diff --git a/.all-contributorsrc b/.all-contributorsrc index 561259e2..b33d332f 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -38,7 +38,8 @@ "profile": "https://github.com/mdhaber", "contributions": [ "code", - "ideas" + "ideas", + "test" ] }, { diff --git a/.dprint.jsonc b/.dprint.jsonc new file mode 100644 index 00000000..c3642905 --- /dev/null +++ b/.dprint.jsonc @@ -0,0 +1,25 @@ +{ + "json": { + "lineWidth": 100, + "array.preferSingleLine": true, + }, + "markdown": { + "lineWidth": 200, + "emphasisKind": "asterisks", + }, + "toml": { + "lineWidth": 100, + }, + "yaml": { + "printWidth": 100, + "formatComments": true, + "braceSpacing": false, + }, + "excludes": ["**/*-lock.json", "**/*.lock", "**/node_modules/", "dist/"], + "plugins": [ + "https://plugins.dprint.dev/g-plane/pretty_yaml-v0.5.1.wasm", + "https://plugins.dprint.dev/json-0.20.0.wasm", + "https://plugins.dprint.dev/markdown-0.19.0.wasm", + "https://plugins.dprint.dev/toml-0.7.0.wasm", + ], +} diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 00000000..014064f0 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,5 @@ + diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index c57eeb4d..68bd3738 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -21,7 +21,7 @@ jobs: with: fetch-depth: 0 - - uses: hynek/build-and-inspect-python-package@b5076c307dc91924a82ad150cdd1533b444d3310 # v2.12.0 + - uses: hynek/build-and-inspect-python-package@c52c3a4710070b50470d903818a7b25115dcd076 # v2.13.0 publish: needs: [dist] @@ -40,7 +40,7 @@ jobs: path: dist - name: Generate artifact attestation for sdist and wheel - uses: actions/attest-build-provenance@db473fddc028af60658334401dc6fa3ffd8669fd # v2.3.0 + uses: actions/attest-build-provenance@e8998f949152b193b063cb0ec769d69d929409be # v2.4.0 with: subject-path: "dist/*" diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 73ab37e1..bcbc67e9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -20,38 +20,35 @@ env: FORCE_COLOR: 3 jobs: - pre-commit-and-lint: - name: Format + lint: + name: Lint runs-on: ubuntu-latest steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 with: fetch-depth: 0 - - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0 - with: - python-version: "3.13.3" - - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 - with: - extra_args: --hook-stage manual --all-files - - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 + + - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 with: - pixi-version: v0.42.1 + pixi-version: v0.49.0 cache: true environments: lint - - name: Run Pylint, Mypy & Pyright - run: | - pixi run -e lint pylint - pixi run -e lint mypy - pixi run -e lint pyright + + - name: Lint (if this step fails, please 'pixi run lint' locally and push the changes) + run: pixi run -e lint lint checks: - name: Check ${{ matrix.environment }} + name: Test ${{ matrix.environment }} runs-on: ${{ matrix.runs-on }} - needs: [pre-commit-and-lint] strategy: fail-fast: false matrix: - environment: [tests-py310, tests-py313, tests-numpy1, tests-backends] + environment: + - tests-py310 + - tests-py313 + - tests-numpy1 + - tests-backends + - tests-nogil runs-on: [ubuntu-latest] steps: @@ -59,16 +56,23 @@ jobs: with: fetch-depth: 0 - - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 + - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 with: - pixi-version: v0.42.1 + pixi-version: v0.49.0 cache: true environments: ${{ matrix.environment }} - name: Test package + # Save some time; also at the moment of writing coverage crashes on python 3.13t + if: ${{ matrix.environment != 'tests-nogil' }} run: pixi run -e ${{ matrix.environment }} tests-ci + - name: Test free-threading + if: ${{ matrix.environment == 'tests-nogil' }} + run: pixi run -e tests-nogil tests --parallel-threads=4 + - name: Upload coverage report - uses: codecov/codecov-action@ad3126e916f78f00edff4ed0317cf185271ccc2d # v5.4.2 + if: ${{ matrix.environment != 'tests-nogil' }} + uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24 # v5.4.3 with: token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index e9da16ec..81073742 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -10,13 +10,16 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 + + - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 with: - pixi-version: v0.42.1 + pixi-version: v0.49.0 cache: true environments: docs + - name: Build Docs run: pixi run -e docs docs + - name: Upload Artifact uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2 with: diff --git a/.github/workflows/docs-deploy.yml b/.github/workflows/docs-deploy.yml index 78a5ada1..844031bd 100644 --- a/.github/workflows/docs-deploy.yml +++ b/.github/workflows/docs-deploy.yml @@ -18,8 +18,9 @@ jobs: name: docs-deploy steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + - name: Download Artifact - uses: dawidd6/action-download-artifact@07ab29fd4a977ae4d2b275087cf67563dfdf0295 # v9 + uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 with: workflow: docs-build.yml name: docs-build diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml deleted file mode 100644 index 7be7a1ca..00000000 --- a/.pre-commit-config.yaml +++ /dev/null @@ -1,84 +0,0 @@ -ci: - autoupdate_commit_msg: "chore: update pre-commit hooks" - autofix_commit_msg: "style: pre-commit fixes" - -exclude: ^.cruft.json|.copier-answers.yml$ - -repos: - - repo: https://github.com/adamchainz/blacken-docs - rev: "1.18.0" - hooks: - - id: blacken-docs - additional_dependencies: [black==24.*] - - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: "v5.0.0" - hooks: - - id: check-added-large-files - - id: check-case-conflict - - id: check-merge-conflict - - id: check-symlinks - - id: check-yaml - - id: debug-statements - - id: end-of-file-fixer - - id: mixed-line-ending - - id: name-tests-test - args: ["--pytest-test-first"] - - id: requirements-txt-fixer - - id: trailing-whitespace - - - repo: https://github.com/pre-commit/pygrep-hooks - rev: "v1.10.0" - hooks: - - id: rst-backticks - - id: rst-directive-colons - - id: rst-inline-touching-normal - - - repo: https://github.com/rbubley/mirrors-prettier - rev: "v3.4.2" - hooks: - - id: prettier - types_or: [yaml, markdown, html, css, scss, javascript, json] - args: [--prose-wrap=always] - - - repo: https://github.com/astral-sh/ruff-pre-commit - rev: "v0.8.2" - hooks: - - id: ruff-format - - id: ruff - args: ["--fix", "--show-fixes"] - - - repo: https://github.com/codespell-project/codespell - rev: "v2.3.0" - hooks: - - id: codespell - exclude: pixi.lock - - - repo: https://github.com/shellcheck-py/shellcheck-py - rev: "v0.10.0.1" - hooks: - - id: shellcheck - - - repo: local - hooks: - - id: disallow-caps - name: Disallow improper capitalization - language: pygrep - entry: PyBind|Numpy|Cmake|CCache|Github|PyTest - exclude: .pre-commit-config.yaml - - - repo: https://github.com/abravalheri/validate-pyproject - rev: "v0.23" - hooks: - - id: validate-pyproject - additional_dependencies: ["validate-pyproject-schema-store[all]"] - - - repo: https://github.com/python-jsonschema/check-jsonschema - rev: "0.30.0" - hooks: - - id: check-github-workflows - - - repo: https://github.com/numpy/numpydoc - rev: "v1.8.0" - hooks: - - id: numpydoc-validation diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index b0f2ffb6..cc93de44 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -10,7 +10,7 @@ This project exists thanks to the following contributors Lucas Colley
Lucas Colley
πŸ’» πŸ“– πŸ’‘ πŸ€” πŸš‡ 🚧 πŸ”§ ⚠️ πŸ› πŸ“¦ πŸ‘€ - Matt Haberland
Matt Haberland
πŸ’» πŸ€” + Matt Haberland
Matt Haberland
πŸ’» πŸ€” ⚠️ Jake Bowhay
Jake Bowhay
πŸ’» πŸ‘€ πŸ”§ Aaron Meurer
Aaron Meurer
πŸ‘€ πŸ€” πŸš‡ Tim Head
Tim Head
πŸ€” diff --git a/README.md b/README.md index 65d19699..1b33322a 100644 --- a/README.md +++ b/README.md @@ -1,32 +1,32 @@ # array-api-extra -[![Actions Status][actions-badge]][actions-link] [![docs - here!][docs-badge]][docs-link] -[![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh) -[![All Contributors](https://img.shields.io/github/all-contributors/data-apis/array-api-extra?color=ee8449&style=flat-square)](#contributors) -[![Typing](https://img.shields.io/pypi/types/array-api-extra)](https://typing.python.org/) -[![codecov](https://codecov.io/github/data-apis/array-api-extra/graph/badge.svg)](https://codecov.io/github/data-apis/array-api-extra) - [![PyPI version][pypi-version]][pypi-link] [![Conda-Forge][conda-badge]][conda-link] [![PyPI platforms][pypi-platforms]][pypi-link] +[![All Contributors](https://img.shields.io/github/all-contributors/data-apis/array-api-extra?color=ee8449&style=flat-square)](#contributors) + +[![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh) +[![Typing](https://img.shields.io/pypi/types/array-api-extra)](https://typing.python.org/) +[![codecov](https://codecov.io/github/data-apis/array-api-extra/graph/badge.svg)](https://codecov.io/github/data-apis/array-api-extra) [![EffVer Versioning](https://img.shields.io/badge/version_scheme-EffVer-0097a7)](https://jacobtomlinson.dev/effver) [![SPEC 8 β€” Securing the Release Process](https://img.shields.io/badge/SPEC-8-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0008/) -[actions-badge]: https://github.com/data-apis/array-api-extra/workflows/CI/badge.svg -[actions-link]: https://github.com/data-apis/array-api-extra/actions -[conda-badge]: https://img.shields.io/conda/vn/conda-forge/array-api-extra -[conda-link]: https://github.com/conda-forge/array-api-extra-feedstock + +[actions-badge]: https://github.com/data-apis/array-api-extra/workflows/CI/badge.svg +[actions-link]: https://github.com/data-apis/array-api-extra/actions +[conda-badge]: https://img.shields.io/conda/vn/conda-forge/array-api-extra +[conda-link]: https://github.com/conda-forge/array-api-extra-feedstock [github-discussions-badge]: https://img.shields.io/static/v1?label=Discussions&message=Ask&color=blue&logo=github -[github-discussions-link]: https://github.com/data-apis/array-api-extra/discussions -[pypi-link]: https://pypi.org/project/array-api-extra/ -[pypi-platforms]: https://img.shields.io/pypi/pyversions/array-api-extra -[pypi-version]: https://img.shields.io/pypi/v/array-api-extra -[docs-badge]: https://img.shields.io/badge/docs-here!-2ea44f -[docs-link]: https://data-apis.org/array-api-extra/index.html +[github-discussions-link]: https://github.com/data-apis/array-api-extra/discussions +[pypi-link]: https://pypi.org/project/array-api-extra/ +[pypi-platforms]: https://img.shields.io/pypi/pyversions/array-api-extra +[pypi-version]: https://img.shields.io/pypi/v/array-api-extra +[docs-badge]: https://img.shields.io/badge/docs-here!-2ea44f +[docs-link]: https://data-apis.org/array-api-extra/index.html @@ -38,7 +38,7 @@ Used by: scientific computing. - [scikit-learn](https://github.com/scikit-learn/scikit-learn)Β β€” Machine Learning in Python. -- _your library? Let us know!_ +- *your library? Let us know!* ## Installation @@ -65,7 +65,7 @@ This project exists thanks to the following contributors Lucas Colley
Lucas Colley
πŸ’» πŸ“– πŸ’‘ πŸ€” πŸš‡ 🚧 πŸ”§ ⚠️ πŸ› πŸ“¦ πŸ‘€ - Matt Haberland
Matt Haberland
πŸ’» πŸ€” + Matt Haberland
Matt Haberland
πŸ’» πŸ€” ⚠️ Jake Bowhay
Jake Bowhay
πŸ’» πŸ‘€ πŸ”§ Aaron Meurer
Aaron Meurer
πŸ‘€ πŸ€” πŸš‡ Tim Head
Tim Head
πŸ€” diff --git a/docs/contributing.md b/docs/contributing.md index 83db0de4..bfcfd0d0 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -61,7 +61,7 @@ development of array-api-extra is made easy with at . - `cd array-api-extra`. - [Install Pixi](https://pixi.sh/latest/#installation). -- To enter a development environment: +- To enter a development environment (if you prefer this to the `pixi run` interface): ``` pixi shell -e dev @@ -73,71 +73,75 @@ pixi shell -e dev pixi run tests ``` -- To generate the coverage report: +- To build the docs locally: ``` -pixi run coverage +pixi run docs ``` -- To generate and display the coverage report: +- To build and preview the docs locally: ``` -pixi run open-coverage +pixi run open-docs ``` -- To build the docs locally: +- To install pre-commit hooks: ``` -pixi run docs +pixi run hooks ``` -- To build and preview the docs locally: +- To run pre-commit checks on staged files: ``` -pixi run open-docs +pixi run pre-commit ``` -- To install a [pre-commit](https://pre-commit.com) hook: +- To run the full lint suite: ``` -pixi run pre-commit-install +pixi run --environment=lint lint ``` -- To run the lint suite: +- To enter an interactive Python prompt: ``` -pixi run -e lint lint +pixi run ipython ``` -- To enter an interactive Python prompt: +- To run individual parts of the lint suite separately (for example): ``` -pixi run ipython +pixi run --environment=lint pyright +pixi run --environment=lint dprint +``` + +- To generate the coverage report: + +``` +pixi run coverage ``` -- To run individual parts of the lint suite separately: +- To generate and display the coverage report: ``` -pixi run -e lint pre-commit -pixi run -e lint pylint -pixi run -e lint mypy -pixi run -e lint pyright +pixi run open-coverage ``` Alternative environments are available with a subset of the dependencies and tasks available in the `dev` environment: ``` -pixi shell -e docs -pixi shell -e tests -pixi shell -e tests-backends -pixi shell -e lint +pixi shell --environment=docs +pixi shell --environment=tests +pixi shell --environment=tests-backends +pixi shell --environment=lint ``` If you run on a host with CUDA hardware, you can enable extra tests: ``` -pixi shell -e dev-cuda -pixi shell -e tests-cuda -pixi run -e tests-cuda tests +pixi shell --environment=dev-cuda +pixi shell --environment=tests-cuda +pixi run --environment=tests-cuda tests ``` diff --git a/docs/contributors.md b/docs/contributors.md index 724cdb77..c8e001d3 100644 --- a/docs/contributors.md +++ b/docs/contributors.md @@ -1,3 +1,2 @@ ```{include} ../CONTRIBUTORS.md - ``` diff --git a/docs/index.md b/docs/index.md index 59615583..5168e973 100644 --- a/docs/index.md +++ b/docs/index.md @@ -17,7 +17,7 @@ well as delegation to existing implementations for known array library backends. The intended users of this library are "array-consuming" libraries which are using [array-api-compat](https://data-apis.org/array-api-compat/) to make their own library's functions array-agnostic. In this library, they will find a set of -tools which provide _extra_ functionality on top of the array API standard, +tools which provide *extra* functionality on top of the array API standard, which other array-consuming libraries in a similar position have found useful themselves. @@ -27,7 +27,7 @@ It is currently used by: scientific computing. - [scikit-learn](https://github.com/scikit-learn/scikit-learn) β€” Machine Learning in Python. -- _your library? Let us know!_ +- *your library? Let us know!* (installation)= @@ -114,8 +114,7 @@ def array_namespace(*xs, **kwargs): See [an example of this in SciPy][scipy-vendor-example]. ``` -[scipy-vendor-example]: - https://github.com/scipy/scipy/blob/main/scipy/_lib/_array_api_compat_vendor.py +[scipy-vendor-example]: https://github.com/scipy/scipy/blob/main/scipy/_lib/_array_api_compat_vendor.py ## Versioning diff --git a/lefthook.yml b/lefthook.yml new file mode 100644 index 00000000..3ae3197d --- /dev/null +++ b/lefthook.yml @@ -0,0 +1,56 @@ +lefthook: pixi run --no-progress --environment=lint lefthook + +templates: + run: run --quiet --no-progress --environment=lint + +colors: true + +output: + - meta # Print lefthook version + - summary # Print summary block (successful and failed steps) + - empty_summary # Print summary heading when there are no steps to run + # - success # Print successful steps + # - failure # Print failed steps printing + # - execution # Print any execution logs + # - execution_out # Print execution output + # - execution_info # Print `EXECUTE > ...` logging + - skips # Print "skip" (i.e. no files matched) + +pre-commit: + parallel: true + jobs: + - name: dprint + glob: "*.{json,jsonc,md,toml,yaml,yml}" + stage_fixed: true + run: pixi {run} dprint + - name: ruff + glob: "*.{py,pyi}" + stage_fixed: true + group: + piped: true + jobs: + - name: ruff check + run: pixi {run} ruff-check {staged_files} + - name: ruff format + run: pixi {run} ruff-format {staged_files} + - name: pyright + glob: "*.{py,pyi}" + run: pixi {run} pyright + - name: mypy + glob: "*.{py,pyi}" + run: pixi {run} mypy + - name: typos + stage_fixed: true + run: pixi {run} typos + - name: actionlint + run: pixi {run} actionlint + - name: blacken-docs + glob: "*.md" + stage_fixed: true + run: pixi {run} blacken-docs {staged_files} + - name: validate-pyproject + glob: "pyproject.toml" + run: pixi {run} validate-pyproject + - name: numpydoc + glob: "*.py" + run: pixi {run} numpydoc {staged_files} diff --git a/pixi.lock b/pixi.lock index 2e8472f4..0183f204 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,21 +11,21 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.12.0-pyhe01879c_0.conda - conda: https://prefix.dev/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda - - conda: https://prefix.dev/conda-forge/noarch/ca-certificates-2025.4.26-hbd8a1cb_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda + - conda: https://prefix.dev/conda-forge/noarch/ca-certificates-2025.6.15-hbd8a1cb_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/ld_impl_linux-64-2.43-h1423503_5.conda - conda: https://prefix.dev/conda-forge/linux-64/libexpat-2.7.0-h5888daf_0.conda - conda: https://prefix.dev/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda - - conda: https://prefix.dev/conda-forge/linux-64/libgcc-15.1.0-h767d61c_2.conda - - conda: 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[tool.pixi.project] channels = ["https://prefix.dev/conda-forge"] platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"] [tool.pixi.dependencies] -python = ">=3.10,<3.14" array-api-compat = ">=1.12.0,<2" [tool.pixi.pypi-dependencies] array-api-extra = { path = ".", editable = true } [tool.pixi.feature.lint.dependencies] -typing-extensions = ">=4.13.2" -pre-commit = ">=4.2.0" +typing-extensions = ">=4.14.1" pylint = ">=3.3.7" -basedmypy = ">=2.10.0" -basedpyright = ">=1.29.1" -numpydoc = ">=1.8.0,<2" +mypy = ">=1.16.1" +basedpyright = ">=1.30.0" +numpydoc = ">=1.9.0,<2" # import dependencies for mypy: -array-api-strict = ">=2.3.1" +array-api-strict = ">=2.3.1,<2.4" numpy = ">=2.1.3" -pytest = ">=8.3.5" -hypothesis = ">=6.131.8" -dask-core = ">=2025.5.0" # No distributed, tornado, etc. +hypothesis = ">=6.135.16" +dask-core = ">=2025.5.1" # No distributed, tornado, etc. +dprint = ">=0.50.0,<0.51" +lefthook = ">=1.12.0,<2" +ruff = ">=0.12.2,<0.13" +typos = ">=1.34.0,<2" +actionlint = ">=1.7.7,<2" +blacken-docs = ">=1.19.1,<2" +pytest = ">=8.4.1,<9" +validate-pyproject = ">=0.24.1,<0.25" # NOTE: don't add cupy, jax, pytorch, or sparse here, # as they slow down mypy and are not portable across target OSs [tool.pixi.feature.lint.tasks] -pre-commit-install = { cmd = "pre-commit install", description = "Install pre-commit"} -pre-commit = { cmd = "pre-commit run --all-files", description = "Run pre-commit"} -mypy = { cmd = "mypy", description="Type check with mypy"} -pylint = { cmd = "pylint array_api_extra", cwd = "src" , description = "Lint using pylint"} -pyright = { cmd = "basedpyright", description = "Type check with basedpyright"} -lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] , description = "Run pre-commit, pylint, mypy, and pyright"} +lefthook = { cmd = "lefthook", description = "Run lefthook" } +hooks = { cmd = "lefthook install", description = "Install pre-commit hooks" } +pre-commit = { cmd = "lefthook run pre-commit", description = "Run pre-commit checks" } +pylint = { cmd = "pylint array_api_extra", cwd = "src", description = "Lint with pylint" } +mypy = { cmd = "mypy", description = "Type check with mypy" } +pyright = { cmd = "basedpyright", description = "Type check with basedpyright" } +ruff-check = { cmd = "ruff check --fix", description = "Lint with ruff" } +ruff-format = { cmd = "ruff format", description = "Format with ruff" } +dprint = { cmd = "dprint fmt", description = "Format with dprint" } +typos = { cmd = "typos --write-changes --force-exclude", description = "Fix typos" } +actionlint = { cmd = "actionlint", description = "Lint actions with actionlint" } +blacken-docs = { cmd = "blacken-docs", description = "Format Python markdown blocks with Black" } +validate-pyproject = { cmd = "validate-pyproject pyproject.toml", description = "Validate pyproject.toml" } +numpydoc = { cmd = "numpydoc lint", description = "Validate docstrings with numpydoc" } +lint = { cmd = "lefthook run pre-commit --all-files --force", description = "Run all linters" } [tool.pixi.feature.tests.dependencies] -pytest = ">=8.3.5" -pytest-cov = ">=6.1.1" -hypothesis = ">=6.131.8" -array-api-strict = ">=2.3.1" +pytest = ">=8.4.1" +pytest-cov = ">=6.2.1" +hypothesis = ">=6.135.16" +array-api-strict = ">=2.3.1,<2.4" numpy = ">=1.22.0" [tool.pixi.feature.tests.tasks] -tests = { cmd = "pytest -v", description = "Run tests"} -tests-cov = { cmd="pytest -v -ra --cov --cov-report=xml --cov-report=term --durations=20", description = "Run tests with coverage"} +tests = { cmd = "pytest -v", description = "Run tests" } +tests-cov = { cmd = "pytest -v -ra --cov --cov-report=xml --cov-report=term --durations=20", description = "Run tests with coverage" } -clean-vendor-compat = { cmd = "rm -rf vendor_tests/array_api_compat", description = "Delete the existing vendored version of array-api-compat"} -clean-vendor-extra = { cmd = "rm -rf vendor_tests/array_api_extra" , description = "Delete the existing vendored version of array-api-extra"} -copy-vendor-compat = { cmd = "cp -r $(python -c 'import site; print(site.getsitepackages()[0])')/array_api_compat vendor_tests/", depends-on = ["clean-vendor-compat"] , description = "Vendor a clean copy of array-api-compat"} -copy-vendor-extra = { cmd = "cp -r src/array_api_extra vendor_tests/", depends-on = ["clean-vendor-extra"] , description = "Vendor a clean copy of array-api-extra"} -tests-vendor = { cmd = "pytest -v vendor_tests", depends-on = ["copy-vendor-compat", "copy-vendor-extra"] , description = "Check that array-api-extra and array-api-compat can be vendored together" } +clean-vendor-compat = { cmd = "rm -rf vendor_tests/array_api_compat", description = "Delete the existing vendored version of array-api-compat" } +clean-vendor-extra = { cmd = "rm -rf vendor_tests/array_api_extra", description = "Delete the existing vendored version of array-api-extra" } +copy-vendor-compat = { cmd = "cp -r $(python -c 'import site; print(site.getsitepackages()[0])')/array_api_compat vendor_tests/", depends-on = ["clean-vendor-compat"], description = "Vendor a clean copy of array-api-compat" } +copy-vendor-extra = { cmd = "cp -r src/array_api_extra vendor_tests/", depends-on = ["clean-vendor-extra"], description = "Vendor a clean copy of array-api-extra" } +tests-vendor = { cmd = "pytest -v vendor_tests", depends-on = ["copy-vendor-compat", "copy-vendor-extra"], description = "Check that array-api-extra and array-api-compat can be vendored together" } -tests-ci = { depends-on = ["tests-cov", "tests-vendor"] , description = "Run tests with coverage and vendor tests"} -coverage = { cmd = "coverage html", depends-on = ["tests-cov"], description = "Generate test coverage html report"} -open-coverage = { cmd = "open htmlcov/index.html", depends-on = ["coverage"] , description = "Open test coverage report"} +tests-ci = { depends-on = ["tests-cov", "tests-vendor"], description = "Run tests with coverage and vendor tests" } +coverage = { cmd = "coverage html", depends-on = ["tests-cov"], description = "Generate test coverage html report" } +open-coverage = { cmd = "open htmlcov/index.html", depends-on = ["coverage"], description = "Open test coverage report" } [tool.pixi.feature.docs.dependencies] sphinx = ">=7.4.7" @@ -105,20 +121,20 @@ myst-parser = ">=4.0.1" sphinx-copybutton = ">=0.5.2" sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc -dask-core = ">=2025.5.0" # No distributed, tornado, etc. -pytest = ">=8.3.5" -typing-extensions = ">=4.13.2" +dask-core = ">=2025.5.1" # No distributed, tornado, etc. +pytest = ">=8.4.1" +typing-extensions = ">=4.14.1" numpy = ">=2.1.3" [tool.pixi.feature.docs.tasks] -docs = { cmd = "sphinx-build -E -W . build/", cwd = "docs" , description = "Build docs"} -open-docs = { cmd = "open build/index.html", cwd = "docs", depends-on = ["docs"] , description = "Open the generated docs"} +docs = { cmd = "sphinx-build -E -W . build/", cwd = "docs", description = "Build docs" } +open-docs = { cmd = "open build/index.html", cwd = "docs", depends-on = ["docs"], description = "Open the generated docs" } [tool.pixi.feature.dev.dependencies] ipython = ">=7.33.0" [tool.pixi.feature.dev.tasks] -ipython = { cmd = "ipython" , description = "Launch ipython"} +ipython = { cmd = "ipython", description = "Launch ipython" } [tool.pixi.feature.py310.dependencies] python = "~=3.10.0" @@ -135,17 +151,17 @@ numpy = "=1.22.0" # Note: JAX and PyTorch will install CPU variants. [tool.pixi.feature.backends.dependencies] pytorch = ">=2.7.0" -dask-core = ">=2025.5.0" # No distributed, tornado, etc. -sparse = ">=0.16.0" +dask-core = ">=2025.5.1" # No distributed, tornado, etc. +sparse = ">=0.17.0" [tool.pixi.feature.backends.target.linux-64.dependencies] -jax = ">=0.5.3" +jax = ">=0.6.0" [tool.pixi.feature.backends.target.osx-64.dependencies] -jax = ">=0.5.3" +jax = ">=0.6.0" [tool.pixi.feature.backends.target.osx-arm64.dependencies] -jax = ">=0.5.3" +jax = ">=0.6.0" [tool.pixi.feature.backends.target.win-64.dependencies] # jax = "*" # unavailable @@ -161,7 +177,7 @@ system-requirements = { cuda = "12" } [tool.pixi.feature.cuda-backends.target.linux-64.dependencies] cupy = ">=13.4.1" -jaxlib = { version = ">=0.5.3", build = "cuda12*" } +jaxlib = { version = ">=0.6.0", build = "cuda12*" } pytorch = { version = ">=2.7.0", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.osx-64.dependencies] @@ -179,6 +195,15 @@ cupy = ">=13.4.1" # jaxlib = { version = "*", build = "cuda12*" } # unavailable pytorch = { version = ">=2.7.0", build = "cuda12*" } +[tool.pixi.feature.nogil.dependencies] +python-freethreading = "~=3.13.0" +pytest-run-parallel = ">=0.4.4" +numpy = ">=2.3.1" +# pytorch = "*" # Not available on Python 3.13t yet +dask-core = ">=2025.5.1" # No distributed, tornado, etc. +# sparse = "*" # numba not available on Python 3.13t yet +# jax = "*" # ml_dtypes not available on Python 3.13t yet + [tool.pixi.environments] default = { features = ["py313"], solve-group = "py313" } lint = { features = ["py313", "lint"], solve-group = "py313" } @@ -197,7 +222,7 @@ tests-cuda = { features = ["py310", "tests", "backends", "cuda-backends"], solve # Ungrouped environments tests-numpy1 = ["py310", "tests", "numpy1"] tests-py310 = ["py310", "tests"] - +tests-nogil = ["nogil", "tests"] # pytest @@ -213,7 +238,6 @@ markers = [ "xfail_xp_backend(library, /, *, reason=None, strict=None): Xfail test for a specific backend", ] - # Coverage [tool.coverage] @@ -227,16 +251,17 @@ python_version = "3.10" warn_unused_configs = true strict = true enable_error_code = ["ignore-without-code", "truthy-bool"] -# https://github.com/data-apis/array-api-typing -disallow_any_expr = false -# false positives with input validation -disable_error_code = ["redundant-expr", "unreachable", "no-any-return"] +disable_error_code = ["no-any-return"] [[tool.mypy.overrides]] # slow or unavailable on Windows; do not add to the lint env module = ["cupy.*", "jax.*", "sparse.*", "torch.*"] ignore_missing_imports = true +[[tool.mypy.overrides]] +module = ["tests/*"] +disable_error_code = ["no-untyped-def"] # test(...) without -> None + # pyright [tool.basedpyright] @@ -265,11 +290,10 @@ reportImportCycles = false reportUnknownLambdaType = false executionEnvironments = [ - { root = "tests", reportPrivateUsage = false }, + { root = "tests", reportPrivateUsage = false, reportUnknownArgumentType = false }, { root = "src" }, ] - # Ruff [tool.ruff] @@ -277,65 +301,64 @@ target-version = "py310" [tool.ruff.lint] extend-select = [ - "B", # flake8-bugbear - "F", # Pyflakes - "I", # isort - "E", # Pycodestyle - "W", # Pycodestyle - "N", # pep8-naming + "B", # flake8-bugbear + "F", # Pyflakes + "I", # isort + "E", # Pycodestyle + "W", # Pycodestyle + "N", # pep8-naming "ARG", # flake8-unused-arguments - "C4", # flake8-comprehensions - "EM", # flake8-errmsg + "C4", # flake8-comprehensions + "EM", # flake8-errmsg "ICN", # flake8-import-conventions "ISC", # flake8-implicit-str-concat - "G", # flake8-logging-format + "G", # flake8-logging-format "PGH", # pygrep-hooks "PIE", # flake8-pie - "PL", # pylint - "PT", # flake8-pytest-style + "PL", # pylint + "PT", # flake8-pytest-style "PTH", # flake8-use-pathlib "RET", # flake8-return "RUF", # Ruff-specific "SIM", # flake8-simplify "T20", # flake8-print - "UP", # pyupgrade + "UP", # pyupgrade "YTT", # flake8-2020 "EXE", # flake8-executable "NPY", # NumPy specific rules - "PD", # pandas-vet - "UP", # Pyupgrade + "PD", # pandas-vet + "UP", # Pyupgrade ] ignore = [ - "PLR09", # Too many <...> + "PLR09", # Too many <...> "PLR2004", # Magic value used in comparison - "ISC001", # Conflicts with formatter - "N801", # Class name should use CapWords convention - "N802", # Function name should be lowercase - "N806", # Variable in function should be lowercase + "ISC001", # Conflicts with formatter + "N801", # Class name should use CapWords convention + "N802", # Function name should be lowercase + "N806", # Variable in function should be lowercase + "PLC0415", # `import` should be at the top-level of a file ] - # Pylint [tool.pylint] py-version = "3.10" reports.output-format = "colorized" messages_control.disable = [ - "design", # ignore heavily opinionated design checks - "fixme", #Β allow FIXME comments - "line-too-long", # ruff handles this - "unused-argument", # ruff handles this + "design", # ignore heavily opinionated design checks + "fixme", # Β allow FIXME comments + "line-too-long", # ruff handles this + "unused-argument", # ruff handles this "missing-function-docstring", # numpydoc handles this - "import-error", # mypy handles this - "import-outside-toplevel", # optional dependencies + "import-error", # mypy handles this + "import-outside-toplevel", # optional dependencies ] - # numpydoc [tool.numpydoc_validation] checks = [ - "all", # report on all checks, except the below + "all", # report on all checks, except the below "EX01", # most docstrings do not need an example "SA01", # data-apis/array-api-extra#87 "ES01", # most docstrings do not need an extended summary diff --git a/renovate.json b/renovate.json index c263292b..d81ec2b4 100644 --- a/renovate.json +++ b/renovate.json @@ -1,10 +1,6 @@ { "$schema": "https://docs.renovatebot.com/renovate-schema.json", - "extends": [ - "config:recommended", - "helpers:pinGitHubActionDigests", - ":automergeMinor" - ], + "extends": ["config:recommended", "helpers:pinGitHubActionDigests", ":automergeMinor"], "dependencyDashboardTitle": "META: Dependency Dashboard", "commitMessagePrefix": "deps:", "labels": ["dependencies"], @@ -13,59 +9,40 @@ "pixi": ">=v0.45.0" }, "minimumReleaseAge": "14 days", - "packageRules": [ - { - "description": "Do not bump deps pinned with '~=' or '='.", - "matchManagers": ["pixi"], - "matchCurrentValue": "/^~?=/", - "enabled": false - }, - { - "description": "Do not bump Python deps in the manifest or requires-python.", - "matchManagers": ["pixi", "pep621"], - "matchPackageNames": ["python"], - "enabled": false - }, - { - "description": "Schedule automerged GHA updates for the 15th of each month.", - "matchManagers": ["github-actions"], - "groupName": "gha", - "schedule": ["* * 15 * *"], - "automerge": true - }, - { - "description": "Block PRs for updates blocked on dropping Python 3.10.", - "matchManagers": ["pixi"], - "matchPackageNames": ["sphinx", "ipython", "sphinx-autodoc-typehints"], - "enabled": false - }, - { - "description": "Waiting for Numba to support NumPy 2.2.", - "matchManagers": ["pixi"], - "matchPackageNames": ["numpy"], - "enabled": false - }, - { - "description": "Block Python CI updates as setup-python lags behind (gh-194).", - "matchManagers": ["github-actions"], - "matchPackageNames": ["python"], - "enabled": false - }, - { - "description": "Group Dask packages.", - "matchPackageNames": ["dask", "dask-core"], - "groupName": "dask" - }, - { - "description": "Group JAX packages.", - "matchPackageNames": ["jax", "jaxlib"], - "groupName": "jax" - }, - { - "description": "Schedule hypothesis monthly as releases are frequent.", - "matchManagers": ["pixi"], - "matchPackageNames": ["hypothesis"], - "schedule": ["* * 10 * *"] - } - ] + "packageRules": [{ + "description": "Do not bump deps pinned with '~=' or '='.", + "matchManagers": ["pixi"], + "matchCurrentValue": "/^~?=/", + "enabled": false + }, { + "description": "Do not bump requires-python.", + "matchManagers": ["pep621"], + "matchPackageNames": ["python"], + "enabled": false + }, { + "description": "Schedule automerged GHA updates for the 15th of each month.", + "matchManagers": ["github-actions"], + "groupName": "gha", + "schedule": ["* * 15 * *"], + "automerge": true + }, { + "description": "Block PRs for updates blocked on dropping Python 3.10.", + "matchManagers": ["pixi"], + "matchUpdateTypes": ["major", "minor"], + "matchPackageNames": ["numpy", "sphinx", "ipython", "sphinx-autodoc-typehints"], + "enabled": false + }, { + "description": "Group Dask packages.", + "matchPackageNames": ["dask", "dask-core"], + "groupName": "dask" + }, { + "description": "Group JAX packages.", + "matchPackageNames": ["jax", "jaxlib"], + "groupName": "jax" + }, { + "description": "Schedule hypothesis monthly as releases are frequent.", + "matchManagers": ["pixi"], + "matchPackageNames": ["hypothesis"], + "schedule": ["* * 10 * *"] + }] } diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index b5654902..ddfc715e 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -17,7 +17,7 @@ ) from ._lib._lazy import lazy_apply -__version__ = "0.8.0" +__version__ = "0.8.1.dev0" # pylint: disable=duplicate-code __all__ = [ diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index 870884b8..fb2d6ab7 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -37,7 +37,7 @@ class _AtOp(Enum): MAX = "max" # @override from Python 3.12 - def __str__(self) -> str: # type: ignore[explicit-override] # pyright: ignore[reportImplicitOverride] + def __str__(self) -> str: # pyright: ignore[reportImplicitOverride] """ Return string representation (useful for pytest logs). diff --git a/src/array_api_extra/_lib/_backends.py b/src/array_api_extra/_lib/_backends.py index f64e1479..936f5dd0 100644 --- a/src/array_api_extra/_lib/_backends.py +++ b/src/array_api_extra/_lib/_backends.py @@ -3,8 +3,14 @@ from __future__ import annotations from enum import Enum +from typing import Any -__all__ = ["Backend"] +import numpy as np +import pytest + +__all__ = ["NUMPY_VERSION", "Backend"] + +NUMPY_VERSION = tuple(int(v) for v in np.__version__.split(".")[:3]) # pyright: ignore[reportUnknownArgumentType] class Backend(Enum): # numpydoc ignore=PR02 @@ -30,12 +36,6 @@ class Backend(Enum): # numpydoc ignore=PR02 JAX = "jax.numpy" JAX_GPU = "jax.numpy:gpu" - def __str__(self) -> str: # type: ignore[explicit-override] # pyright: ignore[reportImplicitOverride] # numpydoc ignore=RT01 - """Pretty-print parameterized test names.""" - return ( - self.name.lower().replace("_gpu", ":gpu").replace("_readonly", ":readonly") - ) - @property def modname(self) -> str: # numpydoc ignore=RT01 """Module name to be imported.""" @@ -44,3 +44,29 @@ def modname(self) -> str: # numpydoc ignore=RT01 def like(self, *others: Backend) -> bool: # numpydoc ignore=PR01,RT01 """Check if this backend uses the same module as others.""" return any(self.modname == other.modname for other in others) + + def pytest_param(self) -> Any: + """ + Backend as a pytest parameter + + Returns + ------- + pytest.mark.ParameterSet + """ + id_ = ( + self.name.lower().replace("_gpu", ":gpu").replace("_readonly", ":readonly") + ) + + marks = [] + if self.like(Backend.ARRAY_API_STRICT): + marks.append( + pytest.mark.skipif( + NUMPY_VERSION < (1, 26), + reason="array_api_strict is untested on NumPy <1.26", + ) + ) + if self.like(Backend.DASK, Backend.JAX): + # Monkey-patched by lazy_xp_function + marks.append(pytest.mark.thread_unsafe) + + return pytest.param(self, id=id_, marks=marks) # pyright: ignore[reportUnknownArgumentType] diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 69dfe6a4..05db6251 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -34,7 +34,7 @@ @overload -def apply_where( # type: ignore[explicit-any,decorated-any] # numpydoc ignore=GL08 +def apply_where( # numpydoc ignore=GL08 cond: Array, args: Array | tuple[Array, ...], f1: Callable[..., Array], @@ -46,7 +46,7 @@ def apply_where( # type: ignore[explicit-any,decorated-any] # numpydoc ignore=G @overload -def apply_where( # type: ignore[explicit-any,decorated-any] # numpydoc ignore=GL08 +def apply_where( # numpydoc ignore=GL08 cond: Array, args: Array | tuple[Array, ...], f1: Callable[..., Array], @@ -57,7 +57,7 @@ def apply_where( # type: ignore[explicit-any,decorated-any] # numpydoc ignore=G ) -> Array: ... -def apply_where( # type: ignore[explicit-any] # numpydoc ignore=PR01,PR02 +def apply_where( # numpydoc ignore=PR01,PR02 cond: Array, args: Array | tuple[Array, ...], f1: Callable[..., Array], @@ -143,7 +143,7 @@ def apply_where( # type: ignore[explicit-any] # numpydoc ignore=PR01,PR02 return _apply_where(cond, f1, f2, fill_value, *args_, xp=xp) -def _apply_where( # type: ignore[explicit-any] # numpydoc ignore=PR01,RT01 +def _apply_where( # numpydoc ignore=PR01,RT01 cond: Array, f1: Callable[..., Array], f2: Callable[..., Array] | None, @@ -268,7 +268,7 @@ def broadcast_shapes(*shapes: tuple[float | None, ...]) -> tuple[int | None, ... for axis in range(-ndim, 0): sizes = {shape[axis] for shape in shapes if axis >= -len(shape)} # Dask uses NaN for unknown shape, which predates the Array API spec for None - none_size = None in sizes or math.nan in sizes + none_size = None in sizes or math.nan in sizes # noqa: PLW0177 sizes -= {1, None, math.nan} if len(sizes) > 1: msg = ( @@ -813,8 +813,7 @@ def pad( else: pad_width_seq = cast(list[tuple[int, int]], list(pad_width)) - # https://github.com/python/typeshed/issues/13376 - slices: list[slice] = [] # type: ignore[explicit-any] + slices: list[slice] = [] newshape: list[int] = [] for ax, w_tpl in enumerate(pad_width_seq): if len(w_tpl) != 2: @@ -826,6 +825,7 @@ def pad( if w_tpl[0] == 0 and w_tpl[1] == 0: sl = slice(None, None, None) else: + stop: int | None start, stop = w_tpl stop = None if stop == 0 else -stop diff --git a/src/array_api_extra/_lib/_lazy.py b/src/array_api_extra/_lib/_lazy.py index d13d08f8..d5095001 100644 --- a/src/array_api_extra/_lib/_lazy.py +++ b/src/array_api_extra/_lib/_lazy.py @@ -22,7 +22,7 @@ import numpy as np from numpy.typing import ArrayLike - NumPyObject: TypeAlias = np.ndarray[Any, Any] | np.generic # type: ignore[explicit-any] + NumPyObject: TypeAlias = np.ndarray[Any, Any] | np.generic else: # Sphinx hack NumPyObject = Any @@ -31,7 +31,7 @@ @overload -def lazy_apply( # type: ignore[decorated-any, valid-type] +def lazy_apply( # type: ignore[valid-type] func: Callable[P, Array | ArrayLike], *args: Array | complex | None, shape: tuple[int | None, ...] | None = None, @@ -43,7 +43,7 @@ def lazy_apply( # type: ignore[decorated-any, valid-type] @overload -def lazy_apply( # type: ignore[decorated-any, valid-type] +def lazy_apply( # type: ignore[valid-type] func: Callable[P, Sequence[Array | ArrayLike]], *args: Array | complex | None, shape: Sequence[tuple[int | None, ...]], @@ -313,7 +313,7 @@ def _is_jax_jit_enabled(xp: ModuleType) -> bool: # numpydoc ignore=PR01,RT01 return True -def _lazy_apply_wrapper( # type: ignore[explicit-any] # numpydoc ignore=PR01,RT01 +def _lazy_apply_wrapper( # numpydoc ignore=PR01,RT01 func: Callable[..., Array | ArrayLike | Sequence[Array | ArrayLike]], as_numpy: bool, multi_output: bool, @@ -331,7 +331,7 @@ def _lazy_apply_wrapper( # type: ignore[explicit-any] # numpydoc ignore=PR01,R # On Dask, @wraps causes the graph key to contain the wrapped function's name @wraps(func) - def wrapper( # type: ignore[decorated-any,explicit-any] + def wrapper( *args: Array | complex | None, **kwargs: Any ) -> tuple[Array, ...]: # numpydoc ignore=GL08 args_list = [] @@ -343,7 +343,7 @@ def wrapper( # type: ignore[decorated-any,explicit-any] if as_numpy: import numpy as np - arg = cast(Array, np.asarray(arg)) # type: ignore[bad-cast] # noqa: PLW2901 + arg = cast(Array, np.asarray(arg)) # pyright: ignore[reportInvalidCast] # noqa: PLW2901 args_list.append(arg) assert device is not None diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index 16a9d102..30e2f1ef 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -110,7 +110,7 @@ def _is_materializable(x: Array) -> bool: return not is_torch_array(x) or x.device.type != "meta" # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] -def as_numpy_array(array: Array, *, xp: ModuleType) -> np.typing.NDArray[Any]: # type: ignore[explicit-any] +def as_numpy_array(array: Array, *, xp: ModuleType) -> np.typing.NDArray[Any]: """ Convert array to NumPy, bypassing GPU-CPU transfer guards and densification guards. """ diff --git a/src/array_api_extra/_lib/_utils/_compat.pyi b/src/array_api_extra/_lib/_utils/_compat.pyi index 48addda4..95c6bc8a 100644 --- a/src/array_api_extra/_lib/_utils/_compat.pyi +++ b/src/array_api_extra/_lib/_utils/_compat.pyi @@ -36,7 +36,7 @@ def is_torch_array(x: object, /) -> TypeGuard[Array]: ... def is_lazy_array(x: object, /) -> TypeGuard[Array]: ... def is_writeable_array(x: object, /) -> TypeGuard[Array]: ... def size(x: Array, /) -> int | None: ... -def to_device( # type: ignore[explicit-any] +def to_device( x: Array, device: Device, # pylint: disable=redefined-outer-name /, diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 3e43fa91..d177b376 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -210,7 +210,7 @@ def asarrays( float: ("real floating", "complex floating"), complex: "complex floating", } - kind = same_dtype[type(cast(complex, b))] # type: ignore[index] + kind = same_dtype[type(cast(complex, b))] if xp.isdtype(a.dtype, kind): xb = xp.asarray(b, dtype=a.dtype) else: @@ -322,26 +322,28 @@ def capabilities( dict Capabilities of the namespace. """ - if is_pydata_sparse_namespace(xp): - # No __array_namespace_info__(); no indexing by sparse arrays - return { - "boolean indexing": False, - "data-dependent shapes": True, - "max dimensions": None, - } out = xp.__array_namespace_info__().capabilities() - if is_jax_namespace(xp) and out["boolean indexing"]: - # FIXME https://github.com/jax-ml/jax/issues/27418 - # Fixed in jax >=0.6.0 - out = out.copy() - out["boolean indexing"] = False - if is_torch_namespace(xp): + if is_pydata_sparse_namespace(xp): + if out["boolean indexing"]: + # FIXME https://github.com/pydata/sparse/issues/876 + # boolean indexing is supported, but not when the index is a sparse array. + # boolean indexing by list or numpy array is not part of the Array API. + out = out.copy() + out["boolean indexing"] = False + elif is_jax_namespace(xp): + if out["boolean indexing"]: # pragma: no cover + # Backwards compatibility with jax <0.6.0 + # https://github.com/jax-ml/jax/issues/27418 + out = out.copy() + out["boolean indexing"] = False + elif is_torch_namespace(xp): # FIXME https://github.com/data-apis/array-api/issues/945 device = xp.get_default_device() if device is None else xp.device(device) if device.type == "meta": # type: ignore[union-attr] # pyright: ignore[reportAttributeAccessIssue,reportOptionalMemberAccess] out = out.copy() out["boolean indexing"] = False out["data-dependent shapes"] = False + return out @@ -456,7 +458,7 @@ def persistent_id( return instances, (f.getvalue(), *rest) -def pickle_unflatten(instances: Iterable[object], rest: FlattenRest) -> Any: # type: ignore[explicit-any] +def pickle_unflatten(instances: Iterable[object], rest: FlattenRest) -> Any: """ Reverse of ``pickle_flatten``. @@ -519,7 +521,7 @@ def __init__(self, obj: T) -> None: # numpydoc ignore=GL08 self.obj = obj @classmethod - def _register(cls): # numpydoc ignore=SS06 + def _register(cls) -> None: # numpydoc ignore=SS06 """ Register upon first use instead of at import time, to avoid globally importing JAX. @@ -581,7 +583,7 @@ def f(x: Array, y: float, plus: bool) -> Array: import jax @jax.jit # type: ignore[misc] # pyright: ignore[reportUntypedFunctionDecorator] - def inner( # type: ignore[decorated-any,explicit-any] # numpydoc ignore=GL08 + def inner( # numpydoc ignore=GL08 wargs: _AutoJITWrapper[Any], ) -> _AutoJITWrapper[T]: args, kwargs = wargs.obj diff --git a/src/array_api_extra/_lib/_utils/_typing.pyi b/src/array_api_extra/_lib/_utils/_typing.pyi index e32a59bd..35c255fc 100644 --- a/src/array_api_extra/_lib/_utils/_typing.pyi +++ b/src/array_api_extra/_lib/_utils/_typing.pyi @@ -95,10 +95,10 @@ class DType(Protocol): # pylint: disable=missing-class-docstring class Device(Protocol): # pylint: disable=missing-class-docstring pass -SetIndex: TypeAlias = ( # type: ignore[explicit-any] +SetIndex: TypeAlias = ( int | slice | EllipsisType | Array | tuple[int | slice | EllipsisType | Array, ...] ) -GetIndex: TypeAlias = ( # type: ignore[explicit-any] +GetIndex: TypeAlias = ( SetIndex | None | tuple[int | slice | EllipsisType | None | Array, ...] ) diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 3979f9dd..d40fea1a 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -9,7 +9,7 @@ import contextlib import enum import warnings -from collections.abc import Callable, Iterator, Sequence +from collections.abc import Callable, Generator, Iterator, Sequence from functools import wraps from types import ModuleType from typing import TYPE_CHECKING, Any, ParamSpec, TypeVar, cast @@ -36,7 +36,7 @@ def override(func): P = ParamSpec("P") T = TypeVar("T") -_ufuncs_tags: dict[object, dict[str, Any]] = {} # type: ignore[explicit-any] +_ufuncs_tags: dict[object, dict[str, Any]] = {} class Deprecated(enum.Enum): @@ -48,7 +48,7 @@ class Deprecated(enum.Enum): DEPRECATED = Deprecated.DEPRECATED -def lazy_xp_function( # type: ignore[explicit-any] +def lazy_xp_function( func: Callable[..., Any], *, allow_dask_compute: bool | int = False, @@ -216,8 +216,11 @@ def test_myfunc(xp): def patch_lazy_xp_functions( - request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch, *, xp: ModuleType -) -> None: + request: pytest.FixtureRequest, + monkeypatch: pytest.MonkeyPatch | None = None, + *, + xp: ModuleType, +) -> contextlib.AbstractContextManager[None]: """ Test lazy execution of functions tagged with :func:`lazy_xp_function`. @@ -233,10 +236,15 @@ def patch_lazy_xp_functions( This function should be typically called by your library's `xp` fixture that runs tests on multiple backends:: - @pytest.fixture(params=[numpy, array_api_strict, jax.numpy, dask.array]) - def xp(request, monkeypatch): - patch_lazy_xp_functions(request, monkeypatch, xp=request.param) - return request.param + @pytest.fixture(params=[ + numpy, + array_api_strict, + pytest.param(jax.numpy, marks=pytest.mark.thread_unsafe), + pytest.param(dask.array, marks=pytest.mark.thread_unsafe), + ]) + def xp(request): + with patch_lazy_xp_functions(request, xp=request.param): + yield request.param but it can be otherwise be called by the test itself too. @@ -245,7 +253,7 @@ def xp(request, monkeypatch): request : pytest.FixtureRequest Pytest fixture, as acquired by the test itself or by one of its fixtures. monkeypatch : pytest.MonkeyPatch - Pytest fixture, as acquired by the test itself or by one of its fixtures. + Deprecated xp : array_namespace Array namespace to be tested. @@ -253,16 +261,48 @@ def xp(request, monkeypatch): -------- lazy_xp_function : Tag a function to be tested on lazy backends. pytest.FixtureRequest : `request` test function parameter. + + Notes + ----- + This context manager monkey-patches modules and as such is thread unsafe + on Dask and JAX. If you run your test suite with + `pytest-run-parallel `_, + you should mark these backends with ``@pytest.mark.thread_unsafe``, as shown in + the example above. """ mod = cast(ModuleType, request.module) mods = [mod, *cast(list[ModuleType], getattr(mod, "lazy_xp_modules", []))] - def iter_tagged() -> ( # type: ignore[explicit-any] - Iterator[tuple[ModuleType, str, Callable[..., Any], dict[str, Any]]] - ): + to_revert: list[tuple[ModuleType, str, object]] = [] + + def temp_setattr(mod: ModuleType, name: str, func: object) -> None: + """ + Variant of monkeypatch.setattr, which allows monkey-patching only selected + parameters of a test so that pytest-run-parallel can run on the remainder. + """ + assert hasattr(mod, name) + to_revert.append((mod, name, getattr(mod, name))) + setattr(mod, name, func) + + if monkeypatch is not None: + warnings.warn( + ( + "The `monkeypatch` parameter is deprecated and will be removed in a " + "future version. " + "Use `patch_lazy_xp_function` as a context manager instead." + ), + DeprecationWarning, + stacklevel=2, + ) + # Enable using patch_lazy_xp_function not as a context manager + temp_setattr = monkeypatch.setattr # type: ignore[assignment] # pyright: ignore[reportAssignmentType] + + def iter_tagged() -> Iterator[ + tuple[ModuleType, str, Callable[..., Any], dict[str, Any]] + ]: for mod in mods: for name, func in mod.__dict__.items(): - tags: dict[str, Any] | None = None # type: ignore[explicit-any] + tags: dict[str, Any] | None = None with contextlib.suppress(AttributeError): tags = func._lazy_xp_function # pylint: disable=protected-access if tags is None: @@ -279,13 +319,26 @@ def iter_tagged() -> ( # type: ignore[explicit-any] elif n is False: n = 0 wrapped = _dask_wrap(func, n) - monkeypatch.setattr(mod, name, wrapped) + temp_setattr(mod, name, wrapped) elif is_jax_namespace(xp): for mod, name, func, tags in iter_tagged(): if tags["jax_jit"]: wrapped = jax_autojit(func) - monkeypatch.setattr(mod, name, wrapped) + temp_setattr(mod, name, wrapped) + + # We can't just decorate patch_lazy_xp_functions with + # @contextlib.contextmanager because it would not work with the + # deprecated monkeypatch when not used as a context manager. + @contextlib.contextmanager + def revert_on_exit() -> Generator[None]: + try: + yield + finally: + for mod, name, orig_func in to_revert: + setattr(mod, name, orig_func) + + return revert_on_exit() class CountingDaskScheduler(SchedulerGetCallable): @@ -313,7 +366,9 @@ def __init__(self, max_count: int, msg: str): # numpydoc ignore=GL08 self.msg = msg @override - def __call__(self, dsk: Graph, keys: Sequence[Key] | Key, **kwargs: Any) -> Any: # type: ignore[decorated-any,explicit-any] # numpydoc ignore=GL08 + def __call__( + self, dsk: Graph, keys: Sequence[Key] | Key, **kwargs: Any + ) -> Any: # numpydoc ignore=GL08 import dask self.count += 1 @@ -321,7 +376,7 @@ def __call__(self, dsk: Graph, keys: Sequence[Key] | Key, **kwargs: Any) -> Any: # offending line in the user's code assert self.count <= self.max_count, self.msg - return dask.get(dsk, keys, **kwargs) # type: ignore[attr-defined,no-untyped-call] # pyright: ignore[reportPrivateImportUsage] + return dask.get(dsk, keys, **kwargs) # type: ignore[attr-defined] # pyright: ignore[reportPrivateImportUsage] def _dask_wrap( @@ -354,7 +409,7 @@ def wrapper(*args: P.args, **kwargs: P.kwargs) -> T: # numpydoc ignore=GL08 # `pytest.raises` and `pytest.warns` to work as expected. Note that this would # not work on scheduler='distributed', as it would not block. arrays, rest = pickle_flatten(out, da.Array) - arrays = dask.persist(arrays, scheduler="threads")[0] # type: ignore[attr-defined,no-untyped-call,func-returns-value,index] # pyright: ignore[reportPrivateImportUsage] + arrays = dask.persist(arrays, scheduler="threads")[0] # type: ignore[attr-defined,no-untyped-call] # pyright: ignore[reportPrivateImportUsage] return pickle_unflatten(arrays, rest) # pyright: ignore[reportUnknownArgumentType] return wrapper diff --git a/tests/conftest.py b/tests/conftest.py index 82a0acbb..76fb7650 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -18,11 +18,10 @@ T = TypeVar("T") P = ParamSpec("P") -NUMPY_VERSION = tuple(int(v) for v in np.__version__.split(".")[2]) np_compat = array_namespace(np.empty(0)) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] -@pytest.fixture(params=tuple(Backend)) +@pytest.fixture(params=[b.pytest_param() for b in Backend]) def library(request: pytest.FixtureRequest) -> Backend: # numpydoc ignore=PR01,RT03 """ Parameterized fixture that iterates on all libraries. @@ -38,13 +37,13 @@ def library(request: pytest.FixtureRequest) -> Backend: # numpydoc ignore=PR01, ("xfail_xp_backend", partial(xfail, request), {"reason", "strict"}), ): for marker in request.node.iter_markers(marker_name): - if len(marker.args) != 1: # pyright: ignore[reportUnknownArgumentType] + if len(marker.args) != 1: msg = f"Expected exactly one positional argument; got {marker.args}" raise TypeError(msg) if not isinstance(marker.args[0], Backend): msg = f"Argument of {marker_name} must be a Backend enum" raise TypeError(msg) - if invalid_kwargs := set(marker.kwargs) - allow_kwargs: # pyright: ignore[reportUnknownArgumentType] + if invalid_kwargs := set(marker.kwargs) - allow_kwargs: msg = f"Unexpected kwarg(s): {invalid_kwargs}" raise TypeError(msg) @@ -53,9 +52,9 @@ def library(request: pytest.FixtureRequest) -> Backend: # numpydoc ignore=PR01, strict: bool | None = marker.kwargs.get("strict", None) if library == elem: - reason = f"{library}: {reason}" if reason else str(library) # pyright: ignore[reportUnknownArgumentType] + reason = f"{library}: {reason}" if reason else str(library) kwargs = {"strict": strict} if strict is not None else {} - skip_or_xfail(reason=reason, **kwargs) # pyright: ignore[reportUnknownArgumentType] + skip_or_xfail(reason=reason, **kwargs) return elem @@ -99,7 +98,7 @@ def as_readonly(o: T) -> T: # numpydoc ignore=PR01,RT01 # This works with namedtuples too if isinstance(o, tuple | list): - return type(o)(*(as_readonly(i) for i in o)) # type: ignore[arg-type,return-value] # pyright: ignore[reportArgumentType,reportUnknownArgumentType] + return type(o)(*(as_readonly(i) for i in o)) # type: ignore[arg-type,return-value] # pyright: ignore[reportArgumentType] return o @@ -112,7 +111,7 @@ def wrapper(*args: P.args, **kwargs: P.kwargs) -> T: # numpydoc ignore=GL08 @pytest.fixture def xp( - library: Backend, request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch + library: Backend, request: pytest.FixtureRequest ) -> Generator[ModuleType]: # numpydoc ignore=PR01,RT03 """ Parameterized fixture that iterates on all libraries. @@ -125,9 +124,6 @@ def xp( yield NumPyReadOnly() # type: ignore[misc] # pyright: ignore[reportReturnType] return - if library.like(Backend.ARRAY_API_STRICT) and NUMPY_VERSION < (1, 26): - pytest.skip("array_api_strict is untested on NumPy <1.26") - xp = pytest.importorskip(library.modname) # Possibly wrap module with array_api_compat xp = array_namespace(xp.empty(0)) @@ -143,16 +139,15 @@ def xp( yield xp return - # On Dask and JAX, monkey-patch all functions tagged by `lazy_xp_function` - # in the global scope of the module containing the test function. - patch_lazy_xp_functions(request, monkeypatch, xp=xp) - if library.like(Backend.JAX): _setup_jax(library) elif library.like(Backend.TORCH): _setup_torch(library) - yield xp + # On Dask and JAX, monkey-patch all functions tagged by `lazy_xp_function` + # in the global scope of the module containing the test function. + with patch_lazy_xp_functions(request, xp=xp): + yield xp def _setup_jax(library: Backend) -> None: @@ -189,26 +184,27 @@ def _setup_torch(library: Backend) -> None: torch.set_default_device("cpu") -@pytest.fixture(params=[Backend.DASK]) # Can select the test with `pytest -k dask` +# Can select the test with `pytest -k dask` +@pytest.fixture(params=[Backend.DASK.pytest_param()]) def da( - request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch -) -> ModuleType: # numpydoc ignore=PR01,RT01 + request: pytest.FixtureRequest, +) -> Generator[ModuleType]: # numpydoc ignore=PR01,RT01 """Variant of the `xp` fixture that only yields dask.array.""" xp = pytest.importorskip("dask.array") xp = array_namespace(xp.empty(0)) - patch_lazy_xp_functions(request, monkeypatch, xp=xp) - return xp + with patch_lazy_xp_functions(request, xp=xp): + yield xp -@pytest.fixture(params=[Backend.JAX, Backend.JAX_GPU]) +@pytest.fixture(params=[Backend.JAX.pytest_param(), Backend.JAX_GPU.pytest_param()]) def jnp( - request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch -) -> ModuleType: # numpydoc ignore=PR01,RT01 + request: pytest.FixtureRequest, +) -> Generator[ModuleType]: # numpydoc ignore=PR01,RT01 """Variant of the `xp` fixture that only yields jax.numpy.""" xp = pytest.importorskip("jax.numpy") _setup_jax(request.param) - patch_lazy_xp_functions(request, monkeypatch, xp=xp) - return xp + with patch_lazy_xp_functions(request, xp=xp): + yield xp @pytest.fixture(params=[Backend.TORCH, Backend.TORCH_GPU]) diff --git a/tests/test_at.py b/tests/test_at.py index 7294a7c4..d9e1bdf9 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -40,7 +40,7 @@ def at_op( just a workaround for when one wants to apply jax.jit to `at()` directly, which is not a common use case. """ - meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) # type: ignore[explicit-any] + meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) return meth(y, copy=copy, xp=xp) @@ -157,7 +157,7 @@ def test_copy_default(xp: ModuleType, library: Backend, op: _AtOp): """ x = xp.asarray([1.0, 10.0, 20.0]) expect_copy = not is_writeable_array(x) - meth = cast(Callable[..., Array], getattr(at(x)[:2], op.value)) # type: ignore[explicit-any] + meth = cast(Callable[..., Array], getattr(at(x)[:2], op.value)) with assert_copy(x, None, expect_copy): _ = meth(2.0) @@ -166,7 +166,7 @@ def test_copy_default(xp: ModuleType, library: Backend, op: _AtOp): # even if the arrays are writeable. expect_copy = not is_writeable_array(x) or library is Backend.DASK idx = xp.asarray([True, True, False]) - meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) # type: ignore[explicit-any] + meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) with assert_copy(x, None, expect_copy): _ = meth(2.0) @@ -178,7 +178,7 @@ def test_copy_invalid(): def test_xp(): - a = cast(Array, np.asarray([1, 2, 3])) # type: ignore[bad-cast] + a = cast(Array, np.asarray([1, 2, 3])) # pyright: ignore[reportInvalidCast] _ = at(a, 0).set(4, xp=np) _ = at(a, 0).add(4, xp=np) _ = at(a, 0).subtract(4, xp=np) @@ -190,7 +190,7 @@ def test_xp(): def test_alternate_index_syntax(): - xp = cast(ModuleType, np) # pyright: ignore[reportInvalidCast] + xp = cast(ModuleType, np) # type: ignore[redundant-cast] # pyright: ignore[reportInvalidCast] a = cast(Array, xp.asarray([1, 2, 3])) xp_assert_equal(at(a, 0).set(4, copy=True), xp.asarray([4, 2, 3])) xp_assert_equal(at(a)[0].set(4, copy=True), xp.asarray([4, 2, 3])) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 99da4a2b..769b4119 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -27,18 +27,13 @@ setdiff1d, sinc, ) -from array_api_extra._lib._backends import Backend +from array_api_extra._lib._backends import NUMPY_VERSION, Backend from array_api_extra._lib._testing import xp_assert_close, xp_assert_equal from array_api_extra._lib._utils._compat import device as get_device from array_api_extra._lib._utils._helpers import eager_shape, ndindex from array_api_extra._lib._utils._typing import Array, Device from array_api_extra.testing import lazy_xp_function -from .conftest import NUMPY_VERSION - -# some xp backends are untyped -# mypy: disable-error-code=no-untyped-def - lazy_xp_function(apply_where) lazy_xp_function(atleast_nd) lazy_xp_function(cov) @@ -99,8 +94,8 @@ def test_broadcast(self, xp: ModuleType): actual = apply_where( cond, (x, y), - lambda x, _: x, # pyright: ignore[reportUnknownArgumentType] - lambda _, y: y, # pyright: ignore[reportUnknownArgumentType] + lambda x, _: x, + lambda _, y: y, ) expect = xp.where(cond, x, y) xp_assert_equal(actual, expect) @@ -120,7 +115,7 @@ def test_dtype_propagation(self, xp: ModuleType, library: Backend): cond, (x, y), self.f1, - lambda x, y: mxp.astype(x - y, xp.int64), # pyright: ignore[reportArgumentType,reportUnknownArgumentType] + lambda x, y: mxp.astype(x - y, xp.int64), # pyright: ignore[reportArgumentType] ) assert actual.dtype == xp.int64 @@ -167,8 +162,8 @@ def test_dont_run_on_false(self, xp: ModuleType): actual = apply_where( x == 0, (x, y), - lambda x, y: x / y, # pyright: ignore[reportUnknownArgumentType] - lambda x, y: y / x, # pyright: ignore[reportUnknownArgumentType] + lambda x, y: x / y, + lambda x, y: y / x, ) xp_assert_equal(actual, xp.asarray([0.0, 1.5, 0.0])) @@ -213,7 +208,7 @@ def test_device(self, xp: ModuleType, device: Device): p=st.floats(min_value=0, max_value=1), data=st.data(), ) - def test_hypothesis( # type: ignore[explicit-any,decorated-any] + def test_hypothesis( self, n_arrays: int, rng_seed: int, @@ -416,7 +411,7 @@ def test_complex(self, xp: ModuleType): expect = xp.asarray([[1.0, -1.0j], [1.0j, 1.0]], dtype=xp.complex128) xp_assert_close(actual, expect) - @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="matmul with nan fillvalue") + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="sparse#877") def test_empty(self, xp: ModuleType): with warnings.catch_warnings(record=True): warnings.simplefilter("always", RuntimeWarning) @@ -451,7 +446,7 @@ def test_xp(self, xp: ModuleType): ) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="backend doesn't have arange") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no arange", strict=False) class TestOneHot: @pytest.mark.parametrize("n_dim", range(4)) @pytest.mark.parametrize("num_classes", [1, 3, 10]) @@ -816,7 +811,7 @@ def test_bool_dtype(self, xp: ModuleType): isclose(xp.asarray(True), b, atol=1), xp.asarray([True, True, True]) ) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="unknown shape") def test_none_shape(self, xp: ModuleType): a = xp.asarray([1, 5, 0]) @@ -825,7 +820,7 @@ def test_none_shape(self, xp: ModuleType): a = a[a < 5] xp_assert_equal(isclose(a, b), xp.asarray([True, False])) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="unknown shape") def test_none_shape_bool(self, xp: ModuleType): a = xp.asarray([True, True, False]) @@ -1141,10 +1136,10 @@ def test_xp(self, xp: ModuleType): class TestSinc: - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no linspace") def test_simple(self, xp: ModuleType): xp_assert_equal(sinc(xp.asarray(0.0)), xp.asarray(1.0)) - w = sinc(xp.linspace(-1, 1, 100)) + x = xp.asarray(np.linspace(-1, 1, 100)) + w = sinc(x) # check symmetry xp_assert_close(w, xp.flip(w, axis=0)) @@ -1153,11 +1148,12 @@ def test_dtype(self, xp: ModuleType, x: int | complex): with pytest.raises(ValueError, match="real floating data type"): _ = sinc(xp.asarray(x)) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no arange") def test_3d(self, xp: ModuleType): - x = xp.reshape(xp.arange(18, dtype=xp.float64), (3, 3, 2)) - expected = xp.zeros((3, 3, 2), dtype=xp.float64) - expected = at(expected)[0, 0, 0].set(1.0) + x = np.arange(18, dtype=np.float64).reshape((3, 3, 2)) + expected = np.zeros_like(x) + expected[0, 0, 0] = 1 + x = xp.asarray(x) + expected = xp.asarray(expected) xp_assert_close(sinc(x), expected, atol=1e-15) def test_device(self, xp: ModuleType, device: Device): diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 74a0ec93..9f5c924d 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -24,7 +24,7 @@ from .conftest import np_compat -if TYPE_CHECKING: +if TYPE_CHECKING: # pragma: no cover # TODO import from typing (requires Python >=3.12) from typing_extensions import override else: @@ -32,7 +32,6 @@ def override(func): return func -# mypy: disable-error-code=no-untyped-usage T = TypeVar("T") @@ -40,7 +39,7 @@ def override(func): lazy_xp_function(in1d, jax_jit=False) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no unique_inverse") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no unique_inverse") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="no unique_inverse") class TestIn1D: # cover both code paths @@ -235,10 +234,10 @@ def test_device(self, xp: ModuleType, library: Backend, device: Device): # Test that we're accepting anything that is accepted by the # device= parameter in other functions - actual = capabilities(xp, device=device.type) # type: ignore[attr-defined] # pyright: ignore[reportUnknownArgumentType,reportAttributeAccessIssue] + actual = capabilities(xp, device=device.type) # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] -class Wrapper(Generic[T]): +class Wrapper(Generic[T]): # noqa: PLW1641 """Trivial opaque wrapper. Must be pickleable.""" x: T @@ -264,7 +263,7 @@ def __reduce__(self) -> tuple[object, ...]: # Note: NotHashable() instances can be reduced to an # unserializable local class - class NotHashable: + class NotHashable: # noqa: PLW1641 @override def __eq__(self, other: object) -> bool: return isinstance(other, type(self)) and other.__dict__ == self.__dict__ @@ -332,16 +331,16 @@ def test_flattened_stream(self): obj2 = [Wrapper(2), Wrapper(3)] instances1, rest1 = pickle_flatten(obj1, Wrapper) instances2, rest2 = pickle_flatten(obj2, Wrapper) - it = iter(instances1 + instances2 + [Wrapper(4)]) # pyright: ignore[reportUnknownArgumentType] - assert pickle_unflatten(it, rest1) == obj1 # pyright: ignore[reportUnknownArgumentType] - assert pickle_unflatten(it, rest2) == obj2 # pyright: ignore[reportUnknownArgumentType] - assert list(it) == [Wrapper(4)] # pyright: ignore[reportUnknownArgumentType] + it = iter(instances1 + instances2 + [Wrapper(4)]) + assert pickle_unflatten(it, rest1) == obj1 + assert pickle_unflatten(it, rest2) == obj2 + assert list(it) == [Wrapper(4)] def test_too_short(self): obj = [Wrapper(1), Wrapper(2)] instances, rest = pickle_flatten(obj, Wrapper) with pytest.raises(ValueError, match="Not enough"): - pickle_unflatten(instances[:1], rest) # pyright: ignore[reportUnknownArgumentType] + pickle_unflatten(instances[:1], rest) def test_recursion(self): obj: list[object] = [Wrapper(1)] @@ -350,7 +349,7 @@ def test_recursion(self): instances, rest = pickle_flatten(obj, Wrapper) assert instances == [Wrapper(1)] - obj2 = pickle_unflatten(instances, rest) # pyright: ignore[reportUnknownArgumentType] + obj2 = pickle_unflatten(instances, rest) assert len(obj2) == 2 assert obj2[0] is obj[0] assert obj2[1] is obj2 @@ -387,7 +386,7 @@ def test_static_hashable(self, jnp: ModuleType): """Static argument/return value is hashable, but not serializable""" class C: - def __reduce__(self) -> object: # type: ignore[explicit-override,override] # pyright: ignore[reportIncompatibleMethodOverride,reportImplicitOverride] + def __reduce__(self) -> object: # type: ignore[override] # pyright: ignore[reportIncompatibleMethodOverride,reportImplicitOverride] raise Exception() @jax_autojit @@ -399,12 +398,12 @@ def f(x: object) -> object: assert out is inp # Serializable opaque input contains non-serializable object plus array - inp = Wrapper((C(), jnp.asarray([1, 2]))) - out = f(inp) + winp = Wrapper((C(), jnp.asarray([1, 2]))) + out = f(winp) assert isinstance(out, Wrapper) - assert out.x[0] is inp.x[0] - assert out.x[1] is not inp.x[1] - xp_assert_equal(out.x[1], inp.x[1]) # pyright: ignore[reportUnknownArgumentType] + assert out.x[0] is winp.x[0] + assert out.x[1] is not winp.x[1] + xp_assert_equal(out.x[1], winp.x[1]) def test_arraylikes_are_static(self): pytest.importorskip("jax") diff --git a/tests/test_lazy.py b/tests/test_lazy.py index f97062f0..07904a33 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -141,7 +141,7 @@ def f(x: Array) -> Array: xp = array_namespace(x) return xp.sum(x, axis=0) + x - x_np = cast(Array, np.arange(15).reshape(5, 3)) # type: ignore[bad-cast] + x_np = cast(Array, np.arange(15).reshape(5, 3)) # pyright: ignore[reportInvalidCast] expect = da.asarray(f(x_np)) x_da = da.asarray(x_np).rechunk(3) @@ -187,8 +187,8 @@ def f(x: Array) -> Array: return x + 1 y = lazy_apply(f, x_da) - assert array_namespace(y._meta) is cp # type: ignore[attr-defined] # pyright: ignore[reportUnknownArgumentType,reportAttributeAccessIssue] - xp_assert_equal(y.compute(), x_cp + 1) # type: ignore[attr-defined] # pyright: ignore[reportUnknownArgumentType,reportAttributeAccessIssue] + assert array_namespace(y._meta) is cp # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + xp_assert_equal(y.compute(), x_cp + 1) # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] def test_dask_key(da: ModuleType): @@ -230,7 +230,7 @@ def test_lazy_apply_none_shape_in_args(xp: ModuleType, library: Backend): # Single output with ctx: values = lazy_apply(mxp.unique_values, x, shape=(None,)) - xp_assert_equal(values, xp.asarray([1, 2])) + xp_assert_equal(xp.sort(values), xp.asarray([1, 2])) with ctx: # Multi output @@ -396,7 +396,7 @@ def test_lazy_apply_kwargs(xp: ModuleType, library: Backend, as_numpy: bool): with numpy arrays, and leave the rest untouched.""" x = xp.asarray(0) expect_cls = np.ndarray if as_numpy or library is Backend.DASK else type(x) - actual = check_lazy_apply_kwargs(x, expect_cls, as_numpy) # pyright: ignore[reportUnknownArgumentType] + actual = check_lazy_apply_kwargs(x, expect_cls, as_numpy) xp_assert_equal(actual, x + 1) diff --git a/tests/test_testing.py b/tests/test_testing.py index 43d6e8ae..3a93e287 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -18,9 +18,8 @@ is_jax_namespace, ) from array_api_extra._lib._utils._typing import Array, Device -from array_api_extra.testing import lazy_xp_function +from array_api_extra.testing import lazy_xp_function, patch_lazy_xp_functions -# mypy: disable-error-code="decorated-any, explicit-any" # pyright: reportUnknownParameterType=false,reportMissingParameterType=false @@ -140,7 +139,7 @@ def test_assert_less(self, xp: ModuleType): xp_assert_less(xp.asarray([1, 1]), xp.asarray([2, 1])) @pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="boolean indexing") def test_none_shape(self, xp: ModuleType, func: Callable[..., None]): """On Dask and other lazy backends, test that a shape with NaN's or None's @@ -295,9 +294,9 @@ def test_lazy_xp_function_deprecated_static_argnames(): # Test an arbitrary Cython ufunc (@cython.vectorize). # When SCIPY_ARRAY_API is not set, this is the same as # scipy.special.erf. - from scipy.special._ufuncs import erf # type: ignore[import-not-found] + from scipy.special._ufuncs import erf # type: ignore[import-untyped] - lazy_xp_function(erf) # pyright: ignore[reportUnknownArgumentType] + lazy_xp_function(erf) except ImportError: erf = None @@ -449,3 +448,23 @@ def test_lazy_xp_modules(xp: ModuleType, library: Backend): else: y = wrapped.f(x) xp_assert_equal(y, x) + + +def test_patch_lazy_xp_functions_deprecated_monkeypatch( + request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch +): + xp = pytest.importorskip("dask.array") + + x = xp.asarray([1.0, 2.0]) + y = non_materializable5(x) + xp_assert_equal(y, x) + + with pytest.warns(DeprecationWarning, match="`monkeypatch` parameter"): + _ = patch_lazy_xp_functions(request, monkeypatch, xp=xp) + + with pytest.raises(AssertionError, match=r"dask\.compute.* 1 times"): + _ = non_materializable5(x) + + monkeypatch.undo() + y = non_materializable5(x) + xp_assert_equal(y, x) diff --git a/typos.toml b/typos.toml new file mode 100644 index 00000000..34233590 --- /dev/null +++ b/typos.toml @@ -0,0 +1,8 @@ +[files] +extend-exclude = [".git/", ".pixi/"] +ignore-hidden = false + +[default.extend-words] +nd = "nd" +typ = "typ" +cardinalis = "cardinalis" diff --git a/vendor_tests/_array_api_compat_vendor.py b/vendor_tests/_array_api_compat_vendor.py index cd31a9c4..9bc129b5 100644 --- a/vendor_tests/_array_api_compat_vendor.py +++ b/vendor_tests/_array_api_compat_vendor.py @@ -1,4 +1,5 @@ """This file is a hook imported by `src/array_api_extra/_lib/_compat.py`.""" +# pyright: reportUnknownParameterType=false, reportMissingParameterType=false from .array_api_compat import * # noqa: F403 from .array_api_compat import array_namespace as array_namespace_compat diff --git a/vendor_tests/test_vendor.py b/vendor_tests/test_vendor.py index 374cba11..e43c82fb 100644 --- a/vendor_tests/test_vendor.py +++ b/vendor_tests/test_vendor.py @@ -1,3 +1,7 @@ +# pyright: reportAttributeAccessIssue=false + +from typing import Any + import array_api_strict as xp from numpy.testing import assert_array_equal @@ -53,13 +57,13 @@ def test_vendor_extra(): x = xp.asarray(1) y = atleast_nd(x, ndim=0) - assert_array_equal(y, x) + assert_array_equal(y, x) # pyright: ignore[reportUnknownArgumentType] def test_vendor_extra_testing(): from .array_api_extra.testing import lazy_xp_function - def f(x): + def f(x: Any) -> Any: return x lazy_xp_function(f) pFad - Phonifier reborn

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