feat: experimental openfe gather-septop & openfe gather-abfe support
#1710
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* 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>
…-gather-improvements
…-gather-improvements
* 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>
* only apply precision rounding at the end * clean up code
* update abfe names parsing * update septop names parsing * add todo * get names from alchemical_components * remove todo
* 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
* 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
…-gather-improvements
* add warnings for experimental gathering * use click to make output look nicer, not a true warning * add warning text * make yellow * add tests
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1710 +/- ##
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- Coverage 95.47% 93.09% -2.39%
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Files 187 189 +2
Lines 16241 16536 +295
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- Hits 15506 15394 -112
- Misses 735 1142 +407
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atravitz
changed the title
IAlibay
requested changes
Dec 1, 2025
7 tasks
7 tasks
mikemhenry
changed the title
mikemhenry
changed the title
openfe gather-septop & openfe gather-abfe support
#1712) * gather septop/abfe output headers accurately reflect error type * split into func * label all uncertainty columns more specifically * add docstring * update test data
IAlibay
approved these changes
Dec 3, 2025
atravitz
changed the title
openfe gather-septop & openfe gather-abfe supportopenfe gather-septop & openfe gather-abfe support
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No API break detected ✅ |
This was referenced Dec 4, 2025
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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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