MDAnalysis 2.9.0__tar.gz → 2.11.0__tar.gz

{mdanalysis-2.9.0 → mdanalysis-2.11.0}/AUTHORS

@@ -192,7 +192,7 @@ Chronological list of authors
   - Mingyi Xue
   - Meghan Osato
   - Anirvinya G
-  - Rishabh Shukla  
+  - Rishabh Shukla
   - Manish Kumar
   - Aditi Tripathi
   - Sukeerti T
@@ -246,8 +246,47 @@ Chronological list of authors
   - Matthew Davies
   - Jia-Xin Zhu
   - Tanish Yelgoe
- 2025
+2025
   - Joshua Raphael Uy
+  - Namir Oues
+  - Pavel Buslaev
+  - Lexi Xu
+  - BHM-Bob G
+  - Yu-Yuan (Stuart) Yang
+  - James Rowe
+  - Debasish Mohanty
+  - Abdulrahman Elbanna
+  - Tulga-Erdene Sodjargal
+  - Gareth Elliott
+  - Marc Schuh
+  - Sirsha Ganguly
+  - Amruthesh Thirumalaiswamy
+  - Ch Zhang
+  - Raúl Lois-Cuns
+  - Pranay Pelapkar
+  - Shreejan Dolai
+  - Tanisha Dubey
+  - Brady Johnston
+  - Pradyumn-cloud
+2026
+  - Mohammad Ayaan
+  - Khushi Phougat
+  - Kushagar Garg
+  - Jeremy M. G. Leung
+  - Harshit Gajjela
+  - Kunj Sinha
+  - Ayush Agarwal
+  - Parth Uppal
+  - Olivier Languin--Cattoën
+  - Amarendra Mohan
+  - Shubham Mittal  
+  - Charity Grey
+  - Sai Udayagiri
+  - Apoorva Verma
+  - Aryaman Chaudhri
+  - Francesco Siciliani
+  - Akshit Boora
+
 
 External code
 -------------

{mdanalysis-2.9.0 → mdanalysis-2.11.0}/CHANGELOG

@@ -14,6 +14,237 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
+10/21/26 IAlibay, orbeckst, marinegor, tylerjereddy, ljwoods2,
+         spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
+         harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
+         ollyfutur, Amarendra22, charity-g, ParthUppal523, apoorva-01, RMeli,
+         raulloiscuns, Aryaman-Chaudhri, sici17, AkshitBoora
+
+ * 2.11.0
+
+Fixes
+ * Fixed PBC handling in triclinic boxes in `_triclinic_pbc()` (used by
+   `distances.apply_PBC()`) and `lib.nsgrid.NSGrid` (used by `capped_distance`
+   and `self_capped_distance`):
+   - `apply_PBC()`, `AtomGroup.wrap()`/`pack_into_box()`, `center*(wrap=True)`,
+     `AtomGroup.unwrap()` with `reference="com"`/`"cog"` and the
+     `transformations.wrap` transformation could leave atoms (or compound
+     centers) outside the primary unit cell in boxes with both b_x and c_y
+     non-zero (e.g. truncated octahedra); they were shifted by whole box
+     vectors, so periodic distances were unaffected, but results that depend on
+     absolute wrapped positions (e.g. dipole moments, densities, written
+     coordinates) may change.
+   - `capped_distance()` and `self_capped_distance()` with the `nsgrid` or
+     `pkdtree` methods (and hence bond guessing, distance-based selections)
+     could miss pairs within the cutoff; `nsgrid` was affected in triclinic
+     boxes with two or more non-90º angles (e.g. rhombic dodecahedron),
+     `pkdtree` in boxes with both b_x and c_y non-zero (e.g. truncated
+     octahedron).
+   (Issue #4906, PR #5496)
+ * `InterRDF_s` with a parallel backend returned wrong counts for one
+   pair of groups and failed for more than two (`nested_array_sum`
+   summed exactly two pairs) (Issue #5496, PR #5497)
+ * Fixed `HydrogenBondAutoCorrel.run()` returning NaN when a run starts
+   without hydrogen bonds. Such runs are now skipped with a RuntimeWarning,
+   and a ValueError is raised if all runs are skipped (Issue #5483, PR #5492)
+ * `GNMAnalysis` silently and wrongly reduced the split `eigenvectors` array
+   via hstack instead of vstack when using multiprocessing, and would raise
+   an error with uneven split of frames across workers (Issue #5494, PR #5495)
+ * `AnalysisBase.run()` now interprets NumPy boolean arrays passed to `frames`
+   as frame masks instead of integer frame indices (Issue #5472)
+ * Mass (u) has been added to MDAnalysis base units and clarified that physical
+   constants use CODATA 2010 values (Issue #3944, PR #5439)
+ * Added `.gitattributes` to enforce LF (\n) as line endings and renormalized
+   existing files to conform (Issue #5315, PR #5446)
+ * `AtomGroup.rotate()` and the `rotateby` trajectory transformation now
+   also rotate velocities and forces besides positions. This also affects
+   `MDAnalysis.analysis.align.alignto()` and `AlignTraj`, since they
+   apply their fit via `AtomGroup.rotate()`. Note: this changes existing
+   behavior, as velocities/forces were previously left untouched by
+   rotation. (Issue #5421, PR #5452)
+ * Fix FileLock tests for XTC and TRR: lock file is no longer removed (#5382)
+ * InterRDF now correctly returns bins in parallel (PR #5344)
+ * `Merge()` no longer raises a TypeError on Universes that have a `cmaps`
+   attribute; cmaps are now combined like the other connection attributes
+   (bonds, angles, dihedrals, impropers) (Issue #3672).
+ * The `principal_axes` method in :class:`Masses` now uses
+   `np.linalg.eigh` instead of `np.linalg.eig`, improving numerical
+   stability. This may lead to slightly different results from previous
+   version of MDAnalysis (#5403, PR #5404).
+ * `MDAnalysis.analysis.nucleicacids.WatsonCrickDist`, `MinorPairDist`,
+   and `MajorPairDist` now match residue names against the full resname
+   instead of only the first character, fixing incorrect behaviour with
+   multi-character names such as CHARMM ``DG``/``DA`` or ``GUA``/``ADE``
+   (Issue #5360). Note: users relying on the previous truncation
+   behaviour must now pass explicit residue names via the ``g_name``,
+   ``a_name``, etc. keyword arguments.
+ * `MDAnalysis.analysis.atomicdistances.AtomicDistances` results are now
+   consistent with expected `analysis` documentation data type = Results
+   (Issue #4819, PR #5347)
+   Note: This fix is backwards-incompatible.
+ * DSSP now correctly handles periodic boundary conditions in hydrogen bond
+   detection; previously, hydrogen bonds across periodic boundaries were
+   missed (PR #5182)
+ * Fix mixed-case atom types in guess_bonds (Issue #5342, PR #5343)
+ * Fixes msd for non-linear frames, when non_linear is not explicitly
+   provided (Issue #5100, PR #5254)
+ * 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)
+ * HydrogenBondAnalysis: Fixed `count_by_time()` when using `run(FrameIterator)` that
+   results in `self.start` and `self.end` being None (Issue #5200, PR #5202)
+ * NoJump shows a more informative message and fails  when applied
+   outside of the first frame (Issue #4915, PR #5201)
+ * DSSP now explicitly checks for a minimum of 6 residues and raises a clear
+   error message, unlike the previous behavior where it would fail with an
+   incomprehensible broadcasting error at execution time (Issue #5046, PR #5163)
+ * Fixes the verbose=False in EinsteinMSD, and only shows progress bar when
+   verbose=True (Issue #5144, PR #5153)
+ * Fix incorrect assignment of topology_format to format (and vice versa)
+   when a parsing class is provided to either (Issue #5147, PR #5148)
+ * Fix incorrect TPR file parsing for GROMACS topologies produced prior
+   to version 5.1.0 (Issue #5145, PR #5146)
+ * Fixes incorrect assignment of secondary structure to proline residues in
+   DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913)
+
+Enhancements
+ * Add reading single-frame files from mmCIF, also known as PDBx format, using
+   crystallographic library `gemmi` as a backend (Issue #2367 and extension of
+   #4303, also solves #5089, PR #4712).
+ * Added ASV benchmark for XYZ trajectory reading (PR #5441)
+ * Added ASV benchmark for PDB trajectory reading (PR #5394)
+ * Read Linear Angle bonded interaction entries from GROMACS TPR files and
+   add the angles to the topology (Issue #5361, PR #5372)
+ * Enables parallelization for analysis.atomicdistances.AtomicDistances
+   (Issue #4662, PR #4822)
+ * DSSP uses ``capped_distance`` and ``calc_bonds`` for faster distance
+   calculations and supports ``backend`` selection (e.g. ``"distopia"``)
+   (PR #5182)
+ * Added ASV benchmark for `MDAnalysis.analysis.contacts` (PR #5291)
+ * Improved performance of inverse index mapping in AtomGroup using an optimized
+   Cython implementation in lib._cutils.inverse_int_index()
+   (Issue #3387, PR #5252)
+ * Added documentation for all keyword in select_atoms() and
+   selections.rst (Issue #5317, PR #5325)
+ * Added HydrogenBondAnalysis benchmark for performance tracking (PR #5309)
+ * Added `select=None` in `analysis.rms.RMSD` to perform no selection on
+   the input `atomgroup` and `reference` (Issue #5300, PR #5296)
+ * MOL2Parser now reads unit cell dimensions from @<TRIPOS>CRYSIN records (Issue #3341)
+ * Reduces duplication of code in _apply() function (Issue #5247, PR #5294)
+ * 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
+   (Issue #4679, PR #4745)
+ * TPRReader now reads box vectors from TPR files and exposes them as
+   ``Universe.dimensions`` (Issue #5375)
+
+Changes
+ * The msd.py inside analysis is changed, and ProgressBar is implemented inside
+   _conclude_simple and _conclude_fft functions instead of tqdm (Issue #5144, PR #5153)
+
+Deprecations
+
+
+10/18/25 IAlibay, orbeckst, BHM-Bob, TRY-ER, Abdulrahman-PROG, pbuslaev,
+         yuxuanzhuang, yuyuan871111, tanishy7777, tulga-rdn, Gareth-elliott,
+         hmacdope, tylerjereddy, cbouy, talagayev, DrDomenicoMarson, amruthesht,
+         p-j-smith, gitzhangch, raulloiscuns, lexi-x, namiroues, jpkrowe, schuhmc,
+         gitsirsha, Pradyumn-cloud
+
+ * 2.10.0
+
+Fixes
+ * Fix incorrect conversion factors for speed units A/fs, A/us, A/ms
+   in MDAnalysis.units (Issue #5051, PR #5053)
+ * `analysis.polymer.sort_backbone` is now working for discontinuous polymers
+   and does not result in an infinite loop (Issue #5112, PR #5113)
+ * Fix atom selection parsing to allow escaping keywords with a backslash
+   (Issue #5111, PR #5119)
+ * Fix DCDWriter to correctly write unit cell angles as cosines following
+   NAMD/VMD convention (Issue #5069)
+ * Fixed an integer overflow in large DCD file seeks on Windows
+   (Issue #4879, PR #5086)
+ * Fix compile failure due to numpy issues in transformations.c (Issue #5061, PR #5068)
+ * Fix incorrect `self.atom` assignment in SingleFrameReaderBase (Issue #5052, PR #5055)
+ * Fixes bug in `analysis/hydrogenbonds.py`: `_donors` and `_hydrogens`
+   were not updated when the `acceptors_sel` and `hydrogens_sel` were provided
+   after initialization. (Issue #5010, PR #5018)
+ * Fixes bug in `analysis/gnm.py`: `closeContactGNMAnalysis`: correct the
+   `residue_index_map` generation when selection is not `protein`.
+   (Issue #4924, PR #4961)
+ * Reads `segids` column in `PDBParser` from 73-76 instead of 67-76 to
+   align the standard of a PDBReader (e.g., Chimera, CHARMM, Gemmi).
+   (Issue #4948, PR #5001)
+ * Fixes the benchmark `SimpleRmsBench` in `benchmarks/analysis/rms.py`
+   by changing the way weights for RMSD are calculated, instead of
+   directly passing them. (Issue #3520, PR #5006)
+
+Enhancements
+ * Add conversion factor for speed unit A/ns and additional representations (Å/fs, A/µs,
+   Å/μs, Å/ms) (PR #5053)
+ * Improved performance of `analysis.rdf.InterRDF_s` > 20-fold
+   by using vectorized NumPy calculations. (Issue #5067, PR #5073)
+ * Parallelize `analysis.rdf.InterRDF` and `analysis.rdf.InterRDF` (Issue #4675)
+ * Support for Python 3.14 was added (PR #5121).
+ * Added support for reading and processing streamed data in `coordinates.base`
+   with new `StreamFrameIteratorSliced` and `StreamReaderBase` (Issue #4827, PR #4923)
+ * New coordinate reader: Added `IMDReader` for reading real-time streamed
+   molecular dynamics simulation data using the IMDv3 protocol - requires
+   `imdclient` package (Issue #4827, PR #4923)
+ * Added capability to calculate MSD from frames with irregular (non-linear)
+   time spacing in analysis.msd.EinsteinMSD with keyword argument
+   `non_linear=True` (Issue #5028, PR #5066)
+ * Support has been added for reading positions and velocities
+   from GROMACS TPR files, between GROMACS version 4.x and 2025
+   (Issue #464, PR #4873)
+ * Added `TemplateInferrer` and `RDKitInferrer` dataclasses to the
+   `RDKitInferring` module to be used by the RDKit converter. (PR #4305)
+ * Improve speed of GROMOS11 (TRC) reader (Issue #5079, PR #5080)
+ * Improve parsing of topology information from LAMMPS dump files to allow
+   reading of mass, charge and element attributes. (Issue #3449, PR #4995)
+ * Added timestep support for XDR writers and readers (Issue #4905, PR #4908)
+ * New feature in `Universe`: `set_groups`. This function allows updating
+   `_topology`, `residues` (ResidueGroup), `segments` (SegmentGroup) in
+   the `Universe` using user-provided atomwise `resids` and/or `segids`.
+   (Issue #4948 #2874, PR #4965)
+ * Adds an argument `force_chainids_to_segids` in `PDBParser`: this will
+   force the use of ChainID as the segID when reading PDB (it is helpful
+   if the segment IDs (segids) are partially missing in the PDB file).
+   (Issue #4948 #2874, PR #4965)
+ * Enables parallelization for analysis.lineardensity.LinearDensity
+   (Issue #4678, PR #5007)
+ * Enabled selection of backend for distance calculations in RDF classes
+   (PR #5038)
+ * Modified functions in lib.distances to add the backend keyword,
+   so that it gets passed through from the calling functions and classes
+   (PR #5038)
+ * Moved distopia checking function to common import location in
+   MDAnalysisTest.util (PR #5038)
+ * Enables parallelization for `analysis.polymer.PersistenceLength` (Issue #4671, PR #5074)
+
+
+Changes
+ * Output precision for LAMMPS Data files set to 10 decimals (PR #5053)
+ * Support for Python 3.10 was removed, in line with SPEC0 (PR #5121).
+ * Refactored the RDKit converter code to move the inferring code in a separate
+   `RDKitInferring` module. The bond order and charges inferrer has been move to
+   an `MDAnalysisInferrer` dataclass in there. (PR #4305)
+ * Removed undocumented and unused attribute
+   `analysis.lineardensity.LinearDensity.totalmass` (PR #5007)
+ * Remove `default` channel from RTD conda env. (Issue # 5036, PR # 5037)
+
+
+Deprecations
+ * The RDKit converter parameter `NoImplicit` has been deprecated in favour of
+   `implicit_hydrogens` and `inferrer` parameters. `max_iter` has been moved
+   under `MDAnalysisInferrer`. (PR #4305)
+
+
 03/11/25 IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy,
          marinegor, hmacdope, jauy123, al42and
 
@@ -29,16 +260,19 @@ Fixes
    the function to prevent shared state. (Issue #4655)
 
 Enhancements
- * Improve distopia backend support in line with new functionality available 
+ * 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)
+ * Added `precision` for XYZWriter (Issue #4775, PR #4771)
  * Add check and warning for empty (all zero) coordinates in RDKit converter
    (PR #4824)
- * Added `precision` for XYZWriter (Issue #4775, PR #4771) 
+ * Added `precision` for XYZWriter (Issue #4775, PR #4771)
 
 Changes
  * MDAnalysis.analysis.psa, MDAnalysis.analysis.waterdynamics and
@@ -52,13 +286,15 @@ Changes
 
 11/11/24 IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
-         tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher, 
+         tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher,
          yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst, MattTDavies,
          talagayev, aya9aladdin
 
  * 2.8.0
 
 Fixes
+ * Fix `test_imd.py` test failures after imdclient 0.2.4
+   increased default timeout by ensuring EOF sent (Issue #5442, PR #5443)
  * Allows bond/angle/dihedral connectivity to be guessed additively with
    `to_guess`, and as a replacement of existing values with `force_guess`.
    Also updates cached bond attributes when updating bonds. (Issue #4759, PR #4761)
@@ -118,7 +354,7 @@ Enhancements
  * 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) 
+   (Issue #4673)
  * 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)
@@ -151,9 +387,9 @@ Changes
  * As per NEP29, the minimum version of numpy has been raised to 1.23.
    We have opted to pin to 1.23.2 to ensure the same minimum numpy version
    is used from python 3.9 to 3.11 (Issue #4401, PR #4402)
- * updated tests that used assert_almost_equal(..., decimal={N}) with 
+ * updated tests that used assert_almost_equal(..., decimal={N}) with
    equivalent assert_allclose(...  rtol=0, atol=1.5e-{N}) (issue modernize
-   testing code #3743, PR Replaced numpy.testing.assert_almost_equal to 
+   testing code #3743, PR Replaced numpy.testing.assert_almost_equal to
    numpy.testing.assert_allclose #4438)
 
 Deprecations
@@ -185,8 +421,8 @@ Deprecations
    (PR #4403)
 
 
-12/26/23 IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, 
-         richardjgowers, lilyminium, ALescoulie, hmacdope, HeetVekariya, 
+12/26/23 IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith,
+         richardjgowers, lilyminium, ALescoulie, hmacdope, HeetVekariya,
          JoStoe, jennaswa, ljwoods2
 
  * 2.7.0
@@ -204,7 +440,7 @@ Fixes
     RMSD of None
   * Fixes hydrogenbonds tutorial path to point to hbonds (Issue #4285, PR #4286)
   * Fix atom charge reading in PDBQT parser (Issue #4282, PR #4283)
-  * Fix doctests failing from separated blocks of imports and 
+  * Fix doctests failing from separated blocks of imports and
     execution and incorrectly formatted test output (Issue #3925, PR #4366)
 
 Enhancements
@@ -220,8 +456,8 @@ Enhancements
   * Added a warning about charge neutrality to the documentation of
     `DielectricConstant` (Issue #4262, PR #4263)
   * Add support for reading chainID info from prmtop amber topologies (PR #4007)
-  * Add support for reading chainID info from GROMACS TPR topologies 
-    (Issue #3994, PR #4281)  
+  * Add support for reading chainID info from GROMACS TPR topologies
+    (Issue #3994, PR #4281)
   * Add support for reading chainID info from Autodock PDBQT files (Issue #4207,
     PR #4284)
 
@@ -235,7 +471,7 @@ Changes
     replacing the now deprecated `xdrlib` core Python library
     (PR #4271)
   * ConverterBase class moved from coordinates/base.py to converters/base.py (Issue #3404)
-  * Results for WatsonCrickDist nucleic acids analysis are now stored in 
+  * Results for WatsonCrickDist nucleic acids analysis are now stored in
     `analysis.nucleicacids.WatsonCrickDist.results.distances` (Issue #3720, PR #3735)
 
 Deprecations
@@ -252,7 +488,7 @@ Deprecations
     in favor of using `ResidueGroup`: using `List[Residue]` will be removed in release
     3.0.0; instead use a `ResidueGroup` (Issue #3720, PR #3735)
   * In `nucleicacids.WatsonCrickDist` the result `results.pair_distances` was
-    deprecated and will be removed in 3.0.0; use `results.distances` (Issue #3720, 
+    deprecated and will be removed in 3.0.0; use `results.distances` (Issue #3720,
     PR #3735)
 
 
@@ -304,7 +540,7 @@ Changes
     of NEP29 (PR #4108).
   * Removed `-ffast-math` compiler flag to avoid potentially incorrect
     floating point results in MDAnalysis *and* other codes when
-    MDAnalysis shared libraries are loaded --- see 
+    MDAnalysis shared libraries are loaded --- see
     https://moyix.blogspot.com/2022/09/someones-been-messing-with-my-subnormals.html
     (Issues #3821, #4211)
   * Atom ID representation order updated to match that of associated
@@ -335,7 +571,7 @@ Deprecations
     32 bit compatible versions. (Issue #3858, PR #4176)
 
 
-05/28/23 IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae, 
+05/28/23 IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae,
          ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler, jbarnoud, jandom,
          xhgchen, jaclark5, DrDomenicoMarson, AHMED-salah00, schlaicha,
          SophiaRuan, g2707, p-j-smith, tylerjereddy, xiki-tempula, richardjgowers,
@@ -399,13 +635,13 @@ Enhancements
   * Add distopia distance calculation library bindings as a selectable backend
     for `calc_bonds` in `MDA.lib.distances`. (Issue #3783, PR #3914)
   * AuxReaders are now pickle-able and copy-able (Issue #1785, PR #3887)
-  * Add pickling support for Atom, Residue, Segment, ResidueGroup 
+  * Add pickling support for Atom, Residue, Segment, ResidueGroup
     and SegmentGroup. (PR #3953)
 
 Changes
   * As per NEP29 the minimum supported Python version has been raised to 3.9
     (PR #4115).
-  * einsum method for Einstein summation convention introduced to increase 
+  * einsum method for Einstein summation convention introduced to increase
     performance (Issue #2063, PR #4089)
   * Add progress bars to track the progress of _conclude() functions
     (_conclude_simple() and _conclude_fft()) in msd.py (Issue #4070, PR #4072)
@@ -465,16 +701,16 @@ Fixes
  * 2.4.0
 
 Fixes
-  * Update hbond analysis doc string to use exclusive bound language 
+  * Update hbond analysis doc string to use exclusive bound language
     (Issue #3847)
   * XTC and TRR readers now fail with IOError when a status except EOK (=0) is
     detected on reading a frame instead of silently continuing
   * Consolidate license files across MDAnalysis library packages (PR #3939)
   * Kwargs passed through to `MemoryReader` when using `transfer_to_memory()`
     and `in_memory=True`.
-  * NoDataError raised on empty atomgroup provided to `DCDReader.timeseries` 
+  * NoDataError raised on empty atomgroup provided to `DCDReader.timeseries`
     was changed to ValueError (see #3901). A matching ValueError was added to
-    `MemoryReader.timeseries`(PR #3890). 
+    `MemoryReader.timeseries`(PR #3890).
   * Removes ``pbc`` kwarg from ``AtomGroup.wrap`` (Issue #3909)
   * LAMMPSDump Reader translates the box to the origin (#3741)
   * hbond analysis: access hbonds results through new results member in count_by_ids() and count_by_type()
@@ -482,7 +718,7 @@ Fixes
     behaviour for cutoff values < -1 (PR # 3749)
   * Fixes distances.between not always returning AtomGroup (Issue #3794)
   * Upgrade to chemfiles 0.10.3 (Issue #3798)
-  * fixes guessed_attributes and read_attributes methods of the Topology class, as 
+  * fixes guessed_attributes and read_attributes methods of the Topology class, as
     those methods were giving unexpected results for some topology attributes
     (e.g. bonds, angles) (PR #3779).
 
@@ -491,12 +727,12 @@ Enhancements
     (Issue #3841, PR #3842)
   * MDAnalysis now follows PEP621 (PR #3528)
   * Added a reader for GROMACS TNG files based on PyTNG (PR #3765,
-    Issue #3237, partially addressing Issue #865) 
-  * Added ability for hbond analysis to use types when resnames are not 
+    Issue #3237, partially addressing Issue #865)
+  * Added ability for hbond analysis to use types when resnames are not
     present (Issue #3847)
   * Added explanatory warnings when hbond analysis doesn't find any hbonds
     (Issue #3847)
-  * Improve C content of libxdr Cython, add `read_direct` methods to read 
+  * Improve C content of libxdr Cython, add `read_direct` methods to read
     coordinates, velocities and forces directly into memoryviews of `Timestep`
     attributes, make `TRR` timestep have positions, velocities and forces on
     `__init__`. (Issue #3891 PR  #3892).
@@ -504,11 +740,11 @@ Enhancements
   * The timeseries method for exporting coordinates from multiple frames to a
     NumPy array was added to ProtoReader (PR #3890)
   * MDAnalysis now officially supports py3.11 (Issue #3878)
-  * LAMMPSDump Reader optionally unwraps trajectories with image flags upon 
+  * LAMMPSDump Reader optionally unwraps trajectories with image flags upon
     loading (Issue #3843)
   * LAMMPSDump Reader now imports velocities and forces (Issue #3843)
   * Minimum NumPy version for py3.11 is now set to 1.23.2.
-  * Added decorator to check for an empty atom group, applied in topological 
+  * Added decorator to check for an empty atom group, applied in topological
     attributes(Issue #3837)
   * AuxReaders now have a memory_limit parameter to control when memory usage
     warnings are issued. (PR # 3749)