Lily Wang

Great, thank you for those links!

pyyaml 6.0 (released 27 days ago) now raises an error upon loading without a Loader. You may need to start pinning dependencies in releases or update the code.

The loader in `analyze.py`: https://github.com/choderalab/yank/blob/aef24d9f413e646a3c4e65581198e0b67ae7a21b/Yank/analyze.py#L298-L301 I noticed it because openff-evaluator uses it :-)

> File "/root/miniconda3/lib/python3.9/site-packages/yank/analyze.py", line 297, in init raise RuntimeError(err_msg) RuntimeError: Cannot find analysis.yaml script in experiments I think the underlying cause of this error might be the lack of an...

3.5, I think 3.7 is when it got a lot better, and `numpy.typing` is only supported from 1.20.0 onwards, which is IIRC 3.7+.

@hmacdope please go ahead! [Here is a notebook](https://lilyminium.github.io/UserGuide/examples/analysis/volumetric/linear_density.html) that shows a bit of the current behaviour of the class. #2507 has some notes about the units of the output.

@1krishnasharma welcome to MDAnalysis! Are you a GSOC or Outreachy applicant? If so, please introduce yourself on our mailing list (https://groups.google.com/g/mdnalysis-devel) As a first step, have a look through the...

User guide points to a branch for now, but it's no work at all to make it point to a tag instead.

However, I'd probably branch the user guide for individual releases as it's more living than the codebase or docs.

@richardjgowers I'm not sure you can blindly enforce dtypes without also giving a preferred actual type; the dtype of string arrays is set to `object`, which an integer also is....