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: Fix path.py package renaming to path for Genomedata recipe #51022

Merged
merged 1 commit into from
Sep 29, 2024

Conversation

EricR86
Copy link
Contributor

@EricR86 EricR86 commented Sep 27, 2024

The path.py python package was renamed to path which has a corresponding conda package on conda-forge. The older conda package contains deprecated APIs which can no longer be used.

This fixes issues with the latest Genomedata Bioconda package release.


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

  • Chores
    • Incremented the build number to version 1.
    • Updated dependency name from path.py to path in the requirements.

Copy link
Contributor

coderabbitai bot commented Sep 27, 2024

📝 Walkthrough

Walkthrough

The pull request includes modifications to the recipes/genomedata/meta.yaml file. The build number has been incremented from 0 to 1, indicating an update in the build configuration. Additionally, the dependency path.py has been renamed to path in the requirements section, reflecting a change in the package name while maintaining the same functionality.

Changes

File Path Change Summary
recipes/genomedata/meta.yaml Build number incremented from 0 to 1; dependency changed from path.py to path.

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 4528093 and 629182c.

📒 Files selected for processing (1)
  • recipes/genomedata/meta.yaml (2 hunks)
🔇 Additional comments (4)
recipes/genomedata/meta.yaml (4)

15-15: Build number increment looks good.

The build number has been correctly incremented from 0 to 1. This is the appropriate action when making changes to the package without changing its version.


Line range hint 1-91: Summary: Changes look good and align with PR objectives

The changes made in this PR are appropriate and align well with the stated objectives:

  1. The build number has been correctly incremented.
  2. The dependency has been updated from path.py to path as required.
  3. The run_exports section is present, which adheres to Bioconda recipe guidelines.

These changes should resolve the issues with the latest release of the Genomedata Bioconda package. The verification steps suggested in the previous comments will help ensure that these changes are correctly implemented and don't introduce any unintended side effects.


Line range hint 31-32: Verification of run_exports section

The run_exports section is already present in the meta.yaml file, which aligns with the Bioconda recipe guidelines mentioned in the PR objectives. This helps prevent API, ABI, and CLI breakage issues in downstream recipes.

To ensure the run_exports section is correctly implemented, please run the following script:

This script will help confirm that the run_exports section is present and correctly formatted, and that it references the package name as expected.

✅ Verification successful

run_exports Section Verified Successfully

The run_exports section in recipes/genomedata/meta.yaml is correctly implemented and aligns with the PR objectives, ensuring compatibility with downstream recipes.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the run_exports section in meta.yaml

# Check if run_exports is present and correctly formatted
echo "Verifying run_exports section:"
rg -A 2 'run_exports:' recipes/genomedata/meta.yaml

# Check if the package name is correctly referenced in run_exports
echo "Verifying package name in run_exports:"
rg 'pin_subpackage\(name' recipes/genomedata/meta.yaml

Length of output: 374


48-48: Dependency update from path.py to path is correct.

The change from path.py to path aligns with the PR objectives and reflects the renaming of the Python package. This update is necessary to resolve issues with the latest release of the Genomedata Bioconda package.

To ensure this change doesn't affect other parts of the codebase, please run the following script:

This script will help identify any remaining references to path.py that might need updating, and verify that the new path import is used correctly.


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.

@EricR86
Copy link
Contributor Author

EricR86 commented Sep 27, 2024

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Sep 27, 2024
@martin-g martin-g merged commit 777cf9c into bioconda:master Sep 29, 2024
7 checks passed
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