New options for visualization #136
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| name: Test build and publish Cobramod to PyPI | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "0 5 * * 1" | |
| pull_request: | |
| types: [ opened, synchronize, reopened, closed ] | |
| branches: | |
| - master | |
| jobs: | |
| lint-format: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.7 | |
| - name: Install dependencies | |
| run: python -m pip install tox | |
| - name: Linter | |
| run: python -m tox -e lint | |
| - name: Format | |
| run: python -m tox -e format | |
| types: | |
| needs: [ lint-format ] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [ "3.10", "3.11", "3.12" ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: python -m pip install tox | |
| - name: Run type-checking | |
| run: python -m tox -e types | |
| build: | |
| needs: [ types ] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| cache: "pip" | |
| - name: Set up JS & build js | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: 20 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel build | |
| yarn install | |
| - name: Build JS | |
| run: yarn run vite build | |
| - name: Build package | |
| run: python -m build | |
| - name: Archive package as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: cobramod-dist | |
| path: | | |
| dist | |
| unittest: | |
| needs: [build] | |
| strategy: | |
| matrix: | |
| os: [ ubuntu-latest, macos-latest, windows-latest ] | |
| python-version: [ "3.10", "3.11", "3.12" ] | |
| runs-on: ${{ matrix.os}} | |
| steps: | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Display Python version | |
| run: python -c "import sys; print(sys.version)" | |
| - name: Download package as artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: cobramod-dist | |
| - name: Get file path | |
| id: path | |
| run: | | |
| file_path = $(find -name cobramod-*.whl) | |
| echo "file-path=$file_path" >> "$GITHUB_OUTPUT" | |
| echo $file_path | |
| echo ${{ steps.path.outputs.file-path }} | |
| - name: Install CobraMod & dependencies from wheel | |
| run: pip install ${{ steps.path.outputs.file-path }} | |
| - name: Install tox | |
| run: python -m pip install tox | |
| - name: Setup test suite | |
| run: tox -vv --notest | |
| - name: Credentials | |
| run: echo "${{ secrets.BIOCYC_USER }}\n${{ secrets.BIOCYC_PASS }}" >> credentials.txt | |
| - name: Run test suite | |
| run: tox --skip-pkg-install -e py | |
| build-publish: | |
| needs: [unittest] | |
| name: Build and publish the package to PyPI | |
| if: github.event.pull_request.merged == true && github.event_name != 'schedule' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Download package as artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: cobramod-dist | |
| path: | | |
| dist | |
| - name: Check the package | |
| run: twine check dist/* | |
| - name: Publish to PyPI | |
| env: | |
| TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} | |
| TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} | |
| run: | |
| twine upload --non-interactive dist/* |