setup bump Python version

[davmlaw]

The generate code uses newer type annotations which are >3.8 which is what is listed as min python version

[YasirKusay]

Please also add the following packages:

ijson, pyhgvs, HTSeq, biopython

Also, I am getting this warning when running cdot_json.py gtf_to_json:

WARNING:root:Skipping chrom/contig conversion. File won't work with Biocommons HGVS
WARNING:root:Your version of HTSeq (2.0.9) can not handle duplicated tags. Some will be lost See https://github.com/htseq/htseq/issues

[davmlaw]

@YasirKusay - Does the message say what you quoted, or did you cut off the end part? Code seems to say:

See https://github.com/htseq/htseq/issues/83 - see https://github.com/SACGF/cdot/blob/main/generate_transcript_data/gff_parser.py#L405

The current state of that issue is that there was a pull request applied to master in GitHub, but not released, so you'll need to run:

pip install --upgrade git+https://github.com/htseq/htseq

I have just raised an issue to try and get them to make a new HTSeq release. Otherwise - can just use git commit in my dependencies

---

For those packages - I don't want to add those packages to default as they are not required by 99% of users, only those that build their own transcripts. I'll make a separate requirements for that (cdot-build or something) - probably switch to pyproject.toml

[davmlaw]

HTSeq has been updated to 2.1.2