Fix workflow YAML syntax error #26
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| name: Unit Test in NSLS-II Conda Environment | ||
| on: | ||
| workflow_call: | ||
| inputs: | ||
| conda_env_name: | ||
| description: 'Name of the conda environment to use for running the test' | ||
| required: true | ||
| type: string | ||
| zenodo_id: | ||
| description: 'Zenodo ID for the archived conda environment' | ||
| required: true | ||
| type: string | ||
| md5_checksum: | ||
| description: 'MD5 checksum for the archived conda environment' | ||
| required: true | ||
| type: string | ||
| python-version: | ||
| description: 'Python version ID to use for running the test' | ||
| required: true | ||
| type: string | ||
| jobs: | ||
| test-in-conda-env: | ||
| runs-on: ubuntu-latest | ||
| defaults: | ||
| run: | ||
| shell: "bash -l {0}" | ||
| steps: | ||
| - name: Set env vars | ||
| run: | | ||
| export REPOSITORY_NAME="${GITHUB_REPOSITORY#*/}" # just the repo, as opposed to org/repo | ||
| echo "REPOSITORY_NAME=${REPOSITORY_NAME}" >> $GITHUB_ENV | ||
| export CONDA_ENV_NAME=${{ inputs.conda_env_name }} | ||
| echo "CONDA_ENV_NAME=${CONDA_ENV_NAME}" >> $GITHUB_ENV | ||
| export ZENODO_ID=${{ inputs.zenodo_id }} | ||
| echo "ZENODO_ID=${ZENODO_ID}" >> $GITHUB_ENV | ||
| export MD5_CHECKSUM=${{ inputs.md5_checksum }} | ||
| echo "MD5_CHECKSUM=${MD5_CHECKSUM}" >> $GITHUB_ENV | ||
| # Workaround for unset GDAL env variables used by newer conda envs | ||
| export GDAL_DATA="${GDAL_DATA-''}" | ||
| echo "GDAL_DATA=${GDAL_DATA}" >> $GITHUB_ENV | ||
| export GDAL_DRIVER_PATH="${GDAL_DRIVER_PATH-''}" | ||
| echo "GDAL_DRIVER_PATH=${GDAL_DRIVER_PATH}" >> $GITHUB_ENV | ||
| export GEOTIFF_CSV="${GEOTIFF_CSV-''}" | ||
| echo "GEOTIFF_CSV=${GEOTIFF_CSV}" >> $GITHUB_ENV | ||
| # Workaround for unset MKL env variables used by newer conda envs | ||
| export MKL_INTERFACE_LAYER="${MKL_INTERFACE_LAYER-''}" | ||
| echo "MKL_INTERFACE_LAYER=${MKL_INTERFACE_LAYER}" >> $GITHUB_ENV | ||
| - name: Check out the code repo | ||
| uses: actions/checkout@v4 | ||
| - name: "Workaround: Fix .condarc MultipleKeysError" | ||
| run: | | ||
| sed -i '/auto_activate_base/d' /home/runner/.condarc || true | ||
| sed -i '/auto_activate:/d' /home/runner/.condarc || true | ||
| - name: Set up Python ${{ inputs.python-version }} with conda | ||
| uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| activate-environment: ${{ env.REPOSITORY_NAME }}-py${{ inputs.python-version }} | ||
| auto-update-conda: true | ||
| miniconda-version: "latest" | ||
| python-version: ${{ inputs.python-version }} | ||
| mamba-version: "*" | ||
| channels: conda-forge | ||
| - name: Cache the archived conda environment | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: ~/miniconda/envs/${{ env.CONDA_ENV_NAME }} | ||
| key: ${{ env.CONDA_ENV_NAME }}-${{ runner.os }}-${{ env.MD5_CHECKSUM }}-${{ env.CACHE_NUMBER }} | ||
| env: | ||
| # Increase this value to reset cache if ${CONDA_ENV_NAME}.tar.gz has not changed | ||
| CACHE_NUMBER: 0 | ||
| id: cache-conda-archive | ||
| - name: Download and install the archived conda environment | ||
| if: steps.cache-conda-archive.outputs.cache-hit != 'true' | ||
| run: | | ||
| set -vxeuo pipefail | ||
| conda activate "${{ env.REPOSITORY_NAME }}-py${{ inputs.python-version }}" | ||
| url="https://zenodo.org/record/${ZENODO_ID}/files/${CONDA_ENV_NAME}.tar.gz?download=1" | ||
| wget --progress=dot:giga ${url} -O ${CONDA_ENV_NAME}.tar.gz | ||
| status=$? | ||
| if [ $status -gt 0 ]; then | ||
| echo "Cannot download from ${url}. Exit code: ${status}" | ||
| exit $status | ||
| fi | ||
| echo "${MD5_CHECKSUM} ${CONDA_ENV_NAME}.tar.gz" > checksum.txt | ||
| md5sum --check checksum.txt | ||
| mkdir -p $HOME/miniconda/envs/${CONDA_ENV_NAME} | ||
| tar -xf ${CONDA_ENV_NAME}.tar.gz -C $HOME/miniconda/envs/${CONDA_ENV_NAME} | ||
| - name: Activate and inspect the archived conda environment | ||
| run: | | ||
| set -vxeuo pipefail | ||
| conda activate $HOME/miniconda/envs/${CONDA_ENV_NAME} | ||
| conda unpack | ||
| conda info -a | ||
| conda env list | ||
| conda list | ||
| pip list | ||
| - name: Install the package and its dependencies | ||
| run: | | ||
| set -vxeuo pipefail | ||
| conda activate $HOME/miniconda/envs/${CONDA_ENV_NAME} | ||
| echo "Using conda environment at ${CONDA_PREFIX}" | ||
| pip install --upgrade pip setuptools wheel | ||
| # Fix backports issue | ||
| pip uninstall -y backports || true | ||
| pip install backports.tarfile | ||
| pip install -r requirements-dev.txt | ||
| pip install -r requirements-extras.txt | ||
| pip install -e . | ||
| pip list | ||
| - name: Test with pytest | ||
| run: | | ||
| set -vxeuo pipefail | ||
| conda activate $HOME/miniconda/envs/${CONDA_ENV_NAME} | ||
| echo "Using conda environment at ${CONDA_PREFIX}" | ||
| coverage run --source=csxtools run_tests.py | ||
| coverage xml | ||
| - name: Upload coverage to Codecov | ||
| uses: codecov/codecov-action@v2 | ||
| with: | ||
| file: ./coverage.xml | ||
| flags: conda-env-unittests | ||
