deprecation remove

[stevenhua0320]

Safe Merge these files

[sbillinge]

I checked the CI output and it looks as if we may be missing this deprecation fix in basebuilder.py: $ conda install -c conda-forge mongodb/usr/share/miniconda/envs/test/lib/python3.12/site-packages/regolith/builders/basebuilder.py:8: DeprecationWarning: Use xonsh.api.subprocessinstead ofxonsh.lib.subprocess.

Also there is a problem with the CI script that it is not loading mongod and running the mongo client tests. Please can you make an issue for that and we can fix it on a separate PR.

There are a bunch of other warning too, of issues with the exemplar datase (things not found). Let's also make an issue to clean that up, but it is low priority. Maybe a new person can do that under your guidance.