py-ci.yml

on:
  push:
    branches:
      - master
    tags:
      - "*"
  pull_request:
  merge_group:
jobs:
  linter:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.7'
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip setuptools
          python -m pip install 'pylint==2.10.2' 'pycodestyle>=2.6.1'
      - name: Run pylint
        run: |
          pylint $(find -name '*.py' -not -path './venv/*')
      - name: Run pycodestyle
        run: |
          pycodestyle $(find -name '*.py' -not -path './venv/*')

  isort:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.7'
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip setuptools
          python -m pip install isort
      - name: Run isort
        run: |
          isort --check --diff .

  test-gendocs:
    runs-on: ubuntu-latest
    env:
      QUILT_DISABLE_USAGE_METRICS: true
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          # on newer versions it crashes with
          # TypeError: <classmethod(<function Package.install at 0x105219f30>)> is not a callable object
          python-version: '3.9'
      - name: install deps
        run: |
          python -m pip install --upgrade pip setuptools
          python -m pip install api/python nbconvert git+https://github.com/quiltdata/pydoc-markdown.git@quilt
      - name: generate docs
        run: cd gendocs && python build.py
      - name: show invisible changes via cat
        run: git diff | cat -A
      - name: check there are no changes
        run: git diff --exit-code

  test-testdocs:
    runs-on: ubuntu-latest
    env:
      QUILT_DISABLE_USAGE_METRICS: true
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.10'
      - name: install poetry
        run: python -m pip install poetry
      - name: install deps
        run: cd testdocs && poetry install
      - name: test codeblocks
        run: cd testdocs && poetry run pytest --codeblocks ../docs

  test-client:
    strategy:
      matrix:
        os: [ubuntu-latest, windows-latest]
        python-version: ['3.9', '3.10', '3.11', '3.12']
    runs-on: ${{ matrix.os }}
    env:
      QUILT_DISABLE_USAGE_METRICS: true
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip setuptools
          python -m pip install -e api/python[tests]
      - name: Run Pytest
        run: |
          pytest --cov=api/python api/python
      - uses: codecov/codecov-action@v4
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
          OS: ${{ matrix.os }}
          PYTHON_VERSION: ${{ matrix.python-version }}
        with:
          flags: api-python
          name: ${{ github.job }}
          env_vars: OS,PYTHON_VERSION

  pypi-release-tag-check:
    needs: test-client
    runs-on: ubuntu-latest
    outputs:
      check: ${{ steps.check.outputs.check }}
    if: github.ref_type == 'tag'
    steps:
      - name: check git tag
        id: check
        run: |
          if [[ ${{ github.ref_name }} =~ ^[0-9]+(\.[0-9]+)*([abrc]+[0-9]+)?$ ]]; then
            echo ::set-output name=check::true
          fi

  pypi-release:
    needs: pypi-release-tag-check
    if: github.ref_type == 'tag' && needs.pypi-release-tag-check.outputs.check == 'true'
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: api/python
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.7'
      - name: verify git tag vs. version
        env:
          CIRCLE_TAG: ${{ github.ref_name }}
        run: python setup.py verify
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip setuptools
          python -m pip install build==0.8.0 twine==4.0.0
      - name: build
        run: python -m build
      - name: upload to PyPI
        env:
          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
        run: twine upload dist/*

  test-lambda:
    strategy:
      fail-fast: false
      matrix:
        path:
          - access_counts
          - indexer
          - molecule
          - pkgevents
          - pkgpush
          - pkgselect
          - preview
          - s3hash
          - s3select
          - shared
          - status_reports
          - tabular_preview
          - thumbnail
          - transcode
    runs-on: ubuntu-latest
    env:
      QUILT_DISABLE_USAGE_METRICS: true
      PYTHONPATH: deps
      JUPYTER_PATH: deps/share/jupyter  # Jupyter is not smart enough to handle custom Python paths
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version-file: lambdas/${{ matrix.path }}/.python-version
      - name: Install dependencies
        run: |
          # Due to behavior change in pip>=23.1 installing tifffile==0.15.1
          # from thumbnail lambda fails whithout installed wheel.
          # See https://github.com/pypa/pip/issues/8559.
          python -m pip install wheel
          if [ ${{ matrix.path }} == "shared" ]
            python -m pip install -e lambdas/shared[tests]
          then
            python -m pip install -e lambdas/shared
            python -m pip install -e lambdas/${{ matrix.path }}
          fi
          python -m pip install -r lambdas/${{ matrix.path }}/test-requirements.txt

          # Try to simulate the lambda .zip file:
          # - Use --no-deps to ensure that second-order dependencies are included in the requirements file
          # - Remove "tests" directories
          # - Run "strip" on shared libraries
          python -m pip install -t deps --no-deps -r lambdas/${{ matrix.path }}/requirements.txt
          find deps -name tests -type d -exec rm -r \{} \+
          find deps \( -name '*.so.*' -o -name '*.so' \) -type f -exec strip \{} \+
      - name: Pytest
        run: |
          pytest --cov=lambdas lambdas/${{ matrix.path }}
      - uses: codecov/codecov-action@v4
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
          LAMBDA: ${{ matrix.path }}
        with:
          flags: lambda
          name: ${{ github.job }}
          env_vars: LAMBDA