Gene Symbols from Ensembl or custom source + better handling of identifiers and orthology translation

[deeenes]

Hi @PauBadiaM,

Here I implemented the stuff that the email discussion was about, now the user has 5 choices:

• Use the gene symbols from the web service (the original behaviour)
• Update them from Ensembl
• Update them from UniProt
• Provide a dict[str, set[str]] with any custom mapping
• Use UniProt IDs instead of gene symbols

I checked all omnip.get_* functions with various options, and everything looks alright for me. If you agree, feel free to merge this to main.

[PauBadiaM]

Better bump to 1.6.2

[PauBadiaM]

Hi Denes, thanks for the changes!
Looks fantastic but could you have a look at the build error? With the new changes, whenever a user types an unsupported organism they get a rather obscure error message TypeError: object of type 'NoneType' has no len() compared to the previous version.

[deeenes]

That particular error I've just fixed in pypath a few days ago; however, I expect another error due to OMA API change, that too will be fixed very soon.