merge and fix conflicts

.github/workflows/CI.yaml

@@ -26,7 +26,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba (Linux)
@@ -42,7 +42,7 @@ jobs:
         run: python -m pytest -v -nauto --cov=foyer --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs foyer
 
       - name: Upload Coverage Report
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v4
         with:
           name: Foyer-Coverage
           verbose: true
@@ -63,7 +63,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba (Linux)
@@ -95,7 +95,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba

.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()]

environment-dev.yml

@@ -14,7 +14,6 @@ dependencies:
   - parmed>=3.4.3
   - ele
   - openff-toolkit >=0.11
-  - gmso
   - pip
   - pre-commit
   - pytest

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: