pytest-with-coverage.yaml

name: pytest-with-coverage

on:
  push:
    branches: ['*']
  # Enable workflow to be triggered from GitHub CLI, browser, or via API
  # primarily for testing conda env solution for new Python versions
  workflow_dispatch:

jobs:
  pytest-with-coverage:
    permissions:
      contents: read
      pull-requests: write
    strategy:
      fail-fast: false
      matrix:
        python-version: [ '3.12' ]
    runs-on: 'ubuntu-latest'
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Set up Conda environment with Micromamba
        uses: mamba-org/setup-micromamba@422500192359a097648154e8db4e39bdb6c6eed7
        with:
           environment-file: envs/environment-test.yaml
           environment-name: salishsea-nowcast-test
           # environment caching does not play nicely with --editable installed packages
           cache-environment: false
           cache-downloads: true
           # persist downloads cache for 1 day
           cache-downloads-key: downloads-${{ steps.date.outputs.date }}
           create-args: >-
             python=${{ inputs.python-version }}

      - name: Install editable-mode dependency packages
        shell: bash -l {0}
        run: |
          python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/43ravens/NEMO_Nowcast.git#egg=NEMO_Nowcast
          python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/UBC-MOAD/moad_tools#egg=moad_tools
          python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/UBC-MOAD/Reshapr#egg=Reshapr
          python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/NEMO-Cmd.git#egg=NEMO-Cmd
          python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/SalishSeaCmd.git#egg=SalishSeaCmd
          python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable "git+https://github.com/SalishSeaCast/tools#egg=SalishSeaTools&subdirectory=SalishSeaTools"
          python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/FVCOM-Cmd.git#egg=FVCOM-Cmd
          # OPPTools is a private GitLab repo, so an access token is required
          python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://oauth2:${{ secrets.GITLAB_ACCESS_TOKEN }}@gitlab.com/mdunphy/OPPTools.git@6c784a4dc44dd9030aafe9a8519e5ae0b6cc3183#egg=OPPTools
          python3 -m pip install --editable $GITHUB_WORKSPACE

      - name: pytest package with coverage
        shell: bash -l {0}
        run: |
          pytest --cov=$GITHUB_WORKSPACE --cov-report=xml

      - name: Upload coverage report to Codecov
        uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be
        with:
          file: ./coverage.xml
          flags: unittests
          token: ${{ secrets.CODECOV_TOKEN }}