Merge pull request #856 from choderalab/release/0.9.2

Release 0.9.2
choderalab · Aug 31, 2021 · 5c5a228 · 5c5a228
2 parents 2d39e8d + 159707e
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diff --git 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
@@ -11,15 +11,15 @@ 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
 
 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
@@ -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 <https://github.com/choderalab/perses/releases>`_.
 
+0.9.2 - Bugfix release
+-----------------------
+Bugfixes
+^^^^^^^^
+- (PR `#835 <https://github.com/choderalab/perses/pull/835>`_)
+ Write out YAML file after all options are parsed and set. Saved as YAML original file name + date + time. Resolves
+ `#817 <https://github.com/choderalab/perses/issues/817>`_.
+- (PR `#840 <https://github.com/choderalab/perses/pull/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 <https://github.com/choderalab/perses/pull/841>`_)
+ Minor improvements to PolymerProposalEngine.
+- (PR `#844 <https://github.com/choderalab/perses/pull/844>`_)
+ Minimal examples of amino acid (small molecule), protein-ligand and ligand mutations, with automated testing.
+- (PR `#849 <https://github.com/choderalab/perses/pull/849>`_)
+ Use an instance of ContextCache instead of the default global instance.
+ More info at `#613 (comment) <https://github.com/choderalab/perses/issues/613#issuecomment-899746348>`_.
+
+New features
+^^^^^^^^
+- (PR `#708 <https://github.com/choderalab/perses/pull/708>`_)
+ Create visualization module for generating PyMOL movies.
+- (PR `#834 <https://github.com/choderalab/perses/pull/834>`_)
+ Enable protein mutation transformations involving nonstandard amino acids, specifically: ASH, GLH, HID, HIE, HIP, LYN.
+- (PR `#838 <https://github.com/choderalab/perses/pull/838>`_)
+ Official Docker image hosted on docker hub ``docker pull choderalab/perses:0.9.2``.
+ Resolves `#832 <https://github.com/choderalab/perses/pull/832>`_.
 
 0.9.1 - Bugfix release
 -----------------------