MDAnalysis 2.8.0__tar.gz → 2.9.0__tar.gz

{mdanalysis-2.8.0 → mdanalysis-2.9.0}/AUTHORS

@@ -82,7 +82,7 @@ Chronological list of authors
   - Shantanu Srivastava
   - Pedro Reis
   - Zhenbo Li
- 2017
+2017
   - Ruggero Cortini
   - Kashish Punjani
   - Utkarsh Bansal
@@ -233,7 +233,7 @@ Chronological list of authors
   - Lawson Woods
   - Johannes Stöckelmaier
   - Jenna M. Swarthout Goddard
-  2024
+2024
   - Aditya Keshari
   - Philipp Stärk
   - Kai Niklas Spauszus
@@ -244,7 +244,10 @@ Chronological list of authors
   - Fabian Zills
   - Laksh Krishna Sharma
   - Matthew Davies
-
+  - Jia-Xin Zhu
+  - Tanish Yelgoe
+ 2025
+  - Joshua Raphael Uy
 
 External code
 -------------

{mdanalysis-2.8.0 → mdanalysis-2.9.0}/CHANGELOG

@@ -14,6 +14,42 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
+03/11/25 IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy,
+         marinegor, hmacdope, jauy123, al42and
+
+ * 2.9.0
+
+Fixes
+ * Add support for TPR files produced by GROMACS 2024.4 and GROMACS 2025.0
+ * Fixes invalid default unit from Angstrom to Angstrom^{-3} for
+   convert_density() function. (Issue #4829)
+ * Fixes deprecation warning Array to scalar convertion. Replaced atan2()
+   with np.arctan2() (Issue #4339)
+ * Replaced mutable defaults with None and initialized them within
+   the function to prevent shared state. (Issue #4655)
+
+Enhancements
+ * Improve distopia backend support in line with new functionality available 
+   in distopia >= 0.3.1 (PR #4734)
+ * 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)
+ * Add check and warning for empty (all zero) coordinates in RDKit converter
+   (PR #4824)
+ * Added `precision` for XYZWriter (Issue #4775, PR #4771) 
+
+Changes
+ * MDAnalysis.analysis.psa, MDAnalysis.analysis.waterdynamics and
+   MDAnalysis.analysis.hole2 are now no longer available by default in
+   MDAnalysis. You will need to install their respective MDAKits to
+   keep using them. Please note that they will be fully removed in
+   MDAnalysis v3.0 (Issue #4899, PR #4953).
+ * Changed `fasteners` dependency to  `filelock` (Issue #4797, PR #4800)
+ * Codebase is now formatted with black (version `24`) (PR #4886)
+
+
 11/11/24 IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
          tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher, 
@@ -79,11 +115,11 @@ Enhancements
  * Introduce parallelization API to `AnalysisBase` and to `analysis.rms.RMSD` class
    (Issue #4158, PR #4304)
  * Enables parallelization for analysis.gnm.GNMAnalysis (Issue #4672)
- * explicitly mark `analysis.pca.PCA` as not parallelizable (Issue #4680)
- * enables parallelization for analysis.bat.BAT (Issue #4663)
- * enable parallelization for analysis.dihedrals.{Dihedral,Ramachandran,Janin}
+ * Explicitly mark `analysis.pca.PCA` as not parallelizable (Issue #4680)
+ * Enables parallelization for analysis.bat.BAT (Issue #4663)
+ * Enable parallelization for analysis.dihedrals.{Dihedral,Ramachandran,Janin}
    (Issue #4673) 
- * enables parallelization for analysis.dssp.dssp.DSSP (Issue #4674)
+ * Enables parallelization for analysis.dssp.dssp.DSSP (Issue #4674)
  * Enables parallelization for analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis (Issue #4664)
  * Improve error message for `AtomGroup.unwrap()` when bonds are not present.(Issue #4436, PR #4642)
  * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)

{mdanalysis-2.8.0 → mdanalysis-2.9.0}/MDAnalysis/__init__.py

@@ -150,8 +150,7 @@ the OPLS/AA force field.
 
 """
 
-__all__ = ['Universe', 'Writer',
-           'AtomGroup', 'ResidueGroup', 'SegmentGroup']
+__all__ = ["Universe", "Writer", "AtomGroup", "ResidueGroup", "SegmentGroup"]
 
 import logging
 import warnings
@@ -161,10 +160,11 @@ from typing import Dict
 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 @@ _PARSER_HINTS: Dict = {}
 _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 @@ logging.getLogger("MDAnalysis").addHandler(log.NullHandler())
 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 . import converters
 
 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

{mdanalysis-2.8.0 → mdanalysis-2.9.0}/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",
 ]

{mdanalysis-2.8.0 → mdanalysis-2.9.0}/MDAnalysis/analysis/align.py

@@ -1592,9 +1592,12 @@ def get_matching_atoms(ag1, ag2, tol_mass=0.1, strict=False, match_atoms=True):
         rsize_mismatches = np.absolute(rsize1 - rsize2)
         mismatch_mask = (rsize_mismatches > 0)
         if np.any(mismatch_mask):
-            def get_atoms_byres(g, match_mask=np.logical_not(mismatch_mask)):
+
+            def get_atoms_byres(g, match_mask=None):
                 # not pretty... but need to do things on a per-atom basis in
                 # order to preserve original selection
+                if match_mask is None:
+                    match_mask = np.logical_not(mismatch_mask)
                 ag = g.atoms
                 good = ag.residues.resids[match_mask]  # resid for each residue
                 resids = ag.resids                     # resid for each atom

{mdanalysis-2.8.0 → mdanalysis-2.9.0}/MDAnalysis/analysis/backends.py

@@ -35,6 +35,7 @@ Classes
 -------
 
 """
+
 import warnings
 from typing import Callable
 from MDAnalysis.lib.util import is_installed
@@ -102,8 +103,9 @@ class BackendBase:
             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 @@ class BackendSerial(BackendBase):
             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 @@ class BackendDask(BackendBase):
         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 @@ class BackendDask(BackendBase):
         """
         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