* Add absolute alchemical settings
* Expose settings in AFE protocols
* expose settings in septop
* Fix up settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* add some tests
* Add septop tests for sterics force settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Add news item
* add an extra parameterize option
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* 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 bf32aa3c6e.
* 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>
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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
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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
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Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
* Disable JAX acceleration by default
* ruff fmt
* add logging info
* fix url
* fix list
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* add example of error message
* added note about disabling jax acel by default
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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* updating install recommendations to prioritize miniconda and conda-lock
* fix formatting
* Update docs/installation.rst
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* recommend openfe test
* remove miniforge
* update language and clean up install instructions
* add link
* adding news item
* add back miniforge instructions at the end
* make testing its own section
* clearer language and formatting
* why is rst like this
* why is rst like this??
* one sentence per line!
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* add return type hints
* first pass at using pd dataframes
* add helper function
* it works but is ugly
* fix copy pasta
* do it better with pandas
* docstrings
* var names
* add docstring
* add example to docstring
* make string check more rigorous
* do we test this at all?
* start of logging improvements
* first pass at logging, worried about performance
* setup a base class + add type hints
* add placeholder url ref
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* update to new logging control
* Fix imports
* remove bit left over from being able to delete these log controlers
* looks like ... is used more than pass
* formatting fix
* Grab new format rule from main
* run ruff check --fix on conflicting files
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Added tests
* see if this fixes the doc build
* add back debugging code
* update openmm doc url
* add note about jax warning
* bump
* Remove debugging code to see if that fixes doc build
* ruff format
* Add url
* switch to using module instead of class w/ static methods
* Update docs/guide/troubleshooting.rst
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* ruff fixes
* Ruff fix
* Added news entry
* Refactor to move things to private namespace
---------
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* Create Pooch Cache
* not exactly sure where the cache will be on osx
* print some debug info
* update cache clearing action
* Debug osx location now
* allow errors when deugging
* lets see what is in the cache
* see if the cache actually works
* since the cache is in 2 different locations, we need to include the OS in the key
* test cache
* it works!!!
