Mypy complains about redefining a variable, but this issue existed before my changes. Fixing it would also result in multiple return statements, which I tried to avoid. How would you like to proceed?

Mypy complains about redefining a variable, but this issue existed before my changes. Fixing it would also result in multiple return statements, which I tried to avoid. How would you like to proceed?

Just remove the type hint on line 295, and it should be fixed @liannette

Now the static typing passes :) but I think that this tests error: FAILED tests/unit/genomics/test_podp_antismash_downloader.py::test_jgi_id - ValueError: No antiSMASH data found for any genome should be fixed before merging. I can look into that next week, in the meantime feel free to do it yourself @liannette

I looked into the test failure, and it doesn’t seem to be related to my changes. My updates only affect the functionality for converting GenBank to RefSeq accessions.

From what I can tell, the error happens earlier in the test—during the conversion of a JGI_Genome_ID to a GenBank accession in the _resolve_jgi_accession function. The logs show that the request to https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=640427140 timed out:

[2025-02-13 12:07:22] WARNING  Timed out        podp_antismash_downloader.py:328
                               waiting for                                      
                               result of                                        
                               JGI_Genome_ID                                    
                               lookup

It looks like an httpx.ReadTimeout issue while waiting for a response from their website. I have the impression the site has been having issues for a few days now, but retrying the test later should hopefully resolve it.

It looks like an httpx.ReadTimeout issue while waiting for a response from their website. I have the impression the site has been having issues for a few days now, but retrying the test later should hopefully resolve it.

Sorry for the delay. I've verified that the failing test should not be related to the edits in this PR.

Great! Could you also merge it? 🙏