Skip to content

feat: Allow default configuration of retrieve behaviour#60

Merged
johanneskoester merged 1 commit intosnakemake:mainfrom
MattMonk:local_and_retrieve
Mar 14, 2025
Merged

feat: Allow default configuration of retrieve behaviour#60
johanneskoester merged 1 commit intosnakemake:mainfrom
MattMonk:local_and_retrieve

Conversation

@MattMonk
Copy link
Copy Markdown
Contributor

@MattMonk MattMonk commented Mar 13, 2025 •
edited by coderabbitai bot
Loading

This allows for the retrieve argument to be set for a storage_provider the same way that keep_local can be already.

This is useful for example with the XRootD storage plugin where we typically want retrieve=False so this modification makes it easier to specify this instead of the deafult retrieve=True behaviour.

Required for snakemake/snakemake#3410.

Summary by CodeRabbit

  • New Features
    • Improved storage functionality now offers enhanced flexibility in controlling data retrieval. Users benefit from a default retrieval mode that can be easily overridden for a more tailored experience.

@MattMonk MattMonk self-assigned this Mar 13, 2025
@coderabbitai
Copy link
Copy Markdown
Contributor

coderabbitai bot commented Mar 13, 2025 •
edited
Loading

📝 Walkthrough

Walkthrough

The pull request introduces a new retrieve parameter to the __init__ method of the StorageProviderBase class with a default value of True. It also updates the object method, changing the retrieve parameter from a non-optional boolean with a default of True to an optional boolean defaulting to None. When None is passed to the object method, it now inherits the value from the instance attribute set during initialization. These changes allow for more flexible default behavior regarding object retrieval.

Changes

File Change Summary
snakemake_interface_storage_plugins/storage_provider.py Updated StorageProviderBase.__init__ to include a new parameter retrieve (default True) and assign it to self.retrieve; modified object method to accept retrieve as an optional boolean (default None) and use self.retrieve when not provided

Sequence Diagram(s)

sequenceDiagram
    participant Caller
    participant StorageProvider as StorageProviderBase
    Caller->>StorageProvider: Call __init__(..., retrieve=True)
    Caller->>StorageProvider: Call object(query, retrieve: None)
    StorageProvider-->>StorageProvider: Check if retrieve is None
    StorageProvider-->>StorageProvider: Set retrieve = self.retrieve
    StorageProvider-->>Caller: Return object data
Loading

Possibly related PRs

Suggested reviewers

  • chrisburr
  • johanneskoester

Tip

⚡🧪 Multi-step agentic review comment chat (experimental)
  • We're introducing multi-step agentic chat in review comments. This experimental feature enhances review discussions with the CodeRabbit agentic chat by enabling advanced interactions, including the ability to create pull requests directly from comments.
    - To enable this feature, set early_access to true under in the settings.
📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 860f976 and 9be64fb.

📒 Files selected for processing (1)
  • snakemake_interface_storage_plugins/storage_provider.py (4 hunks)
🧰 Additional context used
📓 Path-based instructions (1)
`**/*.py`: Do not try to improve formatting. Do not suggest ...

**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

  • snakemake_interface_storage_plugins/storage_provider.py
⏰ Context from checks skipped due to timeout of 90000ms (1)
  • GitHub Check: formatting
🔇 Additional comments (4)
snakemake_interface_storage_plugins/storage_provider.py (4)

61-62: LGTM: Added new parameter to allow default retrieve behavior configuration.

The addition of the retrieve parameter with a default value of True maintains backward compatibility while enabling users to configure the default behavior.

74-74: LGTM: Properly storing the retrieve parameter as an instance attribute.

The retrieve parameter is correctly stored as an instance attribute, making it available for use in other methods.

171-171: LGTM: Modified retrieve parameter to be optional.

Changing the retrieve parameter to be Optional with a default value of None allows it to utilize the default value set during initialization when not explicitly provided.

183-185: LGTM: Properly implementing instance-level default for retrieve parameter.

This check correctly handles the case when retrieve is None by using the instance-level default value. This follows the same pattern used for the keep_local parameter, maintaining consistency in the codebase.

✨ Finishing Touches
  • 📝 Generate Docstrings

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ 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 generate docstrings to generate docstrings for this 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.

@MattMonk MattMonk mentioned this pull request Mar 13, 2025
Merged
2 tasks
@MattMonk MattMonk moved this from In progress to In review in Snakemake Hackathon March 2025 Mar 14, 2025
@johanneskoester johanneskoester merged commit a30f957 into snakemake:main Mar 14, 2025
6 checks passed
@github-project-automation github-project-automation bot moved this from In review to Done in Snakemake Hackathon March 2025 Mar 14, 2025
@github-actions github-actions bot mentioned this pull request Mar 14, 2025
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@johanneskoester johanneskoester johanneskoester approved these changes

Assignees

@MattMonk MattMonk

Labels

None yet

Projects

Snakemake Hackathon March 2025
Status: Done

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@MattMonk @johanneskoester