Csse layout 550 error #871
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: 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_536a' --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_pyd2_warnings' --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/github-pages-deploy-action@4.1.1 | |
| 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 |