python-request.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Python on pull request

on:
  pull_request:
  schedule:
    # * is a special character in YAML so you have to quote this string
    - cron:  '0 0 1 * *'

jobs:
  build:

    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest]
        python-version: [3.11]
    env:
      OS: ${{ matrix.os }}
      PYTHON: ${{ matrix.python-version }}
    defaults:
      run:
        shell: bash -l {0}

    steps:
    - uses: actions/checkout@v4
    - name: Set up mamba ${{ matrix.python-version }}
      uses: mamba-org/setup-micromamba@v1
      with:
        micromamba-version: 'latest'
        environment-file: environment.yml
        init-shell: bash
        environment-name: pyTMD
        cache-environment: true
        post-cleanup: 'all'
        create-args: >-
          blas
          boto3
          python=${{ matrix.python-version }}
          flake8
          pytest
          pytest-cov
          cython
          geopandas
          jplephem
          octave
          oct2py
          pyarrow
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
    - name: "Check if repository secrets are accessible"
      id: secrets
      run: |
        if [ "${{ secrets.EARTHDATA_USERNAME }}" == '' ] ; then
            echo "accessible=false" >> $GITHUB_OUTPUT;
            echo "::debug::GitHub secrets unavailable for Actions";
        else
            echo "accessible=true" >> $GITHUB_OUTPUT;
            echo "::debug::GitHub secrets available for Actions";
        fi
    - name: Checkout Matlab TMD Toolbox
      if: steps.secrets.outputs.accessible == 'true'
      uses: actions/checkout@v4
      with:
        repository: EarthAndSpaceResearch/TMD_Matlab_Toolbox_v2.5
        path: TMD_Matlab_Toolbox
        ref: master
    - name: Test with pytest
      if: steps.secrets.outputs.accessible == 'true'
      run: |
        pip install --no-deps .
        pytest --verbose --capture=no --cov=./ --cov-report=xml \
            --username=${{ secrets.EARTHDATA_USERNAME }} \
            --password=${{ secrets.EARTHDATA_PASSWORD }} \
            --aws-access=${{ secrets.AWS_ACCESS_KEY_ID }} \
            --aws-secret=${{ secrets.AWS_SECRET_ACCESS_KEY }} \
            --aws-region=${{ secrets.AWS_REGION_NAME }}
    - name: Upload coverage to Codecov
      if: steps.secrets.outputs.accessible == 'true'
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml
        flags: unittests
        env_vars: OS,PYTHON
        name: codecov-umbrella
        fail_ci_if_error: true
        verbose: true
    - name: Archive code coverage results
      if: steps.secrets.outputs.accessible == 'true'
      uses: actions/upload-artifact@v3
      with:
        name: code-coverage-report
        path: ./coverage.xml