Merge branch 'develop' into fasteners_to_filelock

MDAnalysis · Jan 10, 2025 · 40d09cc · 40d09cc
2 parents 2fb9b69 + bdfb2c9
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -1,2 +1,43 @@
-# black
-83e5f99051d86ca354b537be8854c40f9b6ce172
+##### git-blame shows what revision and author last modified each line of a file
+##### The ".git-blame-ignore-revs" file is used to ignore certain revisions from being
+##### shown in the output of git blame (also on GitHub blame view).
+#
+# ~~~ Commits that only change the formatting of the code should be ignored. ~~~
+#
+# --- Automated Formatting with `black` ---
+# MDAnalysis was automatically formatted with `black` (end of 2024, beginning of 2025).
+# Formatting PRs (should) contain "[fmt]" in the title (and so do the related commits).
+# See https://github.com/MDAnalysis/mdanalysis/issues/2450 for more details.
+# The following commits are squash commits that contain only^ formatting changes.
+#    ^ This is not strictly true. See PRs for the nitty gritty details.
+#.     PR numbers are listed just above the commit being ignored.
+#4725 
+571431a169e5881f7d09930c4d7e633df0f2cd40
+#4726
+46be788d84a6cb149d90e4493a726c3a30b3cca0
+#4802
+441e2c67abdb8a0a5ffac4a0bc5e88bc7c329aa8
+#4804
+25e755fd78e0a6fb71a91c9d3d989328f021f34b
+#4809
+557f27d658ff0d4011bbe0efa03495f18aa2c1ce
+#4848
+b710e57a64654bed5250eb771f0f27a2dddfeebf
+#4850
+9110a6efe2765802856d028e650ebb0117d336bf
+#4851
+a10e23e681023f383baac7582c39dce4180e2263
+#4856
+c08cb797fd1a2cb45bc0b9e4522cabb15d1f36bd
+#4857
+29deccc9b43a09d2ec3b456bb9c70aae4c34c2cd
+#4859
+9312fa67f163ec055a66f5756a182206fbea3130
+#4861
+55cce24003d4c0975b1bba387b9e6ac20638780e
+#4874
+5eef34165b03281515e08a69159f6504e3a2ff8b
+#4875
+b8fe34b73c9df9330c1608229b2f8cddc6e275b4
+#4885
+263bbe65047e535fbad981852ad9c7327826f93d
diff --git a/maintainer/active_files_package.lst b/maintainer/active_files_package.lst
diff --git a/maintainer/active_files_testsuite.lst b/maintainer/active_files_testsuite.lst
diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -14,8 +14,8 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
-??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev,
-         tylerjereddy
+??/??/?? IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy,
+         marinegor
 
  * 2.9.0
 
@@ -37,6 +37,7 @@ Enhancements
 
 Changes
  * Changed `fasteners` dependency to  `filelock` (Issue #4797, PR #4800)
+ * Codebase is now formatted with black (version `24`) (PR #4886)
 
 Deprecations
 

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