Merge branch 'develop' into broken-link

Author: orbeckst

LICENSE

@@ -8,10 +8,14 @@
 
 MDAnalysis is a Python toolkit to analyse molecular dynamics files and trajectories in `many popular formats`_. MDAnalysis can write most of these formats, too, together with atom selections for use in visualisation tools or other analysis programs. It provides a fast framework for complex analysis tasks, as well as flexible tooling to construct your own analyses.
 
-This repository contains the `user guide`_ for MDAnalysis. The user guide originated as a `project for Google Season of Docs 2019-2020`_ .
+This repository contains the `user guide`_ for MDAnalysis. The user guide originated as a `project for Google Season of Docs 2019-2020`_.
+
+The code in the user guide is released under the `GNU LGPL v2.1+` license, while text and images are released under the `CC BY-SA 4.0 DEED`_ license.
 
 .. Footnotes
 
+.. _`CC BY-SA 4.0 DEED`: https://creativecommons.org/licenses/by-sa/4.0/
+.. _`GNU LGPL v2.1+`: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html
 .. _`user guide`: https://www.mdanalysis.org/UserGuide/index.html
 .. _`many popular formats`: https://www.mdanalysis.org/UserGuide/formats/index.html
 .. _MDAnalysis: https://www.mdanalysis.org

README.rst

@@ -85,8 +85,8 @@ Getting started with Git
 setting up your SSH key, and configuring git.  All these steps need to be completed before
 you can work seamlessly between your local repository and GitHub.
 
-.. _`mdnalysis-discussion`:
-   http://groups.google.com/group/mdnalysis-discussion
+.. _`GitHub Discussions`:
+   https://github.com/MDAnalysis/mdanalysis/discussions
 .. _`Code of Conduct`: https://www.mdanalysis.org/pages/conduct/
 .. _`Issue Tracker`: https://github.com/MDAnalysis/mdanalysis/issues
 .. _`MDAKits registry`: https://mdakits.mdanalysis.org/mdakits.html

doc/source/contributing.rst

@@ -39,7 +39,7 @@ The typical use case for MDAnalysis is to manipulate or analyse molecular dynami
 Participating
 =============
 
-MDAnalysis welcomes all contributions from its users. There are many ways you can help improve MDAnalysis, from asking questions on the `mdnalysis-discussion`_ mailing list, to raising issues on the `Issue Tracker`_, to adding your own code. Please see :ref:`contributing` for an introduction and guide to contributing to the code and documentation.
+MDAnalysis welcomes all contributions from its users. There are many ways you can help improve MDAnalysis, from asking questions on `GitHub Discussions`_, to raising issues on the `Issue Tracker`_, to adding your own code. Please see :ref:`contributing` for an introduction and guide to contributing to the code and documentation.
 
 .. important::
 
@@ -55,7 +55,7 @@ MDAnalysis welcomes all contributions from its users. There are many ways you ca
 Communications
 --------------
 
-Questions and discussions about MDAnalysis take place on `GitHub Discussions`_ and this repository’s `Issue Tracker`_. Anybody is welcome to join these conversations. Please ask questions about the usage of MDAnalysis on the `mdnalysis-discussion`_ mailing list, and report problems on the `Issue Tracker`_.
+Questions and discussions about MDAnalysis take place on `GitHub Discussions`_ and this repository’s `Issue Tracker`_. Anybody is welcome to join these conversations. Please ask questions about the usage of MDAnalysis on `GitHub Discussions`_, and report problems on the `Issue Tracker`_.
 
 Wherever possible, do not take these conversations to private channels, including contacting the maintainers directly. Keeping communication public means everybody can benefit and learn from the conversation.
 

doc/source/index.rst

@@ -1,6 +1,40 @@
 # MDAnalysis Release Notes
 
 
+## Release 2.8.0 of MDAnalysis
+
+This a minor release of MDAnalysis.
+
+As of this release MDAnalysis is packaged under a [LGPLv3+ license](https://www.gnu.org/licenses/lgpl-3.0.en.html), and all code contributions are provided under the [LGPLv2.1+ license](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html).
+
+This release supports NumPy 2.0+ and offers backwards compatibility through to NumPy 1.23.2
+
+Supported Python versions:
+  - 3.10, 3.11, 3.12, 3.13
+
+### Major features
+
+See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.8.0/package/CHANGELOG) and our [release blog post](https://www.mdanalysis.org/blog/#mdanalysis-2.8-is-out) for more details.
+
+* The MDAnalysis package license has changed from GPLv3+ to LGPLv3+ and all code contributions are now under LGPLv2.1+
+* MDAnalysis now has a brand new guesser API (PR #3753). See the DefaultGuesser class for more information. Please note that default guessing of types and masses will change in MDAnalysis v3.0.
+* DSSP analysis `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP) was added.
+* An iterative average structure method was added to `analysis.align` based on DOI 10.1021/acs.jpcb.7b11988. 
+* The TPR reader has been updated to support Gromacs 2024.
+* The AnalysisBase class was enhanced through the introduction of a parallelization API (Issue #4158, PR #4304). Various analyses now support parallel computation, including; RMSD, GNMAnalysis, BAT, dihdral calculations, DSSP, and HydrogenBondAnalysis.
+
+### Notable changes / upcoming deprecations
+
+* MMTF support is now deprecated and will be removed in MDAnalysis v3.0. The `fetch_mmtf` method has been disabled as it no longer works.
+* MDAnalysis.analysis.hole2 has been moved to its own mdakit ([mdahole2](https://github.com/MDAnalysis/mdahole2)) and will be fully removed from the core library in MDAnalysis v3.0.
+* MDAnalysis.analysis.encore has been deprecated in favour of its own mdakit ([mdaencore](https://github.com/MDAnalysis/mdaencore/)) and will be removed in MDAnalysis v3.0.
+* MDAnalysis.analysis.waterdynamics has been deprecated in favour of its own mdakit ([waterdynamics](https://github.com/MDAnalysis/waterdynamics)) and will be removed in MDAnalysis v3.0.
+* MDAnalysis.analysis.psa has been deprecated in favour of its own mdakit ([PathSimAnalysis](https://github.com/MDAnalysis/pathsimanalysis)) and will be removed in MDAnalysis v3.0.
+* 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.
+* MDAnalysis.topology.guessers and MDAnalysis.topology.tables are deprecated in favour of the new Guessers API and will be removed in MDAnalysis v3.0.
+* Unknown masses are set to 0.0 for current version, this will be depracated in MDAnalysis v3.0.0 and replaced by :class:`Masses`' no_value_label attribute (np.nan).
+
 ## Release 2.7.0 of MDAnalysis
 
 This a minor release of MDAnalysis.

doc/source/releases.md

@@ -139,6 +139,12 @@
       '',
       ':ref:`DATA <DATA-format>`, :ref:`GSD <GSD-format>`, :ref:`PSF <PSF-format>`, :ref:`TOP, PRMTOP, PARM7 <TOP-format>`, :ref:`TPR <TPR-format>`, :ref:`XML <XML-format>`',
     ]),
+    list([
+      'mass',
+      'masses',
+      '',
+      ':ref:`CONFIG <CONFIG-format>`, :ref:`CRD <CRD-format>`, :ref:`DATA <DATA-format>`, :ref:`DMS <DMS-format>`, :ref:`GMS <GMS-format>`, :ref:`GRO <GRO-format>`, :ref:`GSD <GSD-format>`, :ref:`HISTORY <HISTORY-format>`, :ref:`IN, FHIAIMS <IN-format>`, :ref:`LAMMPSDUMP <LAMMPSDUMP-format>`, :ref:`MMTF <MMTF-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDB, ENT <PDB-format>`, :ref:`PDBQT <PDBQT-format>`, :ref:`PQR <PQR-format>`, :ref:`PSF <PSF-format>`, :ref:`TOP, PRMTOP, PARM7 <TOP-format>`, :ref:`TPR <TPR-format>`, :ref:`TXYZ, ARC <TXYZ-format>`, :ref:`XML <XML-format>`, :ref:`XPDB <XPDB-format>`, :ref:`XYZ <XYZ-format>`',
+    ]),
     list([
       'model',
       'models',
@@ -217,6 +223,12 @@
       'B-factor',
       ':ref:`CRD <CRD-format>`, :ref:`MMTF <MMTF-format>`, :ref:`PDB, ENT <PDB-format>`, :ref:`PDBQT <PDBQT-format>`, :ref:`XPDB <XPDB-format>`',
     ]),
+    list([
+      'type',
+      'types',
+      '',
+      ':ref:`CONFIG <CONFIG-format>`, :ref:`CRD <CRD-format>`, :ref:`DATA <DATA-format>`, :ref:`DMS <DMS-format>`, :ref:`GMS <GMS-format>`, :ref:`GRO <GRO-format>`, :ref:`GSD <GSD-format>`, :ref:`HISTORY <HISTORY-format>`, :ref:`IN, FHIAIMS <IN-format>`, :ref:`LAMMPSDUMP <LAMMPSDUMP-format>`, :ref:`MMTF <MMTF-format>`, :ref:`MOL2 <MOL2-format>`, :ref:`PDB, ENT <PDB-format>`, :ref:`PDBQT <PDBQT-format>`, :ref:`PQR <PQR-format>`, :ref:`PSF <PSF-format>`, :ref:`TOP, PRMTOP, PARM7 <TOP-format>`, :ref:`TPR <TPR-format>`, :ref:`TXYZ, ARC <TXYZ-format>`, :ref:`XML <XML-format>`, :ref:`XPDB <XPDB-format>`, :ref:`XYZ <XYZ-format>`',
+    ]),
     list([
       'type_index',
       'type_indices',
@@ -319,8 +331,11 @@
     'masses': set({
       ':ref:`CONFIG <CONFIG-format>`',
       ':ref:`CRD <CRD-format>`',
+      ':ref:`DATA <DATA-format>`',
+      ':ref:`DMS <DMS-format>`',
       ':ref:`GMS <GMS-format>`',
       ':ref:`GRO <GRO-format>`',
+      ':ref:`GSD <GSD-format>`',
       ':ref:`HISTORY <HISTORY-format>`',
       ':ref:`IN, FHIAIMS <IN-format>`',
       ':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
@@ -329,7 +344,11 @@
       ':ref:`PDB, ENT <PDB-format>`',
       ':ref:`PDBQT <PDBQT-format>`',
       ':ref:`PQR <PQR-format>`',
+      ':ref:`PSF <PSF-format>`',
+      ':ref:`TOP, PRMTOP, PARM7 <TOP-format>`',
+      ':ref:`TPR <TPR-format>`',
       ':ref:`TXYZ, ARC <TXYZ-format>`',
+      ':ref:`XML <XML-format>`',
       ':ref:`XPDB <XPDB-format>`',
       ':ref:`XYZ <XYZ-format>`',
     }),
@@ -408,13 +427,24 @@
     'types': set({
       ':ref:`CONFIG <CONFIG-format>`',
       ':ref:`CRD <CRD-format>`',
+      ':ref:`DATA <DATA-format>`',
       ':ref:`DMS <DMS-format>`',
       ':ref:`GMS <GMS-format>`',
       ':ref:`GRO <GRO-format>`',
+      ':ref:`GSD <GSD-format>`',
       ':ref:`HISTORY <HISTORY-format>`',
       ':ref:`IN, FHIAIMS <IN-format>`',
+      ':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
+      ':ref:`MMTF <MMTF-format>`',
+      ':ref:`MOL2 <MOL2-format>`',
       ':ref:`PDB, ENT <PDB-format>`',
+      ':ref:`PDBQT <PDBQT-format>`',
       ':ref:`PQR <PQR-format>`',
+      ':ref:`PSF <PSF-format>`',
+      ':ref:`TOP, PRMTOP, PARM7 <TOP-format>`',
+      ':ref:`TPR <TPR-format>`',
+      ':ref:`TXYZ, ARC <TXYZ-format>`',
+      ':ref:`XML <XML-format>`',
       ':ref:`XPDB <XPDB-format>`',
       ':ref:`XYZ <XYZ-format>`',
     }),
@@ -437,13 +467,13 @@
     list([
       ':ref:`DATA <DATA-format>`',
       'LAMMPS data file',
-      'angles, bonds, charges, dihedrals, impropers',
+      'angles, bonds, charges, dihedrals, impropers, masses, types',
       '',
     ]),
     list([
       ':ref:`DMS <DMS-format>`',
       'DESRES Molecular Structure file',
-      'atomnums, bonds, chainIDs, charges, names, resnames',
+      'atomnums, bonds, chainIDs, charges, masses, names, resnames',
       'types',
     ]),
     list([
@@ -461,7 +491,7 @@
     list([
       ':ref:`GSD <GSD-format>`',
       'HOOMD GSD file',
-      'angles, bonds, charges, dihedrals, impropers, names, radii, resnames',
+      'angles, bonds, charges, dihedrals, impropers, masses, names, radii, resnames, types',
       '',
     ]),
     list([
@@ -479,19 +509,19 @@
     list([
       ':ref:`LAMMPSDUMP <LAMMPSDUMP-format>`',
       'LAMMPS ascii dump file',
+      'masses, types',
       '',
-      'masses',
     ]),
     list([
       ':ref:`MMTF <MMTF-format>`',
       'MMTF file',
-      'altLocs, bonds, charges, icodes, models, names, occupancies, resnames, tempfactors',
+      'altLocs, bonds, charges, icodes, models, names, occupancies, resnames, tempfactors, types',
       'masses',
     ]),
     list([
       ':ref:`MOL2 <MOL2-format>`',
       'Tripos MOL2 file',
-      'bonds, charges, elements, names, resnames',
+      'bonds, charges, elements, names, resnames, types',
       'masses',
     ]),
     list([
@@ -503,7 +533,7 @@
     list([
       ':ref:`PDBQT <PDBQT-format>`',
       'PDBQT file',
-      'altLocs, chainIDs, charges, icodes, names, occupancies, record_types, resnames, tempfactors',
+      'altLocs, chainIDs, charges, icodes, names, occupancies, record_types, resnames, tempfactors, types',
       'masses',
     ]),
     list([
@@ -515,31 +545,31 @@
     list([
       ':ref:`PSF <PSF-format>`',
       'CHARMM, NAMD, or XPLOR PSF file',
-      'angles, bonds, charges, dihedrals, impropers, names, resnames',
+      'angles, bonds, charges, dihedrals, impropers, masses, names, resnames, types',
       '',
     ]),
     list([
       ':ref:`TOP, PRMTOP, PARM7 <TOP-format>`',
       'AMBER topology file',
-      'angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices',
+      'angles, bonds, charges, dihedrals, impropers, masses, names, resnames, type_indices, types',
       '',
     ]),
     list([
       ':ref:`TPR <TPR-format>`',
       'GROMACS run topology file',
-      'angles, bonds, chainIDs, charges, dihedrals, elements, impropers, molnums, moltypes, names, resnames',
+      'angles, bonds, chainIDs, charges, dihedrals, elements, impropers, masses, molnums, moltypes, names, resnames, types',
       '',
     ]),
     list([
       ':ref:`TXYZ, ARC <TXYZ-format>`',
       'Tinker file',
-      'bonds, elements, names',
+      'bonds, elements, names, types',
       'masses',
     ]),
     list([
       ':ref:`XML <XML-format>`',
       'HOOMD XML file',
-      'angles, bonds, charges, dihedrals, impropers, radii',
+      'angles, bonds, charges, dihedrals, impropers, masses, radii, types',
       '',
     ]),
     list([