John Chodera
John Chodera
A great deal of developer time is spent waiting for CI to pass. Would it make sense to switch to [mambaforge](https://github.com/conda-forge/miniforge#mambaforge), a combination of [mamba](https://github.com/mamba-org/mamba) (a very fast version of...
It would be useful to add some sort of unique token or phrase somewhere in `devtools/` (where users are unlikely to extensively change or delete things) to better track deployments...
I wonder if there might be some way to help automate the update process for ensuring that repos created with the cookiecutter remain up to date with the latest best...
As the cookiecutter is continually being updated, it might make sense to start cutting releases so that projects using the cookiecutter have a clear cookiecutter version they are based on,...
This repo is getting to be pretty large (>1.2GB), so I'd like to suggest we break it up into smaller repos or put files on osf.io and link from here...
It would be super useful to have an easy way to map between FAH project numbers (like 14573) and setup files here just so we can spot-check things and easily...
**Is your feature request related to a problem? Please describe.** Currently, writing many molecules to a file requires (1) conversion to JSON as a string, then (2) writing the string...
We should migrate the [thermodynamic trailblazing code](https://github.com/choderalab/yank/blob/master/Yank/pipeline.py#L2282-L2648) to [openmmtools](http://github.com/choderalab/openmmtools), along with the relevant tests of this functionality. We could use this for relative and absolute free energy calculations. cc @dominicrufa
@mikemhenry : If you can help us update the CI for the yank repo at some point, that would be fantastic.
``` /Users/choderaj/miniconda/lib/python3.6/site-packages/yank/experiment.py:1168: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. ``` See: https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation