add VMD, PGMD/CGMD (#1466) #9165
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Checks | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| concurrency: | |
| # NOTE: the value of `group` should be chosen carefully, | |
| # otherwise we might end up over- or under-canceling workflow runs | |
| # github.head_ref is only defined for pull request events | |
| # so, if it's not present (i.e. event was triggered by push) | |
| # we use github.ref instead | |
| group: ${{ github.workflow }}-${{ github.head_ref || github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| # important to make sure that all commands on Windows are run using Bash | |
| # -l: login shell, needed when using Conda | |
| shell: bash -l {0} | |
| env: | |
| # --color=yes needed for colorized output to be shown in GHA logs | |
| # --pyargs watertap is needed to be able to define CLI options in watertap/conftest.py | |
| PYTEST_ADDOPTS: "--color=yes" | |
| PIP_PROGRESS_BAR: "off" | |
| WATERTAP_KERNEL_NAME: watertap-dev | |
| jobs: | |
| code-formatting: | |
| name: Check code is formatted (Black) | |
| # OS and/or Python version don't make a difference, so we choose ubuntu and 3.8 as defaults | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install Black | |
| # unlike the other jobs, we don't need to install WaterTAP and/or all the dev dependencies, | |
| # but we still want to specify the Black version to use in requirements-dev.txt for local development | |
| # so we extract the relevant line and pass it to a simple `pip install` | |
| run: | | |
| black_requirement="$(grep '^black==' requirements-dev.txt)" | |
| pip --no-cache-dir install "$black_requirement" | |
| - name: Run Black to verify that the committed code is formatted | |
| run: | | |
| black --check . | |
| pylint: | |
| name: Code linting (pylint) | |
| runs-on: ubuntu-latest | |
| needs: [code-formatting] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dev dependencies | |
| run: | | |
| pip install -r requirements-dev.txt | |
| pip list | |
| - name: Run pylint | |
| run: | | |
| pylint watertap | |
| tests: | |
| name: Tests (py${{ matrix.python-version }}/${{ matrix.os }}) | |
| runs-on: ${{ matrix.os-version }} | |
| needs: [code-formatting] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: | |
| - '3.9' | |
| - '3.10' | |
| - '3.11' | |
| os: | |
| - linux | |
| - win64 | |
| # - macos | |
| include: | |
| - os: linux | |
| os-version: ubuntu-20.04 | |
| - os: win64 | |
| os-version: windows-2019 | |
| # - os: macos | |
| # os-version: macos-10.15 | |
| - python-version: '3.10' | |
| # limit uploading coverage report for a single Python version in the matrix | |
| coverage: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: watertap-dev | |
| python-version: ${{ matrix.python-version }} | |
| miniforge-version: latest | |
| - name: Install dependencies | |
| run: | | |
| echo '::group::Output of "conda install" commands' | |
| conda install --quiet --yes pip setuptools wheel pandoc | |
| echo '::endgroup::' | |
| echo '::group::Output of "pip install" commands' | |
| pip install -r requirements-dev.txt | |
| echo '::endgroup::' | |
| echo '::group::Output of "conda install -c conda-forge cyipopt" command' | |
| conda install -c conda-forge cyipopt | |
| echo '::endgroup::' | |
| echo '::group::Display installed packages' | |
| conda list | |
| pip list | |
| pip show idaes-pse | |
| echo '::endgroup::' | |
| echo '::group::Output of "idaes get-extensions" command' | |
| idaes get-extensions --extra petsc --verbose | |
| echo '::endgroup::' | |
| - name: Add coverage report pytest options | |
| if: matrix.coverage | |
| run: | |
| | | |
| echo PYTEST_ADDOPTS="$PYTEST_ADDOPTS --cov --cov-report=xml" >> $GITHUB_ENV | |
| - name: Test with pytest | |
| run: | | |
| pytest --pyargs watertap --idaes-flowsheets --entry-points-group watertap.flowsheets | |
| - name: Upload coverage report as job artifact | |
| if: matrix.coverage | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-report-${{ matrix.os }} | |
| path: coverage.xml | |
| if-no-files-found: error | |
| - name: Test documentation code | |
| run: | | |
| make -C docs doctest -d | |
| # TODO: this should be moved to a dedicated job/workflow | |
| # until then, we can leave this here as a reminder | |
| - name: Test documentation links | |
| if: 'false' | |
| run: | | |
| make -C docs linkcheck -d | |
| upload-coverage: | |
| name: Upload coverage report (Codecov) | |
| needs: [tests] | |
| runs-on: ubuntu-latest | |
| steps: | |
| # the checkout step is needed to have access to codecov.yml | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| pattern: coverage-report-* | |
| - name: Upload coverage report to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| fail_ci_if_error: true | |
| verbose: true | |
| # NOTE: secrets are not available for pull_request workflows | |
| # However, as of 2024-02-10, Codecov is still allowing tokenless upload from PRs | |
| # but does require token for other workflows e.g. merge to `main` | |
| # see https://github.com/codecov/codecov-action/issues/1274#issuecomment-1934437359 | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| # downgrading after v0.7.0 broke tokenless upload | |
| # see codecov/codecov-action#1487 | |
| version: v0.6.0 | |
| user-mode-pytest: | |
| name: pytest (user mode) (py${{ matrix.python-version }}/${{ matrix.os }}) | |
| runs-on: ${{ matrix.os-version }} | |
| needs: [code-formatting] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: | |
| - '3.9' | |
| - '3.11' | |
| os: | |
| - linux | |
| - win64 | |
| include: | |
| - os: linux | |
| os-version: ubuntu-20.04 | |
| - os: win64 | |
| os-version: windows-2019 | |
| steps: | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: watertap | |
| python-version: ${{ matrix.python-version }} | |
| - name: Define install URL (default) | |
| env: | |
| _repo_full_name: watertap-org/watertap | |
| _ref_to_install: main | |
| run: | | |
| echo "_install_url=https://github.com/${_repo_full_name}/archive/${_ref_to_install}.zip" >> $GITHUB_ENV | |
| - name: Define install URL (for PRs) | |
| if: github.event.pull_request | |
| env: | |
| _repo_full_name: ${{ github.event.pull_request.head.repo.full_name }} | |
| _ref_to_install: ${{ github.event.pull_request.head.sha }} | |
| run: | |
| echo "_install_url=https://github.com/${_repo_full_name}/archive/${_ref_to_install}.zip" >> $GITHUB_ENV | |
| - name: Install watertap and testing dependencies | |
| run: | | |
| echo '::group::Output of "pip install" commands' | |
| pip install "watertap @ ${_install_url}" pytest | |
| echo '::endgroup::' | |
| echo '::group::Display installed packages' | |
| conda list | |
| pip list | |
| pip show idaes-pse | |
| echo '::endgroup::' | |
| echo '::group::Output of "idaes get-extensions" command' | |
| idaes get-extensions --extra petsc --verbose | |
| echo '::endgroup::' | |
| - name: Run pytest | |
| run: | | |
| pytest --pyargs watertap | |
| notebooks: | |
| name: Test notebooks (py${{ matrix.python-version }}/${{ matrix.os }}) | |
| runs-on: ${{ matrix.os-version }} | |
| needs: [code-formatting] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: | |
| - '3.9' | |
| - '3.11' | |
| os: | |
| - linux | |
| - win64 | |
| include: | |
| - os: linux | |
| os-version: ubuntu-20.04 | |
| - os: win64 | |
| os-version: windows-2019 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: watertap-dev | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| echo '::group::Output of "conda install" commands' | |
| conda install --quiet --yes pip setuptools wheel pandoc | |
| echo '::endgroup::' | |
| echo '::group::Output of "pip install" commands' | |
| pip install -r requirements-dev.txt | |
| echo '::endgroup::' | |
| echo '::group::Display installed packages' | |
| conda list | |
| pip list | |
| pip show idaes-pse | |
| echo '::endgroup::' | |
| echo '::group::Output of "idaes get-extensions" command' | |
| idaes get-extensions --extra petsc --verbose | |
| echo '::endgroup::' | |
| - name: Install Jupyter kernel | |
| run: | | |
| jupyter kernelspec list | |
| python -m ipykernel install --user --name "${{ env.WATERTAP_KERNEL_NAME }}" | |
| jupyter kernelspec list | |
| - name: Run pytest with nbmake | |
| run: | | |
| pytest --nbmake --nbmake-kernel="${{ env.WATERTAP_KERNEL_NAME }}" **/*.ipynb | |
| macos: | |
| name: macOS setup (EXPERIMENTAL) | |
| runs-on: macos-13 | |
| needs: [code-formatting] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: | |
| - '3.9' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: watertap | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install WaterTAP (dev) without idaes get-extensions | |
| run: | | |
| echo '::group::Output of "conda install" commands' | |
| conda install --quiet --yes pip=21.1 wheel setuptools pandoc | |
| echo '::endgroup::' | |
| echo '::group::Output of "pip install" commands' | |
| pip install -r requirements-dev.txt | |
| echo '::endgroup::' | |
| echo '::group::Display installed packages' | |
| conda list | |
| pip list | |
| pip show pyomo idaes-pse | |
| echo '::endgroup::' | |
| - name: Install Ipopt from conda-forge | |
| run: | |
| conda install --quiet --yes -c conda-forge ipopt=3.14.11 | |
| - name: Build Pyomo extensions | |
| run: | | |
| conda install --quiet --yes cmake | |
| # some failures are expected, but this should succeed as long as pynumero is built correctly | |
| pyomo build-extensions || python -c "from pyomo.contrib.pynumero.asl import AmplInterface; exit(0) if AmplInterface.available() else exit(1)" | |
| - name: Run pytest | |
| run: | | |
| pytest --pyargs watertap -k 'not (nf_dspmde.nf_ui or nf_dspmde.nf_with_bypass_ui or mvc.mvc_single_stage_ui or full_water_resource_recovery_facility.BSM2_P_extension_ui )' |