James Stevenson

Eliminate "extra" dependencies

5

I'm not sure if a firm decision has been made on this but I've heard a few thoughts expressed on the matter: * Rename "extras" to something more expressive ("tools"...

We (me, @jarbesfeld) have been refactoring a mapping pipeline, which previously created VRS 1.3 alleles and haplotypes, to use more up-to-date tooling. This means we're programmatically tied to VRS 2a,...

**Describe the bug** As of #176, three test modules fail: * `test_eutils_xmlfacades_dbsnp.py` * `test_eutils_xmlfaces_esearchresult.py` * `test_eutils_xmlfacades_gi.py` **To Reproduce** `make test` **Expected behavior** They should probably be passing with minimal interventions....

**Describe the bug** Running code verbatim from both "Fetching gene information" and "Fetch PubMed information" raises an IndexError and an AttributeError, respectively. **To Reproduce** Run code in https://eutils.readthedocs.io/en/stable/using.html#examples in a...

Implement client interface for `elink`

1

**Is your feature request related to a problem? Please describe.** I think it's technically possible to get some cross-referential information in more roundabout ways, but [elink](https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ELink) is helpful for eg...

**Is your feature request related to a problem? Please describe.** The IPython dependency, and its sub-dependencies, makes the SeqRepo install footprint bigger than I'd expect it to be. On my...

**Describe the bug** I'm getting set up on a fresh machine, and pulling the 2024 snapshot seems to expect a `/usr/local/seqrepo` directory to exist already: ``` [ main ⚙ .venv]...

**Describe the bug** Same issue as https://github.com/biocommons/eutils/issues/173: Importing raises a ModuleNotFoundError: ``` >>> import biocommons.seqrepo Traceback (most recent call last): File "", line 1, in File "/Users/jss009/code/mavemap/tmp-venv/lib/python3.12/site-packages/biocommons/seqrepo/__init__.py", line 5, in...

Sqlite3 timestamp converter is deprecated as of Python 3.12

1

I can circle back and flesh this one out in greater detail later (trying to get something else done currently, but wanted to put it on paper before I forget)....