Update abismal to 3.2.4

[BiocondaBot]

Update abismal: 3.2.3 → 3.2.4

Info	Link or Description
Recipe	recipes/abismal (click to view/edit other files)
Summary	abismal is a fast and memory-efficient mapper for short bisulfite sequencing reads.

Home | https://github.com/smithlabcode/abismal
Releases |
Recipe Maintainer(s) | @andrewdavidsmith, @guilhermesena1
Author | @smithlabcode

---

This pull request was automatically generated (see docs).

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request involves an update to the meta.yaml file for the abismal package. The version number has been changed from "3.2.3" to "3.2.4". Alongside this version increment, the source URL has been updated to reflect the new version, changing from abismal-3.2.3.tar.gz to abismal-3.2.4.tar.gz. Additionally, the SHA256 checksum for the source file has been modified, updating from 0698ca408feb7e2650468e66dfdd4615e9405f64cd5496272fe2226cefd21322 to 822e5efe322f989c561a1fb728bd6f57f49d94033620eb1bc5046f22a8492544. There are no other modifications to the logic, error handling, or control flow in this update.

Possibly related PRs

• Update tissuumaps to 3.2.1.10 #51109: Involves updating the version and SHA256 checksum in the meta.yaml file, similar to the changes in the main PR for the abismal package.
• Update peaks2utr to 1.3.3 #51170: Updates the version and SHA256 checksum in the meta.yaml file, reflecting a similar type of change as seen in the main PR.
• Update bactopia-py to 1.2.1 #51226: Contains version and SHA256 checksum updates in the meta.yaml file for the bactopia-py package, aligning with the main PR changes.
• Update phylodm to 3.2.0 #51232: Updates the version and SHA256 checksum in the meta.yaml file, paralleling the updates in the main PR.
• Update civicpy to 3.1.2 #51252: Features version and SHA256 checksum changes in the meta.yaml file for the civicpy package, consistent with the main PR updates.
• Update picard to 3.3.0 #51282: Involves a version and SHA256 checksum update in the meta.yaml file, similar to the changes in the main PR.
• Update picard-slim to 3.3.0 #51286: Includes updates to the version and SHA256 checksum in the meta.yaml file, reflecting the same type of modifications as in the main PR.
• Update biobb_cmip to 5.0.0 #51455: Updates the version and SHA256 checksum in the meta.yaml file, consistent with the changes made in the main PR.
• Update pybbi to 0.4.1 #51483: Features version and SHA256 checksum updates in the meta.yaml file for the pybbi package, analogous to the changes in the main PR.

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 8dd05cc and 21d7063.

📒 Files selected for processing (1)

• recipes/abismal/meta.yaml (2 hunks)

🧰 Additional context used

🪛 yamllint

recipes/abismal/meta.yaml

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

🔇 Additional comments (5)

recipes/abismal/meta.yaml (5)

1-1: Version update looks good.

The version number has been correctly updated to 3.2.4, which aligns with the PR objective.

🧰 Tools

🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

---

1-1: Note on YAML syntax:

The static analysis tool (yamllint) reported a syntax error for the '%' character at the beginning of the file. This is a false positive. The '%' is part of a Jinja2 template syntax, which is commonly used in Conda recipes. The YAML file is correct and follows the expected format for Conda recipes.

🧰 Tools

🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

---

Line range hint 1-16: Summary: Version update changes look good

The changes in this file are consistent with updating the abismal package to version 3.2.4:

1. The version number has been updated.
2. The source URL has been modified to point to the new version.
3. The SHA256 checksum has been updated for the new version.

These changes are appropriate for a version bump, and no other modifications were made to the file. Please ensure to run the verification steps suggested in the previous comments to confirm the validity of the URL and checksum.

🧰 Tools

🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

---

15-15: Source URL update is correct.

The source URL has been properly updated to reflect the new version 3.2.4.

To ensure the URL is valid and the file exists, you can run the following command:

This command will perform a HEAD request to check if the file exists without downloading it. A successful response (HTTP 200) indicates that the file is accessible.

✅ Verification successful

Source URL accessibility verified.

The updated source URL is accessible and returns a successful HTTP 200 status code.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Verify that the source URL is accessible
curl -I https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz

Length of output: 682

---

Script:

#!/bin/bash
# Verify that the source URL is accessible by performing a HEAD request
curl -I https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz

Length of output: 4732

---

Script:

#!/bin/bash
# Verify that the source URL is accessible by performing a HEAD request and following redirects
curl -I -L https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz

Length of output: 5642

---

16-16: SHA256 checksum has been updated.

The SHA256 checksum has been changed to match the new version of the package.

To verify the correctness of the new SHA256 checksum, you can run the following commands:

This script will download the package and verify its checksum. If the verification passes, it confirms that the provided checksum is correct.

---

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.