Merge branch 'develop' into stderr-skip

.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
 

.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: |

doc/source/AUTHORS

@@ -40,3 +40,4 @@ Chronological list of authors
 2023
   - Jan Domanski
   - Micaela Matta
+  - Mike Henry

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.

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",

doc/source/scripts/tests/snapshot/__snapshots__/test_gen_format_overview_classes.ambr

@@ -211,6 +211,12 @@
       '✓',
       '✓',
     ]),
+    list([
+      ':ref:`TRC <TRC-format>`',
+      'GROMOS11 trajectory file',
+      '',
+      '',
+    ]),
     list([
       ':ref:`TRJ <TRJ-format>`',
       'AMBER ASCII trajectories',
@@ -593,6 +599,14 @@
       '✓',
       '',
     ]),
+    list([
+      ':ref:`TRC <TRC-format>`',
+      'GROMOS11 trajectory file',
+      '',
+      '✓',
+      '✓',
+      '',
+    ]),
     list([
       ':ref:`TRJ <TRJ-format>`',
       'AMBER ASCII trajectories',