Do not call python setup.py

.github/workflows/CI.yml

@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - 3.8
+          - 3.9
         cfg:
           - os: ubuntu-latest
             conda-env: basic
@@ -60,7 +60,7 @@ jobs:
 
       - name: Install Package
         run: |
-          python setup.py develop --no-deps
+          python -m pip install .
 
       - name: Conda Environment Information
         run: |

.github/workflows/Lint.yaml

@@ -30,8 +30,8 @@ jobs:
 
       - name: Run isort
         run: |
-          isort --recursive --check-only openff
+          isort --check-only openff
 
       - name: Run black
         run: |
-          black openff --check
+          black --check openff

.gitignore

@@ -103,4 +103,7 @@ ENV/
 .mypy_cache/
 
 # PyCharm
-.idea
+.idea
+
+# macOS
+.DS_Store

openff/qcsubmit/common_structures.py

@@ -366,7 +366,6 @@ def to_string(self) -> str:
 
 
 class QCSpec(ResultsConfig):
-
     method: constr(strip_whitespace=True) = Field(
         "B3LYP-D3BJ",
         description="The name of the computational model used to execute the calculation. This could be the QC method or the forcefield name.",
@@ -450,7 +449,6 @@ def __init__(
             gaff_forcefields = GAFFTemplateGenerator.INSTALLED_FORCEFIELDS
 
         except ModuleNotFoundError:
-
             gaff_forcefields = [
                 "gaff-1.4",
                 "gaff-1.8",
@@ -536,7 +534,6 @@ def dict(
         exclude_defaults: bool = False,
         exclude_none: bool = False,
     ) -> "DictStrAny":
-
         data = super().dict(
             include=include,
             exclude=exclude,
@@ -788,7 +785,6 @@ def validate_metadata(self, raise_errors: bool = False) -> Optional[List[str]]:
 
         empty_fields = []
         for field in self.__fields__:
-
             if field == "long_description_url":
                 # The 'long_description_url' is made optional to more easily facilitate
                 # local or private dataset submissions.

openff/qcsubmit/datasets/datasets.py

@@ -51,7 +51,6 @@
 from openff.qcsubmit.utils.visualize import molecules_to_pdf
 
 if TYPE_CHECKING:
-
     from openff.toolkit.typing.engines.smirnoff import ForceField
     from qcportal import FractalClient
     from qcportal.collections.collection import Collection
@@ -353,7 +352,6 @@ def submit(
             from multiprocessing.pool import Pool
 
             with Pool(processes=processes) as pool:
-
                 # add compute specs to the collection
                 for spec_name, spec in self.qc_specifications.items():
                     spec_tasks = 0
@@ -590,7 +588,6 @@ def filter_molecules(
             ]
             self.filtered_molecules[component].molecules.extend(filter_mols)
         else:
-
             filter_data = FilterEntry(
                 off_molecules=molecules,
                 component=component,
@@ -853,7 +850,6 @@ def visualize(
         molecules = []
 
         for data in self.dataset.values():
-
             off_mol = data.get_off_molecule(include_conformers=False)
             off_mol.name = None
 
@@ -1055,9 +1051,7 @@ def _add_entries(self, dataset: ptl.collections.Dataset) -> Tuple[List[str], int
         indices = []
 
         for i, (index, data) in enumerate(self.dataset.items()):
-
             if len(data.initial_molecules) > 1:
-
                 # check if the index has a number tag
                 # if so, start from this tag
                 index, tag = self._clean_index(index=index)
@@ -1365,9 +1359,7 @@ def _add_entries(
         indices = []
 
         for i, (index, data) in enumerate(self.dataset.items()):
-
             if len(data.initial_molecules) > 1:
-
                 # check if the index has a number tag
                 # if so, start from this tag
                 index, tag = self._clean_index(index=index)
@@ -1579,7 +1571,6 @@ def _add_entries(
         indices = []
 
         for i, (index, data) in enumerate(self.dataset.items()):
-
             new_entries += int(
                 self._add_entry(
                     data.initial_molecules, dataset=dataset, name=data.index, data=data

openff/qcsubmit/datasets/entries.py

@@ -266,7 +266,6 @@ def formatted_keywords(self) -> Dict[str, Any]:
             return self.keywords.additional_keywords
 
     def __init__(self, off_molecule: Optional[off.Molecule] = None, **kwargs):
-
         super().__init__(off_molecule, **kwargs)
         # now validate the torsions check proper first
         off_molecule = self.get_off_molecule(include_conformers=False)

openff/qcsubmit/exceptions.py

@@ -10,7 +10,6 @@ class QCSubmitException(Exception):
     header = "QCSubmit Base Error"
 
     def __init__(self, message: str):
-
         super().__init__(message)
 
         self.raw_message = message
@@ -130,7 +129,6 @@ class MolecularComplexError(QCSubmitException):
 
 
 class ConstraintError(QCSubmitException):
-
     error_type = "constraint_error"
     header = "Constraint Error"
 

openff/qcsubmit/factories.py

@@ -526,7 +526,6 @@ def _dataset_type(cls) -> Type[BasicDataset]:
     def _process_molecule(
         self, dataset: T, molecule: off.Molecule, toolkit_registry: ToolkitRegistry
     ) -> None:
-
         # always put the cmiles in the extras from what we have just calculated to ensure correct order
         extras = molecule.properties.get("extras", {})
 

openff/qcsubmit/results/caching.py

@@ -63,11 +63,9 @@ def cached_fractal_client(address: str) -> FractalClient:
     """Returns a cached copy of a fractal client."""
 
     try:
-
         return FractalClient(address)
 
     except ConnectionRefusedError as e:
-
         # Try to handle the case when connecting to a local snowflake.
         try:
             return FractalClient(address, verify=False)
@@ -121,11 +119,9 @@ def _cached_client_query(
     logger.debug(f"query split into {len(batch_query_ids)} batches")
 
     for i, batch_ids in enumerate(batch_query_ids):
-
         logger.debug(f"starting batch query {i}")
 
         for query in getattr(client, query_name)(batch_ids):
-
             found_queries.append(query)
 
             if cache_predicate is not None and not cache_predicate(query):
@@ -226,7 +222,6 @@ def _cached_query_single_structure_results(
     return_values = []
 
     for result in results:
-
         qc_record = qc_records[result.record_id]
         qc_molecule = qc_molecules[qc_record_to_molecule_id[result.record_id]]
 
@@ -286,7 +281,6 @@ def cached_query_optimization_results(
 def _cached_torsion_drive_molecule_ids(
     client_address: str, qc_records: List[TorsionDriveRecord]
 ) -> Dict[Tuple[str, Tuple[int, ...]], str]:
-
     client_address = client_address.rstrip("/")
 
     optimization_ids = {
@@ -315,7 +309,6 @@ def _cached_torsion_drive_molecule_ids(
     qc_optimizations = {}
 
     for i, batch_ids in enumerate(batched_missing_ids):
-
         logger.debug(f"starting batch query {i}")
 
         qc_optimizations.update(
@@ -333,7 +326,6 @@ def _cached_torsion_drive_molecule_ids(
     }
 
     for grid_tuple, optimization_id in missing_optimization_ids.items():
-
         qc_optimization = qc_optimizations[optimization_id]
         found_molecule_ids[grid_tuple] = qc_optimization.final_molecule
 
@@ -392,7 +384,6 @@ def cached_query_torsion_drive_results(
     return_values = []
 
     for result in results:
-
         qc_record = qc_records[result.record_id]
 
         grid_ids = [*qc_record.minimum_positions]