BUG: fix CDS span calculations

[GavinHuttley]

Summary by Sourcery

Fixes CDS span calculations and adds tests to validate the fix. The pull request also updates the CI configuration to include Python 3.13 and updates the test data URL.

Bug Fixes:

• Fixes CDS span calculations to correctly determine the start and stop coordinates of CDS features, addressing issues with relative start and stop positions, especially in multi-exon scenarios.

Build:

• Updates the requires-python field in pyproject.toml to allow Python 3.13.

CI:

• Adds Python 3.13 to the testing matrix in the CI workflow.
• Updates the cache key for test data to invalidate the cache and force a re-download of the test data.
• Updates the test data URL to use a direct download link from Dropbox.

Tests:

• Adds new tests to verify CDS sequence retrieval for single-exon and multi-exon genes, including cases with reverse strand and non-standard exon boundaries.
• Adds a test case for retrieving CDS features for C. elegans.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request fixes CDS span calculations, adds tests for various CDS scenarios, and updates development dependencies and testing workflow to include Python 3.13 and resolve data download issues. The CDS span calculation fix ensures accurate sequence retrieval for both single and multi-exon transcripts.

Sequence diagram for CDS span calculation with single exon

sequenceDiagram
  participant get_transcript_attr_records
  participant LimitExons
  participant cds_spans

  get_transcript_attr_records->>LimitExons: lex.single_exon == True
  alt lex.single_exon == True
    get_transcript_attr_records->>cds_spans: ex_start = cds_spans[0][0] if lex.strand == 1 else cds_spans[0][1]
    get_transcript_attr_records->>cds_spans: start, stop = ex_start + lex.rel_start, ex_start + lex.rel_stop (if lex.strand == 1)
    get_transcript_attr_records->>cds_spans: start, stop = ex_start - lex.rel_stop, ex_start - lex.rel_start (if lex.strand != 1)
    get_transcript_attr_records->>cds_spans: cds_spans[0, :] = start, stop
    get_transcript_attr_records-->>get_transcript_attr_records: yield TranscriptAttrRecord
  end

Loading

File-Level Changes

Change	Details	Files
Corrected CDS span calculations for single and multi-exon transcripts, ensuring accurate sequence retrieval.	Fixed CDS span calculations for single-exon transcripts by correctly adjusting start and stop coordinates based on strand. Corrected CDS span calculations for multi-exon transcripts, ensuring accurate sequence retrieval. Added tests to verify CDS sequence retrieval for single-exon, multi-exon (plus strand), and two-exon (reverse strand) scenarios. Modified get_transcript_attr_records to handle single exon CDS span calculations. Adjusted relative start coordinate calculation in get_limit_exons. Added a property to the LimitExons class to determine if the CDS is single exon.	tests/test_cli.py src/ensembl_tui/_mysql_core_attr.py tests/test_install.py tests/test_genome.py
Updated development dependencies and testing workflow to include Python 3.13 and resolve data download issues.	Added Python 3.13 to the testing matrix in .github/workflows/testing_develop.yml. Updated the test data download URL in tests/conftest.py and .github/workflows/testing_develop.yml to resolve download issues. Added development dependencies to pyproject.toml.	pyproject.toml .github/workflows/testing_develop.yml tests/conftest.py

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[sourcery-ai]

Hey @GavinHuttley - I've reviewed your changes - here's some feedback:

Overall Comments:

• The tests added in this PR are great, but could be improved by using smaller test fixtures rather than loading the entire genome.
• The logic for single exon CDS spans seems overly complex; can it be simplified?

Here's what I looked at during the review

• 🟡 General issues: 1 issue found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟡 Complexity: 1 issue found
• 🟢 Documentation: all looks good

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[coveralls]

Pull Request Test Coverage Report for Build 13556843807

Details

• 14 of 14 (100.0%) changed or added relevant lines in 1 file are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.08%) to 87.673%

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Totals
Change from base Build 13492055593:	0.08%
Covered Lines:	2660
Relevant Lines:	3034

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💛 - Coveralls