Fix/issue 1196 #1229
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Fix/issue 1196 #1229
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* CI minor fixes. Allow codecov to fail. * bump ci --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
ijpulidos
requested changes
Aug 23, 2023
| @@ -753,7 +753,7 @@ def run_setup(setup_options, serialize_systems=True, build_samplers=True): | |||
| def run(yaml_filename=None, override_string=None): | |||
| cli_tool_name = sys.argv[0].split(os.sep)[-1] | |||
| if cli_tool_name == "perses-relative": | |||
| warnings.warn("perses-relative will be removed in 0.11, see https://github.com/choderalab/perses/tree/main/examples/new-cli for new CLI tool", FutureWarning) | |||
| warningg.warn("perses-relative will be removed in 0.11, see https://github.com/choderalab/perses/tree/main/examples/new-cli for new CLI tool", FutureWarning) | |||
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lmao, yes, I was vim-ing
mikemhenry
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Aug 23, 2023
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Sep 14, 2023
* run CI on new 0.10.x branch (#1212) * run CI on new 0.10.x branch * Update .github/workflows/CI.yaml Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> --------- Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> * print perses version on startup (#1176) * Update comments in `RESTCapableHybridTopologyFactory` (#1189) * update comments * bump ci --------- Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> * use python executable from env (#1174) * use python executable from env * run tests using the shell * parmed 4 seems to be giving us some issues * actually I think we want the newer parmed * pin pymbar for now * ooof, parmed != pymbar * add some more debugging to figure out how we are getting old parmed * Update devtools/conda-envs/test_env.yaml * see if shell=True fixes it * removed parmed by mistake * Support pymbar 4 (#1173) * switch to using pymbar 3 & 4 support from openmmtools * fix typo on import * fix yaml * switch to using pymbar 4 * missed a pymbar import * missed another one * bump ci * missed a import * go back to how it was * Update devtools/conda-envs/test_env.yaml --------- Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> * Remove example testing (#1214) * Store initial and final topologies for all phases -- small molecule pipeline (#1210) * Initial and final topologies serialized per phase. * Using properties instead of private attrs. * Fix test * Remove uneeded code/attributes * bump ci * Store phase topologies separately * Fix tests. vacuum topologies expected. * Better docstring. --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> * Improve docker building (#1200) * Added note about example for adding oe license * make docker file much simpler * build images in CI * forgot to add conda-forge * fix permissions on a step * get oe_license file mounted in docker container * mount path must be absolute * setup singulairty to test + fix testing on docker image * add some testing deps to the image * add -v for tests, fix envar * tests are failing, want to test rest of pipeline * use latest openmm version * hardcode perses version for now * bump ci * make sure we can make openeye dir * support a dev build as well * don't hardcode value * fix name clash * forgot to add conda-forge * bump ci * test docker image and fix missing deps * install ps * also push latest tag * don't build on tag since the conda-forge package won't exist yet * don't test the examples * Remove docker deb build, we can do these ourselves * better document container use * build a latest version for apptainer * build with 11.2 to make things more compatable * skip docker test to see if other bits build okay * see if I can get the step to fail if there is an error * skip docker tests to make sure apptainer builds okay * Add mpiplus and mpi4py to docker image * give correct path to oe license * add mpi stuff to docker * clean up diskspace before build * skip tests for singularity now that the only failures come from a package bug * Clean examples -- CLI protein-ligand example for Tyk2 (#1223) * Improving examples dir structure and readme * Adding Tyk2 CLI example * removing new-cli/ripk2 example (deprecated) * fix typo for link * Clarify tyk2 cli example docs * Realtime analysis interval to default to checkpoint interval (#1227) * CI miscellaneous fixes (#1217) * CI minor fixes. Allow codecov to fail. * bump ci --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> * Changing offline freq default to checkpoint interval * Fixing input yaml for example * commenting offline-freq param --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> * MPI example with dipeptide mutation (#1228) * peptide mutation MPI example added * better documentation of motivation * Fix/issue 1194 (#1230) * set cutoff distance in sterics_custom_nonbonded_force * matching cutoff for custom forces. Improving logic. * test for HTF nonbonded cutoff --------- Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> * Fix/issue 1196 (#1229) * CI miscellaneous fixes (#1217) * CI minor fixes. Allow codecov to fail. * bump ci --------- Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com> * added dels to contexts * Update perses/app/setup_relative_calculation.py --------- Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> * Fix spectator support (#1233) * fix spectator support. Enabling test. * Test to run on GPU CI. * pin <4 for pymbar on GPU --------- Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com> Co-authored-by: Ivy Zhang <35546250+zhang-ivy@users.noreply.github.com>
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Description
Back ports some fixes from the OpenFE team.
Motivation and context
Resolves #1196
How has this been tested?
Change log
Explicitly deleted some sampler and energy contexts in
setup_relative_calculation.py