Re-run black (#219)

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Black 23
+94875c5bb13a5734b720f99b181e0d6b8639ba39

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+ci:
+  autoupdate_schedule: "quarterly"
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: check-yaml
+  - id: debug-statements
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+  - id: black
+    files: ^openff
+- repo: https://github.com/PyCQA/isort
+  rev: 5.12.0
+  hooks:
+  - id: isort
+    files: ^openff
+- repo: https://github.com/PyCQA/flake8
+  rev: 6.0.0
+  hooks:
+  - id: flake8
+    files: ^openff

devtools/conda-envs/basic.yaml

@@ -28,7 +28,7 @@ dependencies:
   # openmmforcefields brings in the full toolkit; if that is ever re-packaged
   # this should be changed to openff-toolkit-base
   - openff-toolkit >= 0.12
-  - pydantic
+  - pydantic =1
   - pyyaml
   - qcportal>=0.15.7
   - torsiondrive

openff/qcsubmit/common_structures.py

@@ -6,7 +6,7 @@
 import re
 from datetime import date, datetime
 from enum import Enum
-from typing import Any, ClassVar, Dict, List, Optional, Set, Tuple, Union
+from typing import Any, ClassVar, Dict, List, Optional, Set, Tuple, Union, TYPE_CHECKING
 
 import numpy as np
 import qcportal as ptl
@@ -36,6 +36,8 @@
 from openff.qcsubmit.utils.smirnoff import split_openff_molecule
 
 
+if TYPE_CHECKING:
+    from pydantic import AbstractSetIntStr
 class DatasetConfig(BaseModel):
     """
     The basic configurations for all datasets.

openff/qcsubmit/tests/results/__init__.py

@@ -28,16 +28,13 @@
 
 
 class _FractalClient(BaseModel):
-
     address: str
 
 
 def _mock_molecule(entry: _BaseResult, n_conformers: int = 1) -> Molecule:
-
     molecule: Molecule = Molecule.from_smiles(entry.cmiles)
 
     for _ in range(n_conformers):
-
         molecule.add_conformer(
             numpy.arange(molecule.n_atoms * 3).reshape((molecule.n_atoms, 3))
             * unit.angstrom
@@ -47,7 +44,6 @@ def _mock_molecule(entry: _BaseResult, n_conformers: int = 1) -> Molecule:
 
 
 def mock_basic_result_collection(molecules, monkeypatch) -> BasicResultCollection:
-
     collection = BasicResultCollection(
         entries={
             address: [
@@ -77,7 +73,7 @@ def mock_basic_result_collection(molecules, monkeypatch) -> BasicResultCollectio
                     status=RecordStatusEnum.complete,
                     client=_FractalClient(address=address),
                 ),
-                molecules[address][int(entry.record_id) - 1]
+                molecules[address][int(entry.record_id) - 1],
             )
             for address, entries in self.entries.items()
             for entry in entries
@@ -90,7 +86,6 @@ def mock_basic_result_collection(molecules, monkeypatch) -> BasicResultCollectio
 def mock_optimization_result_collection(
     molecules, monkeypatch
 ) -> OptimizationResultCollection:
-
     collection = OptimizationResultCollection(
         entries={
             address: [
@@ -138,7 +133,6 @@ def mock_optimization_result_collection(
 def mock_torsion_drive_result_collection(
     molecules, monkeypatch
 ) -> TorsionDriveResultCollection:
-
     collection = TorsionDriveResultCollection(
         entries={
             address: [
@@ -190,11 +184,9 @@ def mock_torsion_drive_result_collection(
     )
 
     def get_molecules(self):
-
         return_value = []
 
         for molecule_id in self.initial_molecule:
-
             molecule = copy.deepcopy(molecules[self.client.address][int(self.id) - 1])
             molecule._conformers = [molecule.conformers[int(molecule_id) - 1]]
 

openff/qcsubmit/tests/results/conftest.py

@@ -16,7 +16,6 @@
 
 
 def _smiles_to_molecule(smiles: str) -> Molecule:
-
     molecule: Molecule = Molecule.from_smiles(smiles, allow_undefined_stereo=True)
     molecule.generate_conformers(n_conformers=1)
 
@@ -45,7 +44,8 @@ def tautomer_basic_result_collection(monkeypatch) -> BasicResultCollection:
 
     smiles = {
         "http://localhost:442": [
-            _smiles_to_molecule(smiles) for smiles in ["Oc1nnccn1", "C1=NC(=O)NN=C1", "C1=CN=NC(=O)N1"]
+            _smiles_to_molecule(smiles)
+            for smiles in ["Oc1nnccn1", "C1=NC(=O)NN=C1", "C1=CN=NC(=O)N1"]
         ]
     }
     return mock_basic_result_collection(smiles, monkeypatch)
@@ -116,16 +116,14 @@ def optimization_result_collection(monkeypatch) -> OptimizationResultCollection:
 
 
 @pytest.fixture()
-def optimization_result_collection_duplicates(monkeypatch) -> OptimizationResultCollection:
+def optimization_result_collection_duplicates(
+    monkeypatch,
+) -> OptimizationResultCollection:
     """Create a collection with duplicate enetries accross different addresses which can be reduced to a single entry."""
 
     smiles = {
-        "http://localhost:442": [
-            _smiles_to_molecule(smiles="CCCO")
-        ],
-        "http://localhost:443": [
-            _smiles_to_molecule(smiles="CCCO")
-        ]
+        "http://localhost:442": [_smiles_to_molecule(smiles="CCCO")],
+        "http://localhost:443": [_smiles_to_molecule(smiles="CCCO")],
     }
     return mock_optimization_result_collection(smiles, monkeypatch)
 

openff/qcsubmit/tests/results/test_caching.py

@@ -27,13 +27,11 @@ def test_batched_indices():
 
 
 def test_cached_fractal_client_bad_address():
-
     with pytest.raises(ConnectionRefusedError):
         cached_fractal_client("http://localhost:1234/")
 
 
 def test_cached_fractal_client_snowflake():
-
     from qcfractal import FractalSnowflake
 
     snowflake = FractalSnowflake(start_server=False)
@@ -43,7 +41,6 @@ def test_cached_fractal_client_snowflake():
 
 
 def test_cached_query_procedures(public_client):
-
     assert len(_record_cache) == 0
 
     record_ids = ["32651863", "32651864"]
@@ -62,7 +59,6 @@ def test_cached_query_procedures(public_client):
 
 
 def test_cached_query_molecule(public_client):
-
     assert len(_molecule_cache) == 0
 
     molecule_ids = ["25696236", "25696152"]
@@ -101,10 +97,7 @@ def test_cached_query_molecule(public_client):
         ),
     ],
 )
-def test_record_to_molecule(
-    result, query_function, public_client
-):
-
+def test_record_to_molecule(result, query_function, public_client):
     expected_molecule = Molecule.from_mapped_smiles(result.cmiles)
 
     records = query_function(public_client.address, [result])
@@ -123,7 +116,7 @@ def test_record_to_molecule(
 
     assert numpy.allclose(
         molecule.conformers[0].m_as(unit.bohr),
-        expected_qc_molecule.geometry.reshape((molecule.n_atoms, 3))
+        expected_qc_molecule.geometry.reshape((molecule.n_atoms, 3)),
     )
 
     are_isomorphic, _ = Molecule.are_isomorphic(molecule, expected_molecule)
@@ -136,7 +129,6 @@ def test_record_to_molecule(
 
 
 def test_cached_query_torsion_drive_results(public_client):
-
     assert len(_grid_id_cache) == 0
 
     result = TorsionDriveResult(
@@ -162,10 +154,9 @@ def test_cached_query_torsion_drive_results(public_client):
     }
 
     for grid_id, conformer in zip(molecule.properties["grid_ids"], molecule.conformers):
-
         assert numpy.allclose(
             conformer.m_as(unit.bohr),
-            expected_qc_molecules[grid_id].geometry.reshape((molecule.n_atoms, 3))
+            expected_qc_molecules[grid_id].geometry.reshape((molecule.n_atoms, 3)),
         )
 
     assert len(molecule.properties["grid_ids"]) == 24