Replace deprecated assert_almost_equal with assert_allclose in GNM tests

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

@@ -74,6 +74,8 @@ inputs:
     default: 'networkx'
   openmm:
     default: 'openmm'
+  pooch:
+    default: 'pooch'
   pytng:
     default: 'pytng>=0.2.3'
   rdkit:
@@ -145,6 +147,7 @@ runs:
           ${{ inputs.netcdf4 }}
           ${{ inputs.networkx }}
           ${{ inputs.openmm }}
+          ${{ inputs.pooch }}
           ${{ inputs.pytng }}
           ${{ inputs.rdkit }}
           ${{ inputs.scikit-learn }}

.gitignore

@@ -53,3 +53,5 @@ benchmarks/results
 .idea
 .vscode
 *.lock
+venv/
+package/doc/sphinx/_build/

benchmarks/benchmarks/ag_methods.py

@@ -195,6 +195,7 @@ def time_wrap_compound(self, num_atoms):
         """
         self.ag.wrap(compound="residues")
 
+
 class AtomGroupAttrsBench(object):
     """Benchmarks for the various MDAnalysis
     atomgroup attributes.

benchmarks/benchmarks/analysis/msd.py

@@ -0,0 +1,85 @@
+"""
+Benchmarks for the EinsteinMSD analysis module.
+"""
+
+import numpy as np
+import MDAnalysis as mda
+from MDAnalysis.analysis import msd
+from MDAnalysis.tests.datafiles import RANDOM_WALK_TOPO, RANDOM_WALK
+
+
+class EinsteinMSDCustom:
+    """
+    Benchmark for Mean-Squared Displacement (EinsteinMSD).
+
+    The trajectory is created by using random forces
+    that are generated from a normal distribution
+    and then cumulatively summed to simulate a real random walk.
+    """
+
+    unit = "ms"
+    description = (
+        "Performance of EinsteinMSD calculation using "
+        "custom n_atoms and range of n_frames."
+    )
+
+    timeout = 300.0
+
+    param_names = ["n_frames", "fft"]
+    params = ([100, 1000, 5000], [True, False])
+
+    def setup(self, n_frames, fft):
+        """Setup method for MSD benchmark with custom number of frames."""
+        n_atoms = 100
+
+        rng = np.random.default_rng(42)
+
+        # Random forces are sampled from a normal distribution
+        steps = rng.standard_normal((n_frames, n_atoms, 3), dtype=np.float32)
+
+        # Cumulative sum is taken to simulate positions over time
+        res = np.cumsum(steps, axis=0)
+
+        self.u = mda.Universe.empty(n_atoms, n_frames=n_frames, trajectory=True)
+        self.u.trajectory.set_array(res)
+
+    def time_msd_run_custom(self, n_frames, fft):
+        """
+        Benchmark calculation of Mean-Squared Displacement
+        using a custom trajectory.
+        """
+        msd_var = msd.EinsteinMSD(self.u, select="all", fft=fft)
+        msd_var.run()
+
+
+class EinsteinMSDExample:
+    """
+    Benchmark for Mean-Squared Displacement (EinsteinMSD)
+    using the RANDOM_WALK example trajectory provided in the MDAnalysis testsuite.
+
+    The files for the trajectory can be found in the library at :
+        RANDOM_WALK      - mdanalysis/testsuite/xyz_random_walk.xtc
+        RANDOM_WALK_TOPO - mdanalysis/testsuite/RANDOM_WALK_TOPO.pdb
+    """
+
+    unit = "ms"
+    description = (
+        "Performance of EinsteinMSD calculation using RANDOM_WALK_TOPO and RANDOM_WALK"
+    )
+
+    timeout = 300.0
+
+    param_names = ["fft"]
+    params = [True, False]
+
+    def setup(self, fft):
+        """Setup method for MSD benchmark with RANDOM_WALK example."""
+        self.u = mda.Universe(RANDOM_WALK_TOPO, RANDOM_WALK)
+
+    def time_msd_run_simple(self, fft):
+        """
+        Benchmark calculation of Mean-Squared Displacement
+        using the example trajectory RANDOM_WALK.
+        """
+        msd_var = msd.EinsteinMSD(self.u, fft=fft)
+        msd_var.run()

benchmarks/benchmarks/analysis/rdf.py

@@ -40,6 +40,7 @@ def time_interrdf(self, nbins, range_val, natoms):
         """
         self.rdf.run()
 
+
 class SimpleRdfsBench(object):
     """Benchmarks for MDAnalysis.analysis.rdf.InterRDF_s"""
 
@@ -61,9 +62,8 @@ def setup(self, nbins, range_val, natoms, npairs):
         ags = [[self.sel, self.sel]] * npairs
         self.rdf_s = InterRDF_s(self.u, ags, nbins=nbins, range=range_val)
 
-
     def time_interrdfs(self, nbins, range_val, natoms, npairs):
         """Benchmark a full trajectory parse
         by MDAnalysis.analysis.rdf.InterRDF_s
         """
-        self.rdf_s.run()
+        self.rdf_s.run()

benchmarks/benchmarks/analysis/rms.py

@@ -28,7 +28,9 @@ def setup(self, num_atoms, use_weights, center, superposition):
         self.u.trajectory[-1]
         self.B = self.u.atoms.positions.copy()[:num_atoms]
         self.atoms = self.u.atoms[:num_atoms]
-        self.weights = self.atoms.masses/np.sum(self.atoms.masses) if use_weights else None
+        self.weights = (
+            self.atoms.masses / np.sum(self.atoms.masses) if use_weights else None
+        )
 
     def time_rmsd(self, num_atoms, weights, center, superposition):
         """Benchmark rmsd function using a setup similar to

maintainer/update_json_stubs_sitemap.py

@@ -59,15 +59,13 @@ def write_redirect(file, version="", outfile=None):
     if outfile is None:
         outfile = file
     url = os.path.join(URL, version, file)
-    REDIRECT = textwrap.dedent(
-        f"""
+    REDIRECT = textwrap.dedent(f"""
     <!DOCTYPE html>
     <meta charset="utf-8">
     <title>Redirecting to {url}</title>
     <meta http-equiv="refresh" content="0; URL={url}">
     <link rel="canonical" href="{url}">
-    """
-    )
+    """)
     with open(outfile, "w") as f:
         f.write(REDIRECT)
     print(f"Wrote redirect from {url} to {outfile}")

package/AUTHORS

@@ -273,6 +273,8 @@ Chronological list of authors
   - Kushagar Garg
   - Jeremy M. G. Leung
   - Harshit Gajjela
+  - Kunj Sinha
+  - Ayush Agarwal
 
 External code
 -------------

package/CHANGELOG

@@ -16,11 +16,12 @@ The rules for this file:
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2, marinegor,
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
-         harshitgajjela-droid
+         harshitgajjela-droid, kunjsinha, aygarwal, jauy123
 
  * 2.11.0
 
 Fixes
+ * Fixes TypeError with np.int64 indexing in GSD Reader (Issue #5224)
  * Fixed bug in add_transformations allowing non-callable transformations
    (Issue #2558, PR #2558)
  * Drop/Replace lock file test in test_xdr (Issue #5236, PR #5237)
@@ -41,6 +42,10 @@ Fixes
    DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913)
 
 Enhancements
+ * Added new top-level `MDAnalysis.fetch` module (PR #4943)
+ * Added new function `MDAnalysis.fetch.from_PDB` to download structure files from wwPDB
+   using `pooch` as optional dependency (Issue #4907, PR #4943) 
+ * Added benchmarks for package.MDAnalysis.analysis.msd.EinsteinMSD (PR #5277)
  * Improved performance of `AtomGroup.wrap()` with compounds (PR #5220)
  * Adds support for parsing `.tpr` files produced by GROMACS 2026.0
  * Enables parallelization for analysis.diffusionmap.DistanceMatrix

package/MDAnalysis/__init__.py

@@ -48,10 +48,10 @@
 When using MDAnalysis in published work, please cite
 
     R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
-    D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. 
-    MDAnalysis: A Python package for the rapid analysis of molecular dynamics 
-    simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th 
-    Python in Science Conference, pages 98-105, Austin, TX, 2016. SciPy, 
+    D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
+    MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+    simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th
+    Python in Science Conference, pages 98-105, Austin, TX, 2016. SciPy,
     doi:10.25080/majora-629e541a-00e
 
     N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and
@@ -156,7 +156,6 @@
 import warnings
 from typing import Dict
 
-
 logger = logging.getLogger("MDAnalysis.__init__")
 
 from .version import __version__
@@ -179,9 +178,7 @@
 _CONVERTERS: Dict = {}
 # Registry of TopologyAttributes
 _TOPOLOGY_ATTRS: Dict = {}  # {attrname: cls}
-_TOPOLOGY_TRANSPLANTS: Dict = (
-    {}
-)  # {name: [attrname, method, transplant class]}
+_TOPOLOGY_TRANSPLANTS: Dict = {}  # {name: [attrname, method, transplant class]}
 _TOPOLOGY_ATTRNAMES: Dict = {}  # {lower case name w/o _ : name}
 _GUESSERS: Dict = {}
 
@@ -204,9 +201,7 @@
 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

package/MDAnalysis/analysis/align.py

@@ -89,7 +89,7 @@
 rotational superposition use the superposition keyword. This will calculate a
 minimized RMSD between the reference and mobile structure::
 
-   >>> rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions, 
+   >>> rmsd(mobile.select_atoms('name CA').positions, ref.select_atoms('name CA').positions,
    ...      superposition=True)
    6.809396586471815
 
@@ -138,7 +138,7 @@
    >>> trj = mda.Universe(PSF, DCD)         # trajectory of change 1AKE->4AKE
    >>> alignment = align.AlignTraj(trj, ref, filename='rmsfit.dcd')
    >>> alignment.run()
-   <MDAnalysis.analysis.align.AlignTraj object at ...> 
+   <MDAnalysis.analysis.align.AlignTraj object at ...>
 
 It is also possible to align two arbitrary structures by providing a
 mapping between atoms based on a sequence alignment. This allows
@@ -190,6 +190,7 @@
 .. autofunction:: get_matching_atoms
 
 """
+
 import os.path
 import warnings
 import logging
@@ -361,9 +362,7 @@ def _fit_to(
        where :math:`\bar{X}` is the center.
 
     """
-    R, min_rmsd = rotation_matrix(
-        mobile_coordinates, ref_coordinates, weights=weights
-    )
+    R, min_rmsd = rotation_matrix(mobile_coordinates, ref_coordinates, weights=weights)
 
     mobile_atoms.translate(-mobile_com)
     mobile_atoms.rotate(R)
@@ -845,8 +844,7 @@ def __init__(
 
             if os.path.exists(filename) and not force:
                 raise IOError(
-                    "Filename already exists in path and force is not set"
-                    " to True"
+                    "Filename already exists in path and force is not set" " to True"
                 )
 
         # do this after setting the memory reader to have a reference to the
@@ -1092,9 +1090,7 @@ def __init__(
             )
             logger.exception(err)
             raise SelectionError(err)
-        logger.info(
-            "RMS calculation " "for {0:d} atoms.".format(len(self.ref_atoms))
-        )
+        logger.info("RMS calculation " "for {0:d} atoms.".format(len(self.ref_atoms)))
 
         # store reference to mobile atoms
         self.mobile = mobile.atoms
@@ -1155,9 +1151,7 @@ def _single_frame(self):
     def _conclude(self):
         self.results.positions /= self.n_frames
         self.results.rmsd /= self.n_frames
-        self.results.universe.load_new(
-            self.results.positions.reshape((1, -1, 3))
-        )
+        self.results.universe.load_new(self.results.positions.reshape((1, -1, 3)))
         self._writer.write(self.results.universe.atoms)
         self._writer.close()
         if not self._verbose:
@@ -1465,26 +1459,18 @@ def fasta2select(
             stdout, stderr = run_clustalw()
         except:
             logger.exception("ClustalW %(clustalw)r failed", vars())
-            logger.info(
-                "(You can get clustalw2 from http://www.clustal.org/clustal2/)"
-            )
+            logger.info("(You can get clustalw2 from http://www.clustal.org/clustal2/)")
             raise
         with open(alnfilename) as aln:
             alignment = Bio.AlignIO.read(aln, "clustal")
+        logger.info("Using clustalw sequence alignment {0!r}".format(alnfilename))
         logger.info(
-            "Using clustalw sequence alignment {0!r}".format(alnfilename)
-        )
-        logger.info(
-            "ClustalW Newick guide tree was also produced: {0!r}".format(
-                treefilename
-            )
+            "ClustalW Newick guide tree was also produced: {0!r}".format(treefilename)
         )
 
     nseq = len(alignment)
     if nseq != 2:
-        raise ValueError(
-            "Only two sequences in the alignment can be processed."
-        )
+        raise ValueError("Only two sequences in the alignment can be processed.")
 
     # implict assertion that we only have two sequences in the alignment
     orig_resids = [ref_resids, target_resids]
@@ -1500,9 +1486,7 @@ def fasta2select(
         else:
             orig_resids[iseq] = np.asarray(orig_resids[iseq])
     # add offsets to the sequence <--> resid translation table
-    seq2resids = [
-        resids + offset for resids, offset in zip(orig_resids, offsets)
-    ]
+    seq2resids = [resids + offset for resids, offset in zip(orig_resids, offsets)]
     del orig_resids
     del offsets
 
@@ -1773,9 +1757,7 @@ def get_atoms_byres(g, match_mask=None):
             warnings.warn(msg, category=SelectionWarning)
         else:
             try:
-                mass_mismatches = (
-                    np.absolute(ag1.masses - ag2.masses) > tol_mass
-                )
+                mass_mismatches = np.absolute(ag1.masses - ag2.masses) > tol_mass
             except ValueError:
                 errmsg = (
                     "Failed to find matching atoms: len(reference) = {}, len(mobile) = {} "

package/MDAnalysis/analysis/atomicdistances.py

@@ -150,16 +150,12 @@ class AtomicDistances(AnalysisBase):
     def __init__(self, ag1, ag2, pbc=True, **kwargs):
         # check ag1 and ag2 have the same number of atoms
         if ag1.atoms.n_atoms != ag2.atoms.n_atoms:
-            raise ValueError(
-                "AtomGroups do not " "have the same number of atoms"
-            )
+            raise ValueError("AtomGroups do not " "have the same number of atoms")
         # check ag1 and ag2 are from the same trajectory
         elif ag1.universe.trajectory != ag2.universe.trajectory:
             raise ValueError("AtomGroups are not " "from the same trajectory")
 
-        super(AtomicDistances, self).__init__(
-            ag1.universe.trajectory, **kwargs
-        )
+        super(AtomicDistances, self).__init__(ag1.universe.trajectory, **kwargs)
 
         self._ag1 = ag1
         self._ag2 = ag2