Merge branch 'MDAnalysis:develop' into parallelization_polymer

.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

.github/actions/setup-deps/action.yaml

@@ -21,8 +21,8 @@ inputs:
     default: 'codecov'
   cython:
     default: 'cython'
-  fasteners:
-    default: 'fasteners'
+  filelock:
+    default: 'filelock'
   griddataformats:
     default: 'griddataformats'
   gsd:
@@ -110,7 +110,7 @@ runs:
         CONDA_MIN_DEPS: |
           ${{ inputs.codecov }}
           ${{ inputs.cython }}
-          ${{ inputs.fasteners }}
+          ${{ inputs.filelock }}
           ${{ inputs.griddataformats }}
           ${{ inputs.hypothesis }}
           ${{ inputs.matplotlib }}

.github/workflows/gh-ci-cron.yaml

@@ -237,9 +237,11 @@ jobs:
         fail-fast: false
         matrix:
           # Stick to macos-13 because some of our
-          # optional depss don't support arm64 (i.e. macos-14)
+          # optional deps don't support arm64 (i.e. macos-14)
+          #
+          # add "3.13" once conda-forge packages are available (see #4805)
           os: [ubuntu-latest, macos-13]
-          python-version: ["3.9", "3.10", "3.11", "3.12"]
+          python-version: ["3.10", "3.11", "3.12"]
     steps:
     - uses: actions/checkout@v4
 
@@ -285,11 +287,8 @@ jobs:
         fail-fast: false
         matrix:
           os: [ubuntu-latest, macos-latest, macos-14, windows-latest]
-          python-version: ["3.9", "3.10", "3.11", "3.12"]
+          python-version: ["3.10", "3.11", "3.12", "3.13"]
           wheels: ['true', 'false']
-          exclude:
-          - os: "macos-14"
-            python-version: "3.9"
     steps:
       # Checkout to have access to local actions (i.e. setup-os)
     - uses: actions/checkout@v4

.pep8speaks.yml

@@ -4,7 +4,7 @@ scanner:
 
 pycodestyle:  # Valid if scanner.linter is pycodestyle
     max-line-length: 79
-    ignore: ["E203", "E701"]
+    ignore: ["E203", "E701", "W503"]
     exclude: []
     count: False
     first: False
@@ -17,7 +17,7 @@ pycodestyle:  # Valid if scanner.linter is pycodestyle
 
 flake8:  # Valid if scanner.linter is flake8
     max-line-length: 79
-    ignore: ["E203", "E501", "E701"]
+    ignore: ["E203", "E501", "E701", "W503"]
     exclude: []
     count: False
     show-source: False

azure-pipelines.yml

@@ -90,7 +90,7 @@ jobs:
       scikit-learn
       tqdm
       threadpoolctl
-      fasteners
+      filelock
     displayName: 'Install dependencies'
   # for wheel install testing, we pin to an
   # older NumPy, the oldest version we support and that

maintainer/conda/environment.yml

@@ -7,7 +7,7 @@ dependencies:
   - codecov
   - cython
   - docutils
-  - fasteners
+  - filelock
   - griddataformats
   - gsd
   - h5py>=2.10

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 +37,8 @@ Enhancements
 
 
 Changes
+ * Changed `fasteners` dependency to  `filelock` (Issue #4797, PR #4800)
+ * Codebase is now formatted with black (version `24`) (PR #4886)
 
 Deprecations
 

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

package/MDAnalysis/coordinates/XDR.py

@@ -38,7 +38,7 @@
 import numpy as np
 from os.path import getctime, getsize, isfile, split, join
 import warnings
-import fasteners
+from filelock import FileLock
 
 from . import base
 from ..lib.mdamath import triclinic_box
@@ -121,6 +121,8 @@ class XDRBaseReader(base.ReaderBase):
        Add a InterProcessLock when generating offsets
     .. versionchanged:: 2.4.0
        Use a direct read into ts attributes
+    .. versionchanged:: 2.9.0
+       Changed fasteners.InterProcessLock() to filelock.FileLock
     """
     @store_init_arguments
     def __init__(self, filename, convert_units=True, sub=None,
@@ -195,18 +197,18 @@ def _load_offsets(self):
 
         #  check if the location of the lock is writable.
         try:
-            with fasteners.InterProcessLock(lock_name) as filelock:
+            with FileLock(lock_name) as filelock:
                 pass
         except OSError as e:
             if isinstance(e, PermissionError) or e.errno == errno.EROFS:
                 warnings.warn(f"Cannot write lock/offset file in same location as "
                               f"{self.filename}. Using slow offset calculation.")
-                self._read_offsets(store=True)
+                self._read_offsets(store=False)
                 return
             else:
                 raise
 
-        with fasteners.InterProcessLock(lock_name) as filelock:
+        with FileLock(lock_name) as filelock:
             if not isfile(fname):
                 self._read_offsets(store=True)
                 return

package/MDAnalysis/core/__init__.py

@@ -50,7 +50,7 @@
 and write your own Python code.
 """
 
-__all__ = ['AtomGroup', 'Selection']
+__all__ = ["AtomGroup", "Selection"]
 
 from .groups import AtomGroup
 from .selection import Selection