Virtualenv issues when queueing jobs

[jrs65]

If you submit a job while in one virtual environment to run in a different environment (via the venv key) it will run the linter against the first one even though it should be running against the second one.

[ljgray]

https://bugs.python.org/issue46473
python/importlib_metadata#364

Basically, importlib import_module ignores any egg-link files, so any of our modules which are linked that way won't be checked and importlib will fall back to the active venv path. Explicitly adding the code directories (i.e. ../code/ch_pipeline) gets past this issue, but really we just need to modify how some of our packages are installed to avoid egg-link files in the venv site-packages.

As far as I can tell, only ch_pipeline and the various chimedb packages use egg-link files.

[ljgray]

It seems like the logging uses class names from the current active venv rather than the venv that we're running the pipeline in. For example, if we have class1 in the venv we want to use, and in the active venv we've renamed it class2 and aliased class1 = class2, logs will display class2 even though that doesn't exist in the venv we're running in.