🚧 switch mamba installation #627
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| name: Run unit tests, integration tests, and publish package if tagged | |
| on: | |
| push: | |
| branches: [main, dev] | |
| pull_request: | |
| branches: [main, dev] | |
| release: | |
| types: [published] | |
| schedule: | |
| - cron: '0 2 * * 3,6' | |
| jobs: | |
| run-unit-and-integration-tests-with-conda-install: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", | |
| #"macos-13", | |
| # "windows-latest" # rrcovNA cannot be build from source on windows-server | |
| ] | |
| python-version: ["3.8", "3.9", "3.10"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| # miniforge-variant: Mambaforge | |
| # miniforge-version: latest | |
| # conda-solver: libmamba | |
| # use-mamba: true | |
| # channels: conda-forge,defaults | |
| python-version: ${{ matrix.python-version }} | |
| # mamba-version: "*" | |
| # channels: conda-forge,defaults | |
| channel-priority: strict | |
| environment-file: snakemake_env.yml | |
| activate-environment: snakemake | |
| auto-activate-base: true | |
| auto-update-conda: true | |
| # - uses: mamba-org/setup-micromamba@v1 | |
| # with: | |
| # micromamba-version: 'latest' # any version from https://github.com/mamba-org/micromamba-releases | |
| # environment-file: snakemake_env.yml | |
| # create-args: >- | |
| # python=${{ matrix.python-version }} | |
| # init-shell: >- | |
| # bash | |
| # cache-environment: false | |
| # post-cleanup: 'none' | |
| # - name: inspect-conda-environment | |
| # run: | | |
| # conda info | |
| # conda list | |
| # conda env export --from-history --no-builds > environment.yml | |
| # conda env export --no-builds | |
| # conda env export --no-builds > environment_w_versions.yml | |
| # - name: test-r-kernel-imports | |
| # run: | | |
| # Rscript -e "library(stringi)" | |
| # Rscript -e "library(stringr)" | |
| # Rscript -e "library(reshape2)" | |
| - name: Dry-Run demo workflow (integration test) | |
| run: | | |
| cd project | |
| snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml --use-conda -n | |
| - name: Run demo workflow (integration test) | |
| continue-on-error: true | |
| run: | | |
| cd project | |
| snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda | |
| - name: Show current files in conda snakemake folder | |
| run: ls -l project/.snakemake/conda/ | |
| - name: Run demo workflow again (in case of installation issues) | |
| continue-on-error: true | |
| run: | | |
| cd project | |
| snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda | |
| - name: Run demo workflow again (in case of installation issues) - one thread | |
| run: | | |
| cd project | |
| snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml --use-conda | |
| - name: Archive results | |
| # https://github.com/actions/upload-artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.os }}-${{ matrix.python-version }}-example-workflow-results | |
| path: | | |
| project/runs/example/ | |
| environment.yml | |
| environment_w_versions.yml | |
| run-unit-local-pip-installation: | |
| runs-on: ${{ matrix.os }} | |
| name: test-pip-installation | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest",] | |
| # "macos-latest", "windows-latest"] | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # - uses: actions/setup-python@v5 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| auto-update-conda: true | |
| activate-environment: test | |
| auto-activate-base: true | |
| - name: check conda | |
| run: | | |
| conda info | |
| conda list | |
| conda info -e | |
| which python | |
| conda activate test | |
| which pip | |
| - name: Install build dependencies explicitly | |
| run: | | |
| python -m pip install setuptools_scm | |
| conda list | |
| - name: install pimms | |
| run: python -m pip install . | |
| # - name: install njab | |
| # run: python -m pip install njab | |
| - name: Install pytest | |
| run: pip install pytest pytest-cov | |
| - name: Run pytest | |
| run: pytest . | |
| - name: Install papermill | |
| run: pip install papermill ipykernel | |
| - name: View papermill help message for notebooks (as scripts) | |
| run: | | |
| cd project | |
| papermill 01_0_split_data.ipynb --help-notebook | |
| papermill 01_1_train_VAE.ipynb --help-notebook | |
| papermill 01_1_train_DAE.ipynb --help-notebook | |
| papermill 01_1_train_CF.ipynb --help-notebook | |
| - name: Run tutorial notebooks | |
| run: | | |
| cd project | |
| mkdir runs | |
| papermill 04_1_train_pimms_models.ipynb runs/04_1_train_pimms_models.ipynb | |
| papermill 04_1_train_pimms_models.ipynb runs/04_1_train_pimms_models_no_val.ipynb -p sample_splits False | |
| publish: | |
| name: Publish package | |
| if: startsWith(github.ref, 'refs/tags') | |
| needs: | |
| - run-unit-and-integration-tests-with-conda-install | |
| - run-unit-local-pip-installation | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.8" | |
| - name: Install twine and build | |
| run: python -m pip install --upgrade twine build | |
| - name: Build | |
| run: python -m build | |
| - uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |