Add snakefmt to pre-commit

[MilesCranmer]

Seems like a good addition given the number of snakemake files and the fact that black is already used for Python:

This repository provides formatting for Snakemake files. It follows the design and specifications of Black.

[dfm]

This looks great too! Can you fix the conflicts and try to see what the pre-commit failure is being caused by? Here is the error log:

trim trailing whitespace.................................................Passed
fix end of files.........................................................Passed
isort....................................................................Passed
black-jupyter............................................................Passed
pycln....................................................................Passed
snakefmt.................................................................Failed
- hook id: snakefmt
- exit code: 1

snakefmt.exceptions.InvalidPython: Black error:
```
Cannot parse: 89:0: else:
```

Seems to be a syntax error somewhere, but it's not very clear :D

[MilesCranmer]

This syntax error happens on master as well. It's due to build.smk on this line:

showyourwork/showyourwork/workflow/build.smk

Line 89 in 8038af8

else:

This is at the limits of my snakemake knowledge as I didn't even know you could have rules within if statements. Any idea?

[MilesCranmer]

Nevermind I fixed it. Snakefiles are a little too expressive for my taste; it was some issue where it couldn't tell where a block ended and the next one began, so I put a pass at one indent down so the formatter could figure out it had to exit the scope.

[MilesCranmer]

I just made a second if statement instead of an else. But I'm not sure if onsuccess refers to the original if statement or not?

Also - with this exception raised at the top, does the rest even need to be embedded in an if statement?

[dfm]

I added some tiny inline comments, but this otherwise looks great!

[dfm]

This formatting is wrong. Are there settings that we can change in snakefmt?

[dfm]

After adding the new conditional at the top, this isn't still needed anymore, is it?

[MilesCranmer]

I think you are correct.

Actually, could the entire if statement be removed now, since the check is at the top?

[MilesCranmer]

It looks like this might be a bug in snakefmt: snakemake/snakefmt#190 and snakemake/snakefmt#186

We could wait to merge this until those bugs are fixed, lest it produces a bug on our side due to incorrect formatting. Wdyt?

[dfm]

Sounds like a plan to me!