Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bug fix for another cds spans edge case #198

Merged
merged 2 commits into from
Feb 27, 2025

Conversation

GavinHuttley
Copy link

@GavinHuttley GavinHuttley commented Feb 27, 2025

Summary by Sourcery

Bug Fixes:

  • Fixes an edge case where CDS spans were not correctly handled for single-exon transcripts, ensuring that only the relevant CDS span is processed.

Copy link

sourcery-ai bot commented Feb 27, 2025

Reviewer's Guide by Sourcery

This pull request addresses an edge case in the handling of CDS spans for single-exon transcripts. The code now correctly adjusts the CDS spans by limiting the cds_spans array to the first element when processing single-exon transcripts.

Sequence diagram for CDS span adjustment in single-exon transcripts

sequenceDiagram
  participant MT as _mysql_core_attr.py
  participant lex
  participant cds_spans

  MT->>cds_spans: cds_spans[start_index : start_index + 1]
  MT->>lex: _adjust_single_exon(lex, cds_spans[0])
  MT->>MT: yield TranscriptAttrRecord(...)
Loading

File-Level Changes

Change Details Files
Fixed an edge case where the CDS spans were not being correctly adjusted for single-exon transcripts.
  • Limited the cds_spans array to the first element when processing single-exon transcripts.
  • Ensured that only the relevant CDS span is adjusted, preventing potential errors with multi-exon transcripts.
src/ensembl_tui/_mysql_core_attr.py

Tips and commands

Interacting with Sourcery

  • Trigger a new review: Comment @sourcery-ai review on the pull request.
  • Continue discussions: Reply directly to Sourcery's review comments.
  • Generate a GitHub issue from a review comment: Ask Sourcery to create an
    issue from a review comment by replying to it. You can also reply to a
    review comment with @sourcery-ai issue to create an issue from it.
  • Generate a pull request title: Write @sourcery-ai anywhere in the pull
    request title to generate a title at any time. You can also comment
    @sourcery-ai title on the pull request to (re-)generate the title at any time.
  • Generate a pull request summary: Write @sourcery-ai summary anywhere in
    the pull request body to generate a PR summary at any time exactly where you
    want it. You can also comment @sourcery-ai summary on the pull request to
    (re-)generate the summary at any time.
  • Generate reviewer's guide: Comment @sourcery-ai guide on the pull
    request to (re-)generate the reviewer's guide at any time.
  • Resolve all Sourcery comments: Comment @sourcery-ai resolve on the
    pull request to resolve all Sourcery comments. Useful if you've already
    addressed all the comments and don't want to see them anymore.
  • Dismiss all Sourcery reviews: Comment @sourcery-ai dismiss on the pull
    request to dismiss all existing Sourcery reviews. Especially useful if you
    want to start fresh with a new review - don't forget to comment
    @sourcery-ai review to trigger a new review!
  • Generate a plan of action for an issue: Comment @sourcery-ai plan on
    an issue to generate a plan of action for it.

Customizing Your Experience

Access your dashboard to:

  • Enable or disable review features such as the Sourcery-generated pull request
    summary, the reviewer's guide, and others.
  • Change the review language.
  • Add, remove or edit custom review instructions.
  • Adjust other review settings.

Getting Help

Copy link

@sourcery-ai sourcery-ai bot left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Overall Comments:

  • It's good to see a specific edge case being addressed, but please include details of the bug in the description.
Here's what I looked at during the review
  • 🟢 General issues: all looks good
  • 🟢 Security: all looks good
  • 🟢 Testing: all looks good
  • 🟢 Complexity: all looks good
  • 🟢 Documentation: all looks good

Sourcery is free for open source - if you like our reviews please consider sharing them ✨
Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.

@coveralls
Copy link
Collaborator

Pull Request Test Coverage Report for Build 13561833520

Details

  • 1 of 1 (100.0%) changed or added relevant line in 1 file are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage increased (+0.004%) to 87.677%

Totals Coverage Status
Change from base Build 13558606474: 0.004%
Covered Lines: 2661
Relevant Lines: 3035

💛 - Coveralls

@GavinHuttley GavinHuttley merged commit 4398740 into cogent3:develop Feb 27, 2025
28 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants