Update sequana_pipetools to 1.2.0

[BiocondaBot]

Update sequana_pipetools: 0.9.4 → 1.2.0

Info	Link or Description
Recipe	recipes/sequana_pipetools (click to view/edit other files)
Summary	A set of tools to help building or using Sequana pipelines
Home	https://github.com/sequana/sequana_pipetools
Releases	https://pypi.org/pypi/sequana_pipetools/json
Recipe Maintainer(s)	@cokelaer

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This pull request was automatically generated (see docs).

[dpryan79]

Missing dependencies: easydev, pykwalify

[coderabbitai]

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request introduces significant modifications to the meta.yaml file for the sequana_pipetools package. The version is updated from "0.9.4" to "1.1.0", accompanied by a corresponding SHA256 checksum update. The package name is now consistently in lowercase, and the source URL format has been adjusted to align with the new versioning scheme. In the build section, the script command has been revised to include --no-build-isolation and increased verbosity with -vvv. Entry points for sequana_completion and sequana_slurm_status have been redirected to new script locations. A new run_exports field has been added to pin the subpackage version. The requirements section specifies minimum versions for several dependencies, including the addition of charset-normalizer. The test commands have been simplified by removing output redirection. The about section sees a change in the home URL format, an updated license to "BSD-3-Clause," and the inclusion of a new documentation URL. The recipe-maintainers section remains unchanged except for formatting adjustments.

Possibly related PRs

• Update meta.yaml for spec2vec #49857: This PR updates the meta.yaml file for the spec2vec package, which includes changes to the version and the addition of a run_exports section, similar to the changes made in the main PR for sequana_pipetools.
• Update bactopia-teton to 1.1.0 #51086: The bactopia-teton package's meta.yaml file is updated with a new version and SHA256 checksum, paralleling the version increment and checksum update in the main PR.
• Update sequali to 0.12.0 #51271: The sequali package's meta.yaml file is updated with a new version and SHA256 checksum, reflecting similar changes to those in the main PR.
• Update gempipe to 1.35.4 #51330: The gempipe package's meta.yaml file is updated with a new version and SHA256 checksum, akin to the updates made in the main PR.
• Update seqfu to 1.22.3 #51410: This PR updates the seqfu package's meta.yaml file with a new version and SHA256 checksum, similar to the changes in the main PR.
• Update gempipe to 1.36.0 #51518: The gempipe package is updated again to a new version, reflecting the ongoing versioning changes similar to those in the main PR.
• Update gempipe to 1.37.0 #51600: Another update to the gempipe package's meta.yaml file, continuing the pattern of version updates seen in the main PR.
• Update pbmarkdup to 1.1.0 #51783: The pbmarkdup package's meta.yaml file is updated with a new version and the addition of a run_exports section, mirroring the changes in the main PR.

Suggested labels

please review & merge

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 7fd7d2e and b6938e9.

📒 Files selected for processing (1)

• recipes/sequana_pipetools/meta.yaml (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• recipes/sequana_pipetools/meta.yaml

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[coderabbitai]

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)

recipes/sequana_pipetools/meta.yaml (1)

47-48: Consider keeping test output visible.

The test commands have been simplified by removing output redirection. While this is generally good, it might hide potential warnings or errors. Consider keeping the output visible or redirecting it to a log file for better debugging capabilities.

Suggestion:

  commands:
    - sequana_completion --help > >(tee -a command_output.log) 2> >(tee -a command_error.log >&2)
    - sequana_slurm_status --help > >(tee -a command_output.log) 2> >(tee -a command_error.log >&2)

This will display the output while also saving it to log files.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 0599585 and 7fd7d2e.

📒 Files selected for processing (1)

• recipes/sequana_pipetools/meta.yaml (1 hunks)

🧰 Additional context used

🔇 Additional comments (6)

recipes/sequana_pipetools/meta.yaml (6)

2-3: LGTM: Package metadata updates look good.

The version has been correctly updated to 1.0.6, and the SHA256 checksum has been updated accordingly. The package name is now in lowercase, which is a best practice for conda recipes.

Also applies to: 6-6

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10-11: LGTM: Source URL update is correct.

The source URL has been properly updated to reflect the new version (1.0.6) of the package.

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25-41: Requirements updates look good and address PR comments.

1. The Python version requirement has been appropriately updated to >=3.8.
2. Specific version requirements for dependencies have been added, which helps ensure compatibility.
3. The switch from setuptools to poetry-core reflects a change in the build system.
4. The dependencies mentioned in the PR comment (easydev, pykwalify) are now included, addressing the concern about missing dependencies.

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51-55: LGTM: About section updates are beneficial.

The changes in the about section provide more accurate and up-to-date information:

1. The home URL format has been updated.
2. The license has been correctly specified as BSD-3-Clause.
3. A new documentation URL has been added, which is helpful for users.

These updates improve the metadata quality of the package.

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1-59: Summary of review for sequana_pipetools update

Overall, the changes in this update are positive and align well with the PR objectives. The package has been updated to version 1.0.6 with appropriate modifications throughout the recipe. Key points:

1. Package metadata, source URL, and version have been correctly updated.
2. Build script changes include potential concerns with --no-build-isolation.
3. Requirements have been updated, addressing the PR comment about missing dependencies.
4. Test commands have been simplified, but consider keeping output visible for debugging.
5. About section updates provide more accurate and helpful information.

Main areas requiring attention:

• Verify that --no-build-isolation doesn't cause dependency conflicts.
• Consider modifying test commands to preserve output visibility.

Please address these concerns and make any necessary adjustments before merging.

🧰 Tools

🪛 yamllint

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

(syntax)

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15-21: Build script changes require attention.

1. The addition of --no-build-isolation to the build script might cause issues if there are conflicting dependencies. Please ensure this doesn't lead to unexpected behavior.
2. The -vvv flag increases verbosity, which can be helpful for debugging but may produce excessive output.
3. Entry point updates seem to reflect changes in the package structure. Verify that these new paths are correct.
4. The addition of run_exports is good for maintaining version consistency.

To check for potential dependency conflicts, run: