Merge pull request #997 from openforcefield/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate
openforcefield · Jul 8, 2024 · 65f36d5 · 65f36d5
2 parents a649485 + 5854e84
commit 65f36d5
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -46,7 +46,7 @@ repos:
     exclude: openff/interchange/_version.py|setup.py
     args: ["--py310-plus"]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.9
+  rev: v0.5.1
   hooks:
     - id: ruff
       args: ["check", "--select", "NPY"]
@@ -63,7 +63,7 @@ repos:
       args: ["openff/interchange/", "-e", "openff/interchange/_tests/"]
       pass_filenames: false
 - repo: https://github.com/adamchainz/blacken-docs
-  rev: 1.16.0
+  rev: 1.18.0
   hooks:
   - id: blacken-docs
     files: ^docs/

diff --git a/docs/using/collections.md b/docs/using/collections.md
@@ -83,7 +83,7 @@ The [`Interchange.collections`] attribute maps names to the corresponding collec
 dict_keys(['Bonds', 'Constraints', 'Angles', 'ProperTorsions',
     'ImproperTorsions', 'vdW', 'Electrostatics'])
 >>> # Ethane has no improper torsions, so both maps will be empty
->>> interchange.collections['ImproperTorsions']  # doctest: +NORMALIZE_WHITESPACE,+ELLIPSIS
+>>> interchange.collections["ImproperTorsions"]  # doctest: +NORMALIZE_WHITESPACE,+ELLIPSIS
 SMIRNOFFImproperTorsionCollection(type='ImproperTorsions',
     expression='k*(1+cos(periodicity*theta-phase))',
     key_map={},
@@ -97,7 +97,7 @@ carbon-hydrogen bonds. It's clear from the SMIRKS codes that atoms 0 and 1 are
 the carbon atoms, and atoms 2 through 7 are the hydrogens:
 
 ```pycon
->>> interchange.collections['Bonds'].key_map  # doctest: +NORMALIZE_WHITESPACE,+ELLIPSIS
+>>> interchange.collections["Bonds"].key_map  # doctest: +NORMALIZE_WHITESPACE,+ELLIPSIS
 {TopologyKey(atom_indices=(0, 1), ...): PotentialKey(id='[#6X4:1]-[#6X4:2]', ...),
  TopologyKey(atom_indices=(0, 2), ...): PotentialKey(id='[#6X4:1]-[#1:2]', ...),
  TopologyKey(atom_indices=(0, 3), ...): PotentialKey(id='[#6X4:1]-[#1:2]', ...),
@@ -117,7 +117,7 @@ The bond collection also maps the two potential keys to the appropriate `Potenti
 Here we can read off the force constant and length:
 
 ```pycon
->>> interchange.collections['Bonds'].potentials  # doctest: +NORMALIZE_WHITESPACE,+ELLIPSIS
+>>> interchange.collections["Bonds"].potentials  # doctest: +NORMALIZE_WHITESPACE,+ELLIPSIS
 {PotentialKey(id='[#6X4:1]-[#6X4:2]', ...):
      Potential(parameters={'k': <Quantity(529.242972, 'kilocalorie / angstrom ** 2 / mole')>,
                            'length': <Quantity(1.52190126, 'angstrom')>}, ...),
@@ -135,14 +135,15 @@ the bonds have been updated:
 >>> from openff.units import unit
 >>> # Get the potential from the first C-H bond
 >>> top_key = TopologyKey(atom_indices=(0, 2))
->>> pot_key = interchange.collections['Bonds'].key_map[top_key]
->>> potential = interchange.collections['Bonds'].potentials[pot_key]
+>>> pot_key = interchange.collections["Bonds"].key_map[top_key]
+>>> potential = interchange.collections["Bonds"].potentials[pot_key]
 >>> # Modify the potential
->>> potential.parameters['length'] = 3.1415926 * unit.nanometer
+>>> potential.parameters["length"] = 3.1415926 * unit.nanometer
 >>> # Write out the modified interchange to a GROMACS .top file
 >>> interchange.to_top("out.top")
 >>> with open("out.top") as f:
 ...     print(f.read())  # doctest: +NORMALIZE_WHITESPACE,+ELLIPSIS
+...
 ; Generated by Interchange
     ...
 [ bonds ]