big linting pass

.github/CONTRIBUTING.md

@@ -11,7 +11,7 @@ We are happy to get you started in using our software.
 ## Issues
 
 If you think you have encountered a software issue, please raise this on the "Issues" tab in Github.
-In general the more details you can provide the better, 
+In general the more details you can provide the better,
 we recommend reading section 3.3 of [this article](https://livecomsjournal.org/index.php/livecoms/article/view/v3i1e1473)
 to understand the problem solving process.
 

.github/workflows/ci.yaml

@@ -123,9 +123,9 @@ jobs:
         # we only want to upload a slow report if
         # 1) it isn't a schedule run
         # 2) it wasn't from a PR (we don't run slow tests on PRs)
-        if: ${{ github.repository == 'OpenFreeEnergy/openfe'  
-                && github.event_name != 'schedule'            
-                && github.event_name != 'pull_request' }}     
+        if: ${{ github.repository == 'OpenFreeEnergy/openfe'
+                && github.event_name != 'schedule'
+                && github.event_name != 'pull_request' }}
         uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/clean_cache.yaml

@@ -11,18 +11,18 @@ jobs:
     steps:
       - name: Check out code
         uses: actions/checkout@v3
-        
+
       - name: Cleanup
         run: |
           gh extension install actions/gh-actions-cache
-          
+
           REPO=${{ github.repository }}
           BRANCH="refs/pull/${{ github.event.pull_request.number }}/merge"
 
           echo "Fetching list of cache key"
           cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH | cut -f 1 )
 
-          ## Setting this to not fail the workflow while deleting cache keys. 
+          ## Setting this to not fail the workflow while deleting cache keys.
           set +e
           echo "Deleting caches..."
           for cacheKey in $cacheKeysForPR

.github/workflows/mypy.yaml

@@ -50,4 +50,4 @@ jobs:
           micromamba list
 
       - name: "Lint with mypy"
-        run: mypy 
+        run: mypy

Code_of_Conduct.md

@@ -1,6 +1,6 @@
 ## Code of Conduct ##
 
-This project is dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. Members do not tolerate harassment for any reason, but especially harassment based on gender, sexual orientation, disability, physical appearance, body size, race, nationality, sex, color, ethnic or social origin, pregnancy, citizenship, familial status, veteran status, genetic information, religion or belief, political or any other opinion, membership of a national minority, property, age, or preference of text editor. 
+This project is dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. Members do not tolerate harassment for any reason, but especially harassment based on gender, sexual orientation, disability, physical appearance, body size, race, nationality, sex, color, ethnic or social origin, pregnancy, citizenship, familial status, veteran status, genetic information, religion or belief, political or any other opinion, membership of a national minority, property, age, or preference of text editor.
 
 
 ### Expected Behavior ###

devtools/data/gen-serialized-results.py

@@ -9,36 +9,32 @@
 - MDProtocol_json_results.gz
   - used in md_json fixture
 """
+
 import gzip
 import json
 import logging
 import pathlib
 import tempfile
-from openff.toolkit import (
-    Molecule, RDKitToolkitWrapper, AmberToolsToolkitWrapper
-)
-from openff.toolkit.utils.toolkit_registry import (
-    toolkit_registry_manager, ToolkitRegistry
-)
-from openff.units import unit
-from kartograf.atom_aligner import align_mol_shape
-from kartograf import KartografAtomMapper
+
 import gufe
 from gufe.tokenization import JSON_HANDLER
+from kartograf import KartografAtomMapper
+from kartograf.atom_aligner import align_mol_shape
+from openff.toolkit import AmberToolsToolkitWrapper, Molecule, RDKitToolkitWrapper
+from openff.toolkit.utils.toolkit_registry import ToolkitRegistry, toolkit_registry_manager
+from openff.units import unit
+
 import openfe
-from openfe.protocols.openmm_md.plain_md_methods import PlainMDProtocol
 from openfe.protocols.openmm_afe import AbsoluteSolvationProtocol
+from openfe.protocols.openmm_md.plain_md_methods import PlainMDProtocol
 from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocol
 
-
 logger = logging.getLogger(__name__)
 
 LIGA = "[H]C([H])([H])C([H])([H])C(=O)C([H])([H])C([H])([H])[H]"
 LIGB = "[H]C([H])([H])C(=O)C([H])([H])C([H])([H])C([H])([H])[H]"
 
-amber_rdkit = ToolkitRegistry(
-    [RDKitToolkitWrapper(), AmberToolsToolkitWrapper()]
-)
+amber_rdkit = ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])
 
 
 def get_molecule(smi, name):
@@ -58,21 +54,18 @@ def execute_and_serialize(dag, protocol, simname):
             shared_basedir=workdir,
             scratch_basedir=workdir,
             keep_shared=False,
-            n_retries=3
+            n_retries=3,
         )
     protres = protocol.gather([dagres])
 
     outdict = {
         "estimate": protres.get_estimate(),
         "uncertainty": protres.get_uncertainty(),
         "protocol_result": protres.to_dict(),
-        "unit_results": {
-            unit.key: unit.to_keyed_dict()
-            for unit in dagres.protocol_unit_results
-        }
+        "unit_results": {unit.key: unit.to_keyed_dict() for unit in dagres.protocol_unit_results},
     }
 
-    with gzip.open(f"{simname}_json_results.gz", 'wt') as zipfile:
+    with gzip.open(f"{simname}_json_results.gz", "wt") as zipfile:
         json.dump(outdict, zipfile, cls=JSON_HANDLER.encoder)
 
 
@@ -95,27 +88,19 @@ def generate_ahfe_json(smc):
     settings.solvent_simulation_settings.production_length = 500 * unit.picosecond
     settings.vacuum_simulation_settings.equilibration_length = 10 * unit.picosecond
     settings.vacuum_simulation_settings.production_length = 1000 * unit.picosecond
-    settings.lambda_settings.lambda_elec = [0.0, 0.25, 0.5, 0.75, 1.0, 1.0,
-                                            1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0,
-                                            1.0]
-    settings.lambda_settings.lambda_vdw = [0.0, 0.0, 0.0, 0.0, 0.0, 0.12, 0.24,
-                                           0.36, 0.48, 0.6, 0.7, 0.77, 0.85,
-                                           1.0]
+    settings.lambda_settings.lambda_elec = [0.0, 0.25, 0.5, 0.75, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
+    settings.lambda_settings.lambda_vdw = [0.0, 0.0, 0.0, 0.0, 0.0, 0.12, 0.24, 0.36, 0.48, 0.6, 0.7, 0.77, 0.85, 1.0]
     settings.protocol_repeats = 3
     settings.solvent_simulation_settings.n_replicas = 14
     settings.vacuum_simulation_settings.n_replicas = 14
     settings.solvent_simulation_settings.early_termination_target_error = 0.12 * unit.kilocalorie_per_mole
     settings.vacuum_simulation_settings.early_termination_target_error = 0.12 * unit.kilocalorie_per_mole
-    settings.vacuum_engine_settings.compute_platform = 'CPU'
-    settings.solvent_engine_settings.compute_platform = 'CUDA'
+    settings.vacuum_engine_settings.compute_platform = "CPU"
+    settings.solvent_engine_settings.compute_platform = "CUDA"
 
     protocol = AbsoluteSolvationProtocol(settings=settings)
-    sysA = openfe.ChemicalSystem(
-        {"ligand": smc, "solvent": openfe.SolventComponent()}
-    )
-    sysB = openfe.ChemicalSystem(
-        {"solvent": openfe.SolventComponent()}
-    )
+    sysA = openfe.ChemicalSystem({"ligand": smc, "solvent": openfe.SolventComponent()})
+    sysB = openfe.ChemicalSystem({"solvent": openfe.SolventComponent()})
 
     dag = protocol.create(stateA=sysA, stateB=sysB, mapping=None)
 
@@ -133,15 +118,13 @@ def generate_rfe_json(smcA, smcB):
     mapper = KartografAtomMapper(atom_map_hydrogens=True)
     mapping = next(mapper.suggest_mappings(smcA, a_smcB))
 
-    systemA = openfe.ChemicalSystem({'ligand': smcA})
-    systemB = openfe.ChemicalSystem({'ligand': a_smcB})
+    systemA = openfe.ChemicalSystem({"ligand": smcA})
+    systemB = openfe.ChemicalSystem({"ligand": a_smcB})
 
-    dag = protocol.create(
-        stateA=systemA, stateB=systemB, mapping=mapping
-    )
+    dag = protocol.create(stateA=systemA, stateB=systemB, mapping=mapping)
 
     execute_and_serialize(dag, protocol, "RHFEProtocol")
-        
+
 
 if __name__ == "__main__":
     molA = get_molecule(LIGA, "ligandA")

docs/_ext/sass.py

@@ -17,13 +17,11 @@
 from pathlib import Path
 from typing import Optional, Union
 
-
 import sass
 from sphinx.application import Sphinx
 from sphinx.environment import BuildEnvironment
 from sphinx.util import logging
 
-
 logger = logging.getLogger(__name__)
 
 
@@ -44,10 +42,7 @@ def get_targets(app: Sphinx) -> dict[Path, Path]:
     if isinstance(app.config.sass_targets, dict):
         targets = app.config.sass_targets
     else:
-        targets = {
-            path: path.relative_to(src_dir).with_suffix(".css")
-            for path in src_dir.glob("**/[!_]*.s[ca]ss")
-        }
+        targets = {path: path.relative_to(src_dir).with_suffix(".css") for path in src_dir.glob("**/[!_]*.s[ca]ss")}
 
     return {src_dir / src: dst_dir / dst for src, dst in targets.items()}
 

docs/_sass/deflist-flowchart.scss

@@ -263,7 +263,7 @@ ul.deflist-flowchart {
       margin-left: 0;
     }
   }
-  
+
   dl {
     display: flex;
     flex-direction: row-reverse;
@@ -394,4 +394,4 @@ ul.deflist-flowchart {
       }
     }
   }
-}
+}