0.10.2

Bugfix release.

Enhancements

• 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 #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 #1091
• Set aromatic draw style to OEAromaticStyle_Circle in atom mapper rendering by @mikemhenry in #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 #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 #1133
• CLI workflow for replica exchange now uses the faster LangevinMiddleIntegrator via the LangevinDynamicsMove. Tests were updated to reflect the changes. by @ijpulidos in #1138
• Add opencontainers image-spec to Dockerfile by @SauravMaheshkar in #1139
• Updated to support openff-toolkit 0.11, which included API-breaking changes. by @jchodera in #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 #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 #1202

Documentation

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

Bug Fixes

• Fixes bug where if a : was in a key, we could not override the argument in our perses-cli. @mikemhenry in #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 #1163
• Fixes for new openmmtools 0.23.0 by @mikemhenry in #1203

Testing/CI/Packaging

• add python 3.10 to CI by @mikemhenry in #1080
• skip broken tests by @mikemhenry in #1074
• Feat/fix ssl gpu error by @mikemhenry in #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 #1101
• fix issue with test asset name by @mikemhenry in #1102
• Examples and benchmarks template input files now run vacuum, solvent and complex phases in order. by @ijpulidos in #1122
• Add openmm 8 to testing matrix by @mikemhenry in #1124
• Fix resume tests to use new CLI (resolves issue #1150) by @mikemhenry in #1151
• Avoid testing non-examples in CI by @ijpulidos in #1164
• only run dev with newest python version by @mikemhenry in #1165
• remove outdated recipe by @mikemhenry in #1159
• update release process by @mikemhenry in #1162
• add env caching to CI by @mikemhenry in #1178
• Skip failing openmm 8 tests by @mikemhenry in #1186
• Add small molecule repex consistency tests by @zhang-ivy in #1065
• Fix RESTTopologyFactory test by @zhang-ivy in #1188
• enable merge queue by @mikemhenry in #1206
• Using default online analysis interval in GPU repex tests by @ijpulidos in #1207

New Contributors

• @SauravMaheshkar made their first contribution in #1139

Full Changelog: 0.10.1...0.10.2

Benchmark data

Tyk2

From the latest data set in https://github.com/openforcefield/protein-ligand-benchmark (please note that it is not directly comparable to previous releases results)