Support new snakemake keywords prefix and default_target

[koen-vg]

Hi! Thanks for the great project; snakefmt is much appreciated.

Recently two new keywords have been added to snakemake: prefix (in module blocks) and default_target (in rules). This pull request adds support to snakefmt for both. I have also included both in test. All tests pass, and I have also tested this with success on a more involved snakefile I personally work with.

This also closes #130.

Let me know if any improvements are changes are needed or wished for before merging.

[bricoletc]

Hi @koen-vg , thanks for your contribution :) This looks good! By default we merge into dev and then push new versions to master.

I'm just a bit surprised that all tests passed for you, as our current snakemake dependency version fails 'grammar completeness' tests. So I recommend we merge this in dev and I then push an update of snakemake dep. version to latest (OR @koen-vg you push a commit on this branch after running poetry install(see CONTRIBUTING.md) and poetry update snakemake . I checked all tests/lints pass from there (make precommit)

[bricoletc]

@mbhall88 after your review we either wait for @koen-vg to push that snakemake update commit here, or we merge to dev and do it ourselves

[koen-vg]

Right, I did have to update to the latest version of snakemake, 6.15, but seem to have forgotten to document that. I'll try to push the snakemake update, that would be to the poetry.lock file?

[koen-vg]

Alright I have to admit I'm not super familiar with poetry; the latest commit is what I got after updating the snakemake version in pyproject.toml and then running poetry update; hopefully that was the intention.

[codecov]

Codecov Report

Merging #131 (13614af) into dev (97a2b6e) will decrease coverage by 0.01%.
The diff coverage is n/a.

❗ Current head 13614af differs from pull request most recent head c9a00a4. Consider uploading reports for the commit c9a00a4 to get more accurate results

@@            Coverage Diff             @@
##              dev     #131      +/-   ##
==========================================
- Coverage   98.21%   98.20%   -0.02%     
==========================================
  Files          12       12              
  Lines         954      948       -6     
  Branches      175      209      +34     
==========================================
- Hits          937      931       -6     
  Misses         10       10              
  Partials        7        7              

Flag	Coverage Δ
unittests	98.10% <ø> (-0.02%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
snakefmt/parser/grammar.py	100.00% <ø> (ø)
snakefmt/parser/parser.py	96.39% <0.00%> (-0.04%)	⬇️
snakefmt/parser/syntax.py	99.05% <0.00%> (-0.01%)	⬇️
snakefmt/exceptions.py	100.00% <0.00%> (ø)

[mbhall88]

All looks good. @koen-vg could you please add your changes to the CHANGELOG as well?

[bricoletc]

Thanks @koen-vg ! so I've just done two things:

• Fixed CHANGELOG conflict in this PR on dev branch
• Modified your poetry update commit, because you ran poetry update but I would rather we do poetry update snakemake only here (after, as you did, modifying the pyproject.toml snakemake version). I know poetry is not so easy at first (https://python-poetry.org/docs/basic-usage/#specifying-dependencies). For me, no need to update all dependencies, if they ain't broke, let's not change them :-) @mbhall88 thoughts?

@koen-vg I've pushed your changes plus those two points above to dev. You are still author of the fixing and changelog commits. @mbhall88 i would suggest we close this pull request since I've merged the material into dev, if you agree.

[koen-vg]

That all sounds very good. Thanks for making it easy to contribute to this project!

[mbhall88]

For me, no need to update all dependencies, if they ain't broke, let's not change them :-) @mbhall88 thoughts?

Fine by me. This does remind me though, black is now stable so we will need to update that dependency soon. But agree with just updating snakemake here

@koen-vg I've pushed your changes plus those two points above to dev. You are still author of the fixing and changelog commits. @mbhall88 i would suggest we close this pull request since I've merged the material into dev, if you agree.

Ok. Normally I would prefer you push to this PR and we solve conflicts here, but it's done now. So yes, closing this makes sense.

[bricoletc]

For future ref- not sure how I could have pushed a change that removed one of the commits (updating all dependencies), i.e. rewriting history, to the from branch?

If you have suggestions i'll do that next time round

[mbhall88]

Ah didn't realise you had removed a commit. Ignore me.