Update dnaio dependency for cutadapt

[rhpvorderman]

ping @marcelm

This updates the dnaio dependency to 1.2.2 which fixes a bug in the uBAM reader. This will make a new biocontainer available without the bug.

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request involves modifications to the meta.yaml file for the cutadapt package. The package version has been updated to "4.9", and the build number has been incremented from 1 to 2. The source section now includes a specified URL for the package tarball along with a SHA256 checksum for integrity verification. In the requirements section, the minimum version of the dnaio dependency has been revised from >=1.2.0 to >=1.2.2. The build section retains the existing installation script and the stipulation to skip builds for Python versions below 3.8. The test section remains unchanged, including an import test for cutadapt and a command to verify the version. Additionally, the about and extra sections have not been altered, continuing to provide metadata about the package.

Possibly related PRs

• Update dnaio to 1.2.2 #51157: This PR updates the dnaio package version from 1.2.1 to 1.2.2, which is directly related to the main PR's change of the dnaio dependency version from >=1.2.0 to >=1.2.2.

Suggested labels

please review & merge

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 64e6279 and dbaf313.

📒 Files selected for processing (1)

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

🧰 Additional context used

🔇 Additional comments (3)

recipes/cutadapt/meta.yaml (3)

12-12: LGTM: Build number increment is appropriate.

The build number has been correctly incremented from 1 to 2. This change is necessary to ensure that users receive the updated package with the new dnaio dependency when they update their conda environments.

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Line range hint 1-58: Summary: Changes are appropriate and align with PR objectives.

The modifications to the meta.yaml file for cutadapt are minimal and focused:

1. The build number has been incremented from 1 to 2.
2. The dnaio dependency has been updated from >=1.2.0 to >=1.2.2.

These changes align with the PR objectives of updating the dnaio dependency to address a bug in the uBAM reader. The build number increment ensures that users will receive the updated package.

The rest of the file, including other dependencies, build instructions, and metadata, remains unchanged, which is appropriate given the focused nature of this update.

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29-29: LGTM: dnaio dependency update addresses the uBAM reader bug.

The update of the dnaio dependency from >=1.2.0 to >=1.2.2 aligns with the PR objectives and should resolve the reported bug in the uBAM reader. The use of '>=' maintains backwards compatibility.

To ensure this change doesn't introduce any unexpected issues, please run the following verification script:

This script will create a test environment with the updated versions, verify that cutadapt works, and check for any potential conflicts with other packages in the bioconda channel.

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