Add pore analyser to md kits #423
Workflow file for this run
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| name: GH Actions CI | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| # 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-changed-mdakits.outputs.matrix }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - id: get-python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - id: files | |
| name: get changed filed | |
| uses: masesgroup/retrieve-changed-files@v3 | |
| with: | |
| format: 'json' | |
| - id: get-changed-mdakits | |
| name: build mdakit matrix | |
| run: | | |
| echo ${{ steps.files.outputs.all }} | |
| mdakit=$(python utils/get_affected_mdakits.py --json '${{ steps.files.outputs.all }}') | |
| echo ${mdakit} | |
| echo "matrix=${mdakit}" >> $GITHUB_OUTPUT | |
| env_config: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| python-stable: ${{ steps.get-compatible-python.outputs.stable-python }} | |
| python-min: ${{ steps.get-compatible-python.outputs.oldest-python }} | |
| steps: | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.12" | |
| - id: get-compatible-python | |
| uses: MDAnalysis/mdanalysis-compatible-python@main | |
| with: | |
| release: "develop" | |
| mdakit-ci: | |
| needs: [gen_matrix, env_config] | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| mdakit: ${{fromJSON(needs.gen_matrix.outputs.matrix)}} | |
| jobstep: ['latest', 'develop'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - id: get-base-python-deps | |
| name: get-base-python-deps | |
| run: | | |
| pip install requests setuptools packaging pyyaml pydantic PyGithub | |
| - id: check-set-python-bounds | |
| name: check-set-python-bounds | |
| continue-on-error: false | |
| run: | | |
| maxpy=${{needs.env_config.outputs.python-stable}} | |
| minpy=${{needs.env_config.outputs.python-min}} | |
| pyver=$(python utils/check_python_ver.py --mdakit "${{matrix.mdakit}}" --maxpyver ${maxpy} --minpyver ${minpy}) | |
| echo "PYVER=${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: false | |
| 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 ${install} | |
| - id: install-test-deps | |
| name: install-test-deps | |
| continue-on-error: false | |
| run: | | |
| install=$(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: false | |
| with: | |
| version: ${{ matrix.jobstep }} | |
| install-tests: true | |
| installer: mamba | |
| shell: bash -l {0} | |
| - id: run-tests | |
| name: run-tests | |
| continue-on-error: false | |
| run: | | |
| tests=$(python utils/get_runtests.py --mdakit ${{matrix.mdakit}} --runtype ${{matrix.jobstep}}) | |
| echo "tests: ${tests}" | |
| eval ${tests} |