Add multiple-file support to vcfpartition

[Will-Tyler]

Description

This pull request adds support for multiple VCF/BCF files to the vcfpartition command and closes #212.

When the user specifies multiple VCF/BCF files, vcfpartition interprets the number of partitions argument as the total number of partitions among all the files. The partitions are distributed evenly among the files.

Let me know if we should add a section to the vcfpartition that describes how to partition multiple files.

Testing

I added some unit tests to test the changes to the vcfpartition CLI.

I tried to check the documentation changes manually by building the documentation (running make -C docs from the project directory), but I encountered this error:

rm -fR sample.vcz
asciinema-automation cast_scripts/vcf2zarr_convert.sh _static/vcf2zarr_convert.cast
make: asciinema-automation: No such file or directory
make: *** [_static/vcf2zarr_convert.cast] Error 1

I didn't spend much time trying to resolve this, but if you know the fix, that would help!

[coveralls]

coverage: 98.843% (-0.04%) from 98.884%
when pulling 21f142f on Will-Tyler:issue-212
into 31a5935 on sgkit-dev:main.

[coveralls]

coverage: 98.886% (+0.002%) from 98.884%
when pulling 21f142f on Will-Tyler:issue-212
into 31a5935 on sgkit-dev:main.

[Will-Tyler]

Looks like there were some ruff issues because I forgot to setup pre-commit. Should be good now.

[jeromekelleher]

LGTM, thanks @Will-Tyler!

Good to merge after a rebase (I like a linear commit history)

[jeromekelleher]

I tried to check the documentation changes manually by building the documentation (running make -C docs from the project directory), but I encountered this error:

The docs build is very fragile, it needs a good overhaul (#238) once we've figured out a better structure for the actual documentation (#239).

[coveralls]

coverage: 98.843% (-0.04%) from 98.884%
when pulling 99d7f7f on Will-Tyler:issue-212
into 31a5935 on sgkit-dev:main.

[jeromekelleher]

Docs failure is because of numpy 2.0 issues, these should go away once you rebase.

[Will-Tyler]

Thanks, I just rebased this branch. I would like to merge this pull request before #253.

[coveralls]

coverage: 98.843% (-0.04%) from 98.884%
when pulling 6a573a6 on Will-Tyler:issue-212
into a75091e on sgkit-dev:main.