[Python 3.9] Overhaul RMG-RMS Python-Julia dependencies (juliaup and pythoncall), Add Tests for Arkane Network Algorithms

[JacksonBurns]

Replace #2635, targeting a smaller improvement in Python minor version to keep better compatibility with our dependencies.

[JacksonBurns]

I'll update this comment with the path forward for each platform as the errors roll in.

All Platforms

There are Cython errors all over the place, namely because we have incremented Cython to:
cython 3.0.10
from
cython 0.29.33
...oh boy

M1 Macs

The following packages are outright missing, but without any conflicts:

    - nothing provides requested rmg::symmetry
    - nothing provides requested rmg::pyrms
    - nothing provides requested rmg::pydqed >=1.0.3
    - nothing provides requested rmg::pydas >=1.0.3
    - nothing provides requested conda-forge::muq
    - nothing provides requested conda-forge::julia =1.9.1*
    - nothing provides requested rmg::diffeqpy
    - nothing provides julia >=1.5.0 needed by pyjulia-0.6.0-pyhd8ed1ab_0

Anything in the RMG channel we can build for M1 macs, if it comes to that. muq and julia and pyjulia are out of our hands, though.

Ubuntu

We will need to rebuild the rmg channel packages (or just rebase this branch onto #2640, to at least remove a couple of them)

Intel Macs

Same as Ubuntu.

[rwest]

Julia and Pyjulia would be taken care of by #2640 (which would be unblocked if we could get past Python 3.7), so that leave muq? (and the ones that are our responsibility)

[rwest]

Is this faring any better than 3.10 or 3.11? at least it solved the boost - rdkit - muq issue? or do we need to await results on non-M1-platforms?

[JacksonBurns]

Local testing shows that this resolves the muq + rdkit issue. I tried leaving in our packages (rmg channel) to see if the conflict resolution would work, to no avail. I have removed them now to let it (hopefully) suggest solutions to conflicts (if there are any) and then we should have an idea of the path forward.

[JacksonBurns]

@rwest initial tests are done. M1 macs are missing a number of packages that are outside of our control. I think that is a dead end.

Ubuntu and MacOS need the rmg channel packages. If we rebase this on #2640 we can avoid building those we plan to immediately remove afterward (I want to do this).

All platforms will need Cython errors fixed.

[JacksonBurns]

Following some offline discussion, @hwpang and I have agreed that I will rebase this PR onto #2640 and then merge it into the same. This will:

• prevent me having to build packages which we will immediately remove, simplifying this PR: Complete conda-recipes Overhaul conda-recipes#18
• require resolving the Cython compilation errors. This may or may not be very difficult - subsequent work in this PR will focus on addressing the scope of these changes.
• still require building pydas and pydqed, which may or not be difficult, but will handled in separate PRs on their respective repositories.

[JacksonBurns]

This is officially rebased and working in #2741 so I will close this now.