Update dnaapler to 1.0.0

[BiocondaBot]

Update dnaapler: 0.8.1 → 1.0.0

Info	Link or Description
Recipe	recipes/dnaapler (click to view/edit other files)
Summary	Reorients assembled microbial sequences
Home	https://github.com/gbouras13/dnaapler
Releases	https://pypi.org/pypi/dnaapler/json
Recipe Maintainer(s)	@gbouras13

---

This pull request was automatically generated (see docs).

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request introduces several updates to the meta.yaml file for the dnaapler package. The version number is updated from 0.8.1 to 1.0.0, reflecting a major release. Alongside this, the SHA256 checksum for the source tarball is revised to ensure integrity, changing from 0e27734328a1e200c2181f7c02c6c5ffec0ea773bb5fa15eef3a7b2aeafc188b to 29c9aeeabb66c590ddcd7e98c947fb2535ef61307a7ebbbae4f534edd30b5ac3. Additionally, the requirements section sees a notable alteration: the dependency on blast with a version constraint of >=2.10 is removed and replaced with a specific dependency on mmseqs2, fixed at version 13.45111. The other dependencies listed in the run section remain unchanged. Overall, the changes are focused on updating the versioning and modifying a key dependency for the dnaapler package.

Possibly related PRs

• Update pbstarphase to 1.0.0 #51735: This PR involves updating the version number from 0.14.2 to 1.0.0 and modifying the SHA256 checksum, similar to the main PR's version update from 0.8.1 to 1.0.0.
• Update dnaio to 1.2.2 #51157: This PR updates the version of the dnaio package, which is relevant as it also involves changes to the meta.yaml file, although it does not directly relate to the specific dependencies or versioning of dnaapler.
• Update dnaio to 1.2.3 #52055: Similar to the main PR, this PR updates the version of the dnaio package in its meta.yaml file, indicating a pattern of version updates across related packages.

Warning

Rate limit exceeded

@BiocondaBot has exceeded the limit for the number of commits or files that can be reviewed per hour. Please wait 19 minutes and 48 seconds before requesting another review.

⌛ How to resolve this issue?

After the wait time has elapsed, a review can be triggered using the @coderabbitai review command as a PR comment. Alternatively, push new commits to this PR.

We recommend that you space out your commits to avoid hitting the rate limit.

🚦 How do rate limits work?

CodeRabbit enforces hourly rate limits for each developer per organization.

Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout.

Please see our FAQ for further information.

📥 Commits

Reviewing files that changed from the base of the PR and between bc01cb5 and 86b166c.

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between bc01cb5 and 86b166c.

📒 Files selected for processing (1)

• recipes/dnaapler/meta.yaml (2 hunks)

🔇 Additional comments (4)

recipes/dnaapler/meta.yaml (4)

Line range hint 12-19: Build configuration looks good

The package configuration follows conda packaging best practices with appropriate:

• noarch Python package declaration
• entry points configuration
• run exports pinning

🧰 Tools

🪛 yamllint

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

(syntax)

---

2-2: Verify version 1.0.0 availability on PyPI

This is a major version bump which might include breaking changes.

✅ Verification successful

Version 1.0.0 is available on PyPI

The version 1.0.0 exists on PyPI and matches the package's purpose of reorienting assembled microbial sequences. The version bump is valid.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify that version 1.0.0 exists on PyPI and check release notes
# for breaking changes

# Check if the version exists on PyPI
curl -s https://pypi.org/pypi/dnaapler/json | jq '.releases | has("1.0.0")'

# Get release date and information
curl -s https://pypi.org/pypi/dnaapler/1.0.0/json | jq '.info.release_date, .info.summary'

Length of output: 222

---

10-10: Verify SHA256 checksum against PyPI source

Let's ensure the SHA256 checksum matches the source tarball from PyPI.

---

27-27: Significant dependency change: BLAST replaced with MMseqs2

The replacement of blast >=2.10 with mmseqs2 ==13.45111 represents a major change in the underlying sequence search algorithm. Additionally, the exact version pinning of MMseqs2 might be too restrictive for users.

Consider using a more flexible version constraint (e.g., >=13.45111) unless there's a specific reason for exact version pinning.

---

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.