Add prolif test dependencies (#71) #96
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| name: GH Actions Cron CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| # once a week at midnight on Sunday | |
| - cron: "0 3 * * 0" | |
| concurrency: | |
| # Commits to develop/master will cancel each other, but PRs will only cancel | |
| # commits within the same PR | |
| group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}" | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| gen_matrix: | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| matrix: ${{ steps.get-mdakits.outputs.matrix }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - id: get-python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.9 | |
| - id: get-mdakits | |
| run: | | |
| mdakit=$(python utils/get_dir_matrix.py) | |
| echo "matrix=${mdakit}" >> $GITHUB_OUTPUT | |
| mdakit-ci: | |
| needs: gen_matrix | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| mdakit: ${{fromJSON(needs.gen_matrix.outputs.matrix)}} | |
| jobstep: ['latest', 'develop'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - id: prev-python-ver | |
| name: prev-python-ver | |
| uses: MDAnalysis/get-latest-python-version@main | |
| with: | |
| last-n-minor-release: 1 | |
| - id: get-base-python-deps | |
| name: get-base-python-deps | |
| run: | | |
| pip install requests setuptools packaging pyyaml pydantic PyGithub | |
| - id: check-set-python-bounds | |
| name: check-set-python-bounds | |
| continue-on-error: true | |
| run: | | |
| basepy=${{steps.prev-python-ver.outputs.python-version}} | |
| pyver=$(python utils/check_python_ver.py --mdakit "${{matrix.mdakit}}" --maxpyver ${basepy}) | |
| echo "PYVER=${pyver}" >> $GITHUB_ENV | |
| - id: install-conda-env | |
| name: install-conda-env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ env.PYVER }} | |
| add-pip-as-python-dependency: true | |
| architecture: x64 | |
| use-mamba: true | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge, defaults | |
| channel-priority: flexible | |
| auto-update-conda: true | |
| show-channel-urls: true | |
| - id: install-conda-base-deps | |
| name: install-conda-base-deps | |
| run: | | |
| mamba install requests setuptools packaging pyyaml pydantic | |
| pip install PyGithub | |
| - id: install-mdakit | |
| name: install-mdakit | |
| continue-on-error: true | |
| run: | | |
| if [[ ${{ matrix.jobstep }} == "develop" ]]; then | |
| type="src" | |
| else | |
| type="install" | |
| fi | |
| install=$(python utils/get_install.py --itype ${type} --mdakit ${{matrix.mdakit}}) | |
| echo "install=${install}" | |
| eval ${install} | |
| - id: install-test-deps | |
| name: install-test-deps | |
| continue-on-error: true | |
| run: | | |
| install=$(python utils/get_testdeps.py --mdakit ${{matrix.mdakit}}) | |
| echo "install tests:${install}" | |
| eval ${install} | |
| - id: install-mdanalysis | |
| name: install-mdanalysis | |
| uses: MDAnalysis/install-mdanalysis@main | |
| continue-on-error: true | |
| with: | |
| version: ${{ matrix.jobstep }} | |
| install-tests: true | |
| installer: mamba | |
| shell: bash -l {0} | |
| - id: run-tests | |
| name: run-tests | |
| continue-on-error: true | |
| run: | | |
| tests=$(python utils/get_runtests.py --mdakit ${{matrix.mdakit}} --runtype ${{matrix.jobstep}}) | |
| echo "tests: ${tests}" | |
| eval ${tests} | |
| - id: store-errors | |
| name: store-errors | |
| run: | | |
| echo "install_python=${{ steps.check-set-python-bounds.outcome }}" >> $GITHUB_ENV | |
| echo "install_mdakit=${{ steps.install-mdakit.outcome }}" >> $GITHUB_ENV | |
| echo "install_test_deps=${{ steps.install-test-deps.outcome }}" >> $GITHUB_ENV | |
| echo "install_mdanalysis=${{ steps.install-mdanalysis.outcome }}" >> $GITHUB_ENV | |
| echo "run_tests=${{ steps.run-tests.outcome }}" >> $GITHUB_ENV | |
| - id: write-errors | |
| name: write-errors | |
| run: | | |
| python utils/write-ci-status-json.py --tag ${{ matrix.jobstep }} --mdakit ${{ matrix.mdakit }} | |
| - id: upload-artifacts | |
| name: upload-artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: cron-statuses-${{ matrix.mdakit }}-${{ matrix.jobstep }} | |
| path: ${{ matrix.mdakit }}-${{ matrix.jobstep }}-statuses.json | |
| retention-days: 1 | |
| if-no-files-found: error | |
| process_results: | |
| if: ${{ always() }} | |
| needs: mdakit-ci | |
| runs-on: ubuntu-22.04 | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| packages: none | |
| issues: write | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| path: json-statuses/ | |
| - name: list-temp-files | |
| run: ls -l json-statuses/*/ | |
| - id: get-base-python-deps | |
| name: get-base-python-deps | |
| run: | | |
| pip install requests setuptools packaging pyyaml pydantic PyGithub | |
| - id: combine-write-raise-issues | |
| name: combine-write-raise-issues | |
| run: | | |
| python utils/handle-status.py | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| - uses: stefanzweifel/git-auto-commit-action@v4 | |
| with: | |
| commit_message: commit changes to status files | |
| skip_dirty_check: false | |
| skip_fetch: false | |
| deploy_docs: | |
| if: ${{ always() }} | |
| needs: process_results | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: setup_micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: docs/requirements.yaml | |
| environment-name: MDAKitRegistry-docs | |
| create-args: >- | |
| python=3.9 | |
| pip | |
| - name: build_docs | |
| run: | | |
| cd docs && sphinx-build -b html source build | |
| - name: deploy docs | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: ./docs/build | |
| cname: mdakits.mdanalysis.org | |
| user_name: 'github-actions' | |
| user_email: '[email protected]' |