Mdanalysis

This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.1.

Bug fixes

* Fixed an issue where the arguments passed to np.histogramdd in `MDAnalysis.analysis.DensityAnalysis` were not compatible with the 1.24 release of NumPy (PR 3976)
* Fixed upcoming incompatibilities with NumPy 1.25 in `MDAnalysis.visualization.streamlines_3D` and `MDAnalysis.visualization.streamlines` where incorrect comparison of the truth of arrays would have led to failures (PR 3977)

package-2.4.1

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