From 67eab9f0865a955ee23370273bb92ae554ce4210 Mon Sep 17 00:00:00 2001 From: Rocco Meli Date: Sat, 30 Nov 2024 23:38:33 +0100 Subject: [PATCH] release notes and snapshots --- doc/source/releases.md | 34 ++++++++++++ .../test_gen_topologyparser_attrs.ambr | 54 ++++++++++++++----- 2 files changed, 76 insertions(+), 12 deletions(-) diff --git a/doc/source/releases.md b/doc/source/releases.md index e2837008e..123248f9f 100644 --- a/doc/source/releases.md +++ b/doc/source/releases.md @@ -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. diff --git a/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_topologyparser_attrs.ambr b/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_topologyparser_attrs.ambr index 79a63fd0c..8b46763af 100644 --- a/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_topologyparser_attrs.ambr +++ b/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_topologyparser_attrs.ambr @@ -139,6 +139,12 @@ '', ':ref:`DATA `, :ref:`GSD `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`XML `', ]), + list([ + 'mass', + 'masses', + '', + ':ref:`CONFIG `, :ref:`CRD `, :ref:`DATA `, :ref:`DMS `, :ref:`GMS `, :ref:`GRO `, :ref:`GSD `, :ref:`HISTORY `, :ref:`IN, FHIAIMS `, :ref:`LAMMPSDUMP `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB `, :ref:`XYZ `', + ]), list([ 'model', 'models', @@ -217,6 +223,12 @@ 'B-factor', ':ref:`CRD `, :ref:`MMTF `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`XPDB `', ]), + list([ + 'type', + 'types', + '', + ':ref:`CONFIG `, :ref:`CRD `, :ref:`DATA `, :ref:`DMS `, :ref:`GMS `, :ref:`GRO `, :ref:`GSD `, :ref:`HISTORY `, :ref:`IN, FHIAIMS `, :ref:`LAMMPSDUMP `, :ref:`MMTF `, :ref:`MOL2 `, :ref:`PDB, ENT `, :ref:`PDBQT `, :ref:`PQR `, :ref:`PSF `, :ref:`TOP, PRMTOP, PARM7 `, :ref:`TPR `, :ref:`TXYZ, ARC `, :ref:`XML `, :ref:`XPDB `, :ref:`XYZ `', + ]), list([ 'type_index', 'type_indices', @@ -319,8 +331,11 @@ 'masses': set({ ':ref:`CONFIG `', ':ref:`CRD `', + ':ref:`DATA `', + ':ref:`DMS `', ':ref:`GMS `', ':ref:`GRO `', + ':ref:`GSD `', ':ref:`HISTORY `', ':ref:`IN, FHIAIMS `', ':ref:`LAMMPSDUMP `', @@ -329,7 +344,11 @@ ':ref:`PDB, ENT `', ':ref:`PDBQT `', ':ref:`PQR `', + ':ref:`PSF `', + ':ref:`TOP, PRMTOP, PARM7 `', + ':ref:`TPR `', ':ref:`TXYZ, ARC `', + ':ref:`XML `', ':ref:`XPDB `', ':ref:`XYZ `', }), @@ -408,13 +427,24 @@ 'types': set({ ':ref:`CONFIG `', ':ref:`CRD `', + ':ref:`DATA `', ':ref:`DMS `', ':ref:`GMS `', ':ref:`GRO `', + ':ref:`GSD `', ':ref:`HISTORY `', ':ref:`IN, FHIAIMS `', + ':ref:`LAMMPSDUMP `', + ':ref:`MMTF `', + ':ref:`MOL2 `', ':ref:`PDB, ENT `', + ':ref:`PDBQT `', ':ref:`PQR `', + ':ref:`PSF `', + ':ref:`TOP, PRMTOP, PARM7 `', + ':ref:`TPR `', + ':ref:`TXYZ, ARC `', + ':ref:`XML `', ':ref:`XPDB `', ':ref:`XYZ `', }), @@ -437,13 +467,13 @@ list([ ':ref:`DATA `', 'LAMMPS data file', - 'angles, bonds, charges, dihedrals, impropers', + 'angles, bonds, charges, dihedrals, impropers, masses, types', '', ]), list([ ':ref:`DMS `', '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 `', '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 `', 'LAMMPS ascii dump file', + 'masses, types', '', - 'masses', ]), list([ ':ref:`MMTF `', '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 `', 'Tripos MOL2 file', - 'bonds, charges, elements, names, resnames', + 'bonds, charges, elements, names, resnames, types', 'masses', ]), list([ @@ -503,7 +533,7 @@ list([ ':ref:`PDBQT `', '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 `', '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 `', '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 `', '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 `', 'Tinker file', - 'bonds, elements, names', + 'bonds, elements, names, types', 'masses', ]), list([ ':ref:`XML `', 'HOOMD XML file', - 'angles, bonds, charges, dihedrals, impropers, radii', + 'angles, bonds, charges, dihedrals, impropers, masses, radii, types', '', ]), list([