pggb: update vg to v 1.59.0

[AndreaGuarracino]

To address pangenome/pggb#415

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request modifies the meta.yaml file for the pggb package. The primary changes include an increment in the version number from 0 to 1 in the build section. Additionally, the version of the vg dependency is updated from 1.40.0 to 1.59.0 in the requirements section. Minor formatting adjustments are also made, specifically aligning the seqwish and smoothxg dependencies under the run requirements to ensure proper indentation. These changes are aimed at maintaining the package's compatibility and organization.

Possibly related PRs

• Update meta.yaml for spec2vec #49857: The changes in the meta.yaml file for the spec2vec package involve updating the version number and dependencies, similar to the updates made in the meta.yaml for the pggb package in the main PR.

---

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>, please review it.
  • 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 gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
  • @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.

[coderabbitai]

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)

recipes/pggb/meta.yaml (1)

Line range hint 1-49: Overall package recipe looks good.

The structure and content of the meta.yaml file adhere to Conda packaging conventions. The changes made (build number increment and vg version update) are appropriate for addressing the issue mentioned in the PR objectives.

Note: The AI summary mentioned minor formatting adjustments, particularly in the alignment of seqwish and smoothxg dependencies. However, these changes are not visible in the provided diff. If such changes were made, they would contribute to better readability and consistency of the file.

Consider reviewing the entire file to ensure consistent indentation and alignment, particularly for the run requirements section.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 77e9015 and 50ad216.

📒 Files selected for processing (1)

• recipes/pggb/meta.yaml (2 hunks)

🧰 Additional context used

🔇 Additional comments (2)

recipes/pggb/meta.yaml (2)

16-16: LGTM: Build number increment is appropriate.

The build number has been correctly incremented from 0 to 1. This is the expected practice when making changes to a package without altering its version number, which is the case here with the vg dependency update.

---

31-31: Verify compatibility with updated vg version.

The vg dependency has been updated from version 1.40.0 to 1.59.0, which is a significant version jump. While this update likely addresses the issue mentioned in the PR objectives (pangenome repository issue #415), it's important to ensure that this new version is compatible with the current version of pggb (0.6.0).

Please confirm that pggb 0.6.0 has been tested with vg 1.59.0 and functions as expected. You may want to run the following command to check for any compatibility issues:

This will help identify any potential areas where the vg update might affect pggb's functionality.

[AndreaGuarracino]

@bioconda-bot please add label