Reece Hart comments

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                                            Reece Hart

Use entrez gene_ids rather than symbols to link genes and transcripts

This issue was closed by stalebot. It has been reopened to give more time for community review. See [biocommons coding guidelines](https://biocommons.org/contributing/coding-guidelines/) for stale issue and pull request policies. This resurrection...

Update Ensembl data

HGNC Values are Missing on Some Transcripts

am37.c_to_g(hp.parse_hgvs_variant('NM_005117.2:c.295C>T')) fails with Alignment is incomplete.

Support transcript variants with specification of underlying genomic reference

Inconsistent position

There are two errors that many software in this space gets wrong. * **Packages incorrectly assume that exon genomic coordinates from NCBI, UCSC, and Ensembl are identical.** NCBI aligns transcripts...

Inconsistent position

The gff files should work fine as a source. The cigar string appears at the end of the line only for imperfect matches, like this: `NC_000001.10 RefSeq match /.../ ...;pct_identity_ungap=99.9308;Gap=M5230...

Add ruff linter configuration

How about: - set ruff line length = 100 - set black line length = 100 - reformat with `make reformat` ?

Add ruff linter configuration

@ecalifornica : Thanks for contributing this. We're going to incorporate ideas from this PR into the template repo, and then propagate to project repos. https://github.com/biocommons/biocommons.example/issues/3