Merge pull request #573 from chrisjonesBSU/add-ruff

Add ruff to pre-commit hooks

.pre-commit-config.yaml

@@ -8,27 +8,26 @@ ci:
  skip: []
  submodules: false
 repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+ # Ruff version.
+ rev: v0.5.7
+ hooks:
+ # Run the linter.
+ - id: ruff
+ args: [--line-length=80, --fix]
+ # Run the formatter.
+ - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
  rev: v4.6.0
  hooks:
  - id: check-yaml
  - id: end-of-file-fixer
  - id: trailing-whitespace
- exclude: 'setup.cfg'
-- repo: https://github.com/psf/black
- rev: 24.8.0
- hooks:
- - id: black
- args: [--line-length=80]
+ exclude: 'setup.cfg|foyer/tests/files/.*'
 - repo: https://github.com/pycqa/isort
  rev: 5.13.2
  hooks:
  - id: isort
  name: isort (python)
  args: [--profile=black, --line-length=80]
-- repo: https://github.com/pycqa/pydocstyle
- rev: '6.3.0'
- hooks:
- - id: pydocstyle
- exclude: ^(foyer/tests/|docs/|devtools/|setup.py)
- args: [--convention=numpy]
+ exclude: "foyer/tests/files/.*"

docs/source/conf.py

@@ -18,15 +18,15 @@
 import pathlib
 import sys
 
+import sphinx_rtd_theme
+
 sys.path.insert(0, os.path.abspath("../.."))
 sys.path.insert(0, os.path.abspath("sphinxext"))
 
 base_path = pathlib.Path(__file__).parent
 os.system("python {} --name".format((base_path / "../../setup.py").resolve()))
 
 
-import foyer
-
 # -- Project information -----------------------------------------------------
 
 project = "foyer"
@@ -147,7 +147,6 @@
 # a list of builtin themes.
 #
 # html_theme = 'alabaster'
-import sphinx_rtd_theme
 
 html_theme = "sphinx_rtd_theme"
 hhtml_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

foyer/atomtyper.py

@@ -79,9 +79,7 @@ def find_atomtypes(structure, forcefield, max_iter=10):
  topology_graph = TopologyGraph.from_gmso_topology(structure)
 
  if isinstance(forcefield, Forcefield):
- atomtype_rules = AtomTypingRulesProvider.from_foyer_forcefield(
- forcefield
- )
+ atomtype_rules = AtomTypingRulesProvider.from_foyer_forcefield(forcefield)
  elif isinstance(forcefield, AtomTypingRulesProvider):
  atomtype_rules = forcefield
  else:
@@ -110,9 +108,7 @@ def find_atomtypes(structure, forcefield, max_iter=10):
  atomic_number = atom_data.atomic_number
  atomic_symbol = atom_data.element
  try:
- element_from_num = ele.element_from_atomic_number(
- atomic_number
- ).symbol
+ element_from_num = ele.element_from_atomic_number(atomic_number).symbol
  element_from_sym = ele.element_from_symbol(atomic_symbol).symbol
  assert element_from_num == element_from_sym
  system_elements.add(element_from_num)
@@ -210,13 +206,9 @@ def _iterate_rules(rules, topology_graph, typemap, max_iter):
 
 def _resolve_atomtypes(topology_graph, typemap):
  """Determine the final atomtypes from the white- and blacklists."""
- atoms = {
- atom_idx: data for atom_idx, data in topology_graph.atoms(data=True)
- }
+ atoms = {atom_idx: data for atom_idx, data in topology_graph.atoms(data=True)}
  for atom_id, atom in typemap.items():
- atomtype = [
- rule_name for rule_name in atom["whitelist"] - atom["blacklist"]
- ]
+ atomtype = [rule_name for rule_name in atom["whitelist"] - atom["blacklist"]]
  if len(atomtype) == 1:
  atom["atomtype"] = atomtype[0]
  elif len(atomtype) > 1:

foyer/forcefield.py

@@ -146,7 +146,7 @@ def generate_topology(non_omm_topology, non_element_types=None, residues=None):
  return _topology_from_parmed(non_omm_topology, non_element_types)
  elif has_mbuild:
  mb = import_("mbuild")
- if (non_omm_topology, mb.Compound):
+ if all([non_omm_topology, mb.Compound]):
  pmd_comp_struct = non_omm_topology.to_parmed(residues=residues)
  return _topology_from_parmed(pmd_comp_struct, non_element_types)
  else:
@@ -162,16 +162,12 @@ def generate_topology(non_omm_topology, non_element_types=None, residues=None):
 def _structure_from_residue(residue, parent_structure):
  """Convert a ParmEd Residue to an equivalent Structure."""
  structure = pmd.Structure()
- orig_to_copy = (
- dict()
- ) # Clone a lot of atoms to avoid any of parmed's tracking
+ orig_to_copy = dict() # Clone a lot of atoms to avoid any of parmed's tracking
  for atom in residue.atoms:
  new_atom = copy(atom)
  new_atom._idx = atom.idx
  orig_to_copy[atom] = new_atom
- structure.add_atom(
- new_atom, resname=residue.name, resnum=residue.number
- )
+ structure.add_atom(new_atom, resname=residue.name, resnum=residue.number)
 
  for bond in parent_structure.bonds:
  if bond.atom1 in residue.atoms and bond.atom2 in residue.atoms:
@@ -198,10 +194,7 @@ def _topology_from_parmed(structure, non_element_types):
  if pmd_atom.name in non_element_types:
  element = non_element_types[pmd_atom.name]
  else:
- if (
- isinstance(pmd_atom.atomic_number, int)
- and pmd_atom.atomic_number != 0
- ):
+ if isinstance(pmd_atom.atomic_number, int) and pmd_atom.atomic_number != 0:
  element = elem.Element.getByAtomicNumber(pmd_atom.atomic_number)
  else:
  element = elem.Element.getBySymbol(pmd_atom.name)
@@ -221,9 +214,7 @@ def _topology_from_parmed(structure, non_element_types):
  topology.addBond(atom1, atom2)
  atom1.bond_partners.append(atom2)
  atom2.bond_partners.append(atom1)
- if structure.box_vectors and np.any(
- [x._value for x in structure.box_vectors]
- ):
+ if structure.box_vectors and np.any([x._value for x in structure.box_vectors]):
  topology.setPeriodicBoxVectors(structure.box_vectors)
 
  positions = structure.positions
@@ -293,9 +284,7 @@ def _unwrap_typemap(structure, residue_map):
  for res_ref, val in residue_map.items():
  if id(res.name) == id(res_ref):
  for i, atom in enumerate(res.atoms):
- master_typemap[int(atom.idx)]["atomtype"] = val[i][
- "atomtype"
- ]
+ master_typemap[int(atom.idx)]["atomtype"] = val[i]["atomtype"]
  return master_typemap
 
 
@@ -325,9 +314,7 @@ def _separate_urey_bradleys(system, topology):
  ) not in bonds:
  ub_force.addBond(*force.getBondParameters(bond_idx))
  else:
- harmonic_bond_force.addBond(
- *force.getBondParameters(bond_idx)
- )
+ harmonic_bond_force.addBond(*force.getBondParameters(bond_idx))
  system.removeForce(force_idx)
 
  system.addForce(harmonic_bond_force)
@@ -499,9 +486,7 @@ class Forcefield(app.ForceField):
 
  """
 
- def __init__(
- self, forcefield_files=None, name=None, validation=True, debug=False
- ):
+ def __init__(self, forcefield_files=None, name=None, validation=True, debug=False):
  self.atomTypeDefinitions = dict()
  self.atomTypeOverrides = dict()
  self.atomTypeDesc = dict()
@@ -539,13 +524,9 @@ def __init__(
  if len(preprocessed_files) == 1:
  self._version = self._parse_version_number(preprocessed_files[0])
  self._name = self._parse_name(preprocessed_files[0])
- self._combining_rule = self._parse_combining_rule(
- preprocessed_files[0]
- )
+ self._combining_rule = self._parse_combining_rule(preprocessed_files[0])
  elif len(preprocessed_files) > 1:
- self._version = [
- self._parse_version_number(f) for f in preprocessed_files
- ]
+ self._version = [self._parse_version_number(f) for f in preprocessed_files]
  self._name = [self._parse_name(f) for f in preprocessed_files]
  self._combining_rule = [
  self._parse_combining_rule(f) for f in preprocessed_files
@@ -639,9 +620,7 @@ def _parse_name(self, forcefield_file):
  try:
  return root.attrib["name"]
  except KeyError:
- warnings.warn(
- "No force field name found in force field XML file."
- )
+ warnings.warn("No force field name found in force field XML file.")
  return None
 
  def _parse_combining_rule(self, forcefield_file):
@@ -651,9 +630,7 @@ def _parse_combining_rule(self, forcefield_file):
  try:
  return root.attrib["combining_rule"]
  except KeyError:
- warnings.warn(
- "No combining rule found in force field XML file."
- )
+ warnings.warn("No combining rule found in force field XML file.")
  return "lorentz"
 
  def _create_element(self, element, mass):
@@ -679,9 +656,7 @@ def registerAtomType(self, parameters):
  """Register a new atom type."""
  name = parameters["name"]
  if name in self._atomTypes:
- raise ValueError(
- "Found multiple definitions for atom type: " + name
- )
+ raise ValueError("Found multiple definitions for atom type: " + name)
  atom_class = parameters["class"]
  mass = _convertParameterToNumber(parameters["mass"])
  element = None
@@ -846,10 +821,7 @@ def run_atomtyping(self, structure, use_residue_map=True, **kwargs):
 
  # Need to call this only once and store results for later id() comparisons
  for res_id, res in enumerate(structure.residues):
- if (
- structure.residues[res_id].name
- not in residue_map.keys()
- ):
+ if structure.residues[res_id].name not in residue_map.keys():
  tmp_res = _structure_from_residue(res, structure)
  typemap = find_atomtypes(tmp_res, forcefield=self)
  residue_map[res.name] = typemap
@@ -877,9 +849,7 @@ def parametrize_system(
  **kwargs,
  ):
  """Create system based on resulting typemapping."""
- topology, positions = _topology_from_parmed(
- structure, self.non_element_types
- )
+ topology, positions = _topology_from_parmed(structure, self.non_element_types)
 
  system = self.createSystem(topology, *args, **kwargs)
 
@@ -918,9 +888,7 @@ def parametrize_system(
  )
 
  if self.combining_rule == "geometric":
- self._patch_parmed_adjusts(
- structure, combining_rule=self.combining_rule
- )
+ self._patch_parmed_adjusts(structure, combining_rule=self.combining_rule)
 
  total_charge = sum([atom.charge for atom in structure.atoms])
  if not np.allclose(total_charge, 0):
@@ -1032,9 +1000,7 @@ def createSystem(
  elem.hydrogen,
  None,
  ):
- transfer_mass = hydrogenMass - sys.getParticleMass(
- atom2.index
- )
+ transfer_mass = hydrogenMass - sys.getParticleMass(atom2.index)
  sys.setParticleMass(atom2.index, hydrogenMass)
  mass = sys.getParticleMass(atom1.index) - transfer_mass
  sys.setParticleMass(atom1.index, mass)
@@ -1091,9 +1057,7 @@ def createSystem(
  bonded_to = data.bondedToAtom[atom]
  if len(bonded_to) > 2:
  for subset in itertools.combinations(bonded_to, 3):
- data.impropers.append(
- (atom, subset[0], subset[1], subset[2])
- )
+ data.impropers.append((atom, subset[0], subset[1], subset[2]))
 
  # Identify bonds that should be implemented with constraints
  if constraints == AllBonds or constraints == HAngles:
@@ -1188,15 +1152,9 @@ def createSystem(
  site.originWeights[1],
  site.originWeights[2],
  ),
- mm.Vec3(
- site.xWeights[0], site.xWeights[1], site.xWeights[2]
- ),
- mm.Vec3(
- site.yWeights[0], site.yWeights[1], site.yWeights[2]
- ),
- mm.Vec3(
- site.localPos[0], site.localPos[1], site.localPos[2]
- ),
+ mm.Vec3(site.xWeights[0], site.xWeights[1], site.xWeights[2]),
+ mm.Vec3(site.yWeights[0], site.yWeights[1], site.yWeights[2]),
+ mm.Vec3(site.localPos[0], site.localPos[1], site.localPos[2]),
  )
  sys.setVirtualSite(index, local_coord_site)
 
@@ -1263,9 +1221,7 @@ def _write_references_to_file(self, atom_types, references_file):
  for atomtype, dois in atomtype_references.items():
  for doi in dois:
  unique_references[doi].append(atomtype)
- unique_references = collections.OrderedDict(
- sorted(unique_references.items())
- )
+ unique_references = collections.OrderedDict(sorted(unique_references.items()))
  with open(references_file, "w") as f:
  for doi, atomtypes in unique_references.items():
  url = "http://api.crossref.org/works/{}/transform/application/x-bibtex".format(
@@ -1338,11 +1294,7 @@ def get_parameters(self, group, key, keys_are_atom_classes=False):
  if group not in param_extractors:
  raise ValueError(f"Cannot extract parameters for {group}")
 
- key = (
- [key]
- if isinstance(key, str) or not isinstance(key, Iterable)
- else key
- )
+ key = [key] if isinstance(key, str) or not isinstance(key, Iterable) else key
 
  validate_type(key, str)
 
@@ -1367,18 +1319,14 @@ def _extract_non_bonded_params(self, atom_type):
 
  atom_type = atom_type[0]
 
- non_bonded_forces_gen = self.get_generator(
- ff=self, gen_type=NonbondedGenerator
- )
+ non_bonded_forces_gen = self.get_generator(ff=self, gen_type=NonbondedGenerator)
 
  non_bonded_params = non_bonded_forces_gen.params.paramsForType
 
  try:
  return non_bonded_params[atom_type]
  except KeyError:
- raise MissingParametersError(
- f"Missing parameters for atom {atom_type}"
- )
+ raise MissingParametersError(f"Missing parameters for atom {atom_type}")
 
  def _extract_harmonic_bond_params(self, atom_types):
  """Return parameters for a specific HarmonicBondForce between atom types."""
@@ -1548,9 +1496,7 @@ def _extract_rb_proper_params(self, atom_types):
  f"be extracted for four atoms. Provided {len(atom_types)}"
  )
 
- rb_torsion_force_gen = self.get_generator(
- ff=self, gen_type=RBTorsionGenerator
- )
+ rb_torsion_force_gen = self.get_generator(ff=self, gen_type=RBTorsionGenerator)
 
  wildcard = self._atomClasses[""]
  (
@@ -1600,9 +1546,7 @@ def _extract_rb_improper_params(self, atom_types):
  f"be extracted for four atoms. Provided {len(atom_types)}"
  )
 
- rb_torsion_force_gen = self.get_generator(
- ff=self, gen_type=RBTorsionGenerator
- )
+ rb_torsion_force_gen = self.get_generator(ff=self, gen_type=RBTorsionGenerator)
 
  match = self._match_impropers(atom_types, rb_torsion_force_gen)
 
@@ -1622,9 +1566,7 @@ def map_atom_classes_to_types(self, atom_classes_keys, strict=False):
  # When to do this substitution with wildcards?
  substitution = self._atomClasses.get(key)
  if not substitution:
- raise ValueError(
- f"Atom class {key} is missing from the Forcefield"
- )
+ raise ValueError(f"Atom class {key} is missing from the Forcefield")
  atom_type_keys.append(next(iter(substitution)))
 
  return atom_type_keys
@@ -1715,9 +1657,7 @@ def get_generator(ff, gen_type):
  @staticmethod
  def substitute_wildcards(atom_types, wildcard):
  """Return possible wildcard options."""
- return tuple(
- atom_type or next(iter(wildcard)) for atom_type in atom_types
- )
+ return tuple(atom_type or next(iter(wildcard)) for atom_type in atom_types)
 
 
 pmd.Structure.write_foyer = write_foyer