format all (#4885)

MDAnalysis · Jan 8, 2025 · 263bbe6 · 263bbe6
1 parent 5eef341
commit 263bbe6
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Showing 12 changed files with 949 additions and 692 deletions.
diff --git a/package/MDAnalysis/__init__.py b/package/MDAnalysis/__init__.py
@@ -150,8 +150,7 @@
 
 """
 
-__all__ = ['Universe', 'Writer',
-           'AtomGroup', 'ResidueGroup', 'SegmentGroup']
+__all__ = ["Universe", "Writer", "AtomGroup", "ResidueGroup", "SegmentGroup"]
 
 import logging
 import warnings
@@ -161,10 +160,11 @@
 logger = logging.getLogger("MDAnalysis.__init__")
 
 from .version import __version__
+
 try:
     from .authors import __authors__
 except ImportError:
-    logger.info('Could not find authors.py, __authors__ will be empty.')
+    logger.info("Could not find authors.py, __authors__ will be empty.")
     __authors__ = []
 
 # Registry of Readers, Parsers and Writers known to MDAnalysis
@@ -178,16 +178,23 @@
 _SELECTION_WRITERS: Dict = {}
 _CONVERTERS: Dict = {}
 # Registry of TopologyAttributes
-_TOPOLOGY_ATTRS: Dict = {}   # {attrname: cls}
-_TOPOLOGY_TRANSPLANTS: Dict = {}   # {name: [attrname, method, transplant class]}
-_TOPOLOGY_ATTRNAMES: Dict = {}   # {lower case name w/o _ : name}
+_TOPOLOGY_ATTRS: Dict = {}  # {attrname: cls}
+_TOPOLOGY_TRANSPLANTS: Dict = (
+    {}
+)  # {name: [attrname, method, transplant class]}
+_TOPOLOGY_ATTRNAMES: Dict = {}  # {lower case name w/o _ : name}
 _GUESSERS: Dict = {}
 
 # custom exceptions and warnings
 from .exceptions import (
-    SelectionError, NoDataError, ApplicationError, SelectionWarning,
-    MissingDataWarning, ConversionWarning, FileFormatWarning,
-    StreamWarning
+    SelectionError,
+    NoDataError,
+    ApplicationError,
+    SelectionWarning,
+    MissingDataWarning,
+    ConversionWarning,
+    FileFormatWarning,
+    StreamWarning,
 )
 
 from .lib import log
@@ -197,8 +204,9 @@
 del logging
 
 # only MDAnalysis DeprecationWarnings are loud by default
-warnings.filterwarnings(action='once', category=DeprecationWarning,
-                        module='MDAnalysis')
+warnings.filterwarnings(
+    action="once", category=DeprecationWarning, module="MDAnalysis"
+)
 
 
 from . import units
@@ -213,11 +221,17 @@
 
 from .due import due, Doi, BibTeX
 
-due.cite(Doi("10.25080/majora-629e541a-00e"),
-         description="Molecular simulation analysis library",
-         path="MDAnalysis", cite_module=True)
-due.cite(Doi("10.1002/jcc.21787"),
-         description="Molecular simulation analysis library",
-         path="MDAnalysis", cite_module=True)
+due.cite(
+    Doi("10.25080/majora-629e541a-00e"),
+    description="Molecular simulation analysis library",
+    path="MDAnalysis",
+    cite_module=True,
+)
+due.cite(
+    Doi("10.1002/jcc.21787"),
+    description="Molecular simulation analysis library",
+    path="MDAnalysis",
+    cite_module=True,
+)
 
 del Doi, BibTeX
diff --git a/package/MDAnalysis/lib/distances.py b/package/MDAnalysis/lib/distances.py
@@ -403,7 +403,7 @@ def self_distance_array(
                 for j in range(i + 1, n):
                     dist[i, j] = dist[j, i] = d[k]
                     k += 1
-                    
+
     .. versionchanged:: 0.13.0
        Added *backend* keyword.
     .. versionchanged:: 0.19.0