Add meta_eukaryome_detect #51328
Add meta_eukaryome_detect #51328
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/meta_eukaryome_detect/meta.yml (1)
47-47: Remove extra blank line at the end of the file.To improve file consistency and adhere to YAML best practices, please remove the extra blank line at the end of the file.
Apply this change:
extra: recipe-maintainers: - fullama -🧰 Tools
🪛 yamllint
[warning] 47-47: too many blank lines
(1 > 0) (empty-lines)
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📒 Files selected for processing (1)
- recipes/meta_eukaryome_detect/meta.yml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/meta_eukaryome_detect/meta.yml
[warning] 47-47: too many blank lines
(1 > 0) (empty-lines)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/meta_eukaryome_detect/meta.yml (5)
1-10: LGTM! Package and source sections are well-defined.The package name and version are correctly set using Jinja2 variables, which is a good practice for maintainability. The source URL is properly constructed using these variables, following the standard PyPI format. The inclusion of a SHA256 checksum is crucial for verifying the integrity of the downloaded package.
Note: The syntax error reported by yamllint for the '%' character is a false positive. This is valid Jinja2 syntax in YAML and is commonly used in Conda recipes.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
35-42: LGTM! About section is comprehensive and well-documented.The about section provides all necessary metadata:
- Home URL is correctly specified.
- License information is clear (MIT License).
- A concise summary describes the package's functionality.
- Documentation and development URLs are provided.
This information is crucial for users to understand the package's purpose and find additional resources.
44-46: LGTM! Maintainer information is correctly specified.The extra section correctly lists the recipe maintainer as "fullama". This information is crucial for package management and future updates.
19-27: Verify run requirements and consider pandas version constraint.The host requirements look appropriate for building the package. However, for the run requirements:
- Please verify that all listed dependencies (ngless, samtools, pandas, requests) are necessary for the package's functionality.
- Consider if version constraints are needed for ngless, samtools, and requests.
- The pandas version constraint (>= 2.0) is quite recent. Consider if this strict requirement is necessary, as it might limit compatibility with other packages or older systems.
To help verify the dependencies, please run:
#!/bin/bash # Description: Search for import statements and usage of required packages # Test: Search for import statements and usage of required packages rg --type python 'import (ngless|samtools|pandas|requests)' -A 3 rg --type python '(ngless|samtools|pandas|requests)\.' -A 3This will help confirm the usage of these packages in the code and potentially identify any version-specific features being used.
12-17: LGTM! Build section is well-configured.The build configuration looks good:
- Build number is correctly set to 0 for a new package.
- The installation script using pip is appropriate.
- Marking the package as
noarch: pythonis correct if it's compatible with all Python versions and platforms.However, it's important to verify the correctness of the entry point:
Please run the following script to verify the entry point:
This will help ensure that the entry point
meta-eukaryome-detect = meta_eukaryome_detect.meta_eukaryome_detect:mainis correctly defined in the package's configuration.
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (3)
recipes/meta_eukaryome_detect/meta.yml (3)
15-15: Consider using underscores in the entry point name.The entry point name currently uses hyphens (
meta-eukaryome-detect). It's generally recommended to use underscores in Python package names and entry points for better compatibility. Consider changing it tometa_eukaryome_detect.Here's the suggested change:
- - meta-eukaryome-detect = meta_eukaryome_detect.meta_eukaryome_detect:main + - meta_eukaryome_detect = meta_eukaryome_detect.meta_eukaryome_detect:main
20-20: Remove trailing spaces.There are trailing spaces on this line. Please remove them to adhere to YAML best practices and resolve the linting error.
Here's the suggested change:
- +🧰 Tools
🪛 yamllint
[error] 20-20: trailing spaces
(trailing-spaces)
28-28: Fix pandas version requirement.The pandas version requirement has a trailing dot, which should be removed for consistency and to avoid potential issues.
Here's the suggested change:
- - pandas >= 2.0. + - pandas >= 2.0
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📒 Files selected for processing (1)
- recipes/meta_eukaryome_detect/meta.yml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/meta_eukaryome_detect/meta.yml
[error] 20-20: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/meta_eukaryome_detect/meta.yml (4)
1-6: LGTM: Package name and version are correctly defined.The package name and version are properly set using Jinja2 templating, which is the recommended approach for Bioconda recipes.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: LGTM: Source URL and checksum are correctly specified.The source URL is properly constructed using Jinja2 templating, and the SHA256 checksum is provided for package integrity verification.
37-44: LGTM: About section is complete and well-formatted.The about section provides all necessary metadata, including home URL, license information, summary, and documentation links. This follows Bioconda guidelines and best practices.
46-48: LGTM: Recipe maintainer is correctly specified.The extra section properly lists the recipe maintainer, which is important for package maintenance and communication.
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/meta_eukaryome_detect/meta.yml (2)
12-20: LGTM: Build configuration looks good, with a minor formatting issue.The build configuration is correct, including the noarch specification and the addition of the run_exports section for version pinning. However, there's a minor formatting issue to address:
Please remove the trailing space on line 20:
run_exports: {{ pin_subpackage(name, max_pin="x") }} - +🧰 Tools
🪛 yamllint
[error] 20-20: trailing spaces
(trailing-spaces)
31-35: Good improvements, consider adding a version check.The test section has been improved by addressing the inconsistency in naming (using underscores consistently). However, as suggested in previous reviews, it would be beneficial to add a version check for more comprehensive testing.
Consider adding a version check to the test commands:
test: imports: - meta_eukaryome_detect commands: - meta_eukaryome_detect --help + - meta_eukaryome_detect --versionThis addition will help ensure that the package is correctly installed and can report its version.
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📒 Files selected for processing (1)
- recipes/meta_eukaryome_detect/meta.yml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/meta_eukaryome_detect/meta.yml
[error] 20-20: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/meta_eukaryome_detect/meta.yml (4)
1-10: LGTM: Package metadata and source information updated correctly.The package version has been updated to 0.1.1, and the source URL reflects this change. The SHA256 checksum is provided for the new version, which is good practice for ensuring package integrity.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
37-44: LGTM: Comprehensive metadata provided.The about section is well-documented, providing all necessary metadata including the home page, license information, summary, and relevant URLs. The addition of the license family and license file is particularly good for compliance purposes.
46-48: LGTM: Recipe maintainer correctly specified.The extra section properly identifies the recipe maintainer.
1-1: Note on yamllint error: Can be safely ignored.The yamllint tool reports a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' is part of the Jinja2 template syntax, which is valid and commonly used in Conda recipe YAML files. No action is required to address this error.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/meta_eukaryome_detect/meta.yml (2)
12-20: LGTM: Build configuration is well-defined, with a minor formatting issue.The build section is correctly configured with the appropriate entry point, build script, and noarch specification. The inclusion of the
run_exportssection is a good practice for version pinning.However, there's a minor formatting issue:
Remove the trailing space on line 20:
run_exports: {{ pin_subpackage(name, max_pin="x") }} - +🧰 Tools
🪛 yamllint
[error] 20-20: trailing spaces
(trailing-spaces)
30-34: Improve test coverage: Add a version check.The test section looks good, with consistent use of underscores in both the import check and the command. However, to improve test coverage:
Consider adding a version check as suggested in a previous review:
test: imports: - meta_eukaryome_detect commands: - meta_eukaryome_detect --help + - meta_eukaryome_detect --versionThis addition will help ensure that the package is correctly installed and can report its version.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/meta_eukaryome_detect/meta.yml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/meta_eukaryome_detect/meta.yml
[error] 20-20: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/meta_eukaryome_detect/meta.yml (5)
1-10: LGTM: Package and source information are correctly defined.The package name, version, source URL, and SHA256 checksum are all properly specified. The version has been updated to 0.1.1, which matches the information in the PR summary.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
21-29: LGTM: Requirements are well-defined and appropriate.The host and run requirements are correctly specified. The pandas version has been properly updated to
>= 2.0as suggested in a previous review. The Python version requirement of >=3.11 is suitable for a modern package.
36-43: LGTM: About section is comprehensive and well-documented.The about section provides all necessary metadata, including the home page, license information (with family and file), a concise summary, and relevant URLs for documentation and development. This information is valuable for users and maintainers of the package.
45-47: LGTM: Recipe maintainer is correctly specified.The extra section properly identifies "fullama" as the recipe maintainer.
1-1: Note: Ignore yamllint syntax error for Jinja2 template.The yamllint tool reports a syntax error for the '%' character at the beginning of the file. This is a false positive, as the '%' is part of the Jinja2 template syntax, which is valid and commonly used in Conda recipe YAML files. No action is required to address this warning.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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