freesurfer-volume-reader/.github/workflows/python.yml

# sync with https://github.com/fphammerle/ical2vdir/blob/master/.github/workflows/python.yml

# https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions

# shown in badge
# https://help.github.com/en/actions/automating-your-workflow-with-github-actions/configuring-a-workflow#adding-a-workflow-status-badge-to-your-repository
name: tests

on:
  push:
  pull_request:
  schedule:
  - cron: '0 20 * * 5'

jobs:
  code-format:
    runs-on: ubuntu-20.04
    strategy:
      matrix:
        python-version: ['3.9']
    steps:
    - uses: actions/checkout@v3
    - uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}
    - run: pip install --upgrade pipenv==2022.9.21
    - run: pipenv install --python "$PYTHON_VERSION" --deploy --dev
      env:
        PYTHON_VERSION: ${{ matrix.python-version }}
    - run: pipenv graph
    - run: pipenv run black --check .
  tests:
    runs-on: ubuntu-20.04
    strategy:
      matrix:
        python-version:
        - '3.7'
        - '3.8'
        - '3.9'
        - '3.10'
        pandas-version:
        - '' # locked version
        - 0.23.*
        - 0.24.*
        - 0.25.*
        - 1.1.* # pandas does not use semantic versioning
        - 1.*
        exclude:
        # > astroid.exceptions.AttributeInferenceError: '_constructor_expanddim' not found on <ClassDef.Series l.139 at 0x7f314baa6410>.
        # https://github.com/fphammerle/freesurfer-volume-reader/runs/1937182916
        - python-version: 3.7
          pandas-version: 1.1.*
        # no python3.8 wheels for pandas v0.24.2 & v0.23.4 available
        # https://travis-ci.org/github/fphammerle/freesurfer-stats/builds/701952350
        # build takes longer than 10min
        # https://travis-ci.org/github/fphammerle/freesurfer-stats/jobs/702077404#L199
        - python-version: 3.8
          pandas-version: 0.23.*
        - python-version: 3.8
          pandas-version: 0.24.*
        # > astroid.exceptions.AttributeInferenceError: '_constructor_expanddim' not found on <ClassDef.Series l.139 at 0x7f314baa6410>.
        # https://github.com/fphammerle/freesurfer-volume-reader/runs/1937182916
        - python-version: 3.8
          pandas-version: 1.1.*
        - python-version: 3.9
          pandas-version: 0.23.*
        - python-version: 3.9
          pandas-version: 0.24.*
        # > Cython-generated file 'pandas/_libs/algos.c' not found.
        - python-version: 3.9
          pandas-version: 0.25.*
        - python-version: '3.10'
          pandas-version: 0.23.*
        - python-version: '3.10'
          pandas-version: 0.24.*
        - python-version: '3.10'
          pandas-version: 0.25.*
        - python-version: '3.10'
          pandas-version: 1.1.* # building for >4min
      fail-fast: false
    steps:
    - uses: actions/checkout@v3
    - uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}
    - run: pip install --upgrade pipenv==2022.9.21
    # by default pipenv picks the latest version in PATH
    - run: pipenv install --python "$PYTHON_VERSION" --deploy --dev
      env:
        PYTHON_VERSION: ${{ matrix.python-version }}
    # > TypeError: Cannot interpret '<attribute 'dtype' of 'numpy.generic' objects>' as a data type
    - run: pipenv run pip install numpy==1.19.5
      if: startsWith(matrix.pandas-version, '0.')
    # `pipenv install --selective-upgrade "pandas==$PANDAS_VERSION"` was not effective
    - run: '[ -z "$PANDAS_VERSION" ] || pipenv run pip install "pandas==$PANDAS_VERSION"'
      env:
        PANDAS_VERSION: ${{ matrix.pandas-version }}
    - run: pipenv graph
    - run: pipenv run pytest --cov="$(cat *.egg-info/top_level.txt)" --cov-report=term-missing --cov-fail-under=100
    - run: pipenv run pylint --load-plugins=pylint_import_requirements "$(cat *.egg-info/top_level.txt)"
    # workaround pylint reporting:
    # > E0401: Unable to import 'freesurer_volume_reader' (import-error)
    # pyproject.toml broken?
    - run: >-
        printenv GITHUB_WORKSPACE
        | tee "$(pipenv --venv)/lib/python${PYTHON_VERSION}/site-packages/easy-install.pth"
      env:
        PYTHON_VERSION: ${{ matrix.python-version }}
    - run: pipenv run pylint tests
    - run: pipenv run mypy "$(cat *.egg-info/top_level.txt)" tests
    # >=2.1.0 to support GITHUB_TOKEN
    # COVERALLS_REPO_TOKEN required manual configuration of secret
    # https://github.com/TheKevJames/coveralls-python/commit/f597109b62fadaf900af79d4f08a7debee5229e2
    - run: pip install 'coveralls>=2.1.0,<4'
    - run: coveralls
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        # https://github.com/TheKevJames/coveralls-python/issues/240#issuecomment-758336355
        COVERALLS_SERVICE_NAME: github
  install:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v3
    - uses: actions/setup-python@v4
      with: {python-version: 3.9}
    - run: '! freesurfer-volume-reader --help'
    - run: pip install wheel==0.37.1
    - run: python setup.py bdist_wheel
    - run: pip install dist/*.whl
    - run: freesurfer-volume-reader --help
  test-examples: # sync with https://github.com/fphammerle/freesurfer-surface/blob/dev/.github/workflows/python.yml#L73
    runs-on: ubuntu-18.04
    strategy:
      matrix:
        python-version:
        - '3.7'
        - '3.8'
        - '3.9'
        - '3.10'
      fail-fast: false
    defaults:
      run:
        working-directory: examples/
    steps:
    - uses: actions/checkout@v3
    - uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}
    - run: pip install --upgrade pipenv==2022.9.21
    - run: pipenv --python "$(which python)" install --deploy --dev
    - run: pipenv graph
    # > the default behaviour is to abort conversion [...] if one of the cells throws an error
    - run: pipenv run jupyter nbconvert --execute --inplace *.ipynb
    # revert line specifying version of python interpreter
    - run: sudo apt-get update
    - run: sudo apt-get install --yes --no-install-recommends patchutils
    - run: >-
        git diff --unified=0
        | grepdiff --output-matching=hunk '^\(   "version":\|    "execution": {\|       "<img src=\\"data:image/png;base64,\)'
        | patch --reverse
    - run: git diff --exit-code