make gather septop/abfe output headers accurately reflect error type
#1712
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No API break detected ✅ |
atravitz
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gather septop/abfe output headers accurately reflect error type
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## feat/cli-gather-improvements #1712 +/- ##
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- Coverage 93.10% 93.09% -0.01%
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Files 189 189
Lines 16526 16539 +13
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+ Hits 15386 15397 +11
- Misses 1140 1142 +2
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IAlibay
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Dec 2, 2025
openfecli/commands/gather_abfe.py
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| error_name = "MBAR uncertainty (kcal/mol)" | ||
| else: | ||
| error_func = _error_std | ||
| error_name = "uncertainty (kcal/mol)" |
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Thoughts on being more explicit here? Maybe "STDEV uncertainty" or something like that?
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IAlibay
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| unc_col_name = "MBAR uncertainty (kcal/mol)" | ||
| else: | ||
| error_func = _error_std | ||
| unc_col_name = "std dev uncertainty (kcal/mol)" |
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I didn't see any of the test files update with this, are we not testing this code path?
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they're updated! I think you just saw this between commit pushes.
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I think there's a more robust way to do this, but this is at least better than not having mbar/stdev labels. |
IAlibay
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Dec 2, 2025
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…ort (#1710) * feat: support `openfe gather` for septop (#1638) * copy septop analysis notebook over * add todos * add plan and test * format * add failing tests * comment out secondary tests * add cli tmp * clean up imports * fix type hints in gather.py * test passes for gather raw * test passes for ddg * tests pass for dg * pull more error handling into septop * condense code a bit * MBAR uncertainty * remove planning stub * Revert "MBAR uncertainty" This reverts commit bf32aa3. * format * test with tolerances * precommit format * remove accidentally committed file * Apply suggestions from code review Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> --------- Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> * feat: add abfe gathering support first draft (#1686) * add abfe MVP with tests * Apply suggestions from code review Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> * fix incorrect var name * fix abfe legs extraction * fix merge bug * remove unused import --------- Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com> * gather: fix septop rounding (#1696) * only apply precision rounding at the end * clean up code * gather: update names parsing (septop and abfe) (#1698) * update abfe names parsing * update septop names parsing * add todo * get names from alchemical_components * remove todo * gather: refactor/unify rounding behavior (#1697) * format septop outputs with format_df_with_precision * only apply precision rounding at the end * update gather abfe formatting to use format_df_with_precision * remove unused import * switch back to checking final outputs for abfes * clean up code * add rounding for dg mle * simplify code * gather: unify code structure between rbfe, septop, & abfe (#1700) * format septop outputs with format_df_with_precision * only apply precision rounding at the end * update gather abfe formatting to use format_df_with_precision * remove unused import * switch back to checking final outputs for abfes * clean up code * add rounding for dg mle * simplify code * make gather_septop.py code more similar to gather.py * make gather_abfe.py code more similar to gather.py * remove unused function * add stdout message for experimental gathering support (#1703) * add warnings for experimental gathering * use click to make output look nicer, not a true warning * add warning text * make yellow * add tests * remove unused code * add news item * speed up names gathering * names should always return str * add single repeat tests for abfe and septop * remove unused imports * make `gather septop/abfe` output headers accurately reflect error type (#1712) * gather septop/abfe output headers accurately reflect error type * split into func * label all uncertainty columns more specifically * add docstring * update test data * update error calculation --------- Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
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in response to #1710 (comment)
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newsentry, or the changes are not user-facing.pre-commit.ci autofixbefore requesting review.Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).
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