CausalPy/.github/workflows/ci.yml at cc61f137da6c0b34f4c1d40ad9e498b6d30a8fc4 · pymc-labs/CausalPy · GitHub

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name: ci

on:
  pull_request:
    branches: [main]
  push:
    branches: [main]

permissions: {}

jobs:

  prek:
    runs-on: ubuntu-latest
    permissions:
      contents: read
    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
        with:
          # Security: do not set to true — prevents credential leakage (GitHub Advanced Security).
          persist-credentials: false
          fetch-depth: 0
      - name: Set up Python
        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
        with:
          python-version: "3.12"
      - name: Run prek on changed files in PRs
        if: github.event_name == 'pull_request'
        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2.0.2
        with:
          extra-args: --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}
      - name: Run prek on all files on pushes
        if: github.event_name != 'pull_request'
        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2.0.2
        with:
          extra-args: --all-files

  check-environment-yml:
    runs-on: ubuntu-latest
    permissions:
      contents: read
    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
        with:
          # Security: do not set to true — prevents credential leakage (GitHub Advanced Security).
          persist-credentials: false
      - name: Set up Python
        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
        with:
          python-version: "3.12"
      - name: Install pyproject2conda
        run: pip install pyproject2conda
      - name: Regenerate environment.yml (same args as local prek hook config)
        run: |
          pyproject2conda yaml -e dev -o /tmp/environment.generated.yml -n CausalPy \
            -w force --no-header \
            --python-include "python>=3.12" \
            -d make -d pip -d pymc-bart -r "marimo[mcp]"
      - name: Check environment.yml is in sync with pyproject.toml
        run: |
          # Compare YAML body only (skip 9-line autogenerated header in environment.yml)
          tail -n +10 environment.yml > /tmp/environment.current.yml
          diff -u /tmp/environment.current.yml /tmp/environment.generated.yml && echo "environment.yml is in sync with pyproject.toml"

  test:
    runs-on: ubuntu-latest
    permissions:
      contents: read
    strategy:
      matrix:
        python-version: ["3.11", "3.14"]

    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
        with:
          # Security: do not set to true — prevents credential leakage (GitHub Advanced Security).
          persist-credentials: false
      - name: Set up Python
        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
        with:
          python-version: ${{ matrix.python-version }}
      - name: Update pip and setuptools
        run: pip install --upgrade pip setuptools
      - name: Setup environment
        run: pip install -e .[test]
      - name: Run doctests
        run: pytest --doctest-modules --ignore=causalpy/tests/ causalpy/ --config-file=causalpy/tests/conftest.py --no-cov
      - name: Run extra tests
        run: pytest docs/source/.codespell/test_notebook_to_markdown.py --no-cov
      - name: Run tests
        run: pytest --cov-report=xml --no-cov-on-fail
      - name: Check codespell for notebooks
        run: |
          python ./docs/source/.codespell/notebook_to_markdown.py --tempdir tmp_markdown
          codespell
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0
        with:
          token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
          name: ${{ matrix.python-version }}
          fail_ci_if_error: false