chore: pixi

[tristan-f-r]

Pixi recently resolved an issue which was blocking my previous attempt at using pixi (one that, while it seemed to work locally, hangs on GitHub CI).

Other than installing pixi, one just needs to do pixi shell instead of conda init ... and conda activate spras. We also do not need to do pip install . anymore, as pixi automatically installs our local spras dependency - I'm not sure how well this pairs with #332.

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I believe the actual infrastructure changes are otherwise minor and fine: the real review comes into making sure we're good on documenting pixi usage.

[read-the-docs-community]

Documentation build overview

📚 spras | 🛠️ Build #30059945 | 📁 Comparing 68e3b01 against latest (615e6fb)

🔍 Preview build

Show files changed (6 files in total): 📝 6 modified | ➕ 0 added | ➖ 0 deleted

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htcondor.html	📝 modified
install.html	📝 modified
usage.html	📝 modified
contributing/index.html	📝 modified
tutorial/beginner.html	📝 modified
tutorial/introduction.html	📝 modified

[agitter]

I need to take some time to use pixi locally before I can review this. I haven't been able to do that yet.

[tristan-f-r]

There's also a really good chance that this can close #373.

[agitter]

There are two potentially separate decisions here:

1. What should we use to run our CI testing
2. What should we recommend users do to install and run SPRAS

For 1), I don't have strong opinions. Anything that is fast, reliable, maintained, and easy for us to maintain works. If pixi improves on conda in those or other respects I'd like to know how.

For 2), we should give more though to who are users are and what they are accustomed to. Installing software with conda is fairly common for computational and biological users. Should that remain the primary/secondary option and pixi the secondary/primary? Supporting two installation pathways leads to a higher maintenance burden, which I don't like.

[tristan-f-r]

For 2, we can avoid the 'installing conda/pixi' step entirely hopefully with #332, so I'm not too concerned about it. For the time being, encouraging users to use pixi seems fine.

[tristan-f-r]

As for 1, Snakemake itself uses Pixi for CI (and for development!), and unlike Conda, Pixi seems to not have flaky CI. I've had to restart CI in SPRAS for the flaky PCA test, and for flaky conda installations.