Fixes / changes to docs in "Data processing" pages #2129
Workflow file for this run
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| name: Test PR | |
| on: | |
| pull_request: | |
| paths-ignore: ["**/docker.yaml", "docs"] | |
| env: | |
| CONDA_ENV: echopype | |
| NUM_WORKERS: 2 | |
| jobs: | |
| test: | |
| name: ${{ matrix.python-version }}--${{ matrix.runs-on }} | |
| runs-on: ${{ matrix.runs-on }} | |
| if: ${{ !contains(github.event.pull_request.title, '[skip ci]') }} | |
| continue-on-error: ${{ matrix.experimental }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10"] | |
| runs-on: [ubuntu-latest] | |
| experimental: [false] | |
| # TODO: Uncomment when netcdf is unpinned | |
| # include: | |
| # - runs-on: ubuntu-latest | |
| # python-version: "3.11" | |
| # experimental: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| services: | |
| # TODO: figure out how to update tag when there's a new one | |
| minio: | |
| image: cormorack/minioci:latest | |
| ports: | |
| - 9000:9000 | |
| httpserver: | |
| image: cormorack/http:latest | |
| ports: | |
| - 8080:80 | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 # Fetch all history for all branches and tags. | |
| - name: Set environment variables | |
| run: | | |
| echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV | |
| - name: Setup micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: .ci_helpers/py${{ matrix.python-version }}.yaml | |
| environment-name: ${{ env.CONDA_ENV }} | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| - name: Print conda environment | |
| run: | | |
| micromamba info | |
| micromamba list | |
| - name: Remove docker-compose python | |
| if: ${{ matrix.python-version == '3.10' || matrix.python-version == '3.11' }} | |
| run: sed -i "/docker-compose/d" requirements-dev.txt | |
| - name: Install dev tools | |
| run: | | |
| micromamba install -c conda-forge -n ${{ env.CONDA_ENV }} --yes --file requirements-dev.txt | |
| # We only want to install this on one run, because otherwise we'll have | |
| # duplicate annotations. | |
| - name: Install error reporter | |
| if: ${{ matrix.python-version == '3.9' }} | |
| run: | | |
| python -m pip install pytest-github-actions-annotate-failures | |
| - name: Install echopype | |
| run: | | |
| python -m pip install -e .[plot] | |
| - name: Copying test data to services | |
| run: | | |
| python .ci_helpers/docker/setup-services.py --deploy --data-only --http-server ${{ job.services.httpserver.id }} | |
| # Check data endpoint | |
| curl http://localhost:8080/data/ | |
| - name: Finding changed files | |
| id: files | |
| uses: Ana06/[email protected] | |
| with: | |
| format: 'csv' | |
| - name: Print Changed files | |
| run: echo "${{ steps.files.outputs.added_modified_renamed }}" | |
| - name: Running all Tests | |
| if: contains(github.event.pull_request.title, '[all tests ci]') | |
| run: | | |
| pytest -vvv -rx --numprocesses=${{ env.NUM_WORKERS }} --max-worker-restart=3 --cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings |& tee ci_${{ matrix.python-version }}_test_log.log | |
| - name: Running Tests | |
| if: ${{ !contains(github.event.pull_request.title, '[all tests ci]') }} | |
| run: | | |
| python .ci_helpers/run-test.py --pytest-args="--log-cli-level=WARNING,-vvv,-rx,--numprocesses=${{ env.NUM_WORKERS }},--max-worker-restart=3,--disable-warnings" --include-cov ${{ steps.files.outputs.added_modified_renamed }} |& tee ci_${{ matrix.python-version }}_test_log.log | |
| - name: Upload ci test log | |
| if: ${{ success() || failure() }} | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ci_test_log | |
| path: ci_${{ matrix.python-version }}_test_log.log | |
| - name: Upload code coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: ./coverage.xml | |
| flags: unittests | |
| env_vars: RUNNER_OS,PYTHON_VERSION | |
| name: codecov-umbrella | |
| fail_ci_if_error: false |