refactor: update transcript list

[balajtimate]

Description

• Update transcripts.fasta.gz to include transcript sequences from an updated set of small subunit RP genes (RPSA, RPS2, RPS3, RPS9, RPS11, RPS13, RPS14, RPS15, RPS15A, RPS16, RPS18, RPS20, RPS23, RPS29) that are consistent across the domains of Bacteria, Archaea and Eukaryotes (so in the future Bacteria can also be included). The RP genes were selected based on https://bangroup.ethz.ch/research/nomenclature-of-ribosomal-proteins.html. Human genes and their orthologs were downloaded from Ensembl main (Vertebrates), Ensembl Plants, Ensembl Fungi and Ensembl Metazoa. The set now consists of 14410 transcripts from 385 organisms.
• Update to correct current version v0.11.0
• Add disable statement to pylint too-many-positional-arguments in get_read_layout.py (related to changes in pylint v3.3)

Closes #108
Closes #56

Type of change

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)

Checklist

Please carefully read these items and tick them off if the statements are true
or do not apply.

• I have performed a self-review of my own code
• My code follows the existing coding style, lints and generates no new
  warnings
• I have added type annotations to all function/method signatures, and I
  have added type annotations for any local variables that are non-trivial,
  potentially ambiguous or might otherwise benefit from explicit typing.
• I have commented my code in hard-to-understand areas
• I have added ["Google-style docstrings"] to all new modules, classes,
  methods/functions or updated previously existing ones
• I have added tests that prove my fix is effective or that my feature
  works
• New and existing unit tests pass locally with my changes and I have not
  reduced the code coverage relative to the previous state
• I have updated any sections of the app's documentation that are affected
  by the proposed changes

If for some reason you are unable to tick off all boxes, please leave a
comment explaining the issue you are facing so that we can work on it
together.

[balajtimate]

With the updated transcript list and the new set of SRA samples (which does contain 720 samples), we have the best result for library source inference yet:

I think with this we can close #108 and #56 (improving lib source inference with a consistent set of RP genes)

[balajtimate]

Also, the checks are failing because there's an ongoing issue with setup-miniconda as a result of mamba v2 release. There seems to be a fix on the way, should we wait for it or pin mamba to 1.5.10 @uniqueg? That worked in the previous commit.

[uniqueg]

If you think a fix will come within the next few days, then wait - otherwise pin.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (51957ac) to head (a75cfd7).
Report is 1 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff            @@
##               dev      #168   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           13        13           
  Lines         1143      1142    -1     
=========================================
- Hits          1143      1142    -1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.