add save plots option to doc #246
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: GH Actions CI | |
| on: [push] | |
| # push: | |
| # branches: | |
| # - main | |
| # pull_request: | |
| # branches: | |
| # - main | |
| # schedule: | |
| # # Weekly tests at midnight on Sundays run on main by default: | |
| # # Scheduled workflows run on the latest commit on the default or base branch. | |
| # # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule) | |
| # - cron: "0 0 * * 0" | |
| concurrency: | |
| # Specific group naming so CI is only cancelled | |
| # within same PR or on merge to main | |
| group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| environment-config: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| stable-python-version: ${{ steps.get-compatible-python.outputs.stable-python }} | |
| python-matrix: ${{ steps.get-compatible-python.outputs.python-versions }} | |
| steps: | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - id: get-compatible-python | |
| uses: MDAnalysis/mdanalysis-compatible-python@main | |
| main-tests: | |
| if: "github.repository == 'BioMemPhys-FAU/domhmm'" | |
| needs: environment-config | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: [3.11] #${{ fromJSON(needs.environment-config.outputs.python-matrix) }} | |
| mdanalysis-version: ["latest"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build information | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| # More info on options: https://github.com/conda-incubator/setup-miniconda | |
| - name: Install conda dependencies | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| add-pip-as-python-dependency: true | |
| architecture: x64 | |
| miniforge-variant: Mambaforge | |
| use-mamba: true | |
| channels: conda-forge, defaults | |
| activate-environment: domhmm-test | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| show-channel-urls: true | |
| - name: Install MDAnalysis version | |
| uses: MDAnalysis/install-mdanalysis@main | |
| with: | |
| version: ${{ matrix.mdanalysis-version }} | |
| install-tests: false | |
| installer: mamba | |
| shell: bash -l {0} | |
| - name: Install package | |
| run: | | |
| python --version | |
| python -m pip install . --no-deps | |
| - name: Python information | |
| run: | | |
| which python | |
| which pip | |
| pip list | |
| conda info | |
| conda list | |
| - name: Run tests | |
| run: | | |
| pytest -n 2 -v --cov=domhmm --cov-report=xml --color=yes domhmm/tests/ | |
| - name: codecov | |
| if: github.repository == 'BioMemPhys-FAU/domhmm' && github.event_name != 'schedule' | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: coverage.xml | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| verbose: True | |
| pylint_check: | |
| if: "github.repository == 'BioMemPhys-FAU/domhmm'" | |
| needs: environment-config | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ needs.environment-config.outputs.stable-python-version }} | |
| - name: Install Pylint | |
| run: | | |
| which pip | |
| which python | |
| pip install pylint mdanalysis | |
| - name: Run Pylint | |
| env: | |
| PYLINTRC: .pylintrc | |
| run: | | |
| pylint domhmm | |
| pypi_check: | |
| if: "github.repository == 'BioMemPhys-FAU/domhmm'" | |
| needs: environment-config | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ needs.environment-config.outputs.stable-python-version }} | |
| - name: Install dependencies | |
| run: | | |
| pip install setuptools cython numpy twine | |
| - name: Build package | |
| run: | | |
| python setup.py sdist | |
| - name: Check package build | |
| run: | | |
| DISTRIBUTION=$(ls -t1 dist/domhmm-*.tar.gz | head -n 1) | |
| test -n "${DISTRIBUTION}" || { echo "no distribution dist/domhmm-*.tar.gz found"; exit 1; } | |
| echo "twine check $DISTRIBUTION" | |
| twine check $DISTRIBUTION |