diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index dc564dca8..6f28e0d0f 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -16,7 +16,7 @@ dependencies: - numexpr - autograd - pymbar - - openmm >=7.3.1 + - openmm=7.5.1 - openmoltools # may need to sort out ambermini/ambertools/parmed dependencies (we don't want ambertools) - openmmtools # may need to sort out ambermini/ambertools/parmed dependencies - numba diff --git a/docker/README.md b/docker/README.md index a4539f033..2ef231e92 100644 --- a/docker/README.md +++ b/docker/README.md @@ -11,7 +11,7 @@ To do that use the `--mount` option. For example, if you have an `oe_license.txt` file in `$HOME/.openeye/`. ``` -$ docker run --rm --mount type=bind,source=$HOME/.openeye/,target=/perses/,readonly choderalab/perses:0.9.1 python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'" +$ docker run --rm --mount type=bind,source=$HOME/.openeye/,target=/perses/,readonly choderalab/perses:0.9.2 python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'" ``` ## GPU Support @@ -19,7 +19,7 @@ $ docker run --rm --mount type=bind,source=$HOME/.openeye/,target=/perses/,reado Pass the option `--gpus device=0` to use the host's GPU: ``` -$ docker run -it --rm --gpus device=0 --mount type=bind,source=$HOME/.openeye/,target=/openeye/,readonly choderalab/perses:0.9.1 python -m simtk.testInstallation +$ docker run -it --rm --gpus device=0 --mount type=bind,source=$HOME/.openeye/,target=/openeye/,readonly choderalab/perses:0.9.2 python -m simtk.testInstallation OpenMM Version: 7.5.1 Git Revision: a9cfd7fb9343e21c3dbb76e377c721328830a3ee diff --git a/docs/changelog.rst b/docs/changelog.rst index c1adeed68..d3056ba43 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -8,6 +8,33 @@ This section lists features and improvements of note in each release. The full release history can be viewed `at the GitHub perses releases page `_. +0.9.2 - Bugfix release +----------------------- +Bugfixes +^^^^^^^^ +- (PR `#835 `_) + Write out YAML file after all options are parsed and set. Saved as YAML original file name + date + time. Resolves + `#817 `_. +- (PR `#840 `_) + Minor improvements to point mutation executor. Make sure reverse geometry proposal is directly after forward proposal. + Fixes formatting problem for complex positions. +- (PR `#841 `_) + Minor improvements to PolymerProposalEngine. +- (PR `#844 `_) + Minimal examples of amino acid (small molecule), protein-ligand and ligand mutations, with automated testing. +- (PR `#849 `_) + Use an instance of ContextCache instead of the default global instance. + More info at `#613 (comment) `_. + +New features +^^^^^^^^ +- (PR `#708 `_) + Create visualization module for generating PyMOL movies. +- (PR `#834 `_) + Enable protein mutation transformations involving nonstandard amino acids, specifically: ASH, GLH, HID, HIE, HIP, LYN. +- (PR `#838 `_) + Official Docker image hosted on docker hub ``docker pull choderalab/perses:0.9.2``. + Resolves `#832 `_. 0.9.1 - Bugfix release -----------------------