test_stats.py index 0c890f3e..5158d12f 100644 --- a/tests/io/dask/dataframe/test_stats.py +++ b/tests/io/dask/dataframe/test_stats.py @@ -257,7 +257,7 @@ def test_collect_dataset_metadata_fraction_precision(store_factory): def test_collect_dataset_metadata_at_least_one_partition(store_factory): - """Make sure we return at leat one partition, even if none would be + """Make sure we return at least one partition, even if none would be returned by rounding frac * n_partitions.""" df = pd.DataFrame(data={"A": range(100), "B": range(100)}) diff --git a/tests/io/eager/test_commit.py b/tests/io/eager/test_commit.py index e19cafd2..df3f7f55 100644 --- a/tests/io/eager/test_commit.py +++ b/tests/io/eager/test_commit.py @@ -57,7 +57,7 @@ def test_commit_dataset_from_metapartition(dataset_function, store): assert loaded_dataset == updated_dataset # Read the data and check whether the rows above are included. - # This checks whether all necessary informations were updated in the header + # This checks whether all necessary information were updated in the header # (e.g. files attributes of the partitions) actual = read_table(store=store, dataset_uuid=dataset_function.uuid) df_expected = pd.DataFrame( diff --git a/tests/io_components/test_utils.py b/tests/io_components/test_utils.py index e09772db..62e31c61 100644 --- a/tests/io_components/test_utils.py +++ b/tests/io_components/test_utils.py @@ -216,7 +216,7 @@ def test_align_categories_with_missings(): pdt.assert_frame_equal(out[1], expected_1) -def test_sort_cateogrical(): +def test_sort_categorical(): values = ["f", "a", "b", "z", "e"] categories = ["e", "z", "b", "a", "f"] cat_ser = pd.Series(pd.Categorical(values, categories=categories)) @@ -232,7 +232,7 @@ def test_sort_cateogrical(): assert all(sorted_df["cat"].cat.categories == sorted(categories)) -def test_sort_cateogrical_multiple_cols(): +def test_sort_categorical_multiple_cols(): df = pd.DataFrame.from_records( [ {"ColA": "B", "ColB": "Z", "Payload": 1}, diff --git a/tests/serialization/test_parquet.py b/tests/serialization/test_parquet.py index 0e2680ad..beb7f8bc 100644 --- a/tests/serialization/test_parquet.py +++ b/tests/serialization/test_parquet.py @@ -303,7 +303,7 @@ def test_pushdown_binaries(store, dataframe_not_nested, binary_value, chunk_size @pytest.mark.xfail(reason="Requires parquet-cpp 1.5.0.") -def test_pushdown_null_itermediate(store): +def test_pushdown_null_intermediate(store): binary = b"\x8f\xb6\xe5@\x90\xdc\x11\xe8\x00\xae\x02B\xac\x12\x01\x06" df = pd.DataFrame({"byte_with_null": [binary]}) serialiser = ParquetSerializer(chunk_size=1) @@ -473,7 +473,7 @@ def test_reset_dict_cols(store): assert pa.types.is_dictionary(only_a_reset.field("colB").type) -def test_retry_on_IOError(monkeypatch, caplog, store): +def test_retry_on_IOError(monkeypatch, caplog, store): # noqa: N802 """See https://github.com/JDASoftwareGroup/plateau/issues/407 : We are testing a retry-workaround for the above issue here. Once the @@ -504,7 +504,7 @@ def patched__restore_dataframe(**kwargs): pdt.assert_frame_equal(df, df_result) -def test_retries_on_IOError_logs(monkeypatch, caplog, store): +def test_retries_on_IOError_logs(monkeypatch, caplog, store): # noqa: N802 """See https://github.com/JDASoftwareGroup/plateau/issues/407 : We are testing a retry-workaround for the above issue here. Once the diff --git a/tests/utils/test_converters.py b/tests/utils/test_converters.py index cab1fe81..d3cacb3c 100644 --- a/tests/utils/test_converters.py +++ b/tests/utils/test_converters.py @@ -182,9 +182,7 @@ def test_str_tupleset_fail_duplicates(): def test_str_tupleset_fail_unstable(param): with pytest.raises( TypeError, - match="which has type {} has an unstable iteration order".format( - type(param).__name__ - ), + match=f"which has type {type(param).__name__} has an unstable iteration order", ): converter_str_tupleset(param) @@ -508,7 +506,7 @@ def test_get_str_to_python_converter_unknown_type(): ), ], ) -def test_get_str_to_python_converter_failes(s, pa_type): +def test_get_str_to_python_converter_fails(s, pa_type): converter = get_str_to_python_converter(pa_type) with pytest.raises(ValueError): converter(s)