Documentation for installing MUSE (chapter 3.0 to 3.3 in the documentation) should be written clearer

[HarmonicReflux]

The documentation can be improved for clarity.

For example, 3.2 talks about pipx. Then pyenv is dealt with as a subsection of 3.2, but one can perfectly make use of pyenv without ever touching pipx. For example at the moment we have: 3.2. pipx-based installation 3.2.2.1. Installing pyenv

Then, virtual environments are dealt with again in section 3.3, however, it covers conda only. Again, using pyenv along venv, one can perfectly create virutal environments without ever touching conda. Hence, it is confusing to read and sorting chapter 3 better into into clearly separate parts would help clarity.

Specifically, documentation for conda and pyenv should be considered separately.

[alexdewar]

This seems sensible on the face of it.

What does everyone else think? @dalonsoa @tsmbland

[dalonsoa]

I agree that is confusing, but a few notes on this:

• pipx will create a virtual environment to run the tools it installs based on the python version that was used to install pipx to start with, unless you specify another version and that other version is system wide available. Now muse works with Python 3.12, so with any modern python version, but before the last changes, valid python versions were quite constrained. Making sure that the version of python it was being used was a valid one prior to installign pipx was necessary. Hence, including the section on pyenv there. But I agree it will be better in a dedicated section.
• Eitherpyenv+venv or conda can be used to create a virtual environment appropriate for MUSE, so while obviously you don't need conda when using the first approach, it is a perfectly reasonable approach to setup MUSE. Again, I agree the documentation can be organised better, but I think that both approaches should be described in the virtual environments sections.