Csse layout specification #897
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - next2024 | |
| pull_request: | |
| branches: | |
| - master | |
| - next2024 | |
| schedule: | |
| - cron: "9 16 * * 1" | |
| jobs: | |
| build: | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| cfg: | |
| #- conda-env: psi | |
| # python-version: 3.7 | |
| # label: Psi4-1.5 | |
| # runs-on: ubuntu-latest | |
| # pytest: "" | |
| # Note: removed Sep 2024 b/c too hard to reconcile w/pyd v2 | |
| - conda-env: psi-nightly | |
| python-version: "3.10" | |
| label: Psi4-1.6 | |
| runs-on: ubuntu-latest | |
| pytest: "" | |
| - conda-env: psi-cf | |
| python-version: "3.12" | |
| label: Psi4-1.8 | |
| runs-on: windows-latest | |
| pytest: "-k 'not (hes2 or qchem)'" | |
| - conda-env: torchani | |
| python-version: 3.8 | |
| label: ANI | |
| runs-on: ubuntu-latest | |
| pytest: "" | |
| - conda-env: openmm | |
| python-version: 3.8 | |
| label: OpenMM | |
| runs-on: ubuntu-latest | |
| pytest: "" | |
| - conda-env: xtb | |
| python-version: "3.10" | |
| label: xTB | |
| runs-on: ubuntu-latest | |
| pytest: "" | |
| #- conda-env: qcore | |
| # python-version: 3.7 | |
| # label: QCore | |
| # runs-on: ubuntu-latest | |
| # pytest: "" | |
| # Note: removed Sep 2024 b/c too hard to reconcile w/pyd v2. Manby approves. | |
| - conda-env: nwchem | |
| python-version: 3.8 | |
| label: NWChem70 | |
| runs-on: ubuntu-20.04 | |
| pytest: "" | |
| # formerly NWChem v6.6 with python-version: 3.6 & runs-on: ubuntu-16.04 but ubuntu env retired by GH Sep 2021 | |
| - conda-env: nwchem-cf | |
| python-version: 3.12 | |
| label: NWChem | |
| runs-on: ubuntu-latest | |
| pytest: "" | |
| - conda-env: mrchem | |
| python-version: 3.8 | |
| label: MRChem | |
| runs-on: ubuntu-latest | |
| pytest: "" | |
| - conda-env: adcc | |
| python-version: 3.8 | |
| label: ADCC | |
| runs-on: ubuntu-latest | |
| pytest: "" | |
| - conda-env: opt-disp | |
| python-version: 3.8 | |
| label: optimization-dispersion | |
| runs-on: ubuntu-latest | |
| pytest: "" | |
| - conda-env: opt-disp-cf | |
| python-version: 3.11 | |
| label: optimization-dispersion | |
| runs-on: windows-latest | |
| pytest: "-k 'not (hes2 or qchem)'" | |
| # 3.13 | |
| #- conda-env: disp-win | |
| # python-version: 3.12 | |
| # label: disp-win | |
| # runs-on: windows-latest | |
| # pytest: "" | |
| - conda-env: mace | |
| python-version: "3.10" | |
| label: MACE | |
| runs-on: ubuntu-latest | |
| pytest: "" | |
| - conda-env: aimnet2 | |
| python-version: 3.11 | |
| label: AIMNET2 | |
| runs-on: ubuntu-latest | |
| pytest: "" | |
| #- conda-env: nwchem | |
| # python-version: "3.10" | |
| # label: TeraChem | |
| # runs-on: ubuntu-20.04 | |
| # pytest: "" | |
| name: "🐍 ${{ matrix.cfg.python-version }} • ${{ matrix.cfg.label }} • ${{ matrix.cfg.runs-on }}" | |
| runs-on: ${{ matrix.cfg.runs-on }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Create Environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: test | |
| environment-file: devtools/conda-envs/${{ matrix.cfg.conda-env }}.yaml | |
| python-version: ${{ matrix.cfg.python-version }} | |
| auto-activate-base: false | |
| show-channel-urls: true | |
| add-pip-as-python-dependency: true | |
| # note: conda-forge chnl req'd for Mambaforge, but we'll spec in file, not here `channels: conda-forge,...` | |
| # note: any activate/deactivate use the conda cmd. other cmds use mamba cmd. | |
| - name: Special Config - NWChem | |
| if: "(matrix.cfg.label == 'NWChem70')" | |
| run: | | |
| sudo apt-get -y install nwchem | |
| - name: Special Config - QCore | |
| if: "(matrix.cfg.label == 'QCore')" | |
| run: | | |
| qcore --accept-license | |
| #docker.io/mtzgroup/terachem:latest | |
| #Usage: docker exec [OPTIONS] CONTAINER COMMAND [ARG...] | |
| - name: Special Config - QCElemental Dep | |
| #if: false | |
| run: | | |
| conda remove qcelemental --force | |
| python -m pip install 'git+https://github.com/loriab/QCElemental.git@csse_layout_536c' --no-deps | |
| # note: conda remove --force, not mamba remove --force b/c https://github.com/mamba-org/mamba/issues/412 | |
| # alt. is micromamba but not yet ready for setup-miniconda https://github.com/conda-incubator/setup-miniconda/issues/75 | |
| - name: Special Config - QCEngine Dep | |
| if: "(startsWith(matrix.cfg.label, 'Psi4')) || (matrix.cfg.label == 'ADCC') || (matrix.cfg.label == 'optimization-dispersion')" | |
| run: | | |
| conda remove qcengine --force | |
| # QCEngine CI and Psi4 are circularly dependent, so a hack is in order | |
| - name: Special Config - Faux Pydantic Upgrade | |
| if: "((matrix.cfg.label == 'Psi4-1.6') || (matrix.cfg.label == 'optimization-dispersion')) && (runner.os != 'Windows')" | |
| run: | | |
| sed -i s/from\ pydantic\ /from\ pydantic.v1\ /g ${CONDA_PREFIX}/lib/python${{ matrix.cfg.python-version }}/site-packages/psi4/driver/*py | |
| - name: Special Config - Forced Interface Upgrade | |
| if: "(matrix.cfg.label == 'Psi4-1.6')" | |
| run: | | |
| grep -r "local_options" ${CONDA_PREFIX}/lib/python${{ matrix.cfg.python-version }}/site-packages/psi4/driver/ | |
| sed -i "s/local_options/task_config/g" ${CONDA_PREFIX}/lib/python${{ matrix.cfg.python-version }}/site-packages/psi4/driver/procrouting/*py | |
| - name: Install QCEngine | |
| run: | | |
| python -m pip install . --no-deps | |
| - name: Environment Information | |
| run: | | |
| conda info | |
| conda list | |
| python -c "import qcelemental as q;print(q.__file__, q.__version__)" | |
| python -c "import qcengine as q;print(q.__file__, q.__version__)" | |
| git describe | |
| - name: QCEngineRecords | |
| if: "(matrix.cfg.label != 'Psi4-1.6')" | |
| run: | | |
| qcengine info | |
| export QCER_VER=`python -c "import qcengine.testing; print(qcengine.testing.QCENGINE_RECORDS_COMMIT)"` | |
| pip install git+https://github.com/MolSSI/QCEngineRecords.git@${QCER_VER}#egg=qcenginerecords | |
| python -c "import qcengine; print(qcengine.config.global_repr())" | |
| - name: PyTest | |
| run: | | |
| pytest -rws -v ${{ matrix.cfg.pytest }} --cov=qcengine --color=yes --cov-report=xml qcengine/ | |
| - name: CodeCov | |
| uses: codecov/codecov-action@v4 | |
| release_sphinx: | |
| needs: [build] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| cfg: | |
| - conda-env: docs-cf | |
| python-version: "3.10" | |
| label: Sphinx | |
| runs-on: ubuntu-latest | |
| name: "🐍 ${{ matrix.cfg.python-version }} • ${{ matrix.cfg.label }}" | |
| runs-on: ${{ matrix.cfg.runs-on }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Create Environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: test | |
| environment-file: devtools/conda-envs/${{ matrix.cfg.conda-env }}.yaml | |
| python-version: ${{ matrix.cfg.python-version }} | |
| auto-activate-base: false | |
| add-pip-as-python-dependency: true | |
| channels: conda-forge | |
| - name: Special Config - QCElemental Dep | |
| #if: false | |
| run: | | |
| conda remove qcelemental --force | |
| python -m pip install 'git+https://github.com/loriab/QCElemental.git@csse_layout_536c' --no-deps | |
| - name: Environment Information | |
| run: | | |
| conda info | |
| conda list --show-channel-urls | |
| - name: Build Documentation | |
| run: | | |
| python -m pip install . --no-deps | |
| python -c "import qcelemental as q;print(q.__file__, q.__version__)" | |
| python -c "import qcengine as q;print(q.__file__, q.__version__)" | |
| cd docs | |
| make html | |
| - name: GitHub Pages Deploy | |
| uses: JamesIves/[email protected] | |
| if: github.event_name == 'push' && github.repository == 'MolSSI/QCEngine' && ( startsWith( github.ref, 'refs/tags/' ) || github.ref == 'refs/heads/master' ) | |
| with: | |
| branch: gh-pages | |
| folder: docs/build/html |