[pre-commit.ci] pre-commit autoupdate (#333)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 23.12.1 → 24.3.0](psf/black@23.12.1...24.3.0)
- [github.com/PyCQA/flake8: 6.1.0 → 7.0.0](PyCQA/flake8@6.1.0...7.0.0)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
   - id: check-yaml
   - id: debug-statements
 - repo: https://github.com/psf/black
-  rev: 23.12.1
+  rev: 24.3.0
   hooks:
   - id: black
     files: ^openff
@@ -17,7 +17,7 @@ repos:
   - id: isort
     files: ^openff
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
+  rev: 7.0.0
   hooks:
   - id: flake8
     files: ^openff

openff/bespokefit/__init__.py

@@ -1,6 +1,7 @@
 """
 BespokeFit: Creating bespoke parameters for individual molecules.
 """
+
 import logging
 import sys
 

openff/bespokefit/_pydantic.py

@@ -1,4 +1,5 @@
 """A set of common utilities and types useful for building pydantic models."""
+
 import numpy
 
 try:

openff/bespokefit/cli/executor/retrieve.py

@@ -80,13 +80,15 @@ def retrieve_cli(optimization_id, output_file_path, force_field_path):
     if force_field_path is not None:
         message = Padding(
             (
-                f"the bespoke fit {'failed' if results.error else 'is still running'} "
-                f"and so no force field will be saved"
-            )
-            if not results.bespoke_force_field
-            else (
-                f"the bespoke force field has been saved to "
-                f"[repr.filename]{force_field_path}[/repr.filename]"
+                (
+                    f"the bespoke fit {'failed' if results.error else 'is still running'} "
+                    f"and so no force field will be saved"
+                )
+                if not results.bespoke_force_field
+                else (
+                    f"the bespoke force field has been saved to "
+                    f"[repr.filename]{force_field_path}[/repr.filename]"
+                )
             ),
             (1, 0, 1, 0),
         )

openff/bespokefit/cli/executor/run.py

@@ -74,12 +74,12 @@ def _run_cli(
         with handle_common_errors(console) as error_state:
             response_id = _submit(
                 console=console,
-                input_file_path=[input_file_path]
-                if input_file_path is not None
-                else [],
-                molecule_smiles=[molecule_smiles]
-                if molecule_smiles is not None
-                else [],
+                input_file_path=(
+                    [input_file_path] if input_file_path is not None else []
+                ),
+                molecule_smiles=(
+                    [molecule_smiles] if molecule_smiles is not None else []
+                ),
                 force_field_path=force_field_path,
                 target_torsion_smirks=target_torsion_smirks,
                 default_qc_spec=default_qc_spec,

openff/bespokefit/executor/services/coordinator/app.py

@@ -73,23 +73,27 @@ def get_optimizations(
             f"&limit={limit}"
             f"{status_url}"
         ),
-        prev=None
-        if prev_index >= skip
-        else (
-            f"{__settings.BEFLOW_API_V1_STR}/"
-            f"{__settings.BEFLOW_COORDINATOR_PREFIX}"
-            f"?skip={prev_index}"
-            f"&limit={limit}"
-            f"{status_url}"
+        prev=(
+            None
+            if prev_index >= skip
+            else (
+                f"{__settings.BEFLOW_API_V1_STR}/"
+                f"{__settings.BEFLOW_COORDINATOR_PREFIX}"
+                f"?skip={prev_index}"
+                f"&limit={limit}"
+                f"{status_url}"
+            )
         ),
-        next=None
-        if (next_index <= skip or next_index == n_total_tasks)
-        else (
-            f"{__settings.BEFLOW_API_V1_STR}/"
-            f"{__settings.BEFLOW_COORDINATOR_PREFIX}"
-            f"?skip={next_index}"
-            f"&limit={limit}"
-            f"{status_url}"
+        next=(
+            None
+            if (next_index <= skip or next_index == n_total_tasks)
+            else (
+                f"{__settings.BEFLOW_API_V1_STR}/"
+                f"{__settings.BEFLOW_COORDINATOR_PREFIX}"
+                f"?skip={next_index}"
+                f"&limit={limit}"
+                f"{status_url}"
+            )
         ),
         contents=contents,
     )

openff/bespokefit/executor/services/coordinator/models.py

@@ -58,12 +58,14 @@ def from_stage(cls, stage: StageType):
             type=stage.type,
             status=stage.status,
             error=stage.error,
-            results=None
-            if stage_ids is None
-            else [
-                Link(id=stage_id, self=f"{endpoints[stage.type]}{stage_id}")
-                for stage_id in stage_ids
-            ],
+            results=(
+                None
+                if stage_ids is None
+                else [
+                    Link(id=stage_id, self=f"{endpoints[stage.type]}{stage_id}")
+                    for stage_id in stage_ids
+                ]
+            ),
         )
 
 

openff/bespokefit/fragmentation/base.py

@@ -1,6 +1,7 @@
 """
 Register new fragmentation methods with bespokefit
 """
+
 from typing import Dict, List, Type, Union
 
 from openff.fragmenter.fragment import Fragmenter, PfizerFragmenter, WBOFragmenter

openff/bespokefit/optimizers/base.py

@@ -1,6 +1,7 @@
 """
 Here we register all optimizers with bespokefit.
 """
+
 from typing import Dict, List, Type, Union
 
 from openff.bespokefit.exceptions import OptimizerError

openff/bespokefit/optimizers/forcebalance/forcebalance.py

@@ -138,10 +138,12 @@ def _collect_results(cls, root_directory: str) -> OptimizationStageResults:
             provenance=cls.provenance(),
             status=results_dictionary["status"],
             error=results_dictionary["error"],
-            refit_force_field=None
-            if results_dictionary["error"] is not None
-            else force_field_editor.force_field.to_string(
-                discard_cosmetic_attributes=True
+            refit_force_field=(
+                None
+                if results_dictionary["error"] is not None
+                else force_field_editor.force_field.to_string(
+                    discard_cosmetic_attributes=True
+                )
             ),
         )
 

openff/bespokefit/schema/data.py

@@ -104,22 +104,19 @@ def _torsion_drive_record_to_torsion_drive_result(
     @overload
     def from_remote_records(
         cls, qc_records: List[Tuple[TorsiondriveRecord, Molecule]]
-    ) -> "LocalQCData[TorsionDriveResult]":
-        ...
+    ) -> "LocalQCData[TorsionDriveResult]": ...
 
     @classmethod
     @overload
     def from_remote_records(
         cls, qc_records: List[Tuple[OptimizationRecord, Molecule]]
-    ) -> "LocalQCData[OptimizationResult]":
-        ...
+    ) -> "LocalQCData[OptimizationResult]": ...
 
     @classmethod
     @overload
     def from_remote_records(
         cls, qc_records: List[Tuple[BaseRecord, Molecule]]
-    ) -> "LocalQCData[AtomicResult]":
-        ...
+    ) -> "LocalQCData[AtomicResult]": ...
 
     @classmethod
     def from_remote_records(cls, qc_records):

openff/bespokefit/schema/tasks.py

@@ -85,18 +85,15 @@ class Torsion1DTask(Torsion1DTaskSpec):
 
 
 @overload
-def task_from_result(result: AtomicResult) -> HessianTask:
-    ...
+def task_from_result(result: AtomicResult) -> HessianTask: ...
 
 
 @overload
-def task_from_result(result: OptimizationResult) -> OptimizationTask:
-    ...
+def task_from_result(result: OptimizationResult) -> OptimizationTask: ...
 
 
 @overload
-def task_from_result(result: TorsionDriveResult) -> Torsion1DTask:
-    ...
+def task_from_result(result: TorsionDriveResult) -> Torsion1DTask: ...
 
 
 def task_from_result(result):

openff/bespokefit/tests/fragmentation/test_base.py

@@ -1,4 +1,5 @@
 """Test the fragmentation engine registration system."""
+
 import abc
 
 import pytest

openff/bespokefit/tests/optimizers/test_model.py

@@ -1,6 +1,7 @@
 """
 Unit test ability to add and remove new optimizers as well as the various optimizer classes.
 """
+
 import pytest
 from openff.toolkit.typing.engines.smirnoff import ForceField
 

openff/bespokefit/tests/utilities/test_smirnoff.py

@@ -1,6 +1,7 @@
 """
 Test the force field editing tools.
 """
+
 import copy
 import os
 

openff/bespokefit/tests/workflows/test_bespoke.py

@@ -1,6 +1,7 @@
 """
 Test for the bespoke-fit workflow generator.
 """
+
 import os
 
 import pytest

openff/bespokefit/utilities/_settings.py

@@ -83,36 +83,48 @@ class Settings(BaseSettings):
     def fragmenter_settings(self) -> WorkerSettings:
         return WorkerSettings(
             import_path=self.BEFLOW_FRAGMENTER_WORKER,
-            n_cores=None
-            if self.BEFLOW_FRAGMENTER_WORKER_N_CORES == "auto"
-            else self.BEFLOW_FRAGMENTER_WORKER_N_CORES,
-            max_memory=None
-            if self.BEFLOW_FRAGMENTER_WORKER_MAX_MEM == "auto"
-            else self.BEFLOW_FRAGMENTER_WORKER_MAX_MEM,
+            n_cores=(
+                None
+                if self.BEFLOW_FRAGMENTER_WORKER_N_CORES == "auto"
+                else self.BEFLOW_FRAGMENTER_WORKER_N_CORES
+            ),
+            max_memory=(
+                None
+                if self.BEFLOW_FRAGMENTER_WORKER_MAX_MEM == "auto"
+                else self.BEFLOW_FRAGMENTER_WORKER_MAX_MEM
+            ),
         )
 
     @property
     def qc_compute_settings(self) -> WorkerSettings:
         return WorkerSettings(
             import_path=self.BEFLOW_QC_COMPUTE_WORKER,
-            n_cores=None
-            if self.BEFLOW_QC_COMPUTE_WORKER_N_CORES == "auto"
-            else self.BEFLOW_QC_COMPUTE_WORKER_N_CORES,
-            max_memory=None
-            if self.BEFLOW_QC_COMPUTE_WORKER_MAX_MEM == "auto"
-            else self.BEFLOW_QC_COMPUTE_WORKER_MAX_MEM,
+            n_cores=(
+                None
+                if self.BEFLOW_QC_COMPUTE_WORKER_N_CORES == "auto"
+                else self.BEFLOW_QC_COMPUTE_WORKER_N_CORES
+            ),
+            max_memory=(
+                None
+                if self.BEFLOW_QC_COMPUTE_WORKER_MAX_MEM == "auto"
+                else self.BEFLOW_QC_COMPUTE_WORKER_MAX_MEM
+            ),
         )
 
     @property
     def optimizer_settings(self) -> WorkerSettings:
         return WorkerSettings(
             import_path=self.BEFLOW_OPTIMIZER_WORKER,
-            n_cores=None
-            if self.BEFLOW_OPTIMIZER_WORKER_N_CORES == "auto"
-            else self.BEFLOW_OPTIMIZER_WORKER_N_CORES,
-            max_memory=None
-            if self.BEFLOW_OPTIMIZER_WORKER_MAX_MEM == "auto"
-            else self.BEFLOW_OPTIMIZER_WORKER_MAX_MEM,
+            n_cores=(
+                None
+                if self.BEFLOW_OPTIMIZER_WORKER_N_CORES == "auto"
+                else self.BEFLOW_OPTIMIZER_WORKER_N_CORES
+            ),
+            max_memory=(
+                None
+                if self.BEFLOW_OPTIMIZER_WORKER_MAX_MEM == "auto"
+                else self.BEFLOW_OPTIMIZER_WORKER_MAX_MEM
+            ),
         )
 
     @contextmanager

openff/bespokefit/utilities/smirks.py

@@ -221,9 +221,11 @@ def generate_smirks_from_molecule(
         return self.generate_smirks_from_fragment(
             molecule,
             molecule,
-            None
-            if central_bond is None
-            else (central_bond[0] + 1, central_bond[1] + 1),
+            (
+                None
+                if central_bond is None
+                else (central_bond[0] + 1, central_bond[1] + 1)
+            ),
         )
 
     def generate_smirks_from_fragment(
@@ -323,11 +325,13 @@ def _get_existing_parameters(
             for valence_term in self._get_valence_terms(
                 molecule=molecule,
                 smirks_type=smirks_type,
-                torsion_bond=None
-                if molecule_map_indices is None
-                else (
-                    get_atom_index(molecule, molecule_map_indices[0]),
-                    get_atom_index(molecule, molecule_map_indices[1]),
+                torsion_bond=(
+                    None
+                    if molecule_map_indices is None
+                    else (
+                        get_atom_index(molecule, molecule_map_indices[0]),
+                        get_atom_index(molecule, molecule_map_indices[1]),
+                    )
                 ),
             ):
                 requested_smirks.setdefault(smirks_type, []).append(valence_term)
@@ -390,11 +394,13 @@ def _get_bespoke_smirks(
         valence_terms = self._get_valence_terms(
             fragment,
             smirks_type,
-            None
-            if fragment_map_indices is None
-            else (
-                get_atom_index(fragment, fragment_map_indices[0]),
-                get_atom_index(fragment, fragment_map_indices[1]),
+            (
+                None
+                if fragment_map_indices is None
+                else (
+                    get_atom_index(fragment, fragment_map_indices[0]),
+                    get_atom_index(fragment, fragment_map_indices[1]),
+                )
             ),
         )
         valence_groups = [*group_valence_by_symmetry(fragment, valence_terms).values()]

openff/bespokefit/utilities/smirnoff.py

@@ -1,6 +1,7 @@
 """
 Tools for dealing with SMIRNOFF force field manipulation.
 """
+
 import copy
 from enum import Enum
 from typing import TYPE_CHECKING, Dict, List, Tuple, Union

openff/bespokefit/utilities/tempcd.py

@@ -1,4 +1,5 @@
 """"""
+
 import os
 import shutil
 import tempfile