[theamk]

You are doing something right, author does some pretty unusual things:

- Setup custom kernels in Jupyter Notebook

- Hardlink the environments, then install same packages via pip in one and conda in others

- install conda inside conda (!!!) and enter nested environment

- Use tox within conda

I believe as long as you treat the environments as "cattle" (if it goes bad, remove it and re-create from yaml file), you should not have any problems. It's clearly not the case of for the post's author though.

[fluorinerocket]

Yep nuke the bad env and start over. Conda is great only problem are when a package is not available on conda forge or you have to compile and install with setup.py. But then you can blow the env away and start over.