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1 | 1 | # MDAnalysis Release Notes |
2 | 2 |
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3 | 3 |
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| 4 | +## Release 2.7.0 of MDAnalysis |
| 5 | + |
| 6 | +This a minor release of MDAnalysis. |
| 7 | + |
| 8 | +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). |
| 9 | + |
| 10 | +The minimum supported NumPy version is 1.22.3. |
| 11 | + |
| 12 | +Supported Python versions: |
| 13 | + - 3.9, 3.10, 3.11, 3.12 |
| 14 | + |
| 15 | +### Major changes: |
| 16 | + |
| 17 | +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. |
| 18 | + |
| 19 | +#### Fixes: |
| 20 | +* NoJump now properly handles jumps that occur on the second frame of NPT trajectories, PR #4258 |
| 21 | +* Fix charge reading from PDBQT files. PR #4283 |
| 22 | +* Fixed a case where qcprot.CalcRMSDRotationalMatrix would return a RMSD of None. PR #4273 |
| 23 | + |
| 24 | +#### Enhancements: |
| 25 | +* Support was added for reading chainID from prmtop AMBER topologies (PR #4007) |
| 26 | +* Added support for Python 3.12 (PR #4309, #4300, #4301, #4319, #4325, #4327, #4329) |
| 27 | +* Added support for reading `chainID` from PDBQT files (PR #4284) |
| 28 | +* TPR reader now sets `chainID` from `molblock` (PR #4281) |
| 29 | +* Various improvements to the organization and performance of Major and Minor Pair analyses (PR #3735) |
| 30 | +* C distance backend is now exposed via `libmdanalysis.pxd` (PR #4342) |
| 31 | +* Added a GROMOS11 Reader (PR #4294) |
| 32 | + |
| 33 | +#### Changes: |
| 34 | +* Added `mda_xdrlib` as a core dependency to replace the now deprecated Python `xdrlib` code (PR #4271) |
| 35 | +* ConverterBase has been moved to `MDAnalysis.converters.base` (PR #4253) |
| 36 | +* `networkx` is now an optional dependency of MDAnalysis (PR #4331) |
| 37 | +* `BioPython` is now an optional dependency of MDAnalysis (PR #4332) |
| 38 | +* Results for WatsonCrickDist nucleic acids analysis are now stored in `analysis.nucleicacids.WatsonCrickDist.results.distances` (PR #3735) |
| 39 | + |
| 40 | +#### Deprecations: |
| 41 | +* Importing ConverterBase from `MDAnalysis.coordinates.base` will not be possible after MDAnalysis 3.0 (PR #4253) |
| 42 | +* Deprecation with intent of removal in MDAnalysis v3.0 of the X3DNA legacy code (PR #4333) |
| 43 | +* Deprecation with intent of removal in MDAnalysis v3.0 of the TRZ reader and writer (PR #4335) |
| 44 | +* Deprecation with intent of removal in MDAnalysis v3.0 of the `MDAnalysis.lib.util.which` method (PR #4340) |
| 45 | +* The `asel` argument of the `timeseries` attribute of Readers is now deprecated in favour of the `atomgroup` argument (PR #4343) |
| 46 | +* 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) |
| 47 | +* In `nucleicacids.WatsonCrickDist` the result `results.pair_distances` was deprecated and will be removed in 3.0.0; use `results.distances` instead (PR #3735) |
| 48 | + |
| 49 | +## New Contributors |
| 50 | +* [@jennaswa](https://github.com/jennaswa) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4289 |
| 51 | +* [@Sumit112192](https://github.com/Sumit112192) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4346 |
| 52 | +* [@HeetVekariya](https://github.com/HeetVekariya) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4359 |
| 53 | +* [@JoStoe](https://github.com/JoStoe) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4292 |
| 54 | +* [@ljwoods2](https://github.com/ljwoods2) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4366 |
| 55 | + |
4 | 56 | ## Release 2.6.1 of MDAnalysis |
5 | 57 |
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6 | 58 | 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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