add black instead of ruff

MDAnalysis · Oct 25, 2024 · e80632c · e80632c
1 parent b7ada7c
commit e80632c
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Showing 3 changed files with 17 additions and 7 deletions.
diff --git a/package/MDAnalysis/coordinates/MMCIF.py b/package/MDAnalysis/coordinates/MMCIF.py
@@ -15,7 +15,7 @@
 logger = logging.getLogger("MDAnalysis.coordinates.MMCIF")
 
 
-def get_coordinates(model: 'gemmi.Model') -> np.ndarray:
+def get_coordinates(model: "gemmi.Model") -> np.ndarray:
     """Get coordinates of all atoms in the `gemmi.Model` object.
 
     Parameters

diff --git a/package/MDAnalysis/topology/MMCIFParser.py b/package/MDAnalysis/topology/MMCIFParser.py
@@ -61,10 +61,14 @@ def _into_idx(arr: list) -> list[int]:
 
     .. versionadded:: 2.8.0
     """
-    return [idx for idx, (_, group) in enumerate(itertools.groupby(arr)) for _ in group]
+    return [
+        idx
+        for idx, (_, group) in enumerate(itertools.groupby(arr))
+        for _ in group
+    ]
 
 
-def get_Atomattrs(model: 'gemmi.Model') -> tuple[list[AtomAttr], np.ndarray]:
+def get_Atomattrs(model: "gemmi.Model") -> tuple[list[AtomAttr], np.ndarray]:
     """Extract all attributes that are subclasses of :class:`..core.topologyattrs.AtomAttr` from a  ``gemmi.Model`` object,
     and a `residx` index with indices of all atoms in residues.
 
@@ -165,7 +169,9 @@ def get_Atomattrs(model: 'gemmi.Model') -> tuple[list[AtomAttr], np.ndarray]:
     return attrs, residx
 
 
-def get_Residueattrs(model: 'gemmi.Model') -> tuple[list[ResidueAttr], np.ndarray]:
+def get_Residueattrs(
+    model: "gemmi.Model",
+) -> tuple[list[ResidueAttr], np.ndarray]:
     """Extract all attributes that are subclasses of :class:`..core.topologyattrs.ResidueAttr` from a  ``gemmi.Model`` object,
     and a `segidx` index witn indices of all residues in segments.
 
@@ -214,7 +220,7 @@ def get_Residueattrs(model: 'gemmi.Model') -> tuple[list[ResidueAttr], np.ndarra
     return attrs, segidx
 
 
-def get_Segmentattrs(model: 'gemmi.Model') -> SegmentAttr:
+def get_Segmentattrs(model: "gemmi.Model") -> SegmentAttr:
     """Extract all attributes that are subclasses of :class:`..core.topologyattrs.SegmentAttr` from a  ``gemmi.Model`` object.
 
     Parameters

diff --git a/testsuite/MDAnalysisTests/topology/test_mmcif.py b/testsuite/MDAnalysisTests/topology/test_mmcif.py
@@ -35,7 +35,10 @@ def test_chains(mmcif_filename, n_chains):
 @pytest.mark.parametrize(
     "mmcif_filename,sequence",
     [
-        (f"{MMCIF_FOLDER}/1YJP.cif", ["GLY", "ASN", "ASN", "GLN", "GLN", "ASN", "TYR"]),
+        (
+            f"{MMCIF_FOLDER}/1YJP.cif",
+            ["GLY", "ASN", "ASN", "GLN", "GLN", "ASN", "TYR"],
+        ),
         (
             f"{MMCIF_FOLDER}/1YJP.cif.gz",
             ["GLY", "ASN", "ASN", "GLN", "GLN", "ASN", "TYR"],
@@ -47,6 +50,7 @@ def test_chains(mmcif_filename, n_chains):
 def test_sequence(mmcif_filename, sequence):
     u = mda.Universe(mmcif_filename)
     in_structure = [
-        str(res.resname) for res in u.select_atoms("protein and chainid A").residues
+        str(res.resname)
+        for res in u.select_atoms("protein and chainid A").residues
     ]
     assert in_structure == sequence, ":".join(in_structure)