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* Add OpenMM RC to test config matrix. * Fixing typo.
* Comply to Openmm 8 global default values. Test when it doesn't. * Remove old conda-recipe, building on conda-forge now * cleanup CI * fix typo, and cancel concurrent jobs * openmm 7.7 didn't have 3.10 builds * Test behavior only for openmm>=8 * Fix typo in ci file * shorten job name * use dev as key name, not full openmm8 dev version * windows builds are broken with some python 3.8 versions * when testing windows 3.8, use 3.8.10 * also test py 3.9 --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* Make compatible with pymbar 3 and 4 * Try a different syntax * Fix syntax * Update openmmtools/multistate/multistateanalyzer.py Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> * fix pymbar install step * Update `.gitignore` * Update workflow * set env name to match file * fix package spec * remove pymbar pin in envs * Remove unused import * 🧙magic import fixes pymbar 3 🧙 * fix matrix * fix missing statistical_inefficiency conversion and raise an exception so we can figure out what we are trying to catch * missed a doc string * forgot to actually change the name * add note so we can figure out when this error can happen in the wild * lets try and see what excpetions we might be throwing * catught a few more api changes * consolidate all pymbar imports now * Support for both pymbar 3 and 4 in test function * looks like they should be attribute errors * log excpetion thrown * wrap EXP/exp in function to handle different return types * fix syntax error on raising exception * fix typo in function * trim down matrix and update actions/checkout to v3 * see if this magicly fixes the mac builds * looks like the problem is elsewhere * Pinning hdf5 version. Possible fix for macOS CI. --------- Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com> Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
Co-authored-by: Ivy Zhang <35546250+zhang-ivy@users.noreply.github.com> * Not need to retrieve energies for now Co-authored-by: Ivy Zhang <35546250+zhang-ivy@users.noreply.github.com> * Better name. Clarifying test. --------- Co-authored-by: Ivy Zhang <35546250+zhang-ivy@users.noreply.github.com>
…t. (#673) Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
…ter` (#676) * Fix docstring for analysis_particle_indices * Using version 2 for sphinx RTD * Update readthedocs.yml --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* update release notes * fix codecoverage * add module for testing coverage * add a few more args for coverage
* report mode GPU is in and write out gpu UUID * check for Exclusive_Process instead of Default * use try/except to be more robust * Update openmmtools/multistate/multistatesampler.py Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> * make the subprocess throw an exception if there is an error, fix logic in compute mode detection * make debug message more helpful * fix UnboundLocalError: local variable 'cuda_query_output' referenced before assignment * just check the error code * warn method has been deprecated since version 3.2 --------- Co-authored-by: EC2 Default User <ec2-user@ip-10-0-142-194.ec2.internal> Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com>
* Appending real time stats * Validating checkpoint and online analysis intervals * online analysis interval multiple of checkpoint interval in tests --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* Importing everything in utils module * Explicitly importing members of utils.py * sorted * missing comma :) --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* see if tests now pass on osx * commented out too much * run a subset of the tests * test if test_online_analysis_works is okay * see if test_online_analysis_stops works * see if test_real_time_analysis_yaml works * need to incriment cycles * still can run forever, needs to be an and * try more cycles * see if we get the issue in pymbar <4 * test if pymbar 3 fixes things * Start the online analysis early. Fixes MacOS test issues. * skip test on OSX * go back to pymbar 4 * fix syntax issue * clearly I don't use this function a lot * try longer if it is still not converging * skip bad test * See if online interval =2 works * set interations to 10 * enable all tests --------- Co-authored-by: pulidoi <2949729+ijpulidos@users.noreply.github.com>
* update self hosted runner to use new setup * switch to using pytest on gpu * Add token + don't fail if upload fails
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