Perses

Bugfix release.

• Added support for reading input files (ex yaml, sdf, pdbs) from AWS, GCP, and Azure. See the documentation for cloudpathlib for how to setup authentication. Currently only reading the yaml from S3 is unit tested (ie perses-cli --yaml s3://perses-testing/template_s3.yaml), but other cloud providers and input files should work. AzureBlobPath, S3Path and GSPath are supported URI endpoints. Please report any issues on our issue tracker! by @mikemhenry in https://github.com/choderalab/perses/pull/1073
• CUDA platform was hardcoded in geometry engine, generating performance issues by not clearing openmm contexts correctly. Fixed by defaulting to using the faster CPU platform (for the geometry engine) and explicitly deleting context variables after they are used. by @ijpulidos in https://github.com/choderalab/perses/pull/1091
• Set aromatic draw style to OEAromaticStyle_Circle in atom mapper rendering by @mikemhenry in https://github.com/choderalab/perses/pull/1103
• Ligands with atoms changing constrained status were not being handled by mapping proposal. Atoms in bonds that change constrained/unconstrained to unconstrained/constrained during the transformation are now demapped. by @ijpulidos in https://github.com/choderalab/perses/pull/1125
• Now that upstream openmmtools is storing velocities on checkpoint, the small molecule transformation pipeline does not reassign velocities on resume by default. Instead, the velocities are read from the checkpoint file. by @ijpulidos in https://github.com/choderalab/perses/pull/1133
• CLI workflow for replica exchange now uses the faster LangevinMiddleIntegrator via the LangevinDynamicsMove. Tests were updated to reflect the changes. by @ijpulidos in https://github.com/choderalab/perses/pull/1138
• Add opencontainers image-spec to Dockerfile by @SauravMaheshkar in https://github.com/choderalab/perses/pull/1139
• Updated to support openff-toolkit 0.11, which included API-breaking changes. by @jchodera in https://github.com/choderalab/perses/pull/1128
• Make solute-only trajectory writing optional. This option is controlled by the atom_selection option in the yaml file. The syntax uses the MDTraj selection syntax, e.g. not water @mikemhenry in https://github.com/choderalab/perses/pull/1185
• Users can now specify solvent model for simulations using the solvent_model field in the input YAML file. Supported values are tip3p, spce, tip4pew, tip5p, and swm4ndp (polarizable) by @ijpulidos in https://github.com/choderalab/perses/pull/1202

• Document setting ionic_strength in examples/new-cli/template.yaml by @mikemhenry in https://github.com/choderalab/perses/pull/1104
• Add reproducible version of COVID Moonshot example anyone can run as an example by @jchodera in https://github.com/choderalab/perses/pull/1145
• Speed up RTD env generation by @mikemhenry in https://github.com/choderalab/perses/pull/1105
• Fix documentation string for ProteinMutationExecutor, using False for reassign_velocities parameter. by @ijpulidos in https://github.com/choderalab/perses/pull/1169
• Document how to control the log level in the CLI by @mikemhenry in https://github.com/choderalab/perses/pull/1198

• Fixes bug where if a : was in a key, we could not override the argument in our perses-cli. @mikemhenry in https://github.com/choderalab/perses/pull/1062
• Resolves #1157 objects serialized with utils.data.serialize now will be compressed with bzip2 or gzip depending on file name (.gz and .bz2, respectively) by @mikemhenry in https://github.com/choderalab/perses/pull/1163
• Fixes for new openmmtools 0.23.0 by @mikemhenry in https://github.com/choderalab/perses/pull/1203

• add python 3.10 to CI by @mikemhenry in https://github.com/choderalab/perses/pull/1080
• skip broken tests by @mikemhenry in https://github.com/choderalab/perses/pull/1074
• Feat/fix ssl gpu error by @mikemhenry in https://github.com/choderalab/perses/pull/1095
• Previously the keyword argument save_freq in validate_endstate_energies_md was not functional and the value of 250 steps was hard coded. Now, save_freq works and has a default value of 250 steps. by @mikemhenry in https://github.com/choderalab/perses/pull/1101
• fix issue with test asset name by @mikemhenry in https://github.com/choderalab/perses/pull/1102
• Examples and benchmarks template input files now run vacuum, solvent and complex phases in order. by @ijpulidos in https://github.com/choderalab/perses/pull/1122
• Add openmm 8 to testing matrix by @mikemhenry in https://github.com/choderalab/perses/pull/1124
• Fix resume tests to use new CLI (resolves issue #1150) by @mikemhenry in https://github.com/choderalab/perses/pull/1151
• Avoid testing non-examples in CI by @ijpulidos in https://github.com/choderalab/perses/pull/1164
• only run dev with newest python version by @mikemhenry in https://github.com/choderalab/perses/pull/1165
• remove outdated recipe by @mikemhenry in https://github.com/choderalab/perses/pull/1159
• update release process by @mikemhenry in https://github.com/choderalab/perses/pull/1162
• add env caching to CI by @mikemhenry in https://github.com/choderalab/perses/pull/1178
• Skip failing openmm 8 tests by @mikemhenry in https://github.com/choderalab/perses/pull/1186
• Add small molecule repex consistency tests by @zhang-ivy in https://github.com/choderalab/perses/pull/1065
• Fix RESTTopologyFactory test by @zhang-ivy in https://github.com/choderalab/perses/pull/1188
• enable merge queue by @mikemhenry in https://github.com/choderalab/perses/pull/1206
• Using default online analysis interval in GPU repex tests by @ijpulidos in https://github.com/choderalab/perses/pull/1207

• @SauravMaheshkar made their first contribution in https://github.com/choderalab/perses/pull/1139

Full Changelog: https://github.com/choderalab/perses/compare/0.10.1...0.10.2