From 06bbd504577d96ede2e0d0615d75756c7adef914 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Wed, 28 Jun 2023 11:12:38 -0700 Subject: [PATCH] release notes for 0.10.2 (#1208) * release notes for 0.10.2 * fix spelling mistakes, and add more documentation --- docs/changelog.rst | 63 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) diff --git a/docs/changelog.rst b/docs/changelog.rst index e6d4e5a0f..0d1a91d18 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -8,6 +8,69 @@ This section lists features and improvements of note in each release. The full release history can be viewed `at the GitHub perses releases page `_. +0.10.2 - Release +---------------- + +Bugfix release. + +Enhancements +^^^^^^^^^^^^ + +* Added support for reading input files (ex yaml, sdf, pdbs) from AWS, GCP, and Azure. See the documentation for [cloudpathlib](https://cloudpathlib.drivendata.org/stable/authentication/) 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 + +Documentation +^^^^^^^^^^^^^ +* 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 + +Bug Fixes +^^^^^^^^^ + +* 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 + +Testing/CI/Packaging +^^^^^^^^^^^^^^^^^^^^ +* 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 + +New Contributors +^^^^^^^^^^^^^^^^ + +* @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 + + 0.10.1 - Release ----------------