ENH: support tpx 133 (GMX 2024.1) (#4523)

* ENH: support tpx 133 (GMX 2024.1)
* One of my postdocs (Emvia) needs parsing of newer
  `.tpr` files to work; we actually are using tpx version
  `130` internally, but that wasn't from a stable release,
  so I just went for `2024.1` and presumbly we can just use
  `convert-tpr` to "up-version" to the stable release version.
* This patch used `convert-tpr` with GMX `2024.1` to mimic
  Jonathan's changes from gh-4052, when we last bumped `tpx`
  version. The full testsuite passed for me locally at least, so
  maybe we'll be lucky enough to have another simple bump.
* DOC: PR 4523 revisions
* add `CHANGELOG` and TPR docs updates

package/CHANGELOG

@@ -15,11 +15,13 @@ The rules for this file:
 
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
-         ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder
+         ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
+         tyler.je.reddy
 
  * 2.8.0
 
 Fixes
+ * Add support for TPR files produced by Gromacs 2024.1
  * Remove mutable data from ``progressbar_kwargs`` argument in ``AnalysisBase.run()``
    (PR #4459)
  * Fix ChainReader `__repr__()` method when sub-reader is MemoryReader 

package/MDAnalysis/topology/TPRParser.py

@@ -66,6 +66,7 @@
    122        28             2021                 yes
    127        28             2022                 yes
    129        28             2023                 yes
+   133        28             2024.1               yes
    ========== ============== ==================== =====
 
 .. [*] Files generated by the beta versions of Gromacs 2020 are NOT supported.

package/MDAnalysis/topology/tpr/setting.py

@@ -38,7 +38,7 @@
 """
 
 #: Gromacs TPR file format versions that can be read by the TPRParser.
-SUPPORTED_VERSIONS = (58, 73, 83, 100, 103, 110, 112, 116, 119, 122, 127, 129)
+SUPPORTED_VERSIONS = (58, 73, 83, 100, 103, 110, 112, 116, 119, 122, 127, 129, 133)
 
 # Some constants
 STRLEN = 4096

testsuite/MDAnalysisTests/datafiles.py

@@ -82,14 +82,14 @@
     "TPR450", "TPR451", "TPR452", "TPR453", "TPR454", "TPR455", "TPR455Double",
     "TPR460", "TPR461", "TPR502", "TPR504", "TPR505", "TPR510", "TPR2016",
     "TPR2018", "TPR2019B3", "TPR2020B2", "TPR2020", "TPR2020Double",
-    "TPR2021", "TPR2021Double", "TPR2022RC1", "TPR2023",
+    "TPR2021", "TPR2021Double", "TPR2022RC1", "TPR2023", "TPR2024",
     "TPR510_bonded", "TPR2016_bonded", "TPR2018_bonded", "TPR2019B3_bonded",
     "TPR2020B2_bonded", "TPR2020_bonded", "TPR2020_double_bonded",
     "TPR2021_bonded", "TPR2021_double_bonded", "TPR2022RC1_bonded",
-    "TPR334_bonded", "TPR2023_bonded",
+    "TPR334_bonded", "TPR2023_bonded", "TPR2024_bonded",
     "TPR_EXTRA_2021", "TPR_EXTRA_2020", "TPR_EXTRA_2018",
     "TPR_EXTRA_2016", "TPR_EXTRA_407", "TPR_EXTRA_2022RC1",
-    "TPR_EXTRA_2023",
+    "TPR_EXTRA_2023", "TPR_EXTRA_2024",
     "PDB_sub_sol", "PDB_sub_dry",  # TRRReader sub selection
     "TRR_sub_sol",
     "XTC_sub_sol",
@@ -398,6 +398,7 @@
 TPR2021 = (_data_ref / 'tprs/2lyz_gmx_2021.tpr').as_posix()
 TPR2022RC1 = (_data_ref / 'tprs/2lyz_gmx_2022-rc1.tpr').as_posix()
 TPR2023 = (_data_ref / 'tprs/2lyz_gmx_2023.tpr').as_posix()
+TPR2024 = (_data_ref / 'tprs/2lyz_gmx_2024.tpr').as_posix()
 # double precision
 TPR455Double = (_data_ref / 'tprs/drew_gmx_4.5.5.double.tpr').as_posix()
 TPR460 = (_data_ref / 'tprs/ab42_gmx_4.6.tpr').as_posix()
@@ -417,7 +418,9 @@
 TPR2021_double_bonded = (_data_ref / 'tprs/all_bonded/dummy_2021_double.tpr').as_posix()
 TPR2022RC1_bonded = (_data_ref / 'tprs/all_bonded/dummy_2022-rc1.tpr').as_posix()
 TPR2023_bonded = (_data_ref / 'tprs/all_bonded/dummy_2023.tpr').as_posix()
+TPR2024_bonded = (_data_ref / 'tprs/all_bonded/dummy_2024.tpr').as_posix()
 # all interactions
+TPR_EXTRA_2024 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2024.tpr').as_posix()
 TPR_EXTRA_2023 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2023.tpr').as_posix()
 TPR_EXTRA_2022RC1 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2022-rc1.tpr').as_posix()
 TPR_EXTRA_2021 = (_data_ref / 'tprs/virtual_sites/extra-interactions-2021.tpr').as_posix()

testsuite/MDAnalysisTests/topology/test_tprparser.py

@@ -32,14 +32,14 @@
     TPR450, TPR451, TPR452, TPR453, TPR454, TPR455, TPR455Double,
     TPR460, TPR461, TPR502, TPR504, TPR505, TPR510, TPR510_bonded,
     TPR2016, TPR2018, TPR2019B3, TPR2020B2, TPR2020, TPR2020Double,
-    TPR2021, TPR2021Double, TPR2022RC1, TPR2023,
+    TPR2021, TPR2021Double, TPR2022RC1, TPR2023, TPR2024,
     TPR2016_bonded, TPR2018_bonded, TPR2019B3_bonded,
     TPR2020B2_bonded, TPR2020_bonded, TPR2020_double_bonded,
     TPR2021_bonded, TPR2021_double_bonded, TPR334_bonded,
-    TPR2022RC1_bonded, TPR2023_bonded,
+    TPR2022RC1_bonded, TPR2023_bonded, TPR2024_bonded,
     TPR_EXTRA_2021, TPR_EXTRA_2020, TPR_EXTRA_2018,
     TPR_EXTRA_2016, TPR_EXTRA_407, TPR_EXTRA_2022RC1,
-    TPR_EXTRA_2023,
+    TPR_EXTRA_2023, TPR_EXTRA_2024,
     XTC,
 )
 from MDAnalysisTests.topology.base import ParserBase
@@ -57,6 +57,8 @@
     TPR2020_double_bonded,
     TPR2022RC1_bonded,
     TPR2023_bonded,
+    TPR2024_bonded,
+    TPR_EXTRA_2024,
     TPR_EXTRA_2023,
     TPR_EXTRA_2022RC1,
     TPR_EXTRA_2021,
@@ -130,7 +132,8 @@ class TestTPRGromacsVersions(TPRAttrs):
                             TPR407, TPR450, TPR451, TPR452, TPR453, TPR454,
                             TPR455, TPR502, TPR504, TPR505, TPR510, TPR2016,
                             TPR2018, TPR2019B3, TPR2020, TPR2020Double,
-                            TPR2021, TPR2021Double, TPR2022RC1, TPR2023,])
+                            TPR2021, TPR2021Double, TPR2022RC1, TPR2023,
+                            TPR2024])
     def filename(self, request):
         return request.param
 
@@ -257,7 +260,7 @@ def test_all_impropers(topology, impr):
 @pytest.fixture(params=(
     TPR400, TPR402, TPR403, TPR404, TPR405, TPR406, TPR407, TPR450, TPR451,
     TPR452, TPR453, TPR454, TPR502, TPR504, TPR505, TPR510, TPR2016, TPR2018,
-    TPR2023,
+    TPR2023, TPR2024,
 ))
 def bonds_water(request):
     parser = MDAnalysis.topology.TPRParser.TPRParser(request.param).parse()