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

Update recipe for ViroConstrictor #51038

Merged
merged 1 commit into from
Sep 30, 2024

Conversation

florianzwagemaker
Copy link
Contributor

@florianzwagemaker florianzwagemaker commented Sep 30, 2024

Updated the dependencies in the recipe to avoid a broken install and updated the recipe maintainers list.


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
  • PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
  • Please post questions on Gitter or ping @bioconda/core in a comment.

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation).
Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x) {{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions {{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions {{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning {{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

Bot commands for PR management

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please update Merge the master branch into a PR.
@BiocondaBot please add label Add the please review & merge label.
@BiocondaBot please fetch artifacts Post links to CI-built packages/containers.
You can use this to test packages locally.

Note that the @BiocondaBot please merge command is now depreciated. Please just squash and merge instead.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

Summary by CodeRabbit

  • New Features

    • Updated versioning for the ViroConstrictor package to version 1.
    • Standardized entry points for improved clarity.
  • Bug Fixes

    • Consolidated snakemake entry in the run requirements to avoid duplication.
  • Chores

    • Updated maintainership details in the recipe.

Copy link
Contributor

coderabbitai bot commented Sep 30, 2024

📝 Walkthrough

Walkthrough

The pull request introduces several updates to the meta.yaml file of the ViroConstrictor package, including an increment in the version number, specification of a version range for the mamba dependency, and consolidation of the run requirements. Additionally, the entry points in the build section have been standardized, and changes have been made to the extra section regarding recipe maintainers.

Changes

Files Change Summary
recipes/viroconstrictor/meta.yaml - Version number updated from 0 to 1.
- mamba dependency updated to >=1.5.0, <2.0.0.
- Consolidated snakemake entry in run requirements.
- Standardized entry points in build section.
- Updated run_exports section.
- Maintainers updated: removed KHajji, added raaijmag, wolthuisr.

Possibly related PRs

Suggested labels

please review & merge


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
🪧 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.

@florianzwagemaker
Copy link
Contributor Author

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Sep 30, 2024
Copy link
Contributor

@coderabbitai coderabbitai bot left a comment

Choose a reason for hiding this comment

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

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (2)
recipes/viroconstrictor/meta.yaml (2)

43-43: LGTM: Mamba dependency constraint added.

The addition of version constraints for the mamba dependency is a good practice. It helps ensure compatibility and reproducibility. The chosen range (>=1.5.0, <2.0.0) allows for minor updates while preventing potentially breaking changes from major version updates.

Consider adding a comment explaining the rationale behind this specific version range, especially if there are known compatibility issues with certain versions. This can be helpful for future maintenance.


21-22: LGTM: run_exports section added.

The addition of the run_exports section with {{ pin_subpackage('viroconstrictor', max_pin="x") }} is a good practice. It ensures that when ViroConstrictor is used as a dependency in other packages, it will be compatible with minor and patch updates but not major version changes. This aligns well with semantic versioning principles.

Consider adding a brief comment explaining the rationale behind this pinning strategy, especially if there are specific compatibility concerns that drove this decision. This can be helpful for future maintainers.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 2092e27 and 0224088.

📒 Files selected for processing (1)
  • recipes/viroconstrictor/meta.yaml (3 hunks)
🔇 Additional comments (2)
recipes/viroconstrictor/meta.yaml (2)

20-20: LGTM: Build number increment is appropriate.

The build number has been correctly incremented from 0 to 1. This is the proper approach when making changes to a package recipe without altering the package version itself.


66-67: LGTM: New maintainers added.

The addition of 'raaijmag' and 'wolthuisr' as recipe maintainers is a positive change. It can help with the long-term maintenance and support of the package.

The AI summary mentions that 'KHajji' was removed from the maintainers list, but this is not visible in the provided diff. Could you please verify if 'KHajji' was indeed removed? If so, ensure that this removal was intentional and approved by the relevant parties.

✅ Verification successful

Verification Complete: 'KHajji' Removed from Maintainers List

'KHajji' has been successfully removed from the maintainers list in recipes/viroconstrictor/meta.yaml. The addition of 'raaijmag' and 'wolthuisr' as new maintainers is confirmed.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the removal of 'KHajji' from the maintainers list

# Test: Check if 'KHajji' is present in the current version of the file
if grep -q "KHajji" recipes/viroconstrictor/meta.yaml; then
    echo "'KHajji' is still present in the maintainers list."
else
    echo "'KHajji' is not present in the current maintainers list."
fi

# Test: Check the git history for the removal of 'KHajji'
git log -p recipes/viroconstrictor/meta.yaml | grep -B 5 -A 5 "KHajji"

Length of output: 591

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
please review & merge set to ask for merge
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants