diff --git a/.github/workflows/gh-ci-tests.yaml b/.github/workflows/gh-ci-tests.yaml index 92f3e9ed3..8f4968dc6 100644 --- a/.github/workflows/gh-ci-tests.yaml +++ b/.github/workflows/gh-ci-tests.yaml @@ -29,12 +29,19 @@ jobs: steps: - uses: actions/checkout@v3 + - name: Get current date + id: date + run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" + - name: setup micromamba uses: mamba-org/setup-micromamba@v1 with: environment-file: environment.yml environment-name: mda-user-guide cache-environment: true + cache-downloads: true + cache-environment-key: environment-${{ steps.date.outputs.date }} + cache-downloads-key: downloads-${{ steps.date.outputs.date }} create-args: >- hole2 diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 4e3acb7e4..e2a7c49fb 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -37,12 +37,20 @@ jobs: steps: - uses: actions/checkout@v3 + - name: Get current date + id: date + run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" + - name: setup micromamba uses: mamba-org/setup-micromamba@v1 with: environment-file: environment.yml environment-name: mda-user-guide cache-environment: true + cache-downloads: true + cache-environment-key: environment-${{ steps.date.outputs.date }} + cache-downloads-key: downloads-${{ steps.date.outputs.date }} + - name: install_deps run: | diff --git a/doc/source/AUTHORS b/doc/source/AUTHORS index 822227c2f..097338897 100644 --- a/doc/source/AUTHORS +++ b/doc/source/AUTHORS @@ -40,3 +40,4 @@ Chronological list of authors 2023 - Jan Domanski - Micaela Matta + - Mike Henry diff --git a/doc/source/releases.md b/doc/source/releases.md index 233e385ce..e2837008e 100644 --- a/doc/source/releases.md +++ b/doc/source/releases.md @@ -1,6 +1,58 @@ # 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. diff --git a/doc/source/scripts/core.py b/doc/source/scripts/core.py index 0867b6c31..c98aeaa62 100644 --- a/doc/source/scripts/core.py +++ b/doc/source/scripts/core.py @@ -32,6 +32,7 @@ "TNG": "Trajectory Next Generation file", "TOP": "AMBER topology file", "TPR": "GROMACS run topology file", + "TRC": "GROMOS11 trajectory file", "TRJ": "AMBER ASCII trajectories", "TRR": "GROMACS TRR trajectory", "TRZ": "IBIsCO or YASP binary trajectory", diff --git a/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_format_overview_classes.ambr b/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_format_overview_classes.ambr index b180d63ed..f90c19840 100644 --- a/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_format_overview_classes.ambr +++ b/doc/source/scripts/tests/snapshot/__snapshots__/test_gen_format_overview_classes.ambr @@ -211,6 +211,12 @@ '✓', '✓', ]), + list([ + ':ref:`TRC `', + 'GROMOS11 trajectory file', + '', + '', + ]), list([ ':ref:`TRJ `', 'AMBER ASCII trajectories', @@ -593,6 +599,14 @@ '✓', '', ]), + list([ + ':ref:`TRC `', + 'GROMOS11 trajectory file', + '', + '✓', + '✓', + '', + ]), list([ ':ref:`TRJ `', 'AMBER ASCII trajectories',