MDAnalysis 2.7.0__tar.gz → 2.9.0__tar.gz

{MDAnalysis-2.7.0 → 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
@@ -233,11 +233,26 @@ Chronological list of authors
   - Lawson Woods
   - Johannes Stöckelmaier
   - Jenna M. Swarthout Goddard
+2024
+  - Aditya Keshari
+  - Philipp Stärk
+  - Kai Niklas Spauszus
+  - Sampurna Mukherjee
+  - Leon Wehrhan
+  - Valerij Talagayev
+  - Kurt McKee
+  - Fabian Zills
+  - Laksh Krishna Sharma
+  - Matthew Davies
+  - Jia-Xin Zhu
+  - Tanish Yelgoe
+ 2025
+  - Joshua Raphael Uy
 
 External code
 -------------
 
-External code (under a GPL-compatible licence) was obtained from
+External code (under a LGPL-compatible licence) was obtained from
 various sources. The authors (as far as we know them) are listed here.
 
 xdrfile
@@ -249,9 +264,9 @@ xdrfile
   The Gromacs libxdrfile (LGPL-licensed) was used before MDAnalysis
    version 0.8.0.
   Between MDAnalysis versions 0.8.0 and 0.13.0 libxdrfile was replaced by
-   libxdrfile2, our GPLv2 enhanced derivative of libxdrfile.
+   libxdrfile2, our LGPLv2.1+ enhanced derivative of libxdrfile.
   Since version 0.14.0 xdr enhanecments were rebased onto Gromacs'
-   xdrfile 1.1.4 code (now BSD-licensed). Our contributions remain GPLv2
+   xdrfile 1.1.4 code (now BSD-licensed). Our contributions remain LGPLv2.1+
    and were split into files xtc_seek.c, trr_seek.c, xtc_seek.h, and
    trr_seek.h, for clarity (xdrfile 1.1.4 code is distributed with minor
    modifications). Also for clarity we now name the resulting enhanced

{MDAnalysis-2.7.0 → mdanalysis-2.9.0}/CHANGELOG

@@ -14,6 +14,177 @@ 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, 
+         yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst, MattTDavies,
+         talagayev, aya9aladdin
+
+ * 2.8.0
+
+Fixes
+ * 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)
+ * Fixes bug where deleting connections by index would only delete
+   one of multiple, if multiple are present (Issue #4762, PR #4763)
+ * Changes error to warning on Universe creation if guessing fails
+   due to missing information (Issue #4750, PR #4754)
+ * Adds guessed attributes documentation back to each parser page
+   and updates overall guesser docs (Issue #4696)
+ * Fix Bohrium (Bh) atomic mass in tables.py (PR #3753)
+ * set `n_parts` to the total number of frames being analyzed if
+   `n_parts` is bigger. (Issue #4685)
+ * Catch higher dimensional indexing in GroupBase & ComponentBase (Issue #4647)
+ * Do not raise an Error reading H5MD files with datasets like
+   `observables/<particle>/<property>` (part of Issue #4598, PR #4615)
+ * Fix failure in double-serialization of TextIOPicklable file reader.
+   (Issue #3723, PR #3722)
+ * Fix failure to preserve modification of coordinates after serialization,
+   e.g. with transformations
+   (Issue #4633, PR #3722)
+ * Fix PSFParser error when encoutering string-like resids
+ * (Issue #2053, Issue #4189 PR #4582)
+ * Fix `MDAnalysis.analysis.align.AlignTraj` not accepting writer kwargs
+   (Issue #4564, PR #4565)
+ * Fix #4259 via removing argument `parallelizable` of `NoJump` transformation.
+ * Fix doctest errors of analysis/pca.py related to rounding issues
+   (Issue #3925, PR #4377)
+ * Convert openmm Quantity to raw value for KE and PE in OpenMMSimulationReader.
+ * Atomname methods can handle empty groups (Issue #2879, PR #4529)
+ * Add support for TPR files produced by Gromacs 2024.1 (PR #4523)
+ * Remove mutable data from ``progressbar_kwargs`` argument in ``AnalysisBase.run()``
+   (PR #4459)
+ * Fix ChainReader `__repr__()` method when sub-reader is MemoryReader
+   (Issue #3349, PR #4407)
+ * Fix bug in PCA preventing use of `frames=...` syntax (PR #4423)
+ * Fix `analysis/diffusionmap.py` iteration through trajectory to iteration
+   over `self._sliced_trajectory`, hence supporting
+   `DistanceMatrix.run(frames=...)` (PR #4433)
+ * Fix doctest errors of lib/picklable_file_io.py (Issue #3925, PR #4371)
+ * Fix deploy action to use the correct version of the pypi upload action.
+ * Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)
+
+Enhancements
+ * Removed type and mass guessing from all topology parsers (PR #3753)
+ * Added guess_TopologyAttrs() API to the Universe to handle attribute
+   guessing (PR #3753)
+ * Added the DefaultGuesser class, which is a general-purpose guesser with
+   the same functionalities as the existing guesser.py methods (PR #3753)
+ * Added is_value_missing() to `TopologyAttrs` to check for missing
+   values (PR #3753)
+ * Added guessed `Element` attribute to the ITPParser to preserve old mass
+   partial guessing behavior from being broken (PR #3753)
+ * MDAnalysis now supports Python 3.13 (PR #4732)
+ * 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}
+   (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)
+ * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)
+ * Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`
+   (PR #4531)
+ * Improved performance of PDBWriter (Issue #2785, PR #4472)
+ * Added parsing of arbitrary columns of the LAMMPS dump parser. (Issue #3504)
+ * Documented the r0 attribute in the `Contacts` class and added the
+   `n_initial_contacts` attribute, with documentation. (Issue #2604, PR #4415)
+ * Implement average structures with iterative algorithm from
+   DOI 10.1021/acs.jpcb.7b11988. (Issue #2039, PR #4524)
+
+Changes
+ * Relicense code contributions from GPLv2+ to LGPLv2.1+
+   and the package from GPLv3+ to LGPLv3+ (PR #4794)
+ * only use distopia < 0.3.0 due to API changes (Issue #4739)
+ * The `fetch_mmtf` method has been removed as the REST API service
+   for MMTF files has ceased to exist (Issue #4634)
+ * MDAnalysis now builds against numpy 2.0 rather than the
+   minimum supported numpy version (PR #4620)
+ * As per SPEC0 the minimum supported Python version has been raised
+   to 3.10 (PR #4502)
+ * MDAnalysis.analysis.hole2 is now directly imported from the mdakit
+   mdahole2. This module is deprecated and will be fully removed in
+   MDAnalysis version 3.0 (PR #4464)
+ * Testsuite packaging now uses a pyproject.toml file (PR #4463)
+ * Improvement of setuptools packaging, including deduplication of
+   dependency lists (PR #4424)
+ * 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 
+   equivalent assert_allclose(...  rtol=0, atol=1.5e-{N}) (issue modernize
+   testing code #3743, PR Replaced numpy.testing.assert_almost_equal to 
+   numpy.testing.assert_allclose #4438)
+
+Deprecations
+ * The `guess_bonds`, `vdwradii`, `fudge_factor`, and `lower_bound` kwargs
+   are deprecated for bond guessing during Universe creation. Instead,
+   pass `("bonds", "angles", "dihedrals")` into `to_guess` or `force_guess`
+   during Universe creation, and the associated `vdwradii`, `fudge_factor`,
+   and `lower_bound` kwargs into `Guesser` creation. Alternatively, if
+   `vdwradii`, `fudge_factor`, and `lower_bound` are passed into
+   `Universe.guess_TopologyAttrs`, they will override the previous values
+   of those kwargs. (Issue #4756, PR #4757)
+ * MDAnalysis.topology.guessers is deprecated in favour of the new
+   Guessers API and will be removed in version 3.0 (PR #4752)
+ * MDAnalysis.topology.tables is deprecated in favour of
+   MDAnalysis.guesser.tables and will be removed in version 3.0 (PR #4752)
+ * Element guessing in the ITPParser is deprecated and will be removed in version 3.0
+   (Issue #4698)
+ * Unknown masses are set to 0.0 for current version, this will be depracated
+   in version 3.0.0 and replaced by :class:`Masses`' no_value_label attribute(np.nan)
+   (PR #3753)
+ * The MDAnalysis.anaylsis.encore module has been deprecated in favour of the
+   mdaencore MDAKit and will be removed in version 3.0.0 (PR #4737)
+ * The MMTF Reader is deprecated and will be removed in version 3.0
+   as the MMTF format is no longer supported (Issue #4634)
+ * The MDAnalysis.analysis.waterdynamics module has been deprecated in favour
+   of the waterdynamics MDAKit and will be removed in version 3.0.0 (PR #4404)
+ * The MDAnalysis.analysis.psa module has been deprecated in favour of
+   the PathSimAnalysis MDAKit and will be removed in version 3.0.0
+   (PR #4403)
+
+
 12/26/23 IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, 
          richardjgowers, lilyminium, ALescoulie, hmacdope, HeetVekariya, 
          JoStoe, jennaswa, ljwoods2