feat: cli

[tristan-f-r]

This PR adds a very naive SPRAS cli wrapper over Snakemake. Having a wrapping command line interface instead that wraps around Snakemake allows

• generating configuration files without needing to use Snakemake, for automated parameter tuning and seedable configurations in feat!: typed PRA#run #329. This can be done with parameters inside the configuration, but this requires that we have a Snakemake run that immediately stops.
• SPRAS to be installed as a pip module, so SPRAS binaries can be attached with release versions and pip-installable
  • This means users no longer have to clone SPRAS and install conda to use SPRAS, alleviating Can not install yamlfmt in environment.yml in Windows #324.

After the next SPRAS release cycle, one could do:

pip install spras
spras run --configfile config.yaml --cores 8

We use the run subcommand to make extending this CLI easier later. We can easily supply a spras --version or a spras --help which links to the RTD, a spras tune for parameter tuning, etc...

---

This does make local development more annoying if you install SPRAS without python -m pip install -e .[dev]. The pixi PR (#382) helps with this.

We prefer this over Snakemake since it's easier to test separate components outside of Snakemake.

[read-the-docs-community]

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[ntalluri]

Does PR allow for the old version (the conda env version) to still exist or does this PR get rid of it entirely?

Also does this change how Justin set up the CHTC integration?

[ntalluri]

Also what do you mean by this "allows us to generate configuration files without needing to use Snakemake"

[tristan-f-r]

Does PR allow for the old version (the conda env version) to still exist or does this PR get rid of it entirely?

You can still use conda env - this does not remove it. Optimally, once we have #382, using the spras CLI to run snakemake should be the easiest option.

Also does this change how Justin set up the CHTC integration?

This change is backwards compatible, so it won't break Justin's CHTC setup. However, from looking at it earlier, using this CLI might actually be nicer for the CHTC setup (since it avoids hardcoding the SPRAS Snakefile path)

Also what do you mean by this "allows us to generate configuration files without needing to use Snakemake"

For parameter tuning (as far as I'm aware) and configuration seeding, we need to be able to generate configuration files. Refactoring the Snakefile to be able to handle this seems like a lot (especially given its lack of test coverage), so having configuration generation outside of our Snakemake workflow (and inside the CLI) looks like the nicest solution here.

[tristan-f-r]

This CLI should no longer be helpful for parameter tuning - only for determinism and packaging.