debug slow python 3.13 tests #1468
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1468 +/- ##
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- Coverage 95.18% 92.52% -2.67%
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Files 165 165
Lines 12572 12575 +3
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- Hits 11967 11635 -332
- Misses 605 940 +335
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Member
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@atravitz - by any chance, is a different version of openmm being pulled by the slower tests? |
Contributor
Author
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@IAlibay no, I'm not seeing any version discrepancies between the builds other than python/cpython. |
Contributor
Author
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It looks like this is not specifically a ubuntu or python 3.13 thing - test runtime appears to be highly variable, although it's almost always ubuntu python 3.13 that times out. for example: https://github.com/OpenFreeEnergy/openfe/actions/runs/16913427313/job/47921037084 screenshot bc the data will get cleared: 
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Contributor
Author
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thanks @IAlibay for the speed-up! I added some comments so we (hopefully) remember why we did this. merge when you're happy. |
IAlibay
approved these changes
Aug 13, 2025
atravitz
commented
Aug 13, 2025
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No API break detected ✅ |
atravitz
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Sep 23, 2025
* Turn off minimization when we do a dry run --------- Co-authored-by: IAlibay <IAlibay@users.noreply.github.com>
atravitz
added a commit
that referenced
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Oct 7, 2025
* update partial charge tests now that a production NAGL model is available (#1506) * update tests now that a production NAGL model is available * fix mock * clean up mocking * add nagl test news item * debug slow python 3.13 tests (#1468) * Turn off minimization when we do a dry run --------- Co-authored-by: IAlibay <IAlibay@users.noreply.github.com> * update quickrun execution docs and add MPS link (#1483) * add jq cookbook (#1488) * add jq code blocks * use tutorial data * news * debug docs build (#1489) * don't build openmm * mambaforge->miniconda for rtd * artifically small build for debugging * dont build env * just build python * add channels * add sphinx packages to env * add all non-openfe-ecosystem deps * remove shim channel * add openfe package * add everything except openmm and toolkit * add openmm * add openff-toolkit * only openff-toolkit * try openff-toolkit-base * try latest openff * everybody back in * build without openmm * build with openff-toolkit-base * bump rtd * add pip build * remove any openff-toolkit * build w/o openmm * add pip install * build everything without pip install * try no deps * try custom build * only python and pip * try openfe-toolkit-base * add temp deps for build with openff-toolkit-base * add temp deps for build with openff-toolkit-base * mock imports * dont mock with toolkit base * bump toolkit version * Revert "bump toolkit version" This reverts commit 6e3108a. * add mocks * try pinnint to toolkit-base 0.13.0, no mocks * back to >= 0.13.0 toolkit to make sure it wasn't a fluke * mock imports * add pipe example for jq (#1505) * add pipe example for jq * pin to docutil 0.20 * try to avoid memory error * debug rtd build memory error (#1510) * try mambaforge build * Revert "try mambaforge build" This reverts commit 683e07f. * try explicit build * try removing ambertools * use the right env * just add gufe pip install back * add back openfe eco packages * mock py3dmol * add note for pip installs * fix quote * temporarily resort to SettingsBaseModel to get build * specific imports * dont use base settings placeholder * temp pin numpy (#1542) * Removing unnecessary limit on resids (#1539) * Removing unnecessary limit on resids indices gathering * Updated CHANGELOG for 1.6.1 * add summary * update docs theme (#1545) * adding new branding assets * remove images * update theme branch * CantinaPurple accent * lowercase convention * updating text * remove dark mode for now * fix sidebars * fix formatting * capitalization * don't break spaces * bump ci * favicon! * whitespace :( * pin to sphinx release * pin to gufe 1.6.1 * move env info before test imports * bump single file installer to 3.12.11 to match colab --------- Co-authored-by: IAlibay <IAlibay@users.noreply.github.com> Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
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