perf: autobump bio/ucsc/gtfToGenePred

[snakedeploy-bot]

Automatic bump of bio/ucsc/gtfToGenePred.

Summary by CodeRabbit

• New Features
  • Updated the ucsc-gtftogenepred package to version 469, which may include new features and improvements.
• Bug Fixes
  • Upgraded various package dependencies to enhance performance and security, including Python and several libraries.
• Chores
  • Maintained the environment by updating package versions to ensure compatibility and stability.

[coderabbitai]

Walkthrough

The changes involve updates to the package dependencies for the bio/ucsc/gtfToGenePred project. Key modifications include version upgrades for several libraries, including Python, libzlib, openssl, setuptools, and cffi. Additionally, the version of the ucsc-gtftogenepred package has been incremented from 447 to 469, indicating an overall effort to maintain the environment with more recent and potentially more stable versions of the dependencies.

Changes

File	Change Summary
bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt	Updated various package versions, including Python ABI, libgcc, libstdcxx, libzlib, openssl, setuptools, cffi, and others.
bio/ucsc/gtfToGenePred/environment.yaml	Incremented ucsc-gtftogenepred version from 447 to 469.

---

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

Share

• X
• Mastodon
• Reddit
• LinkedIn

Tips

Chat

There are 3 ways to chat with CodeRabbit:

• Review comments: Directly reply to a review comment made by CodeRabbit. Example:
  • I pushed a fix in commit <commit_id>.
  • Generate unit testing code for this file.
  • Open a follow-up GitHub issue for this discussion.
• Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
  • @coderabbitai generate unit testing code for this file.
  • @coderabbitai modularize this function.
• PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
  • @coderabbitai generate interesting stats about this repository and render them as a table.
  • @coderabbitai show all the console.log statements in this repository.
  • @coderabbitai read src/utils.ts and generate unit testing code.
  • @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
  • @coderabbitai help me debug CodeRabbit configuration file.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai full review to do a full review from scratch and review all the files again.
• @coderabbitai summary to regenerate the summary of the PR.
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
• @coderabbitai help to get help.

Other keywords and placeholders

• Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
• Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
• Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (.coderabbit.yaml)

• You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
• Please see the configuration documentation for more information.
• If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

• Visit our Documentation for detailed information on how to use CodeRabbit.
• Join our Discord Community to get help, request features, and share feedback.
• Follow us on X/Twitter for updates and announcements.

[mergify]

Automatically approving successfull autobump

[coderabbitai]

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 44f944f and 8a8fc60.

Files selected for processing (2)

• bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt (2 hunks)
• bio/ucsc/gtfToGenePred/environment.yaml (1 hunks)

Additional comments not posted (4)

bio/ucsc/gtfToGenePred/environment.yaml (1)

6-6: Approved version update for ucsc-gtftogenepred.

The update from version 447 to 469 is noted. Ensure compatibility with other dependencies is maintained.

bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt (3)

8-8: Updated Python ABI version approved.

The update from python_abi-3.12-4_cp312 to python_abi-3.12-5_cp312 is noted. Ensure this update does not affect Python ABI compatibility.

---

22-22: Approved updates to various dependencies.

Updates to libzlib, openssl, libopenssl-static, zlib, setuptools, wheel, cffi, openpyxl, and agate are approved. These updates are important for security and functionality enhancements.

Also applies to: 24-24, 27-27, 33-33, 44-44, 47-47, 50-50, 53-53, 59-59

Verification successful

---

Dependency updates verified successfully.

The versions of libzlib, openssl, libopenssl-static, zlib, setuptools, wheel, cffi, openpyxl, and agate in the environment.linux-64.pin.txt file match the approved updates. These updates are consistent with the review comment's approval for security and functionality enhancements. No issues were found.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify overall stability and compatibility of the updated environment.

# Test: Check for any breaking changes introduced by these updates.
conda list --revisions

Length of output: 97

---

Script:

#!/bin/bash
# Search for the specified dependencies in the environment.linux-64.pin.txt file to verify their versions.
rg 'libzlib|openssl|libopenssl-static|zlib|setuptools|wheel|cffi|openpyxl|agate' bio/ucsc/gtfToGenePred/environment.linux-64.pin.txt

Length of output: 1620

---

12-12: Library version updates approved.

Updates to libgcc, libgcc-ng, and libstdcxx-ng are noted. These updates are crucial for maintaining compatibility and performance.

Also applies to: 13-13, 19-19