ci: add flake to tests, format with black, and add precommit hooks #326
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thanks - I want to dig into this a bit and try it out before committing (heh)! if you separate the fixes from the precommit hooks I'll happily merge those tho! |
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Sure. You want me to just remove precommit hooks but leave everything else? |
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actually, @luizirber is telling me to just go ahead with it 👍 let's give it a try! |
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🎉 |
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I'll let you press the merge button @ctb |
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(I have a similar PR in sourmash: sourmash-bio/sourmash#696 |
ctb
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* split bcalm sorting / input preparation into two steps * fixed pendant removal * simplify offset storage in pickle * add comment * flakes cleanup * change tests to use new workflow; remove bcalm_to_gxt * fix pendant removal code * add debugging script, check-catlas-shadow-vs-cdbg * add some shorter test files based on twofoo * automated tests for twofoo-short checks * update requirements, conda * add test for root shadow nodes <-> unitigs * add comment :) * check md5 on gxt and catlas * ci: switch to github actions, fix some linting issues (#323) Co-authored-by: C. Titus Brown <titus@idyll.org> * ci: add flake to tests, format with black, and add precommit hooks (#326) * ci: add flake to tests, format with black, and add precommit hooks * chore: use precommit hook from flake 8 repo * update with make black and make flakes * update version in setup.py * use MPHF lookup to build { cdbg_id -> reads } index (#322) * switch to a less khmer-specific read indexing approach, using mphf * more frequent reporting is nice * initial switch over to BBHashTable * add use of get_unique_values * rename index_contigs_by_kmer to index_cdbg_by_kmer * bbhash -> bbhash_table * use len(kmer_idx) * fix typo * add sizes output file * switch to using count_cdbg_matches * some fixes * remove khmer thruout * fix some label_cdbg calls * fix tests * update to newer version of bbhash * bbhash >= 0.3 for new release * whoops, bbhash >= 0.3 in requirements.txt * create in sqlite; may not help, doesn't hurt * raise exception when cDBG k-mers that should exist, don't * update requirements to bbhash 0.5 * cleanup, while fixing tests * update version * fix setup.py * Update install requirements, in preparation for conda-forge packaging. (#333) * update version in setup.py * update dependencies * update version to 2.0b3 * fix sourmash dep :) * switch to setuptools scm * remove large files * add long_description * remove cython and mypy * fix spelling * Try moving contig sorting into sqlite (#338) * fix spelling * upgrade for latest sourmash (pre-4.0) * add hacky sqlite-based sorting and storage * rename cdbg directory to include ksize * change bcalm output to be just 'bcalm.unitigs.fa' * ok, I think it's all working now? * update tests; minor cleanup * better remapping * cleanup * clean up / remove print stmts * fix tests * fix test md5 again * output count of all neighbors * remove unused contigs.fa.gz filename setting * sourmash migration -> 4.0 * create offset index too * simplify & streamline neighbor parsing * remove FastaWithOffsetAsDict * misc cleanup * tests save bacon, again * add test for bad bcalm output check * go back to relying on latest sourmash * oops, remove old sourmash req * update comments * moar comment update * fix return codes for tests * reorder tests; rm requirements.txt * use setup.py instead of requirements.txt * update setup to install pre-commit hook foo * swizzle requirements around a bit * update workflow test to be less reliant on sourmash naming details that change in 4.x * cleanup * attempt fix install * update setup * khmer remove ver? * install Cython too * try build_ext -i instead * revert last pile of changes b/c it's getting to be too much * swap test order * adjust @ctb comments * finish updating @ctb flags with docs, cleanup * black & flakes Co-authored-by: Dominik Moritz <domoritz@gmail.com>
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This will cause a bit more work one time (need to run black on prs as well) but then should reduce friction for prs or maintaining style in the future.
I was following https://ljvmiranda921.github.io/notebook/2018/06/21/precommits-using-black-and-flake8/