add stdout message for experimental gathering support #1703
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atravitz
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## feat/cli-gather-improvements #1703 +/- ##
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IAlibay
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Dec 1, 2025
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IAlibay
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Eagerly approving, but a nice to have would be to test these warnings.
atravitz
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Dec 4, 2025
…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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