ENH: support tpx 134 (GMX 2024.4) #4866
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* Fixes MDAnalysisgh-4855. * Add support for reading topology data from `.tpr` files produced by GROMACS 2024.4, corresponding to tpx version `134`. * My approach was similar to the one I used in MDAnalysisgh-4523, except for two things: 1) I retrieved the current generation (`28`) from a `print` in our own binary parser rather than rebuilding GMX from source with added `printf`, and more importantly 2) I had to add some shims because the `.tpr` format has changed. * With regard to the additional field data now stored in the `.tpr` format, I was involved in reviewing it upstream at: https://gitlab.com/gromacs/gromacs/-/merge_requests/4544. You can see that the changes related to the MARTINI functional form made it into the `v2024.4` tag i.e., here: https://gitlab.com/gromacs/gromacs/-/blob/v2024.4/src/gromacs/gmxpreprocess/convparm.cpp?ref_type=tags#L372
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Hello @tylerjereddy! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2024-12-27 17:25:12 UTC |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #4866 +/- ##
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- Coverage 93.65% 93.63% -0.03%
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Files 177 189 +12
Lines 21779 22853 +1074
Branches 3064 3067 +3
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+ Hits 20398 21399 +1001
- Misses 929 1002 +73
Partials 452 452 ☔ View full report in Codecov by Sentry. |
hmacdope
requested changes
Dec 27, 2024
tanishy7777
reviewed
Dec 27, 2024
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I was going through this PR and I am not able to understand why u added an elif for fver>=134. I am a bit new to this repo.
* Remove the periods (`.`) from Tyler's identifier in the `CHANGELOG` to satisfy reviewer comments.
hmacdope
approved these changes
Dec 28, 2024
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Fixes Error: Your tpx version is 134, which this parser does not support, yet #4855.
Add support for reading topology data from
.tprfiles produced by GROMACS 2024.4, corresponding to tpx version134.My approach was similar to the one I used in ENH: support tpx 133 (GMX 2024.1) #4523, except for two things: 1) I retrieved the current generation (
28) from aprintin our own binary parser rather than rebuilding GMX from source with addedprintf, and more importantly 2) I had to add some shims because the.tprformat has changed.With regard to the additional field data now stored in the
.tprformat, I was involved in reviewing it upstream at: https://gitlab.com/gromacs/gromacs/-/merge_requests/4544. You can see that the changes related to the MARTINI functional form made it into thev2024.4tag i.e., here:https://gitlab.com/gromacs/gromacs/-/blob/v2024.4/src/gromacs/gmxpreprocess/convparm.cpp?ref_type=tags#L372
The new
.tprbinary assets added here were produced usinggmx convert-tpras I did for previous adjustments of this type, and I did confirm that the tests failed before adding the source code shims inutils.py.PR Checklist
Developers certificate of origin
📚 Documentation preview 📚: https://mdanalysis--4866.org.readthedocs.build/en/4866/