Merge branch 'MDAnalysis:develop' into devel-relprop

MDAnalysis · Jan 7, 2025 · f960ea7 · f960ea7
2 parents 2b4ab7a + 1eca9f2
commit f960ea7
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diff --git a/.github/workflows/gh-ci-cron.yaml b/.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

diff --git a/.pep8speaks.yml b/.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

diff --git a/package/CHANGELOG b/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)

diff --git a/package/MDAnalysis/analysis/__init__.py b/package/MDAnalysis/analysis/__init__.py
@@ -22,31 +22,31 @@
 #
 
 __all__ = [
-    'align',
-    'backends',
-    'base',
-    'contacts',
-    'density',
-    'distances',
-    'diffusionmap',
-    'dihedrals',
-    'distances',
-    'dielectric',
-    'gnm',
-    'hbonds',
-    'helix_analysis',
-    'hole2',
-    'hydrogenbonds',
-    'leaflet',
-    'lineardensity',
-    'msd',
-    'nuclinfo',
-    'nucleicacids',
-    'polymer',
-    'pca',
-    'psa',
-    'rdf',
-    'results',
-    'rms',
-    'waterdynamics',
+    "align",
+    "backends",
+    "base",
+    "contacts",
+    "density",
+    "distances",
+    "diffusionmap",
+    "dihedrals",
+    "distances",
+    "dielectric",
+    "gnm",
+    "hbonds",
+    "helix_analysis",
+    "hole2",
+    "hydrogenbonds",
+    "leaflet",
+    "lineardensity",
+    "msd",
+    "nuclinfo",
+    "nucleicacids",
+    "polymer",
+    "pca",
+    "psa",
+    "rdf",
+    "results",
+    "rms",
+    "waterdynamics",
 ]
diff --git a/package/MDAnalysis/analysis/backends.py b/package/MDAnalysis/analysis/backends.py
@@ -35,6 +35,7 @@
 -------
 
 """
+
 import warnings
 from typing import Callable
 from MDAnalysis.lib.util import is_installed
@@ -102,8 +103,9 @@ def _get_checks(self):
             checked during ``_validate()`` run
         """
         return {
-            isinstance(self.n_workers, int) and self.n_workers > 0:
-            f"n_workers should be positive integer, got {self.n_workers=}",
+            isinstance(self.n_workers, int)
+            and self.n_workers
+            > 0: f"n_workers should be positive integer, got {self.n_workers=}",
         }
 
     def _get_warnings(self):
@@ -183,8 +185,8 @@ def _get_warnings(self):
             checked during ``_validate()`` run
         """
         return {
-            self.n_workers == 1:
-            "n_workers is ignored when executing with backend='serial'"
+            self.n_workers
+            == 1: "n_workers is ignored when executing with backend='serial'"
         }
 
     def apply(self, func: Callable, computations: list) -> list:
@@ -307,10 +309,12 @@ def apply(self, func: Callable, computations: list) -> list:
         import dask
 
         computations = [delayed(func)(task) for task in computations]
-        results = dask.compute(computations,
-                               scheduler="processes",
-                               chunksize=1,
-                               num_workers=self.n_workers)[0]
+        results = dask.compute(
+            computations,
+            scheduler="processes",
+            chunksize=1,
+            num_workers=self.n_workers,
+        )[0]
         return results
 
     def _get_checks(self):
@@ -326,8 +330,9 @@ def _get_checks(self):
         """
         base_checks = super()._get_checks()
         checks = {
-            is_installed("dask"):
-            ("module 'dask' is missing. Please install 'dask': "
-             "https://docs.dask.org/en/stable/install.html")
+            is_installed("dask"): (
+                "module 'dask' is missing. Please install 'dask': "
+                "https://docs.dask.org/en/stable/install.html"
+            )
         }
         return base_checks | checks