James Stevenson

Cribbing description from https://github.com/biocommons/hgvs/pull/737 > A lot of modern editors will auto-trim trailing whitespace upon save. Unfortunately, if there's a pesky space or two hanging around on some old file,...

build: require python >= 3.10

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pending https://github.com/biocommons/biocommons.example/pull/42

fix: clean up some language regarding citations

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a few possible changes -- let me know if they need to go through additional channels first: * Fix wording on the Citation policy page, which refers to a "Cite"...

`ga4gh_identify` adds `digest` properties in-place regardless of `in_place` argument

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I have a basic allele. If I manually add the VA ID, the compacted JSON dump is 323 chars: ```pycon >>> allele = Allele(location={"end": 44908822, "start": 44908821, "sequenceReference": {"id": "NC_0000019.10",...

ruff hegemony 😎

refactor: resolve timezone-related python 3.12 deprecations

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close #127 * remove two cases of timezone-related deprecations -- one regarding default sqlite3 management of time type conversions back into python, and another from the `utcnow()` method I'd appreciate...

Reintroduce or remove DuplicateFilter

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The only place where it is used was commented out in https://github.com/biocommons/biocommons.seqrepo/commit/f2b48efddeee5303a70d657c156e044826be39e9 Either the class should be removed, or we should start using it again.

**Mondo term (ID and Label):** ampulla of vater neoplasm [http://purl.obolibrary.org/obo/MONDO_0000921] **Xref that should be fixed (ID and label):** `ONCOTREE:AMPULLAOFVATER` (should be `ONCOTREE:AMPULLA_OF_VATER`). The OncoTree API is a little tricky so...

**Describe the bug** The `hgnc` table contains entries for both `ZHX1-C8ORF76` and `ZHX1-C8orf76`. The view `tx_exon_aln_v` contains alignments for each. **To Reproduce** `SELECT * FROM tx_exon_aln_v WHERE hgnc = 'ZHX1-C8ORF76';`...