diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 95e43c62..83cb17f5 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -39,18 +39,11 @@ jobs: - uses: actions/checkout@v3.0.2 - name: Setup Conda Environment - uses: conda-incubator/setup-miniconda@v2.1.1 + uses: mamba-org/provision-with-micromamba@main with: - - python-version: ${{ matrix.python-version }} environment-file: devtools/conda-envs/test_env.yaml - - activate-environment: test - - auto-update-conda: true - auto-activate-base: false - - show-channel-urls: true + extra-specs: | + python=${{ matrix.python-version }} - name: Install OpenEye if: matrix.openeye @@ -58,7 +51,7 @@ jobs: run: | echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE} - conda install -c openeye openeye-toolkits + micromamba install -c openeye openeye-toolkits python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()" env: SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a4fa2d37..c96e8e6e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ ci: autoupdate_schedule: "monthly" repos: - repo: https://github.com/psf/black - rev: 22.3.0 + rev: 22.8.0 hooks: - id: black files: (^openff|^integration-tests) @@ -12,7 +12,7 @@ repos: - id: isort files: (^openff|^integration-tests) - repo: https://github.com/PyCQA/flake8 - rev: 4.0.1 + rev: 5.0.4 hooks: - id: flake8 files: (^openff|^integration-tests) diff --git a/devtools/conda-envs/docs_env.yaml b/devtools/conda-envs/docs_env.yaml index e2741f09..cc033188 100644 --- a/devtools/conda-envs/docs_env.yaml +++ b/devtools/conda-envs/docs_env.yaml @@ -1,7 +1,5 @@ name: evaluator channels: - - conda-forge/label/openff-toolkit_rc - - conda-forge/label/openff-interchange_rc - conda-forge dependencies: # Base depends @@ -10,25 +8,18 @@ dependencies: - pip # Standard dependencies - - openff-toolkit >=0.11.0rc3 - - smirnoff99frosst - - numpy - - pandas - - openmm >=7.6 - - networkx + - openff-toolkit >=0.11.0 - packmol - pymbar >=3.0.5,<4.0.0 - mdtraj >=1.9.3 - dask >=2.7.0 - distributed >=2.7.0 - - dask-jobqueue >=0.7.0 + - dask-jobqueue >=0.7.0,<=0.8.0 - uncertainties - openmmtools - yank >=0.25.2 - pyyaml - requests - - rdkit - - cmiles - python-dateutil - pydantic <2.0.0a0 - paprika diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index 02a1a499..5c01e0e1 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -1,7 +1,6 @@ name: evaluator-test-env channels: - - conda-forge/label/openff-toolkit_rc - - conda-forge/label/openff-interchange_rc + - jaimergp/label/unsupported-cudatoolkit-shim - conda-forge dependencies: # Base depends @@ -17,25 +16,16 @@ dependencies: - coverage >=4.4 # Standard dependencies - - openff-toolkit >=0.11.0rc3 - - smirnoff99frosst - - numpy - - pandas - - openmm >=7.6 - - networkx - - packmol + - openff-toolkit >=0.11.0 - pymbar >=4.0.0 - - mdtraj >=1.9.3 - dask >=2.7.0 - distributed >=2.7.0 - - dask-jobqueue >=0.7.0 + - dask-jobqueue >=0.8.0 - uncertainties - openmmtools - yank >=0.25.2 - pyyaml - requests - - rdkit - - cmiles - python-dateutil - pydantic <2.0.0a0 - paprika diff --git a/openff/evaluator/backends/dask.py b/openff/evaluator/backends/dask.py index 6776c857..62cd679b 100644 --- a/openff/evaluator/backends/dask.py +++ b/openff/evaluator/backends/dask.py @@ -335,7 +335,7 @@ def _get_env_extra(self): The extra commands to run. """ env_extra = dask.config.get( - f"jobqueue.{self._cluster_type}.env-extra", default=[] + f"jobqueue.{self._cluster_type}.job-script-prologue", default=[] ) if self._setup_script_commands is not None: @@ -353,7 +353,7 @@ def _get_job_extra(self): The extra header options to add. """ job_extra = dask.config.get( - f"jobqueue.{self._cluster_type}.job-extra", default=[] + f"jobqueue.{self._cluster_type}.job-extra-directives", default=[] ) if self._extra_script_options is not None: