packaging dep and IcfMetadata.__eq__

[ACEnglish]

Change 1

After creating a clean python3 -m venv b2z and python3 -m pip install . in bio2zarr, running vcf2zarr raised the
error:

<truncated>/python3.13/site-packages/bio2zarr/zarr_utils.py", line 2, in <module>
    from packaging.version import Version
ModuleNotFoundError: No module named 'packaging'

After manually installing python3 -m pip install packaging, the error was no longer raised. Therefore,
adding packaging to the requirements in pyproject.toml, making a new venv, reinstalling, and successfully
ran vcf2zarr.

Change 2

When exploding VCFs with different Header field order, the error was raised

  File "<truncated>/python3.13/site-packages/bio2zarr/vcf2zarr/icf.py", line 328, in scan_vcfs
    raise ValueError("Incompatible VCF chunks")
ValueError: Incompatible VCF chunks

To fix this, add order to relevant dataclasses, add __eq__ on IcfMetadata and call sorted for field comparison

Example data:
test1.vcf

##fileformat=VCFv4.1
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##INFO=<ID=QNAME,Number=1,Type=String,Description="Query name">
##INFO=<ID=QSTART,Number=1,Type=Integer,Description="Query start">
##INFO=<ID=QSTRAND,Number=1,Type=String,Description="Query strand">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
chr21	64506	.	C	CTCCAT	60	.	QNAME=cluster19_000000F;QSTART=25698928;QSTRAND=-	GT	1|0

test2.vcf

##fileformat=VCFv4.1
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##INFO=<ID=QSTART,Number=1,Type=Integer,Description="Query start">
##INFO=<ID=QNAME,Number=1,Type=String,Description="Query name">
##INFO=<ID=QSTRAND,Number=1,Type=String,Description="Query strand">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
chr20	63971	.	TTCCATTCCAC	T	60	.	QNAME=cluster19_000000F;QSTART=25698928;QSTRAND=-	GT	1|0

[coveralls]

coverage: 98.812% (-0.08%) from 98.888%
when pulling 818ced8 on ACEnglish:main
into d851fc3 on sgkit-dev:main.

[jeromekelleher]

This is great, thanks @ACEnglish!

I think the solution is slightly over cooking it, it it's easy enough to just compare on the fields we care about here. We'd like to add your test case to the vcf examples. Can you:

1. Create a new directory, tests/data/vcf/out_of_order_fields and put your test1.vcf and test2.vcf in there (in bgzip format). Also add the csi or tabix indexes, whichever suits best. Add the directory to git.
2. Add a new test class to tests/test_vcf_examples.py TestOutOfOrderFields``, and add a few simple tests to it (following, say, this one:

   bio2zarr/tests/test_vcf_examples.py

   Line 453 in d851fc3

   class TestSmallExampleLocalAlleles:

   ) The details will slightly differ as you'll be passing multiple files to explode.
3. Update the TestDu class here to account for the new files (sorry, this is a stupid test, I really need to think of a better way to do this!)

[jeromekelleher]

Sorting the samples will lead to corruption I think, as we assume that the samples are all in the same order currently (that could be fixed, easily enough, though). How about we just add the sorted on the self.fields attribute, and keep all the others as plain ==?

[jeromekelleher]

I don't think we need order=True here, do we? We're just defining the eq method, and don't need to sort the header definitions.

[ACEnglish]

Hello,

Thanks for the feedback. I've added tests and made some corrections. I was unsure about if Filters/Format fields needed sorting, so I made them very out of order in the input.bcf files and found that indeed they didn't need order=True or sorted to pass the tests.

I also figured out this pre-commit which is new to me so hopefully there won't be any CI/CD fails.

Let me know if there's more to be done. I'm happy to help.

Have a great day,
~/Adam

[jeromekelleher]

Looks great, thanks @ACEnglish ! Good to merge.

It would be nice to squash the commits down to two, if you don't mind (but no big deal if you don't want to/can't be bothered etc)

[ACEnglish]

Commits squished. I'm not sure if the du tests are going to pass. But everything I can see from tests on a mac seems fine.

[jeromekelleher]

Thanks @ACEnglish, this is great. I'll merge it next week and follow up with a release (this week is deadline heavy, I'm afraid!)