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airr-community / airr-standards

AIRR Community Data Standards
https://docs.airr-community.org
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Minor fixes, and fix to the Sphinx build #566

Closed williamdlees closed 2 years ago

williamdlees commented 2 years ago

Some minor changes to germline field names for consistency, and a fix to conf.py which should stop the Sphinx build breaking: names of some of the schema elements needed updating.

closes #561 closes #560

schristley commented 2 years ago

Thanks @williamdlees , I see change for the sphinx doc builds, but are there supposed to be field name changes? I see a commit but maybe the changes were already in master?

williamdlees commented 2 years ago

You are right, they do seem to be there, though I can't see from the change history how they got there from this branch. Perhaps it was something to do with the way you fixed up the changes I over-wrote?

schristley commented 2 years ago

needs more updates to germline.rst

schristley commented 2 years ago

@williamdlees I've added this branch to readthedocs so you can see the documentation changes.

I corrected the sentence, "In the case of a germline inference from a repertoire, ..." to refer to RearrangementSequence instead of UnrearrangedSequence. I think that is correct?

You may want to review the naming paragraph and add reference to you label generator tool. Also, the paragraph references coding_sequence_identifier but it isn't in the schema. I'd filed #561 about that, is that field missing or has it been changed?

williamdlees commented 2 years ago

Thanks @schristley . Sorry I forgot to update the documentation. You are correct about that reference to RearrangedSequence instead of UnrearrangedSequence. coding_sequence_identifier has now disappeared: the approach we're suggesting now is that label should be the IUIS name or a temporary label. I've reflected that in the documentation and added a link to IgLabel.

williamdlees commented 2 years ago

I think everything should be ok now.