Add pre-commit with ruff #36
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Thanks Tom! |
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This should be ready to merge when you're ready @jeromekelleher |
tests/utils.py
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| @@ -114,11 +114,13 @@ def assert_vcfs_close(f1, f2, *, rtol=1e-05, atol=1e-03): | |||
| val2, | |||
| rtol=rtol, | |||
| atol=atol, | |||
| err_msg=f"FORMAT {field} not equal for variants\n{v1}{v2}", | |||
| err_msg=f"FORMAT {field} not equal for \ | |||
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I think ruff is changing the actual strings here. In this program
string = "this is a \
string with\
different levelts of indentation"
print(string)
the leading whitespace isn't removed from the string literal.
Can we change to using string concatenation instead?
(Ruff seems to do this sort of thing quite a bit - it has extremely strong opinions that aren't necessarily all that well supported)
vcztools/vcf_writer.py
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| @@ -54,7 +55,8 @@ | |||
| "HQ": "Haplotype quality", | |||
| "MQ": "RMS mapping quality", | |||
| "PL": "Phred-scaled genotype likelihoods rounded to the closest integer", | |||
| "PP": "Phred-scaled genotype posterior probabilities rounded to the closest integer", | |||
| "PP": "Phred-scaled genotype posterior probabilities rounded to the closest \ | |||
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I fixed it incorrectly before - this should be better now. I think Black didn't change these lines, but Ruff is stricter, as you say. |
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Great - thanks! |
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Based on bio2zarr's set up
(This includes #35 which should be merged first, then I'll rebase this)