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).

package-2.7.0

This a minor release of MDAnalysis.

This release of MDAnalysis is packaged under a [GPLv3+ license](https://www.gnu.org/licenses/gpl-3.0.en.html), additionally all contributions made from commit `44733fc214dcfdcc2b7cb3e3705258781bb491bd` onwards are made under the [LGPLv2.1+ license](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html).

The minimum supported NumPy version is 1.22.3.

Supported Python versions:
- 3.9, 3.10, 3.11, 3.12

Major changes:

See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.7.0/package/CHANGELOG) and our [release blog post](https://www.mdanalysis.org/blog/#mdanalysis-2.7-is-out) for more details.

Fixes:
* NoJump now properly handles jumps that occur on the second frame of NPT trajectories, PR 4258
* Fix charge reading from PDBQT files. PR 4283
* Fixed a case where qcprot.CalcRMSDRotationalMatrix would return a RMSD of None. PR 4273

Enhancements:
* Support was added for reading chainID from prmtop AMBER topologies (PR 4007)
* Added support for Python 3.12 (PR 4309, 4300, 4301, 4319, 4325, 4327, 4329)
* Added support for reading `chainID` from PDBQT files (PR 4284)
* TPR reader now sets `chainID` from `molblock` (PR 4281)
* Various improvements to the organization and performance of Major and Minor Pair analyses (PR 3735)
* C distance backend is now exposed via `libmdanalysis.pxd` (PR 4342)
* Added a GROMOS11 Reader (PR 4294)

Changes:
* Added `mda_xdrlib` as a core dependency to replace the now deprecated Python `xdrlib` code (PR 4271)
* ConverterBase has been moved to `MDAnalysis.converters.base` (PR 4253)
* `networkx` is now an optional dependency of MDAnalysis (PR 4331)
* `BioPython` is now an optional dependency of MDAnalysis (PR 4332)
* Results for WatsonCrickDist nucleic acids analysis are now stored in `analysis.nucleicacids.WatsonCrickDist.results.distances` (PR 3735)

Deprecations:
* Importing ConverterBase from `MDAnalysis.coordinates.base` will not be possible after MDAnalysis 3.0 (PR 4253)
* Deprecation with intent of removal in MDAnalysis v3.0 of the X3DNA legacy code (PR 4333)
* Deprecation with intent of removal in MDAnalysis v3.0 of the TRZ reader and writer (PR 4335)
* Deprecation with intent of removal in MDAnalysis v3.0 of the `MDAnalysis.lib.util.which` method (PR 4340)
* The `asel` argument of the `timeseries` attribute of Readers is now deprecated in favour of the `atomgroup` argument (PR 4343)
* In `nucleicacids.WatsonCrickDist`, accepting lists of `Residue` objects was deprecated in favor of using `ResidueGroup`: using `List[Residue]` will be removed in release 3.0.0; instead use a `ResidueGroup` (PR 3735)
* In `nucleicacids.WatsonCrickDist` the result `results.pair_distances` was deprecated and will be removed in 3.0.0; use `results.distances` instead (PR 3735)

New Contributors
* jennaswa made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4289
* Sumit112192 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4346
* HeetVekariya made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4359
* JoStoe made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4292
* ljwoods2 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4366

package-2.6.1

This is a bugfix release of the 2.6.x version branch of MDAnalysis, it serves as an amendment to the earlier released version 2.6.0.

See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.6.1/package/CHANGELOG) for more details.

Bug fixes and changes

* Reverting the v2.6.0 behaviour, builds are now again made using the oldest supported NumPy version (NumPy 1.22.3 for Python 3.9-3.10, and 1.22.3 for Python 3.11) [PR 4261]
* Uses of numpy `in1d` have been replaced with `isin` in prepartion for NumPy 2.0 [PR 4255]
* Cython DEF statements have been replaced with compile time integer constants as DEF statements are now deprecated in Cython 3.0 [Issue 4237, PR 4246]
* Fix to element guessing code to more accurately interpret atom names split by numbers (i.e. N0A is now recognised as N rather than NA) [Issue 4167, PR 4168]
* Clarification of SurvivalProbability function documentation [Issue 4247, PR 4248]1

New Contributors
* pillose made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4168

package-2.6.0

This a minor release of MDAnalysis.

This release of MDAnalysis is packaged under a [GPLv3+ license](https://www.gnu.org/licenses/gpl-3.0.en.html), additionally all contributions made from commit 44733fc214dcfdcc2b7cb3e3705258781bb491bd onwards are made under the [LGPLv2.1+ license](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html). More details about these license changes will be provided in an upcoming blog post.

The minimum supported NumPy version has been raised to 1.22.3 as per NEP29. Please note that package builds are now made with NumPy 1.25+ which offer backwards runtime compatibility with NEP29 supported versions of NumPy.

Supported Python versions:
- 3.9, 3.10, 3.11

Major changes:

See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.6.0/package/CHANGELOG) and our [release blog post](https://www.mdanalysis.org/blog/#mdanalysis-2.6-is-out) for more details.

Fixes:
* The -ffast-math compiler flag is no longer used by default at build time, avoiding inconsistent (although still scientifically correct) results seen in Intel MacOS systems when calling `AtomGroup.center_of_charge(..., unwrap=True). This also avoids potentially incorrect floating point results as [detailed here](https://moyix.blogspot.com/2022/09/someones-been-messing-with-my-subnormals.html). (https://github.com/MDAnalysis/mdanalysis/pull/4220)
* DATAWriter, CRD, PQR, and PDBQT files can now be correctly written to compressed files. Before this change, any attempt to write to a compressed format (gzip or bzip2) would lead to writing out an uncompressed file. (https://github.com/MDAnalysis/mdanalysis/pull/4163)
* Prevent accidental merging of bond/angle/dihedral types when they are defined as LAMMPS style string integers instead of tuples. This was leading to an incorrect number of bond/angle/dihedral types being written to lammps data files. (https://github.com/MDAnalysis/mdanalysis/pull/4003)

Enhancements:
* An `exclude_same` argument has been added to `InterRDF` allowing pairs of atoms that share the same residue, segment or chain to be excluded from the calculation. (https://github.com/MDAnalysis/mdanalysis/pull/4161)
* LAMMPS reader now supports the `continuous` ChainReader option. (https://github.com/MDAnalysis/mdanalysis/pull/4170)
* AtomGroup representation now returns atom indices in the same order as they are stored in the AtomGroup. (https://github.com/MDAnalysis/mdanalysis/pull/4191)

Changes:
* Package builds now use NumPy 1.25 or higher instead of the lowest supported NumPy version. (https://github.com/MDAnalysis/mdanalysis/pull/4198)
* As per NEP29, the minimum supported runtime version of NumPy has been increased to 1.22.3. (https://github.com/MDAnalysis/mdanalysis/pull/4160)
* The GSD package is now an optional dependency. (https://github.com/MDAnalysis/mdanalysis/pull/4174)
* The MDAnalysis package now only supports GSD versions 3.0.1 or above. (https://github.com/MDAnalysis/mdanalysis/pull/4153)
* MDAnalysis no longer officially supports 32 bit installations. (they are no longer tested in our continuous integration pipelines). Note: no code changes have been made to disable 32 bit, although it is known that new versions of most MDAnalysis core dependencies no longer release 32 bit compatible versions. (https://github.com/MDAnalysis/mdanalysis/pull/4176)
* The package license has been updated to [GPLv3+](https://www.gnu.org/licenses/gpl-3.0.en.html) to better reflect the compatibility of GPLv2+ with Apache and GPLv3 licensed codes. Additionally all new contributions from commit 44733fc214dcfdcc2b7cb3e3705258781bb491bd onwards are made under the [LGPLv2.1+ license](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html). (https://github.com/MDAnalysis/mdanalysis/pull/4219)

Deprecations:
* The misspelt `Boltzman_constant` entry in `MDAnalysis.units` is now deprecated in favour the correctly spelt `Boltzmann_constant`. (https://github.com/MDAnalysis/mdanalysis/pull/4230 and https://github.com/MDAnalysis/mdanalysis/pull/4214)
* `MDAnalysis.analysis.hole2` is now deprecated in favour of a new [HOLE2 MDAKit](https://www.mdanalysis.org/hole2-mdakit/). (https://github.com/MDAnalysis/mdanalysis/pull/4200)

New Contributors
* MohitKumar020291 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4182
* Shubx10 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4184
* ztimol made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4191

package-2.5.0

This a minor release of MDAnalysis.

The minimum Python version has been raised to 3.9 and NumPy to 1.21.0 as per NEP29. We also now package wheels for both linux and osx arm64 machines on PyPi.

Supported Python versions:
- 3.9, 3.10, 3.11

Major changes:

See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.5.0/package/CHANGELOG) and our [release blog post](https://www.mdanalysis.org/blog/#mdanalysis-2.5-is-out) for more details.

Fixes:
* Fixed an issue where transformations were not being properly applied to
Universes with multiple trajectories (i.e. using the ChainReader)
(Issue 3657 4008 PR 3906)
* Fixed an issue with the the `heavy` distance_type for `WaterBridgeAnalysis`
where distance was not correctly assigned when more than one hydrogen
was bonded to a heavy atom (Issue 4040, PR 4066).
* PDB topology parser no longer fails when encountering unknown formal
charges and instead simply does not populate attribute (Issue 4027)
* Fixed an issue where using the `between` keyword of `HydrogenBondAnalysis`
led to incorrect donor-atom distances being returned (PR 4092, Issue 4091)
* Fixed an issue where chi1_selections() ignored atom names CG1 OG OG1 SG
and incorrectly returned `None` for amino acids CYS, ILE, SER, THR, VAL
(Issue 4108, PR 4109)
* Fix H5MD reader to read box vectors rather than returning `None` as the
dimensions (Issue 4075, PR 4076)
* Fix to allow reading NetCDF trajectories which do not have the `time`
variable defined (Issue 4073, PR 4074)
* Allows shape_parameter and asphericity to yield per residue quantities
(Issue 3002, PR 3905)
* Fix EDRReader failing when parsing single-frame EDR files (Issue 3999)
* Add 'PairIJ Coeffs' to the list of sections in LAMMPSParser.py
(Issue 3336)
* PDBReader now defaults atom values for ts.data['occupancy'] to 0.0, rather
than the previous default of 1.0. This now matches the default used when
setting Universe Topology attributes using the first frame's information (PR 3988)

Enchancements:
* ARM64 (osx and linux) wheels are now provided via PyPi (Issue 4054)
* Addition of a new analysis class `analysis.atomicdistances.AtomicDistances`
to provide distances between two atom groups over a trajectory.
(Issue 3654, PR 4105)
* Add kwarg `n_frames` to class method `empty()` in
`MDAnalysis.core.universe`, enabling creation of a blank `Universe` with
multiple frames (PR 4140)
* PDBReader now populates ts.data['tempfactor'] with the tempfactor for
each atom *for each frame*. If an entry is missing for a given atom,
this will default to a `1.0` value. Note, this does not affect the
topology, i.e. `AtomGroup.tempfactors` is not dynamically updated.
(Issue 3825, PR 3988)
* Add writing u.trajectory.ts.data['molecule_tag'] as molecule tags to
LAMMPS data file (Issue 3548)
* Add `progressbar_kwargs` parameter to `AnalysisBase.run` method, allowing
to modify description, position etc of tqdm progressbars. (PR 4085)
* Add a nojump transformation, which unwraps trajectories so that particle
paths are continuous. (Issue 3703, PR 4031)
* Added AtomGroup TopologyAttr to calculate gyration moments (Issue 3904,
PR 3905)
* Add support for TPR files produced by Gromacs 2023 (Issue 4047)
* Add distopia distance calculation library bindings as a selectable backend
for `calc_bonds` in `MDA.lib.distances`. (Issue 3783, PR 3914)
* AuxReaders are now pickle-able and copy-able (Issue 1785, PR 3887)
* Add pickling support for Atom, Residue, Segment, ResidueGroup
and SegmentGroup. (PR 3953)

Changes:
* As per NEP29 the minimum supported Python version has been raised to 3.9
and NumPy has been raised to 1.21 (note: in practice later versions of NumPy
may be required depending on your architecture, operating system, or Python
version) (PRs 4115 and 3983).
* Add progress bars to track the progress of `mds.EinsteinMSD` _conclude()
methods (_conclude_simple() and _conclude_fft()) (Issue 4070, PR 4072)
* The deprecated direct indexing and `times` from the `results` attribute of
analysis.nucleicacids' NucPairDist and WatsonCrickDist classes has been
removed. Please use the `results.pair_distances` and `times` attributes
instead (Issue 3744)
* RDKitConverter changes (part of Issue 3996):
* moved some variables (`MONATOMIC_CATION_CHARGES `and
`STANDARDIZATION_REACTIONS`) out of the related functions to allow users
fine tuning them if necessary.
* changed the sorting of heavy atoms when inferring bond orders and
charges: previously only based on the number of unpaired electrons, now
based on this and the number of heavy atom neighbors.
* use RDKit's `RunReactantInPlace` for the standardization reactions, which
should result in a significant speed improvement as we don't need to use
bespoke code to transfer atomic properties from the non-standardized mol
to the standardized one.

New Contributors
* mglagolev made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3959
* chrispfae made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4009
* ooprathamm made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4010
* MeetB7 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4022
* v-parmar made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4032
* MoSchaeffler made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4049
* jandom made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4043
* xhgchen made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4037
* DrDomenicoMarson made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4074
* AHMED-salah00 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4059
* schlaicha made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4076
* jvermaas made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4031
* SophiaRuan made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4072
* marinegor made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4085
* g2707 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4089
* DanielJamesEvans made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4109

package-2.4.3

This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.2.

Bug fixes
* Fixed DCD reading for large (>2Gb) files (Issue 4039). This was broken for versions 2.4.0, 2.4.1 and 2.4.2.
* Fix element parsing from PSF files tests read via Parmed (Issue 4015)

package-2.4.2