Mike Henry

I'm also in favor of using the `src/package_name` structure

Will the search still work if it is on github pages? readthedocs does some fancy indexing to make the search fast and useful https://docs.readthedocs.io/en/stable/development/search.html they do have all the code...

I also think we should add as many IDEs as possible to make things JustWork :tm: If a user needs/wants to add a file, `git` provides a pretty helpful hint:...

Related to https://github.com/MolSSI/cookiecutter-cms/issues/140 I've ran into the same issues

I am pro these changes, I think that we should aim to be adherent to python packaging best practices, which is to move away from setup.py. I understand that it...

I haven't tested provisioning with micromamba yet, but some data on just the difference in using mamba instead of conda in our CI is here: https://github.com/choderalab/perses/pull/850#issuecomment-906798324 | conda | mamba...

So I've seen nothing but support for this switch, and it will save literally tons of co2, so is there any reason to not do this @Lnaden ? Will you...

Added example notebook here [examples/NEQ_cycling_using_gufe_objects/NEQ_cycling_from_gufe_objs.ipynb](https://github.com/choderalab/perses/pull/1066/files#diff-0d224809db6f63815527c0731d8cdb1d92577c2516d1d982333fa5395ce35308) it is messy, but a start on the notebook that we will want to show people how to use the code in the PR.

Also you can either fix this in your PR, or merge this one in https://github.com/choderalab/pymbar/pull/510 to fix the RTD builds

Can do, I think using `Molecule.to_smiles()` does make the most sense for the key. I've ran into issue juggling different chem informatic toolkits so I think sticking to OpenFF makes...