Add commands for showing OTU data

[igboyes]

• Add commands to list OTUs and show details of a single OTU.
• Clean up CLI module, resolving most Ruff linter errors.
• Remove flaky mark from NCBI tests. The package is not installed and we should be ensuring these tests always pass by making the code more resilient.
• Remove unused async from NCBI tests.
• Remove some log calls. We need to rethink this so it doesn't clutter the output. One idea is logging to stderr or writing log files.

Output of ref-builder otu list:

 NAME                    ACRONYM  ID                                    TAXID
 Abaca bunchy top virus  ABTV     586ba010-4121-48a5-bf0c-f4462cc07b0c  438782
 Abutilon Brazil virus   AbBV     12e98766-2870-4334-a9cd-1705fd8d2066  665102

Output of ref-builder otu get:

Abaca bunchy top virus

 ACRONYM    ABTV
 ID         586ba010-4121-48a5-bf0c-f4462cc07b0c
 LEGACY ID  c93ec9a9
 TAXID      438782

SCHEMA

 SEGMENT  REQUIRED  LENGTH
 DNA N    Yes       1090
 DNA U3   Yes       1057
 DNA S    Yes       1087
 DNA M    Yes       1074
 DNA C    Yes       1015
 DNA R    Yes       1099

ISOLATES

Isolate Q767

 ACCESSION    SEGMENT  DEFINITION
 NC_010314.1  DNA N    Abaca bunchy top virus DNA-N, complete genome
 NC_010315.1  DNA U3   Abaca bunchy top virus segment 2, complete sequence
 NC_010316.1  DNA S    Abaca bunchy top virus DNA-S, complete genome
 NC_010317.1  DNA M    Abaca bunchy top virus DNA-M, complete genome
 NC_010318.1  DNA C    Abaca bunchy top virus DNA-C, complete sequence
 NC_010319.1  DNA R    Abaca bunchy top virus DNA-R, complete genome

Isolate Q1108

 ACCESSION    SEGMENT  DEFINITION
 EF546802.1   DNA N    Abaca bunchy top virus isolate Q1108 segment DNA-N, complete sequence
 EF546803.1   DNA U3   Abaca bunchy top virus isolate Q1108 segment DNA-U3, complete sequence
 EF546804.1   DNA S    Abaca bunchy top virus isolate Q1108 segment DNA-S, complete sequence
 EF546805.1   DNA M    Abaca bunchy top virus isolate Q1108 segment DNA-M, complete sequence
 EF546806.1   DNA C    Abaca bunchy top virus isolate Q1108 segment DNA-C, complete sequence
 EF546807.1   DNA R    Abaca bunchy top virus isolate Q1108 segment DNA-R, complete sequence

[sygao]

I like it!

I do have an opinion on this order though:

Output of ref-builder otu list:

 NAME                    ACRONYM  ID                                    TAXID
 Abaca bunchy top virus  ABTV     586ba010-4121-48a5-bf0c-f4462cc07b0c  438782
 Abutilon Brazil virus   AbBV     12e98766-2870-4334-a9cd-1705fd8d2066  665102

I would prefer the TAXID column to be closer to the left side, since it is the easiest method of entry into ref-builder otu get. I think it risks truncation being so close to the right.

[virtool-bot]

🎉 This PR is included in version 0.2.0 🎉

The release is available on GitHub release

Your semantic-release bot 📦🚀