auto format all the things

.github/workflows/ci.yaml

@@ -31,7 +31,7 @@ jobs:
         pydantic-version: [">1"]
         python-version:
           - "3.10"
-          - "3.11"  
+          - "3.11"
           - "3.12"
         include:
             # Note: pinned to macos-12

.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

devtools/raise-or-close-issue.py

@@ -5,24 +5,24 @@
 #  - TITLE: A string title which the issue will have.
 
 import os
-from github import Github
 
+from github import Github
 
 if __name__ == "__main__":
-    git = Github(os.environ['GITHUB_TOKEN'])
-    status = os.environ['CI_OUTCOME']
-    repo = git.get_repo('OpenFreeEnergy/gufe')
-    title = os.environ['TITLE']
-    
+    git = Github(os.environ["GITHUB_TOKEN"])
+    status = os.environ["CI_OUTCOME"]
+    repo = git.get_repo("OpenFreeEnergy/gufe")
+    title = os.environ["TITLE"]
+
     target_issue = None
     for issue in repo.get_issues():
         if issue.title == title:
             target_issue = issue
-    
+
     # Close any issues with given title if CI returned green
-    if status == 'success':
+    if status == "success":
         if target_issue is not None:
-            target_issue.edit(state='closed')
+            target_issue.edit(state="closed")
     else:
         # Otherwise raise an issue
         if target_issue is None:

docs/CHANGELOG.rst

@@ -28,5 +28,3 @@ v1.1.0
 * Fixed an issue where ProtocolDAG DAG order & keys were unstable /
   non-deterministic between processes under some circumstances (PR #315).
 * Fixed a bug where edge annotations were lost when converting a ``LigandNetwork`` to graphml, all JSON codec types are now supported.
-
-

docs/_static/.gitkeep

@@ -1 +0,0 @@
-

docs/conf.py

@@ -12,14 +12,15 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../'))
+
+sys.path.insert(0, os.path.abspath("../"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'gufe'
-copyright = '2022, The OpenFE Development Team'
-author = 'The OpenFE Development Team'
+project = "gufe"
+copyright = "2022, The OpenFE Development Team"
+author = "The OpenFE Development Team"
 
 
 # -- General configuration ---------------------------------------------------
@@ -28,14 +29,14 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.napoleon',
-    'sphinxcontrib.autodoc_pydantic',
-    'sphinx.ext.intersphinx',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinxcontrib.autodoc_pydantic",
+    "sphinx.ext.intersphinx",
 ]
 
-autoclass_content = 'both'
+autoclass_content = "both"
 
 autodoc_default_options = {
     "members": True,
@@ -47,20 +48,21 @@
 autosummary_generate = True
 
 intersphinx_mapping = {
-    'rdkit': ('https://www.rdkit.org/docs/', None),
+    "rdkit": ("https://www.rdkit.org/docs/", None),
 }
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-autodoc_mock_imports = ["openff.models",
-                        "rdkit",
-                        "networkx",
+autodoc_mock_imports = [
+    "openff.models",
+    "rdkit",
+    "networkx",
 ]
 
 
@@ -77,7 +79,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # replace macros
 rst_prolog = """

docs/guide/overview.rst

@@ -25,7 +25,7 @@ Ligand network setup
 GUFE defines a basic API for the common case of performing alchemical
 transformations between small molecules, either for relative binding free
 energies of relative hydration free energies. This handles how mappings
-between different molecules are defined for alchemical transformations, 
+between different molecules are defined for alchemical transformations,
 by defining both the :class:`.LigandAtomMapping` object that contains the
 details of a specific mapping, and the :class:`.AtomMapper` abstract API for
 an object that creates the mappings.

docs/guide/serialization.rst

@@ -245,7 +245,7 @@ classmethod:
 .. Using JSON codecs outside of JSON
 .. ---------------------------------
 
-.. In a custom recursive storage scheme, 
+.. In a custom recursive storage scheme,
 
 .. TODO: DWHS wants to write something here that describes how to use the
    codecs in your own non-JSON storage scheme. But this is complicated

gufe/__init__.py

@@ -3,40 +3,29 @@
 
 from importlib.metadata import version
 
-from . import tokenization
-
-from . import visualization
-
+from . import tokenization, visualization
+from .chemicalsystem import ChemicalSystem
 from .components import (
     Component,
-    SmallMoleculeComponent,
     ProteinComponent,
-    SolventComponent
-)
-
-from .chemicalsystem import ChemicalSystem
-
-from .mapping import (
-    ComponentMapping,  # how individual Components relate
-    AtomMapping, AtomMapper,  # more specific to atom based components
-    LigandAtomMapping,
+    SmallMoleculeComponent,
+    SolventComponent,
 )
-
-from .settings import Settings
-
-from .protocols import (
+from .ligandnetwork import LigandNetwork
+from .mapping import AtomMapper  # more specific to atom based components
+from .mapping import ComponentMapping  # how individual Components relate
+from .mapping import AtomMapping, LigandAtomMapping
+from .network import AlchemicalNetwork
+from .protocols import Protocol  # description of a method
+from .protocols import ProtocolDAG  # many Units forming a workflow
+from .protocols import ProtocolDAGResult  # the collected result of a DAG
+from .protocols import ProtocolUnit  # the individual step within a method
+from .protocols import ProtocolUnitResult  # the result of a single Unit
+from .protocols import (  # potentially many DAGs together, giving an estimate
     Context,
-    Protocol,  # description of a method
-    ProtocolUnit,  # the individual step within a method
-    ProtocolDAG,  # many Units forming a workflow
-    ProtocolUnitResult,  # the result of a single Unit
-    ProtocolDAGResult,  # the collected result of a DAG
-    ProtocolResult,  # potentially many DAGs together, giving an estimate
+    ProtocolResult,
 )
-
-from .transformations import Transformation, NonTransformation
-
-from .network import AlchemicalNetwork
-from .ligandnetwork import LigandNetwork
+from .settings import Settings
+from .transformations import NonTransformation, Transformation
 
 __version__ = version("gufe")

gufe/chemicalsystem.py

@@ -4,8 +4,8 @@
 from collections import abc
 from typing import Optional
 
-from .tokenization import GufeTokenizable
 from .components import Component
+from .tokenization import GufeTokenizable
 
 
 class ChemicalSystem(GufeTokenizable, abc.Mapping):
@@ -14,14 +14,14 @@ def __init__(
         components: dict[str, Component],
         name: Optional[str] = "",
     ):
-        """A combination of Components that form a system
+        r"""A combination of Components that form a system
 
         Containing a combination of :class:`.SmallMoleculeComponent`,
         :class:`.SolventComponent` and :class:`.ProteinComponent`, this object
         typically represents all the molecules in a simulation box.
 
         Used as a node for an :class:`.AlchemicalNetwork`.
-        
+
         Parameters
         ----------
         components
@@ -55,9 +55,7 @@ def _to_dict(self):
     @classmethod
     def _from_dict(cls, d):
         return cls(
-            components={
-                key: value for key, value in d["components"].items()
-            },
+            components={key: value for key, value in d["components"].items()},
             name=d["name"],
         )
 
@@ -86,7 +84,7 @@ def name(self):
     def total_charge(self):
         """Formal charge for the ChemicalSystem."""
         # This might evaluate the property twice?
-        #return sum(component.total_charge
+        # return sum(component.total_charge
         #           for component in self._components.values()
         #           if component.total_charge is not None)
         total_charge = 0

gufe/components/__init__.py

@@ -1,7 +1,6 @@
 """The building blocks for defining systems"""
 
 from .component import Component
-
-from .smallmoleculecomponent import SmallMoleculeComponent
 from .proteincomponent import ProteinComponent
+from .smallmoleculecomponent import SmallMoleculeComponent
 from .solventcomponent import SolventComponent

gufe/components/explicitmoleculecomponent.py

@@ -1,13 +1,13 @@
 import json
-import numpy as np
 import warnings
-from rdkit import Chem
 from typing import Optional
 
-from .component import Component
+import numpy as np
+from rdkit import Chem
 
 # typing
 from ..custom_typing import RDKitMol
+from .component import Component
 
 
 def _ensure_ofe_name(mol: RDKitMol, name: str) -> str:
@@ -26,10 +26,7 @@ def _ensure_ofe_name(mol: RDKitMol, name: str) -> str:
         pass
 
     if name and rdkit_name and rdkit_name != name:
-        warnings.warn(
-            f"Component being renamed from {rdkit_name}"
-            f"to {name}."
-        )
+        warnings.warn(f"Component being renamed from {rdkit_name}" f"to {name}.")
     elif name == "":
         name = rdkit_name
 
@@ -56,21 +53,23 @@ def _check_partial_charges(mol: RDKitMol) -> None:
       * If partial charges are found.
       * If the partial charges are near 0 for all atoms.
     """
-    if 'atom.dprop.PartialCharge' not in mol.GetPropNames():
+    if "atom.dprop.PartialCharge" not in mol.GetPropNames():
         return
 
-    p_chgs = np.array(
-        mol.GetProp('atom.dprop.PartialCharge').split(), dtype=float
-    )
+    p_chgs = np.array(mol.GetProp("atom.dprop.PartialCharge").split(), dtype=float)
 
     if len(p_chgs) != mol.GetNumAtoms():
-        errmsg = (f"Incorrect number of partial charges: {len(p_chgs)} "
-                  f" were provided for {mol.GetNumAtoms()} atoms")
+        errmsg = (
+            f"Incorrect number of partial charges: {len(p_chgs)} "
+            f" were provided for {mol.GetNumAtoms()} atoms"
+        )
         raise ValueError(errmsg)
 
     if (sum(p_chgs) - Chem.GetFormalCharge(mol)) > 0.01:
-        errmsg = (f"Sum of partial charges {sum(p_chgs)} differs from "
-                  f"RDKit formal charge {Chem.GetFormalCharge(mol)}")
+        errmsg = (
+            f"Sum of partial charges {sum(p_chgs)} differs from "
+            f"RDKit formal charge {Chem.GetFormalCharge(mol)}"
+        )
         raise ValueError(errmsg)
 
     # set the charges on the atoms if not already set
@@ -81,18 +80,24 @@ def _check_partial_charges(mol: RDKitMol) -> None:
         else:
             atom_charge = atom.GetDoubleProp("PartialCharge")
             if not np.isclose(atom_charge, charge):
-                errmsg = (f"non-equivalent partial charges between atom and "
-                          f"molecule properties: {atom_charge} {charge}")
+                errmsg = (
+                    f"non-equivalent partial charges between atom and "
+                    f"molecule properties: {atom_charge} {charge}"
+                )
                 raise ValueError(errmsg)
 
     if np.all(np.isclose(p_chgs, 0.0)):
-        wmsg = (f"Partial charges provided all equal to "
-                "zero. These may be ignored by some Protocols.")
+        wmsg = (
+            f"Partial charges provided all equal to "
+            "zero. These may be ignored by some Protocols."
+        )
         warnings.warn(wmsg)
     else:
-        wmsg = ("Partial charges have been provided, these will "
-                "preferentially be used instead of generating new "
-                "partial charges")
+        wmsg = (
+            "Partial charges have been provided, these will "
+            "preferentially be used instead of generating new "
+            "partial charges"
+        )
         warnings.warn(wmsg)
 
 
@@ -103,6 +108,7 @@ class ExplicitMoleculeComponent(Component):
     representations. Specific file formats, such as SDF for small molecules
     or PDB for proteins, should be implemented in subclasses.
     """
+
     _rdkit: Chem.Mol
     _name: str
 
@@ -121,8 +127,10 @@ def __init__(self, rdkit: RDKitMol, name: str = ""):
             )
 
         if not any(atom.GetAtomicNum() == 1 for atom in rdkit.GetAtoms()):
-            warnings.warn("Molecule doesn't have any hydrogen atoms present. "
-                          "If this is unexpected, consider loading the molecule with `removeHs=False`")
+            warnings.warn(
+                "Molecule doesn't have any hydrogen atoms present. "
+                "If this is unexpected, consider loading the molecule with `removeHs=False`"
+            )
 
         self._rdkit = rdkit
         self._smiles: Optional[str] = None