ENH: support tpx 133 (GMX 2024.1)

[tylerjereddy]

• 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 internally.

• This patch used convert-tpr with GMX 2024.1 to mimic Jonathan's changes from Support TPR files produced by gromacs 2023 #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.

• Note that I did not update the documentation or the CHANGELOG, fell free to push that in here if you're confident of the various tpx generation things, etc.

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

Developers certificate of origin

• I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

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📚 Documentation preview 📚: https://mdanalysis--4523.org.readthedocs.build/en/4523/

[pep8speaks]

Hello @tylerjereddy! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file package/MDAnalysis/topology/tpr/setting.py:

Line 41:80: E501 line too long (83 > 79 characters)

• In the file testsuite/MDAnalysisTests/datafiles.py:

Line 423:80: E501 line too long (90 > 79 characters)

Comment last updated at 2024-03-25 22:24:16 UTC

[github-actions]

Linter Bot Results:

Hi @tylerjereddy! Thanks for making this PR. We linted your code and found the following:

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.63%. Comparing base (0582265) to head (26098bb).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4523      +/-   ##
===========================================
- Coverage    93.65%   93.63%   -0.03%     
===========================================
  Files          168      180      +12     
  Lines        21215    22294    +1079     
  Branches      3908     3908              
===========================================
+ Hits         19869    20875    +1006     
- Misses         888      961      +73     
  Partials       458      458              

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[IAlibay]

Thanks for working on this @tylerjereddy - I was also looking at this a few weeks back (got as far as John telling me to use convert-tpr 😅) and got distracted, I'll try to give it a review as soon as possible.

[orbeckst]

If the test files are TPR 133 and all tests pass then that looks good enough for me.

We'd just need the docs + CHANGELOG. Could you quickly add those in, please?

[tylerjereddy]

We'd just need the docs + CHANGELOG. Could you quickly add those in, please?

@orbeckst

I pushed in what I could, but as I noted above, I don't know how to find out the tpx generation of a .tpr file (not the same as the tpr version). Comically, when I asked Google Gemini, it told me to use MDAnalysis to do it, presumably because it had slurped up this exact docs table. I just put in ?? for now--IMO it is the .tpr version proper that really means something to folks anyway.

[IAlibay]

@tylerjereddy if I remember correctly this is the enum class that gets used for the generation: https://gitlab.com/gromacs/gromacs/-/blob/main/src/gromacs/fileio/tpxio.cpp?ref_type=heads#L190

Should still be 28 I think? (sorry it's late and I'm not in a C++ frame of mind)

[IAlibay]

Just briefly putting this here because it's something @jbarnoud mentioned in a DM but I didn't get a chance to dig into it - apparently there are (edit: ITP?) input files for "all bonded" and "virtual sites" TPR tests somewhere that might need adding too?

[tylerjereddy]

apparently there are input files for "all bonded" and "virtual sites" TPR tests somewhere that might need adding too?

pretty sure I did that in the diff already, I'll see if I can dig up the obscure generation thing

[IAlibay]

apparently there are input files for "all bonded" and "virtual sites" TPR tests somewhere that might need adding too?

pretty sure I did that in the diff already, I'll see if I can dig up the obscure generation thing

🤦🏾‍♂️ Sorry I'm not paying attention - I saw the dummy one but somehow my brain just ignored it completely

[tylerjereddy]

Ok, I added the generation as 28 based on a fresh compilation of GROMACS 2024.1 with this adjustment:

--- a/src/gromacs/fileio/tpxio.cpp
+++ b/src/gromacs/fileio/tpxio.cpp
@@ -1034,6 +1034,7 @@ static void do_inputrec(gmx::ISerializer* serializer, t_inputrec* ir, int file_v
 
     ir->tpxFileVersion = file_version;
 
+    fprintf(stderr, "****** Note: tpx_generation %d\n", tpx_generation);
     if (file_version != tpx_version)
     {
         /* Give a warning about features that are not accessible */

Then used one of the .tpr files here as follows:

gmx mdrun -s dummy_2024.tpr

which includes in its output:

<snip>
Reading file dummy_2024.tpr, VERSION 2024.1-spack (single precision)
****** Note: tpx_generation 28
****** Note: tpx_generation 28
<snip>