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Add 2.7.0 release notes (#353)
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* Add 2.7.0 release notes
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IAlibay authored Jan 4, 2024
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# MDAnalysis Release Notes


## Release 2.7.0 of MDAnalysis

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](https://github.com/jennaswa) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4289
* [@Sumit112192](https://github.com/Sumit112192) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4346
* [@HeetVekariya](https://github.com/HeetVekariya) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4359
* [@JoStoe](https://github.com/JoStoe) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4292
* [@ljwoods2](https://github.com/ljwoods2) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4366

## Release 2.6.1 of MDAnalysis

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.
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