This is the first version of MDAnalysis to solely support python 3.6+
Supported python versions:
- 3.6, 3.7, 3.8, 3.9
Please note that starting with the next minor version, MDAnalysis will be following [NEP29](https://numpy.org/neps/nep-0029-deprecation_policy.html).
Notes:
* This is a major release and introduces major advertised API breaks. Caution is advised when upgrading to 2.0.0.
Major changes:
Enhancements:
- LAMMPSDumpReader can now read coordinates in all different LAMMPS coordinate conventions (Issue 3358)
- New `Results` class for storing analysis results (Issue 3115)
- New OpenMM coordinate and topology converters (Issue 2863, PR 2917)
- New `intra_bonds`,`intra_angles`, `intra_dihedrals`, etc... methods to return connections involve atoms within AtomGroups instead of including atoms outside of it (Issue 1264, 2821, PR 3200)
- Support for Groamcs 2021 TPR files (Issue 3180)
- Adds preliminary support for ppc64le and aarch64 [ARM] (Issue 3127, PR 2956 3149)
- New selection operators (Issue 3054, PR 2927)
- New refactor of helix analysis class as `analysis.helix_analysis` (Issue 2452)
- New converter between RDKit molecules and MDAnalysis AtomGroup objects (Issue 2468). Also includes `from_smiles` Universe generator method, and the aromatic and smarts selection.
- New analysis method for calculating Mean Squared Dsiplacements (Issue 2438)
- New converter between Cartesian and Bond-Angle-Torsion coordinates (PR 2668)
- Universes and readers can now be `pickled` paving the way to easier parallel analyses (Issue 2723)
- New H5MDReader and H5MDWriter (Issue 762, 2866)
Fixes:
- Fixes an issue where `select_atom`, AtomGroup.unique, ResidueGroup.unique, and SegmentGroup.unique did not sort the output atoms (Issues 3364 2977)
- GRO files now only support unit cells defined with 3 or 9 entries (Issue 3305)
- Fixes the sometimes wrong sorting of atoms into fragments when unwrapping (Issue 3352)
- Fixes issue when atttempting to use/pass mean positions to PCA analysis (Issue 2728)
- Fixes support for DL_POLY HISTORY files that contain cell information even if there are no periodic boundary conditions (Issue 3314)
- Fixes issue with WaterBridgeAnalysis double counting waters (Issue 3119)
- PDBWriter will use chainID instead of segID (Issue 3144)
- PDBParser and PDBWriter now assign and use the element attribute (Issues 3030 2422)
- AtomGroup.center now works correctly for compounds + unwrapping (Issue 2984)
- Documents and fixes the `density` keyword for `rdf.InterRDF_s` (Isuse 2811)
- Fixed Janin analysis residue filtering, including CYSH (Issue 2898)
Changes:
- New converter API for all MDAnalysis converters under MDAnalysis.converters
- Timestep now stores information in 'C' memory layout instead of the previous 'F' default (PR 1738)
- `hbonds.hbond_analysis` has been remove din favour of `hydrogenbonds.hbond_analysis` (Issues 2739, 2746)
- TPRParser now loads TPR files with `tpr_resid_from_one=True` by deafult, which starts TPR resid indexing from 1 (instead of 0 as in previous MDAnalysis versions) (Issue 2364, PR 3152)
- `analysis.hole` has now been removed in favour of `analysis.hole2.hole` (Issue 2739)
- `Writer.write(Timestep)` and `Writer.write_next_timestep` have been removed. Please use `write()` instead (Issue 2739)
- Removes deprecated density_from_Universe, density_from_PDB, Bfactor2RMSF, and notwithin_coordinates_factory from MDAnalysis.analysis.density (Issue 2739)
- Changes the minimum numpy supported version to 1.16.0 (Issue 2827)
- Removes deprecated `waterdynamics.HydrogenBondLifetimes` (PR 2842)
- `hbonds.WaterBridgeAnalysis` has been moved to `hydrogenbonds.WaterBridgeAnalysis` (Issue 2739 PR 2913)
Deprecations:
- The `bfactors` attribute is now aliased to `tempfactors` and will be removed in 3.0.0 (Issue 1901)
- `WaterBridgeAnalysis.generate_table()` now returns table information, with the `table` attribute being deprecated
- Various analysis result attributes which are now stored in `Results` will be deprecated in 3.0.0 (Issue 3261)
- In 3.0.0 the ParmEd classes will only be accessible from the `MDAnalysis.converters` module
- In 2.1.0 the TRZReader will default to a dt of 1.0 ps when failing to read it from the input TRZ trajectory
See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.0.0/package/CHANGELOG) for more changes and details.
Known issues:
- Windows builds
* For some compilers (seen on MVC v.19xx), differences in floating point precision leads to PBC wrapping differing from expected outcomes. This leads to failures in the `MDAnalysisTests.lib.test_augment` tests. To our knowledge this does not significantly affect results (as all other tests pass). We will aim to fix this in version 2.1.0.
release-1.1.1
Final bugfix release for 1.0.x
Python support is kept the same as 1.0.0, with python 3.9 not supported.
Supported python versions:
- 2.7, 3.5, 3.6, 3.7, 3.8
Please note that python 2.7 and 3.5 support will be dropped in the upcoming 2.0.0 release.
Major changes:
Bug fixes
- Re-enables support for Windows (Issue 3129)
- NSGrid distance search backend is re-enabled, with a brand new code fixing previously seen issues (Issues 2670 2229 2345 2919)
- Adds support for numpy 1.20 for compatible python versions
- Fixes bug where the exclusion matrix of hbond_autocorrel was not applied correctly (Issue 2987 PR 3242)
Deprecations:
- NCDFWriter `scale_factor` writing behaviour will change in 2.x (Issue 2327)
- PDBWriter will no longer use the last letter of SegID for the chainID in 2.x (Issue 3144)
- In 2.x, the universe attributes `tempfactors` and `bfactors` will stop being separate (Issue 1901)
- `MDAnalysis.analysis.hbonds.WaterBridgeAnalysis` will be moved to `MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis` in 2.x (PR 3111)
- In 2.x the TPRParser will index residues from 1 instead of 0. The `tpr_resid_from_one` keyword has been added to modify this behaviour (Issue 2364)
Enhancements:
- The `get_connections` method has been added to more easily get bonds, angles, dihedrals, etc.. for a group (Issues 1264 2821)
See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-1.1.1/package/CHANGELOG) for more changes and details.
Known issues:
- Windows builds
* For some compilers (seen on MVC v.19xx), differences in floating point precision leads to PBC wrapping differing from expected outcomes. This leads to failures in the `MDAnalysisTests.lib.test_augment` tests. To our knowledge this does not significantly affect results (as all other tests pass). We will aim to fix this in version 2.0.
* For python 3.5 only, extra tests failures are seen. These mostly relate to deprecations and warnings being raised upstream (primarily by `os.path`). As far as we know they do not affect the validity of the code. The following tests are affected:
* `MDAnalysisTests.analysis.test_base::test_analysis_class_decorator`
* `MDAnalysisTests.analysis.test_dihedrals::TestRamachandran::test_protein_ends`
* `MDAnalysisTests.analysis.test_helanal::test_warnings`
* `MDAnalysisTests.coordinates.test_chainreader::TestChainReaderContinuous::test_easy_trigger_warning`
* `MDAnalysisTests.utils.test_streamio::TestNamedStream_filename_behaviour::test_func[abspath]`
Notes:
* Release 1.1.1 fixes an installation issue with 1.1.0. There is no published release for version 1.1.0.
* As detailed in the 1.0.0 release, the 1.x releases only include bug fix changes. New features are being developed for MDAnalysis 2.x.
release-1.0.1
First bugfix release for 1.0.x
Python support is kept the same as 1.0.0, with python 3.9 not supported.
Supported python versions:
- 2.7, 3.5, 3.6, 3.7, 3.8
Major changes:
Bug fixes
- Temporary disabling of the default nsgrid backend (in favour of PDKTree) to the `capped_distance` code due to a bug affecting accuracy (2930)
- Fixes issues with importing matplotlib versions > 3.3 (2938)
- TRZ reader and writer now checks and writes `n_atoms` (2817)
- The density keyword for `rdf.InterRDF_s` is now documented and has been fixed to give correct results (2811)
- Fixed reading of masses and charges from hoomdxml files (2888)
- The DMSParser now handles the creation of multiple segids sharing residues with identical resids (1387)
Deprecations:
- `waterdynamics.HydrogenBondLifetimes` will be replaced with `hydrogenbonds.HydrogenBondAnalysis.lifetime` in 2.0.0 (2547)
- `analysis.helanal` will be removed in 2.0.0 and will be replaced with `analysis.helix_analysis` (2622)
- `lib.util.echo` and `core.universe.as_Universe` will be removed in 2.0.0.
- `analysis.leaflets.LeafletFinder` will no longer accept non-Universe inputs as of version 2.0.0.
Performance improvements:
- Fixes a performance regression seen in 1.0.0 when doing string selections with `select_atoms` (2751)
- Performance improvements to the TPR parser and ParmEd converter (2804 and 3028)
See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-1.0.1/package/CHANGELOG) for more changes and details.
Known issues:
- PyPI and conda-forge releases of 1.0.1 are not compatible with Windows OS due to issues with our `setup.py`. We aim to fix this for the upcoming 1.0.2 release (3129)
As detailed in the 1.0.0 release, the 1.x releases only include bug fix changes. New features are being developed for MDAnalysis 2.x.
release-1.0.0
First major stable release of MDAnalysis. The API will be stable for all 1.x releases.
- supports
- Python ≥3.5
- Python 2.7 (last major release to do so, see the [Roadmap](https://www.mdanalysis.org/2019/11/06/roadmap/))
- new [User Guide](https://userguide.mdanalysis.org/) documentation
- many new features
- new hydrogen bonding and HOLE analysis modules, improved density analysis
- new file formats (Chemfiles reader, NAMD binary coordinates, FHI-AIMS, Gromacs ITP, Gromacs 2020 TPR), improved PDB parsing
- package interoperablity layer ("converters"): interface to ParmEd
- bug fixes
- better support for Windows 32 bit
- removed features and constructs that were previously deprecated
See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-1.0.0/package/CHANGELOG) for details.
**Note that 1.x will not be further developped, with only occasional bug fixes being backported** as described in the [Roadmap](https://www.mdanalysis.org/2019/11/06/roadmap/).
The main development is geared towards MDAnalysis 2.x, which will only support Python 3.x and remove any code that was deprecated in 1.0.
release-0.20.1
Major enhancements and fixes.
See [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-0.20.1/package/CHANGELOG) for details.
(Note: 0.20.1 fixed an installation issue with 0.20.0 so there's no published 0.20.0 release.)
release-0.19.2
Added full support for Windows platform.
See [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-0.19.2/package/CHANGELOG) for details.
release-0.19.1
release-0.19.0
release-0.18.0
[pypidoc.zip](https://github.com/MDAnalysis/mdanalysis/files/1935925/pypidoc.zip)
release-0.17.0
release-0.16.2
Minor bug fixes and deprecations (for 0.17.0 and 1.0).
See the [Release Notes for 0.16.2](https://github.com/MDAnalysis/mdanalysis/wiki/ReleaseNotes0162) for details.
release-0.16.1
Bugfix release for 0.16.
Zipped docs available at:
https://github.com/MDAnalysis/docs/releases
release-0.16.0
[Release Notes](https://github.com/MDAnalysis/mdanalysis/wiki/ReleaseNotes0160)
[Blog Post](http://www.mdanalysis.org/2017/04/10/release-0.16.0/)
release-0.15.0
For full changes see the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/wiki/ReleaseNotes0150)
Documentation is attached
release-0.14.0
Full changelog [here](https://github.com/MDAnalysis/mdanalysis/wiki/ReleaseNotes0140)
release-0.13.0
Changelog available [here](https://github.com/MDAnalysis/mdanalysis/wiki/ReleaseNotes0130)
release-0.12.1