MDAnalysis 2.6.1__tar.gz → 2.8.0__tar.gz

{MDAnalysis-2.6.1 → mdanalysis-2.8.0}/AUTHORS

@@ -42,6 +42,7 @@ Chronological list of authors
   - Lukas Stelzl
   - Jinju Lu
   - Joshua L. Phillips
+  - David van der Spoel
 2013
   - Zhuyi Xue
   - Xavier Deupi
@@ -80,6 +81,7 @@ Chronological list of authors
   - Tone Bengtsen
   - Shantanu Srivastava
   - Pedro Reis
+  - Zhenbo Li
  2017
   - Ruggero Cortini
   - Kashish Punjani
@@ -98,6 +100,7 @@ Chronological list of authors
   - Micaela Matta
   - Jose Borreguero
   - Sören von Bülow
+  - Brigitta Sipőcz
 2018
   - Nabarun Pal
   - Mateusz Bieniek
@@ -124,6 +127,8 @@ Chronological list of authors
   - Lily Wang
   - Matthijs Tadema
   - Joao Miguel Correia Teixeira
+  - Michael Gecht
+  - Bradley Dice
 2020
   - Charlie Cook
   - Yuanyu Chang
@@ -152,7 +157,9 @@ Chronological list of authors
   - Ramon Crehuet
   - Haochuan Chen
   - Karthikeyan Singaravelan
+  - David Minh
 2021
+  - Ian M. Kenney
   - Aditya Kamath
   - Leonardo Barneschi
   - Henrik Jäger
@@ -221,11 +228,28 @@ Chronological list of authors
   - Shubham Kumar
   - Zaheer Timol
   - Geongi Moon
+  - Sumit Gupta
+  - Heet Vekariya
+  - 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
+
 
 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
@@ -237,9 +261,9 @@ 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-2.6.1 → mdanalysis-2.8.0}/CHANGELOG

@@ -10,10 +10,217 @@ The rules for this file:
   * keep the format consistent (79 char width, M/D/Y date format) and do not
     use tabs but use spaces for formatting
   * accompany each entry with github issue/PR number (Issue #xyz)
-  * release numbers follow "Semantic Versioning" http://semver.org
+  * release numbers follow "Semantic Versioning" https://semver.org
 
-------------------------------------------------------------------------------
-28/08/23 IAlibay, hmacdope, pillose, jaclark5, tylerjereddy
+
+-------------------------------------------------------------------------------
+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
+
+ * 2.7.0
+
+Fixes
+  * Fix doctest errors of lib/transformations.py (Issue #3925, PR #4370)
+  * Fix documentation building errors due to `html_static_path` and unindented
+    block of code (Issue #4362, PR #4365)
+  * Updated cimport for numpy to maintain cimport consistency (Issue #3908)
+  * Fix `NoJump` unwrapping for jumps on the second frame in a
+    trajectory (PR #4258, Issue #4257)
+  * Deprecated np.float_ and np.NaN aliases have been replaced with
+    their original type value (np.float64 and np.nan) (PR #4272)
+  * Fixes a case where qcprot.CalcRMSDRotationalMatrix would return a
+    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 
+    execution and incorrectly formatted test output (Issue #3925, PR #4366)
+
+Enhancements
+  * Added a reader for GROMOS11 TRC trajectories (PR #4292 , Issue #4291)
+  * Document the usage of NoDataError in its docstring (Issue #3901, PR #4359)
+  * Refactor c_distances backend to have a cython .pxd header and expose in
+    libmdanalysis (Issue #4315, PR #4324)
+  * Add faster nucleic acid Major and Minor pair distance calculators using
+    AnalysisBase for updated nucleicacids module (Issue #3720, PR #3735)
+  * Adds external sidebar links (Issue #4296)
+  * Updated lib.qcprot.CalcRMSDRotationalMatrix to accept either float32 or float64
+    inputs (PR #4273, part of #3927)
+  * 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 Autodock PDBQT files (Issue #4207,
+    PR #4284)
+
+Changes
+  * Biopython is now an optional dependency (Issue #3820, PR #4332)
+  * Networkx is now an optional dependency (Issue #3822).
+  * High memory tests (enabled through the environment variable
+    `ENABLE_HIGH_MEM_UNIT_TESTS` are now only enabled if the environment variable
+    is set to "true") (PR #4295)
+  * The `mda-xdrlib` module is now a core dependency of MDAnalysis
+    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 
+    `analysis.nucleicacids.WatsonCrickDist.results.distances` (Issue #3720, PR #3735)
+
+Deprecations
+  * The `asel` argument to timeseries will be renamed to `atomgroup` in 3.0.0.
+    (Issue #3911)
+  * MDAnalysis.lib.util is deprecated and will be removed in version 3.0
+    (Issue #3649)
+  * The TRZ reader & writer are deprecated and will be removed in version 3.0
+    (PR #4335)
+  * X3DNA has been deprecated and will be removed in 3.0.0 (Issue #3788)
+  * coordinates.base.ConverterBase has been deprecated and will be removed in 3.0.0;
+    use converters.base.ConvertBase instead (Issue #3404)
+  * In `nucleicacids.WatsonCrickDist`, accepting lists of `Residue` objects was deprecated
+    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, 
+    PR #3735)
+
+
+08/28/23 IAlibay, hmacdope, pillose, jaclark5, tylerjereddy
 
  * 2.6.1
 
@@ -21,10 +228,11 @@ Fixes
   * Fix Atom type guessing error (PR #4168, Issue #4167)
 
 Enhancements
+  * Allow `set_dimensions` transformation to handle NPT trajectories (PR #4258)
 
 Changes
   * Reverts PR #4108, builds are now again made using the oldest
-    supported Python version.
+    supported NumPy version.
   * NumPy `in1d` replaced with `isin` in preparation for NumPy
     `2.0` (PR #4255)
   * Update documentation for SurvivalProbabilty to be more clear
@@ -36,7 +244,7 @@ Deprecations
 
 
 08/15/23 IAlibay, jaclark5, MohitKumar020291, orionarcher, xhgchen,
-         ztimol, orbeckst
+         ztimol, orbeckst, Shubx10
 
  * 2.6.0
 
@@ -95,7 +303,7 @@ Deprecations
          ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler, jbarnoud, jandom,
          xhgchen, jaclark5, DrDomenicoMarson, AHMED-salah00, schlaicha,
          SophiaRuan, g2707, p-j-smith, tylerjereddy, xiki-tempula, richardjgowers,
-         cbouy
+         cbouy, DanielJamesEvans, jvermaas, egormarin
 
  * 2.5.0
 
@@ -352,7 +560,7 @@ Deprecations
          HenokB, umak1106, tamandeeps, Mrqeoqqt, megosato, AnirG, rishu235,
          mtiberti, manishsaini6421, Sukeerti1, robotjellyzone, markvrma, alescoulie,
          mjtadema, PicoCentauri, Atharva7K, aditi2906, orbeckst, yuxuanzhuang,
-         rsexton2, rafaelpap, richardjgowers, orioncohen
+         rsexton2, rafaelpap, richardjgowers, orioncohen, mdpoleto
 
  * 2.2.0
 
@@ -977,7 +1185,7 @@ Deprecations
          Yuan-Yu, xiki-tempula, HTian1997, Iv-Hristov, hmacdope, AnshulAngaria,
          ss62171, Luthaf, yuxuanzhuang, abhishandy, mlnance, shfrz, orbeckst,
          wvandertoorn, cbouy, AmeyaHarmalkar, Oscuro-Phoenix, andrrizzi, WG150,
-         tylerjereddy, Marcello-Sega
+         tylerjereddy, Marcello-Sega, mimischi, mquevill, siddharthjain1611
 
   * 1.0.0
 
@@ -1190,9 +1398,10 @@ Fixes
 
 
 08/28/19 micaela-matta, xiki-tempula, zemanj, mattwthompson, orbeckst, aliehlen,
-         dpadula85, jbarnoud, manuel.nuno.melo, richardjgowers, mattwthompson,
+         dpadula85, jbarnoud, manuel.nuno.melo, richardjgowers,
          ayushsuhane, picocentauri, NinadBhat, bieniekmateusz, p-j-smith, Lp0lp,
-         IAlibay, tyler.je.reddy, aakognole, RMeli, lilyminium
+         IAlibay, tyler.je.reddy, aakognole, RMeli, lilyminium, fenilsuchak,
+         Yibo-Zhang
 
   * 0.20.0
 
@@ -1646,7 +1855,7 @@ Changes
     they are part of the Universe topology (Issue #1092 PR #1186)
 
 
-06/29/17 richardjgowers, rathann, jbarnoud, orbeckst, utkbansal
+06/29/17 richardjgowers, rathann, jbarnoud, orbeckst, utkbansal, bsipocz
 
   * 0.16.2
 
@@ -1721,7 +1930,7 @@ Changes
 04/10/17 kain88-de, fiona-naughton, richardjgowers, tyler.je.reddy, jdetle
          euhruska, orbeckst, rbrtdlg, jbarnoud, wouterboomsma, shanmbic,
          dotsdl, manuel.nuno.melo, utkbansal, vedantrathore, shobhitagarwal1612,
-         xiki-tempula, kash1102, vedantrathore
+         xiki-tempula, kash1102, Akshay0724, bsipocz, jeiros, tbengtsen
 
   * 0.16.0
 
@@ -1891,7 +2100,7 @@ Testsuite
 
 05/15/16 jandom, abhinavgupta94, orbeckst, kain88-de, hainm, jbarnoud,
          dotsdl, richardjgowers, BartBruininks, jdetle, pedrishi,
-         fiona-naughton, jdetle
+         fiona-naughton, jdetle, Endle
 
   * 0.15.0
 
@@ -3026,7 +3235,7 @@ Testsuite
     removal in 0.8
   * uses cython instead of pyrex
 
-11/05/10 orbeckst, denniej0, tyler.je.reddy, danny.parton, joseph.goose
+11/05/10 orbeckst, denniej0, tyler.je.reddy, danny.parton, joseph.goose, dspoel
   * major release 0.7.0
     (includes changes that can BREAK BACKWARDS COMPATIBILITY)
   * Removed ALL DEPRECATED code:

{MDAnalysis-2.6.1 → mdanalysis-2.8.0}/INSTALL

@@ -53,9 +53,9 @@ file) and README and check the MDAnalysis project pages at
 in particular https://github.com/MDAnalysis/mdanalysis/wiki/Install
 and related pages.
 
-You can always ask questions on the MDAnalysis mailing list:
+You can always ask questions on GitHub Discussions:
 
-      http://groups.google.com/group/mdnalysis-discussion
+      https://github.com/MDAnalysis/mdanalysis/discussions/categories/installation
 
 People there are very happy to help. When posting please remember to
 mention the release of MDAnalysis you are trying to install (e.g. "tar