Add new subtopic pattern for datamart directory structure change (#305) #437
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| 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@06375d89d211a1232ef63355742e9e2e564bc7f7 | |
| 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@015f24e6818733317a2da2edd6290ab26238649a | |
| with: | |
| file: ./coverage.xml | |
| flags: unittests | |
| token: ${{ secrets.CODECOV_TOKEN }} |