fix some errors in github action, and add python 3.12

[graphenn]

Not all issues fixed. The left issue can be test with code below.

from cyvcf2 import VCF, Writer

VCF_PATH ="./cyvcf2/tests/test.vcf.gz"

def test():
    input_vcf = VCF('./cyvcf2/tests/seg.vcf.gz')
    output_vcf = Writer('./test.vcf', input_vcf)
    for v in input_vcf:
        v.genotypes = [[1,1,False]]
        output_vcf.write_record(v)
    output_vcf.close()

def test2():
    vcf = VCF(VCF_PATH)
    for variant in vcf:
        print(variant)
        break

    print("11")
    vcf.close()
    print("22")

test()
test2()

It may be same issue with these, on htslib 1.18

Fixed possible double frees when handling errors in bcf_hdr_add_hrec(), if particular memory allocations fail. (PR samtools/htslib#1637)

Ensure that bcf_hdr_remove() clears up all pointers to the items removed from dictionaries. Failing to do this could have resulted in a call requesting a deleted item via bcf_hdr_get_hrec() returning a stale pointer. (PR samtools/htslib#1637)

I tried but failed to upgrade htslib version.

[graphenn]

Add build test case for the offical python docker image, arm64/amd64 + debian #274

It can pass pytest if remove test_write_missing_contig case in test_reader.py (the left issue). Arm64 + debain build issue also fixed.

[graphenn]

I have found a solution to decouple the compilation of cyvcf2 and htslib, which now enables the upgrade of htslib. Additionally, by statically linking to the htslib library, we can avoid redundant compilations. This approach ensures a smoother and more efficient development process. I have tested htslib 1.18, but the test_write_missing_contig test case still error.

Do you want me to submit this changes here or later?

[graphenn]

everything works now! And I will submit decouple the compilation of cyvcf2 and htslib at another PR later.

[brentp]

This is amazing! thanks so much. PR for decoupling would be great!

[brentp]

not all heroes wear capes, but, fittingly, your avatar does. 🦸