Added piechart figure for the pypi description #60
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| name: build | |
| on: | |
| workflow_dispatch: | |
| push: | |
| pull_request: | |
| release: | |
| types: [created] | |
| jobs: | |
| pymaboss_test: | |
| name: Testing pyMaBoSS (Linux) | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| python: | |
| - "3.8" | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| - "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| python-version: ${{ matrix.python }} | |
| - name: Install MaBoSS | |
| run: | | |
| conda install -c colomoto maboss | |
| - name: Test MaBoSS | |
| run: | | |
| MaBoSS --version | |
| - name: Install dependencies | |
| run: | | |
| pip3 install pip coveralls --upgrade | |
| - name: Launch MaBoSS Server docker | |
| run: | | |
| docker run -p 7777:7777 --network host -d sysbiocurie/maboss | |
| - name: Install pyMaBoSS | |
| run: | | |
| pip3 install . | |
| - name: Test pyMaBoSS | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| coverage run -m unittest discover -v | |
| coveralls --service=github | |
| pymaboss_scripts: | |
| name: Testing pyMaBoSS scripts (Linux) | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| python: | |
| - "3.8" | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| - "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| python-version: ${{ matrix.python }} | |
| - name: Install MaBoSS | |
| run: | | |
| conda install -c colomoto maboss | |
| - name: Test MaBoSS | |
| run: | | |
| MaBoSS --version | |
| - name: Install dependencies | |
| run: | | |
| pip3 install pip coveralls --upgrade | |
| - name: Launch MaBoSS Server docker | |
| run: | | |
| docker run -p 7777:7777 --network host -d sysbiocurie/maboss | |
| - name: Install pyMaBoSS | |
| run: | | |
| pip3 install . | |
| - name: Test pyMaBoSS | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| coverage run -a scripts/MBSS_FormatTable.py test/p53_Mdm2.bnd test/p53_Mdm2_runcfg.cfg | |
| coverage run -a scripts/UpPMaBoSS.py test/CellFateModel.bnd test/CellFateModel_1h.cfg test/CellFate_1h.upp | |
| coveralls --service=github | |
| pymaboss_test_macos: | |
| name: Testing pyMaBoSS (MacOS) | |
| runs-on: macos-11 | |
| strategy: | |
| matrix: | |
| python: | |
| - "3.8" | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| - "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| python-version: ${{ matrix.python }} | |
| - name: Install MaBoSS | |
| run: | | |
| conda install -c colomoto maboss | |
| - name: Test MaBoSS | |
| run: | | |
| MaBoSS --version | |
| - name: Install dependencies | |
| run: | | |
| pip3 install pip coveralls --upgrade | |
| - name: Install pyMaBoSS | |
| run: | | |
| pip3 install . | |
| - name: Test pyMaBoSS | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| coverage run -m unittest test.test_conversion | |
| coverage run -m unittest test.test_ensemble | |
| coverage run -m unittest test.test_loadmodels | |
| coverage run -m unittest test.test_probtrajs | |
| coverage run -m unittest test.test_statdist | |
| coverage run -m unittest test.test_types | |
| coverage run -m unittest test.test_uppmaboss | |
| coverage run -m unittest test.test_pipelines | |
| coveralls --service=github | |
| pymaboss_scripts_macos: | |
| name: Testing pyMaBoSS scripts (MacOS) | |
| runs-on: macos-11 | |
| strategy: | |
| matrix: | |
| python: | |
| - "3.8" | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| - "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: s-weigand/setup-conda@v1 | |
| with: | |
| update-conda: true | |
| python-version: ${{ matrix.python }} | |
| - name: Install MaBoSS | |
| run: | | |
| conda install -c colomoto maboss | |
| - name: Test MaBoSS | |
| run: | | |
| MaBoSS --version | |
| - name: Install dependencies | |
| run: | | |
| pip3 install pip coveralls --upgrade | |
| - name: Install pyMaBoSS | |
| run: | | |
| pip3 install . | |
| - name: Test pyMaBoSS | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| coverage run -a scripts/MBSS_FormatTable.py test/p53_Mdm2.bnd test/p53_Mdm2_runcfg.cfg | |
| coverage run -a scripts/UpPMaBoSS.py test/CellFateModel.bnd test/CellFateModel_1h.cfg test/CellFate_1h.upp | |
| coveralls --service=github | |
| conda_pymaboss: | |
| name: pyMaBoSS Conda package | |
| runs-on: ubuntu-20.04 | |
| needs: [pymaboss_test, pymaboss_scripts, pymaboss_test_macos, pymaboss_scripts_macos] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: s-weigand/setup-conda@v1 | |
| - name: Install conda-build and anaconda-client | |
| run: conda install conda-build anaconda-client | |
| - name: Build pyMaBoSS Anaconda package | |
| run: | | |
| conda build conda -c colomoto | |
| - name: Upload Anaconda package to colomoto's repo | |
| if: github.event_name == 'release' && github.event.action == 'created' && github.repository == 'colomoto/pyMaBoSS' | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /usr/share/miniconda/conda-bld/noarch/*.tar.bz2 --force; | |
| - name: Upload Anaconda package to vincent-noel's repo | |
| if: github.repository == 'vincent-noel/pyMaBoSS' && github.ref == 'refs/heads/master' | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /usr/share/miniconda/conda-bld/noarch/*.tar.bz2 --force; | |
| pypi_pymaboss: | |
| name: pyMaBoSS PyPi package | |
| runs-on: ubuntu-20.04 | |
| needs: [pymaboss_test, pymaboss_scripts, pymaboss_test_macos, pymaboss_scripts_macos] | |
| if: github.event_name == 'release' && github.event.action == 'created' && github.repository == 'colomoto/pyMaBoSS' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install twine | |
| run: pip3 install twine | |
| - name: Build pyMaBoSS PyPi package | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }} | |
| run: | | |
| python3 setup.py sdist bdist_wheel | |
| python3 -m twine upload --skip-existing dist/* |