Re-enable mamba in CI

[IAlibay]

Fixes #3048

Changes made in this Pull Request:

• Enable mamba for GH actions CI

Testing on some cron jobs I'll push to MDA later, it looks like it works now (not sure if it's that stable, but I guess we can always disable again if it fails).

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[IAlibay]

The gains here are modest (~ minute and a half).

Personally I think we should go ahead with it anyways, it adds up to ~ 10 mins of CPU time which is a non-insignificant environmental impact.

[codecov]

Codecov Report

Merging #3177 (4154695) into develop (8a5ef48) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop    #3177   +/-   ##
========================================
  Coverage    92.81%   92.81%           
========================================
  Files          170      170           
  Lines        22801    22801           
  Branches      3239     3239           
========================================
  Hits         21162    21162           
  Misses        1591     1591           
  Partials        48       48           

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[lilyminium]

LGTM.
By the way, mdtraj has nuked conda/mamba for nix. That could be something we could look at if installation remains slow.

https://github.com/mdtraj/mdtraj/blob/master/.github/workflows/main.yaml

[IAlibay]

Thanks @lilyminium I'm going to temporarily switch to draft though because I think my latest commit caused a performance regression.

By the way, mdtraj has nuked conda/mamba for nix. That could be something we could look at if installation remains slow.

Yeah, for now we should be fine, we're sub 1 minute for dependency installs on linux. Annoyingly MacOS takes much longer.

[orbeckst]

nix looks interesting and is available for Linux and macOS.

Is it a disadvantage to recommend, say, conda for users but use another package manager for the bulk of our testing?

[IAlibay]

Alright, I think this is as optimised as I can get it.

Main changes are:

• addition of mamba in places where we do lots of dependency installs
• setting the number of macOS processors to 3 instead of 2 (this doesn't have a noticeable influence since the performance differs a lot between runs, but in some cases it can make it run a bit faster)
• Switching the channel priorities around (which is something that's being introduced in the chemfiles PR)

Quick timing summary:

Linux:

full: ~ 2 mins less compared to current develop

miniconda setup: ~ 1 min
deps install: ~ 1 min

min: ~ 1 min less compared to current develop

miniconda_setup: ~ 1 min
deps install: ~ 20s

build_docs: ~ 3 mins less compared to current develop

setup_miniconda: ~ 1 min
install_deps: ~ 1 min

pylint: ~ same as current develop

setup_miniconda: 46s
deps install: 5s

pypi_check: same as current develop

setup_miniconda: 32s
deps install: 10s

macOS:

full: for setup ~ 7 mins less compared to current develop

setup_miniconda: 1m 9s
install_deps: 1m 43s
run_tests: ~ 15 - 25 mins (same as current develop? sometimes faster?)

[lilyminium]

LGTM. Thanks for commenting why it's a conda install in pypi_check.