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* Add dependencies to pixi.toml * Pixi-ize pre-commit * Add pixi tasks * Update CI * Fix build dependencies * update lockfile * Fix doctest * Try to fix readthedocs * Use latest pixi on conda-forge * Find some minimum versions * Bump minimum formulaic version * Find minimum numpy version * Make polars a test dependency * Update lockfile * Fix typing issues * Fix benchmarks * Update contributing docs * Make ruff happy * Remove unnecessary pre-commit option from CI
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| @@ -0,0 +1,2 @@ | ||
| # GitHub syntax highlighting | ||
| pixi.lock linguist-language=YAML linguist-generated=true |
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@@ -3,87 +3,55 @@ on: [push] | |
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| jobs: | ||
| pre-commit-checks: | ||
| name: pre-commit checks | ||
| name: Linux - pre-commit checks | ||
| 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@f8b8a1e23a26f60a44c853292711bacfd3eac822 | ||
| - name: Add micromamba to GITHUB_PATH | ||
| run: echo "${HOME}/micromamba-bin" >> "$GITHUB_PATH" | ||
| - name: Install Python 3.10 | ||
| uses: actions/setup-python@v5 | ||
| - name: Set up pixi | ||
| uses: prefix-dev/[email protected] | ||
| with: | ||
| python-version: "3.10" | ||
| - name: Run pre-commit checks | ||
| uses: pre-commit/[email protected] | ||
| environments: lint default | ||
| - name: pre-commit | ||
| run: pixi run -e lint pre-commit-run --color=always --show-diff-on-failure | ||
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| unit-tests: | ||
| name: Tests - ${{ matrix.os }} - Py${{ matrix.python-version }} - ${{ matrix.note }} | ||
| name: Tests | ||
| runs-on: ${{ matrix.os }} | ||
| env: | ||
| CI: True | ||
| strategy: | ||
| fail-fast: true | ||
| matrix: | ||
| include: | ||
| - { os: ubuntu-latest, python-version: '3.9', note: 'Default Builds' } | ||
| - { os: ubuntu-latest, python-version: '3.10', note: 'Default Builds' } | ||
| - { os: ubuntu-latest, python-version: '3.11', note: 'Default Builds' } | ||
| - { os: ubuntu-latest, python-version: '3.12', note: 'Default Builds' } | ||
| - { os: ubuntu-latest, python-version: '3.12', note: 'Nightly Builds' } | ||
| - { os: macos-latest, python-version: '3.12', note: 'Default Builds' } | ||
| - { os: windows-latest, python-version: '3.12', note: 'Default Builds' } | ||
| - { os: ubuntu-latest, environment: 'py310' } | ||
| - { os: ubuntu-latest, environment: 'py311' } | ||
| - { os: ubuntu-latest, environment: 'py312' } | ||
| - { os: windows-latest, environment: 'py312' } | ||
| - { os: macos-latest, environment: 'py312' } | ||
| - { os: ubuntu-latest, environment: 'oldies' } | ||
| - { os: ubuntu-latest, environment: 'nightly' } | ||
| steps: | ||
| - name: Checkout branch | ||
| uses: actions/checkout@v4 | ||
| - name: Set up conda env | ||
| uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822 | ||
| - name: Set up pixi | ||
| uses: prefix-dev/setup-pixi@992a3081e2f87829e0fff9fb29f4fe6a5d1e80a2 | ||
| with: | ||
| environment-file: ${{ matrix.os == 'windows-latest' && 'environment-win.yml' || 'environment.yml' }} | ||
| init-shell: ${{ matrix.os == 'windows-latest' && 'powershell' || 'bash' }} | ||
| cache-environment: true | ||
| create-args: >- | ||
| python=${{ matrix.python-version }} | ||
| environments: ${{ matrix.environment }} | ||
| - name: Install nightlies | ||
| if: matrix.note == 'Nightly Builds' | ||
| shell: bash -el {0} | ||
| run: | | ||
| PRE_WHEELS="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/" | ||
| for pkg in numpy pandas scipy; do | ||
| echo "Installing $pkg nightly" | ||
| micromamba remove -y --force $pkg | ||
| pip install --pre --no-deps --only-binary :all: --upgrade --timeout=60 -i $PRE_WHEELS $pkg | ||
| done | ||
| micromamba remove -y --force formulaic | ||
| pip install --no-deps git+https://github.com/matthewwardrop/formulaic | ||
| micromamba list | ||
| - name: Install repository (unix) | ||
| if: matrix.os != 'windows-latest' | ||
| shell: bash -el {0} | ||
| run: pip install --no-use-pep517 --no-deps --disable-pip-version-check -e . | ||
| - name: Install repository (windows) | ||
| if: matrix.os == 'windows-latest' | ||
| shell: powershell | ||
| run: pip install --no-use-pep517 --no-deps --disable-pip-version-check -e . | ||
| - name: Run pytest (unix) | ||
| if: matrix.os != 'windows-latest' | ||
| shell: bash -el {0} | ||
| run: pytest -nauto tests -m "not high_memory" --doctest-modules src/ | ||
| - name: Run pytest (windows) | ||
| if: matrix.os == 'windows-latest' | ||
| shell: powershell | ||
| run: pytest -nauto tests -m "not high_memory" | ||
| if: matrix.NOTE == 'Nightly Builds' | ||
| run: pixi run -e ${{ matrix.environment }} install-nightlies | ||
| - name: Install repository | ||
| run: pixi run -e ${{ matrix.environment }} postinstall | ||
| - name: Run pytest | ||
| run: pixi run -e ${{ matrix.environment }} test -nauto -m "not high_memory" | ||
| - name: Run doctest | ||
| if: matrix.os != 'windows-latest' | ||
| shell: bash -el {0} | ||
| # Check that the readme example will work by running via doctest. | ||
| # We run outside the repo to make the test a bit more similar to | ||
| # a user running after installing with conda. | ||
| run: | | ||
| mkdir ../temp | ||
| cp README.md ../temp | ||
| cd ../temp | ||
| python -m doctest -v README.md | ||
| pixi run --manifest-path ../tabmat/pixi.toml -e ${{ matrix.environment }} python -m doctest -v README.md | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,47 @@ | ||
| exclude: ^.pixi$ | ||
| repos: | ||
| - repo: https://github.com/Quantco/pre-commit-mirrors-ruff | ||
| rev: 0.6.2 | ||
| - repo: local | ||
| hooks: | ||
| - id: ruff-conda | ||
| - id: ruff-format-conda | ||
| - repo: https://github.com/Quantco/pre-commit-mirrors-mypy | ||
| rev: "1.10.1" | ||
| hooks: | ||
| - id: mypy-conda | ||
| - repo: https://github.com/Quantco/pre-commit-mirrors-cython-lint | ||
| rev: 0.16.2 | ||
| hooks: | ||
| - id: cython-lint-conda | ||
| args: [--no-pycodestyle] | ||
| - id: double-quote-cython-strings-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 | ||
| - id: mypy | ||
| name: mypy | ||
| entry: pixi run -e default mypy --allow-redefinition | ||
| exclude: (^tests/) | ||
| language: system | ||
| types: [python] | ||
| require_serial: true | ||
| # cython-lint | ||
| - id: cython-lint | ||
| name: cython-lint | ||
| entry: pixi run -e lint cython-lint --no-pycodestyle | ||
| language: system | ||
| types: [cython] | ||
| require_serial: true | ||
| - id: cython-double-quote | ||
| name: cython-double-quote | ||
| entry: pixi run -e lint double-quote-cython-strings | ||
| language: system | ||
| types: [cython] | ||
| require_serial: true |
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@@ -28,51 +28,51 @@ Releases | |
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| Development installation | ||
| ------------------------ | ||
| For development, you should do an editable installation: | ||
| We use [pixi](https://prefix.dev/) for setting up the project dependencies. [Install it](https://pixi.sh/latest/#installation) first if you do not have it already. The following commands will set up the project for development: | ||
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| ```bash | ||
| # First, make sure you have conda-forge as your primary conda channel: | ||
| conda config --add channels conda-forge | ||
| # And install pre-commit | ||
| conda install -y pre-commit | ||
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| git clone [email protected]:Quantco/tabmat.git | ||
| cd tabmat | ||
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| # Set up our pre-commit hooks for ruff, mypy, and cython-lint. | ||
| pre-commit install | ||
| pixi run pre-commit-install | ||
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| # Set up a pixi environment with the dependencies and install the package in editable mode. | ||
| pixi run postinstall | ||
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| # If you want to install the dependencies necessary for benchmarking against other GLM packages: | ||
| pixi run -e benchmark postinstall | ||
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| # Set up a conda environment with name "tabmat" | ||
| conda env create | ||
| # If you want to work on the documentation: | ||
| pixi run -e docs postinstall | ||
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| # Install this package in editable mode. | ||
| conda activate tabmat | ||
| pip install --no-use-pep517 --disable-pip-version-check -e . | ||
| # You can run any command in the pixi environment with `pixi run <command>`. For example: | ||
| pixi run [-e ENVIRONMENT] ipython | ||
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| # Alternatively, you can create a shell with the pixi environment activated: | ||
| pixi shell | ||
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| # A number of pixi tasks are available for commonly used commands. | ||
| # You can run them with `pixi run <task>`. | ||
| # To get a list of available tasks, run: | ||
| pixi task list | ||
| ``` | ||
|
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| Testing and continuous integration | ||
| -------------------------------------------------- | ||
| The test suite is in ``tests/`` and can be run using ``pytest``. | ||
| The test suite is in ``tests/`` and can be run using ``pixi run test``. | ||
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| Developing the documentation | ||
| ---------------------------------------- | ||
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| The documentation is built with Sphinx. To develop the documentation: | ||
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| :: | ||
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| cd docs | ||
| make html | ||
| python -m http.server --directory _build/html | ||
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| Then, navigate to `<http://localhost:8000>`_ to view the documentation. | ||
| The documentation is built with Sphinx. To develop the documentation: ``pixi run serve-docs``. Then, navigate to `<http://localhost:8000>`_ to view the documentation. | ||
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| Alternatively, if you install `entr <http://eradman.com/entrproject/>`_, then you can auto-rebuild the documentation any time a file changes with: | ||
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| :: | ||
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| ```bash | ||
| cd docs | ||
| ./dev | ||
| ``` | ||
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| Conda-forge packaging | ||
| --------------------- | ||
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