Merge branch 'develop' into fmt-blame

.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

package/CHANGELOG

@@ -27,6 +27,7 @@ Fixes
    the function to prevent shared state. (Issue #4655)
 
 Enhancements
+ * Addition of 'water' token for water selection (Issue #4839)
  * Enables parallelization for analysis.density.DensityAnalysis (Issue #4677, PR #4729)
  * Enables parallelization for analysis.contacts.Contacts (Issue #4660)
  * Enable parallelization for analysis.nucleicacids.NucPairDist (Issue #4670)

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

package/MDAnalysis/core/_get_readers.py

@@ -22,9 +22,15 @@
 import copy
 import inspect
 
-from .. import (_READERS, _READER_HINTS,
-                _PARSERS, _PARSER_HINTS,
-                _MULTIFRAME_WRITERS, _SINGLEFRAME_WRITERS, _CONVERTERS)
+from .. import (
+    _READERS,
+    _READER_HINTS,
+    _PARSERS,
+    _PARSER_HINTS,
+    _MULTIFRAME_WRITERS,
+    _SINGLEFRAME_WRITERS,
+    _CONVERTERS,
+)
 from ..lib import util
 
 
@@ -80,8 +86,8 @@ def get_reader_for(filename, format=None):
         return format
 
     # ChainReader gets returned even if format is specified
-    if _READER_HINTS['CHAIN'](filename):
-        format = 'CHAIN'
+    if _READER_HINTS["CHAIN"](filename):
+        format = "CHAIN"
     # Only guess if format is not specified
     if format is None:
         for fmt_name, test in _READER_HINTS.items():
@@ -103,7 +109,9 @@ def get_reader_for(filename, format=None):
             "           Use the format keyword to explicitly set the format: 'Universe(...,format=FORMAT)'\n"
             "           For missing formats, raise an issue at "
             "https://github.com/MDAnalysis/mdanalysis/issues".format(
-                format, filename, _READERS.keys()))
+                format, filename, _READERS.keys()
+            )
+        )
         raise ValueError(errmsg) from None
 
 
@@ -158,7 +166,7 @@ def get_writer_for(filename, format=None, multiframe=None):
        The `filename` argument has been made mandatory.
     """
     if filename is None:
-        format = 'NULL'
+        format = "NULL"
     elif format is None:
         try:
             root, ext = util.get_ext(filename)
@@ -172,18 +180,24 @@ def get_writer_for(filename, format=None, multiframe=None):
         else:
             format = util.check_compressed_format(root, ext)
 
-    if format == '':
-        raise ValueError((
-            'File format could not be guessed from {}, '
-            'resulting in empty string - '
-            'only None or valid formats are supported.'
-            ).format(filename))
+    if format == "":
+        raise ValueError(
+            (
+                "File format could not be guessed from {}, "
+                "resulting in empty string - "
+                "only None or valid formats are supported."
+            ).format(filename)
+        )
 
     format = format.upper()
     if multiframe is None:
         # Multiframe takes priority, else use singleframe
-        options = copy.copy(_SINGLEFRAME_WRITERS)  # do copy to avoid changing in place
-        options.update(_MULTIFRAME_WRITERS)  # update overwrites existing entries
+        options = copy.copy(
+            _SINGLEFRAME_WRITERS
+        )  # do copy to avoid changing in place
+        options.update(
+            _MULTIFRAME_WRITERS
+        )  # update overwrites existing entries
         errmsg = "No trajectory or frame writer for format '{0}'"
     elif multiframe is True:
         options = _MULTIFRAME_WRITERS
@@ -192,9 +206,11 @@ def get_writer_for(filename, format=None, multiframe=None):
         options = _SINGLEFRAME_WRITERS
         errmsg = "No single frame writer for format '{0}'"
     else:
-        raise ValueError("Unknown value '{0}' for multiframe,"
-                         " only True, False, None allowed"
-                         "".format(multiframe))
+        raise ValueError(
+            "Unknown value '{0}' for multiframe,"
+            " only True, False, None allowed"
+            "".format(multiframe)
+        )
 
     try:
         return options[format]
@@ -252,10 +268,13 @@ def get_parser_for(filename, format=None):
                 "   See https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats\n"
                 "   For missing formats, raise an issue at \n"
                 "   https://github.com/MDAnalysis/mdanalysis/issues".format(
-                    format, _PARSERS.keys()))
+                    format, _PARSERS.keys()
+                )
+            )
             raise ValueError(errmsg) from None
         else:
-            return _PARSERS['MINIMAL']
+            return _PARSERS["MINIMAL"]
+
 
 def get_converter_for(format):
     """Return the appropriate topology converter for ``format``.
@@ -276,6 +295,6 @@ def get_converter_for(format):
     try:
         writer = _CONVERTERS[format]
     except KeyError:
-        errmsg = f'No converter found for {format} format'
+        errmsg = f"No converter found for {format} format"
         raise TypeError(errmsg) from None
     return writer

package/MDAnalysis/core/accessors.py

@@ -168,6 +168,7 @@ class ConverterWrapper:
         be accessed as a method with the name of the package in lowercase, i.e.
         `convert_to.parmed()`
     """
+
     _CONVERTERS = {}
 
     def __init__(self, ag):
@@ -199,6 +200,8 @@ def __call__(self, package, *args, **kwargs):
         try:
             convert = getattr(self, package.lower())
         except AttributeError:
-            raise ValueError(f"No {package!r} converter found. Available: "
-                             f"{' '.join(self._CONVERTERS.keys())}") from None
+            raise ValueError(
+                f"No {package!r} converter found. Available: "
+                f"{' '.join(self._CONVERTERS.keys())}"
+            ) from None
         return convert(*args, **kwargs)