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

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

.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

@@ -105,9 +105,9 @@ 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

@@ -15,10 +15,10 @@
 import pathlib
 import tempfile
 from openff.toolkit import (
-    Molecule, RDKitToolkitWrapper, AmberToolsToolkitWrapper
+    Molecule, RDKitToolkitWrapper, AmberToolsToolkitWrapper,
 )
 from openff.toolkit.utils.toolkit_registry import (
-    toolkit_registry_manager, ToolkitRegistry
+    toolkit_registry_manager, ToolkitRegistry,
 )
 from openff.units import unit
 from kartograf.atom_aligner import align_mol_shape
@@ -37,7 +37,7 @@
 LIGB = "[H]C([H])([H])C(=O)C([H])([H])C([H])([H])C([H])([H])[H]"
 
 amber_rdkit = ToolkitRegistry(
-    [RDKitToolkitWrapper(), AmberToolsToolkitWrapper()]
+    [RDKitToolkitWrapper(), AmberToolsToolkitWrapper()],
 )
 
 
@@ -58,7 +58,7 @@ 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])
 
@@ -69,7 +69,7 @@ def execute_and_serialize(dag, protocol, simname):
         "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:
@@ -95,12 +95,16 @@ 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
@@ -111,10 +115,10 @@ def generate_ahfe_json(smc):
 
     protocol = AbsoluteSolvationProtocol(settings=settings)
     sysA = openfe.ChemicalSystem(
-        {"ligand": smc, "solvent": openfe.SolventComponent()}
+        {"ligand": smc, "solvent": openfe.SolventComponent()},
     )
     sysB = openfe.ChemicalSystem(
-        {"solvent": openfe.SolventComponent()}
+        {"solvent": openfe.SolventComponent()},
     )
 
     dag = protocol.create(stateA=sysA, stateB=sysB, mapping=None)
@@ -137,11 +141,11 @@ def generate_rfe_json(smcA, smcB):
     systemB = openfe.ChemicalSystem({'ligand': a_smcB})
 
     dag = protocol.create(
-        stateA=systemA, stateB=systemB, mapping=mapping
+        stateA=systemA, stateB=systemB, mapping=mapping,
     )
 
     execute_and_serialize(dag, protocol, "RHFEProtocol")
-        
+
 
 if __name__ == "__main__":
     molA = get_molecule(LIGA, "ligandA")

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 {
       }
     }
   }
-}
+}