* Disable JAX acceleration by default
* ruff fmt
* add logging info
* fix url
* fix list
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* add example of error message
* added note about disabling jax acel by default
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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* 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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* 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
for more information, see https://pre-commit.ci
* 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: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
* SepTop docs improvements lambda schedule and restraint selection
* Remove set_openmm_threads_1 logic from test_septop_slow
* change femto acknowledgements
* update method docstring limitations
* Make sure we fail when we have virtual sites and reassign_velocities is False
* clean up usage of openmm imports
* clean up equil settings output indices so that it enforces all
* generate smc_off_B on the fly
* Update enforcement of all output indices
* Simulation overview unclear on if the same restraint is used between repeats
* Add test for output indices validation
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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* updates to cli from_json
* replacing dump instances with to_json
* Remove unnecessary imports of JSON_HANDLER
* addressing review
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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: David L. Dotson <dotsdl@gmail.com>
