Mdanalysis

This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.0.

Bug fixes

* The minimum version of biopython has been raised to 1.80 for pip installs
* pytng has been added as an optional dependency


package-2.4.0

This a minor release of MDAnalysis, as per our once-every-three-months schedule.

The minimum NumPy and Python versions remain largely unchanged, however the minimum version of `biopython` has been raised to 1.80. This is also the first release to officially support Python 3.11.

Supported Python versions:
- 3.8, 3.9, 3.10, 3.11

Major changes:

See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.4.0/package/CHANGELOG) and our [release blog post](https://www.mdanalysis.org/blog/#mdanalysis-2.4-is-out) for more details.

Fixes:

Enchancements:
* As part of their [outreachy project](https://www.mdanalysis.org/2022/12/15/uma_outreachy/) umak has started adding type annotations throughout the MDAnalysis codebase
* As part of their [GSoC project](https://www.mdanalysis.org/2022/11/20/bjarne_gsoc/) BFedder has added an auxialliary reader for EDR files (PR #3749)
* As part of their [GSoC project](https://www.mdanalysis.org/2022/12/09/Aya-gsoc-final-report/) aya9aladdin has fixed various issues with guessing and and attribute reading. This will be followed by the introduction of a new guesser system in a future release.
* A reader for TNG files has been added by hmacdope, follow up on his previous [GSoC 2020](https://www.mdanalysis.org/2020/09/02/final-report-hugo/) work on creating a python library for reading TNG files (PR 3765)
* Addition of a new isolayer selection method (PR 3846)
* Various enchancements and fixes to the LAMMPS DUMP Parser (allowing box translation on reading, allowing coordinates to be unwrapped based on dump image flags, and importing of forces and velocities) (PR 3844)
* All readers now have a timeseries attribute (PR 3890)
* ReaderBase file formats now accept pathlib inputs (PR 3935)
* Added ability for hbond analysis to use types when resnames are not present (PR 3848)

Changes:
* The deprecated setup.py `extra_requires` `AMBER` entry has been removed in favor of `extra_formats` (PR 3810)
* Various issues with the auxilliary reader, this should not be much more robust (PR 3749)
* The Cython headers have been moved to MDAnalysis.lib.libmdanalysis (PR 3913)
* The `MDAnalysis.analysis.align.sequence_alignment` now uses Bio.Align.PairwiseAligner instead of the deprecated Bio.pairwise2 (PR 3951)

Deprecations:
* The MemoryReader's timeseries inclusive indexing will be changed to exclusive in version 3.0.0 (PR 3894)
* The `sequence_aligment()` method has been deprecated and will be removed in version 3.0.0 (PR 3951)
* MDAnalysis.analysis.nucleicacids' direct indexing of selection indices to obtain pair distances results has been deprecated in favor of accessing `results.pair_distances` (PR 3958)

New Contributors
* jaclark5 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3846
* pgbarletta made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3876
* jfennick made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3832
* Hakarishirenai made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3956



package-2.3.0

This a minor release of MDAnalysis, as per our once-every-three-months schedule.

The minimum NumPy version has been raised to 1.20.0 (1.21 for macosx-arm64) in line with [NEP29](https://numpy.org/neps/nep-0029-deprecation_policy.html).


Supported python versions:
- 3.8, 3.9, 3.10


Major changes:

See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.3.0/package/CHANGELOG) and our [release blog post](https://www.mdanalysis.org/blog/#mdanalysis-2.3-is-out) for more details.


Fixes:
- Fixed reading error when dealing with corrupt PDB CONECT records, and an issue where MDAnalysis would write out unusable CONECT records with index>100000 (Issue 988).


Enhancements:
- Formal charges are now read from PDB files and stored in a `formalcharge` attribute (PR 3755).
- A new normalizing `norm` parameter for the `InterRDF` and `InterRDF_s` analysis methods (Issue 3687).
- Improved Universe serialization performance (Issue 3721, PR 3710).


Changes:
- To install optional packages for different file formats supported by MDAnalysis, use `pip install ./package[extra_formats]` (Issue 3701, PR 3711).


Deprecations:
- The `extra_requires` target `AMBER` for `pip install ./package[AMBER]` will be removed in 2.4.0. Use `extra_formats` (Issue 3701, PR 3711).


CZI EOSS Performance Improvements:

A series of performance improvements to the MDAnalysis library's backend have been made as per planned work under MDAnalysis' CZI EOSS4 grant. Further details about these will be provided in a future blog post.

- `MDAnalysis.lib.distances` now accepts `AtomGroups` as well as NumPy arrays (PR 3730).
- Timestep has been converted to a Cython Extension type (PR 3683).

package-2.2.0

In line with NEP29, this version of MDAnalysis drops support for Python 3.7 and raises the minimum NumPy version to 1.19.0. Minimum version support has also been changed for the following packages; `networkx>=2.0`, `scipy>=1.5.0`, `gsd>=1.9.3`. Further details on MDAnalysis future support strategy and NEP29 will be released shortly.

Supported python versions:
- 3.8, 3.9, 3.10

Major changes:

See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.2.0/package/CHANGELOG) and our [release blog post](https://www.mdanalysis.org/blog/#mdanalysis-2.2-is-out) for more changes and details.

Enhancements:
- The `frames` argument was added to AnalysisBase-derived classes (i.e. modern analysis classes) allowing for specific frames to be defined when running an analysis. (PR 3415)
- DL_POLY classic HISTORY files are now supported (Issue 3678)
- Python wheels are now made available through PyPI for x86_64 architectures (Issue 1300, PR 3680)
- Added a `center_of_charge` attribute for AtomGroups (PR 3671)
- LinearDensity now work with UpdatingAtomGroups (Issue 2508, PR 3617)
- Addition of a PCA transformation and an associated inverse-PCA transformation was added to the PCA analysis class (PR 3596, Issue 2703)
- Major improvements to the RDKitConverter's accuracy (PR 3044)
- Accuracy of 99.14% when benchmarked against ChEMBL30
- AtomGroups containing monatomic ion charges and edge cases with nitrogen, sulfur, phosphorus and conjugated systems should now have correctly assigned bond orders and charges.
- Addition of a new AnalysisBase derived Watson-Crick distance analysis class (PR 3611)

Fixes:
- Fixed issues where calling the `copy` method of Readers did not preserve optional arguments (Issue 3664, PR 3685)
- Fixed several issues where iterating trajectories had undefined behaviour
- Iterating (not in memory) SingleFrame readers now reset modified trajectory attributes (Issue 3423)
- Iterating using defined indices did not rewind the trajectory (Issue 3416)
- Fixed issues with competing processes writing to an XTC offset file leading to offset corruption (Issue 1988, PR 3375)
- Fixed issue preventing OpenMMTopologyParsers from parsing systems with missing elements (Issue 3317, PR 3511)
- Fixed issue with encore.covariance.covariance_matrix not working when providing an external reference (Issue 3539, PR 3621)
- Fixed issue with broken code paths for "residues" and "segment" groupings for LinearDensity (Issue 3571, PR 3572)
- Improved the flexibility of MOL2 reading, allowing for optional columns (`subst_id`, `subst_name` and `charge`) not to be provided (Issue 3385, PR 3598)
- Fixed several issues related to converting AtomGroups to RDKit molecules (PR 3044):
- Atoms are now in the same order
- `atom.GetMonomerInfor().GetName()` now follows the guidelines for PDB files
- Using `NoImplicit=False` no longer throws a `SanitizationError`
- Fixed issues with incorrect reading of triclinic boxes from DUMP files (Issue 3386, PR 3403)
- Fixed issue with the BAT method modifying input coordinate data (Issue 3501)

Changes:
- The number of matches allowed when doing a smarts selection has been increased from the default
1000 to max(1000, n_atoms * 10), an additional set of `smarts_kwargs` can now also be passed
to override this behaviour (Issue 3469, PR 3470)
- The `fasteners` package is now a core dependency (PR 3375)
- LinearDensity now saves the histogram bin edges for easier plotting as `hist_bin_edges for
each dimension in the results dictionary (Issue 2508, PR 3617)
- ContactAnalysis now accepts AtomGroups (Issue 2666, PR 3565)

Deprecations:
- The following results attribute for LinearDensity are now deprecated: (Issue 2508, PR 3617)
- `pos` is now `mass_density`
- `char` is now `charge_density`
- `std` entries are now `stddev`

Known test failures:
- Windows builds
* In some cases users may get permission errors with tests involving symlinks. This should not impact the behaviour of MDAnalysis but may impact the creation of temporary files when using HOLE2 (see: https://github.com/MDAnalysis/mdanalysis/issues/3556).

package-2.1.0

In line with ongoing attempts to align with NEP29, this version of MDAnalysis drops support for Python 3.6 and raises the minimum NumPy version to 1.18.0.

Please note that at time of release whilst all the MDAnalysis core functionality supports Python 3.10, some optional modules do not due to a lack of support by dependencies which they require. We hope that this support will gradually be added as more of these dependencies release new versions compatible with Python 3.10.

Supported python versions:
- 3.7, 3.8, 3.9, 3.10

Major changes:

See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.1.0/package/CHANGELOG) and our [release blog post](https://www.mdanalysis.org/blog/#mdanalysis-2.1-is-out) for more changes and details.

Enhancements:
- Addition of a new dielectric analysis module (PR 2118)
- The TPR parser now supports reading files from GROMACS 2022 (PR 3514)
- The H5MDReader can now load trajectories without a topology (PR 3466)
- Custom compiler flags can be used when building MDAnalysis from source (PR 3429)
- The RDKit reader now supports parsing R/S chirality (PR 3445)
- A new method to apply the minimum image convention to a collection of vectors, `minimize_vectors`, has been introduced (PR 3472)

Fixes:
- Fixed various integer overflow issues in the distance calculation backend of MDAnalysis which would prevent calculations on large systems (Issues 3183, 3512).
- Fixed issues with the creation of VMD surfaces in HOLE2 when using a non-contiguous start/stop/step.
- Fixes reading of charges with the ITPParser (Issue 3419).
- Fixed issue with the creation of a Universe from a custom object which only provides a topology (Issue 3443).
- Fixed issue with accessing newly created values added via `add_Segment` or `add_Residue` (Issue 3437).

Changes:
- `packaging` is now a core dependency of MDAnalysis.
- Indexing a Group (AtomGroup, ResidueGroup, SegmentGroup) with `None` now raises a `TypeError`. Prior to this indexing by `None` would incorrectly return the whole Group but claim to have a length of 1 atom (Issue 3092).
- The TRZReader now defaults to a `dt` value of 1.0 ps instead of the previous 0.0 ps (Issue 3257).

Deprecations:
- The `pbc` keyword argument for various Group methods has been deprecated in favor of `wrap`. The deprecated keyword will be removed in version 3.0.0 (Issue 1760).

Known test failures:
- `pytest-xdist` and more than 4 workers
* Under these conditions a test related to logging for HydrogenBondAnalysis can fail. This is not thought to impact the validity of MDAnalysis. See here for more details: https://github.com/MDAnalysis/mdanalysis/issues/3543
- Windows builds
* In some cases users may get permission errors with tests involving symlinks. This should not impact the behaviour of MDAnalysis but may impact the creation of temporary files when using HOLE2 (see: https://github.com/MDAnalysis/mdanalysis/issues/3556).

release-2.0.0

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