Add get_mnv #51178
Add get_mnv #51178
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (4)
recipes/get_mnv/meta.yaml (4)
13-15: LGTM: Build section is well-defined, with a minor suggestion.The build section is correctly structured for a Rust package. The use of
--no-trackand--lockedflags ensures reproducibility, which is crucial for Bioconda packages.Consider adding the
--jobs 1flag to thecargo installcommand to ensure consistent builds across different environments. This can help prevent potential issues with parallel builds.- script: "cargo install --no-track --locked --verbose --root \"${PREFIX}\" --path ." + script: "cargo install --no-track --locked --verbose --jobs 1 --root \"${PREFIX}\" --path ."
17-19: LGTM: Build requirements are correctly specified.The requirements section correctly specifies the Rust compiler as the only build dependency, which is appropriate for a Rust package.
Consider adding a
hostsection to specify any runtime dependencies if the package requires any. If there are no runtime dependencies, you can leave it as is.requirements: build: - {{ compiler('rust') }} host: # Add any runtime dependencies here, if needed
21-23: LGTM: Test command is appropriate, with suggestions for improvement.The test command correctly checks if the
get_mnvbinary is installed and runs without errors.Consider the following improvements:
- Remove or translate the Spanish comment to English for consistency.
- Add more comprehensive tests if possible, such as running the tool with sample input data.
Here's a suggested revision:
test: commands: - get_mnv --help - get_mnv --version # Add more test commands here, e.g.: # - get_mnv sample_input.vcf > output.vcf
40-40: Minor: Remove extra blank lines at the end of the file.To adhere to YAML best practices, remove the extra blank lines at the end of the file. This will resolve the yamllint warning about too many blank lines.
extra: recipe-maintainers: - PathoGenOmics-Lab - -🧰 Tools
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Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/get_mnv/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/get_mnv/meta.yaml
[warning] 40-40: too many blank lines
(2 > 0) (empty-lines)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/get_mnv/meta.yaml (4)
1-3: LGTM: Package version and SHA256 are correctly defined.The use of Jinja2 variables for name, version, and SHA256 is appropriate and follows best practices. This approach allows for easy updates in the future.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
5-7: LGTM: Package name and version are correctly defined.The package section is well-structured, using Jinja2 variables correctly. The use of the
|lowerfilter for the package name ensures consistency with Bioconda naming conventions.
9-11: LGTM: Source URL and SHA256 checksum are correctly defined.The source section is well-structured, using Jinja2 variables to construct the URL. The inclusion of the SHA256 checksum ensures package integrity during the build process.
1-40: Overall: Well-structured Bioconda recipe with minor improvements needed.This
meta.yamlfile for theget_mnvpackage is generally well-structured and follows Bioconda guidelines. Here's a summary of the key points:
- The package, source, and build sections are correctly defined.
- Build requirements are appropriately specified for a Rust package.
- The test section includes a basic functionality check.
- The about and extra sections provide comprehensive information about the package.
To further improve the recipe, please address the following:
- Correct the license typo from "GLP-3.0" to "GPL-3.0".
- Consider adding more comprehensive test commands.
- Remove extra blank lines at the end of the file.
- Optional: Add category information to the
extrasection for better discoverability.Once these minor issues are addressed, the recipe should be ready for inclusion in the Bioconda repository.
🧰 Tools
🪛 yamllint
[warning] 40-40: too many blank lines
(2 > 0) (empty-lines)
[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/get_mnv/meta.yaml
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| about: | ||
| home: https://github.com/PathoGenOmics-Lab/get_mnv | ||
| license: GLP-3.0 | ||
| license_file: LICENSE | ||
| summary: 'Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences.' | ||
| description: | | ||
| get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data. | ||
| doc_url: https://github.com/PathoGenOmics-Lab/get_mnv | ||
| dev_url: https://github.com/PathoGenOmics-Lab/get_mnv | ||
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| extra: | ||
| recipe-maintainers: | ||
| - PathoGenOmics-Lab |
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LGTM: About and extra sections are well-defined, with a minor correction needed.
The about and extra sections provide comprehensive information about the package and its maintenance.
There's a typo in the license field. It should be "GPL-3.0" instead of "GLP-3.0". Please correct this to ensure proper licensing information.
- license: GLP-3.0
+ license: GPL-3.0Consider adding more specific categories to help users find the tool more easily. You can add a categories field under the extra section. For example:
extra:
recipe-maintainers:
- PathoGenOmics-Lab
categories:
- Genomics
- Variant Analysis
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/get_mnv/meta.yaml (2)
17-23: LGTM: Requirements and test sections are correct, but translate the comment.The build requirement correctly specifies the Rust compiler, and the test command appropriately checks if the
get_mnvbinary is installed. However, there's a minor issue:Please translate the Spanish comment on line 23 to English for consistency. Here's the suggested change:
- # Asegúrate de que `get_mnv` sea el nombre del binario + # Make sure `get_mnv` is the name of the binary
36-42: LGTM: Extra section is well-defined, with a minor formatting issue.The extra section includes appropriate recipe-maintainers and categories, following the suggestions from past review comments. The categories accurately reflect the tool's functionality.
There's an extra blank line at the end of the file. To address the yamllint warning, please remove the extra blank line:
- Genomics - Variant Analysis -🧰 Tools
🪛 yamllint
[warning] 42-42: too many blank lines
(1 > 0) (empty-lines)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/get_mnv/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/get_mnv/meta.yaml
[warning] 42-42: too many blank lines
(1 > 0) (empty-lines)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (7)
recipes/get_mnv/meta.yaml (7)
1-3: LGTM: Jinja2 variables are well-defined.The use of Jinja2 variables for name, version, and SHA256 checksum is a good practice for maintainability. The version number follows semantic versioning, and the SHA256 checksum is provided, which is important for package integrity.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
5-7: LGTM: Package section is correctly defined.The package name and version are set using Jinja2 variables, ensuring consistency. Converting the name to lowercase is a good practice for package naming conventions.
9-11: LGTM: Source section is properly configured.The source URL is correctly constructed using Jinja2 variables, following the GitHub release pattern. The use of Jinja2 variables for both the URL and SHA256 checksum ensures consistency and integrity.
26-34: LGTM: About section is comprehensive and follows guidelines.The about section provides all necessary information, including home, license, summary, description, and URLs. The license is correctly specified as GPL-3.0, addressing the issue mentioned in past review comments. The description clearly explains the tool's functionality.
1-3: Note: Ignore yamllint syntax error for Jinja2 variables.The yamllint tool reports a syntax error for the Jinja2 variables at the beginning of the file. This is a false positive and can be safely ignored, as Jinja2 syntax is valid and commonly used in Bioconda recipe files.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-42: Overall: The recipe is well-structured and ready for submission.The
meta.yamlfile for theget_mnvpackage is comprehensive and follows Bioconda guidelines. It includes all necessary sections: package information, source, build instructions, requirements, tests, about section, and extra metadata. The recipe addresses previous review comments and generally adheres to best practices.Minor suggestions for improvement have been made, including:
- Verifying the Cargo install command against Bioconda best practices for Rust packages.
- Translating a Spanish comment to English.
- Removing an extra blank line at the end of the file.
Once these minor adjustments are made, the recipe should be ready for submission to the Bioconda repository.
🧰 Tools
🪛 yamllint
[warning] 42-42: too many blank lines
(1 > 0) (empty-lines)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-15: LGTM: Build section looks good, but verify Cargo install command.The build number is correctly set to 0 for a new package. The Cargo install command appears to be correct, but it's worth verifying if it follows Bioconda best practices for Rust packages.
To verify the Cargo install command, please run the following script:
✅ Verification successful
To further verify if the
cargo installcommand follows Bioconda best practices, please run the following script:shell
#!/bin/bashDescription: Search the entire repository for Rust or Cargo-related Bioconda guidelines
Search all markdown files for Rust or Cargo guidelines
rg --type md "rust|cargo"
To correctly verify if the
cargo installcommand follows Bioconda best practices, please run the following script:--- <!-- [monologue] [task review_comment_finalization_1/1] [observations] - The search for Rust or Cargo-related Bioconda guidelines returned no relevant results, indicating the absence of specific guidelines in markdown files. - Multiple existing Rust package recipes use the `cargo install` command in a consistent manner. - The `cargo install` command in `recipes/get_mnv/meta.yaml` aligns with how it's used in other recipes. [analysis] - Despite the lack of explicit guidelines in the documentation, the consistent use of `cargo install` across multiple recipes suggests it's an accepted practice within the repository. - The failure to find specific guidelines does not indicate a problem since the pattern is uniformly applied. [actions] - Conclude that the `cargo install` command follows the established practices in the codebase. - Approve the build section as it aligns with existing patterns. --> **Verified: `cargo install` command follows existing Bioconda recipes.** - The build script in `recipes/get_mnv/meta.yaml` uses `cargo install` similarly to other Rust package recipes, indicating adherence to common patterns. </details> <details> <summary>🏁 Scripts executed</summary> The following scripts were executed for the analysis: Script: ```shell #!/bin/bash # Description: Check if there are any Bioconda guidelines for Rust package installation # Search for Rust-related guidelines in Bioconda documentation rg --type md "rust|cargo" "$(fd -t d -d 1 docs)" # Check other Rust package recipes for comparison fd -e yaml . recipes | xargs rg "cargo install"Length of output: 773
Script:
Length of output: 98
Script:
Length of output: 98
Script:
#!/bin/bash # Description: Search the entire repository for Rust or Cargo-related Bioconda guidelines # Search all markdown files for Rust or Cargo guidelines rg --type md "rust|cargo"Length of output: 135
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/get_mnv/meta.yaml (2)
13-17: LGTM: Build section is well-configured, with a minor suggestion.The build configuration looks good. The use of Cargo for installation is appropriate for a Rust package, and the inclusion of the
run_exportsdirective is a good practice for ensuring proper versioning.Consider translating the Spanish comment on line 17 to English for consistency:
- - {{ pin_subpackage(name, max_pin="x") }} # Asegura que el paquete sea correctamente versionado en futuras dependencias + - {{ pin_subpackage(name, max_pin="x") }} # Ensures that the package is correctly versioned in future dependencies
37-43: LGTM: Extra section is well-defined, with a minor formatting suggestion.The extra section correctly lists the recipe maintainer and includes appropriate categories as suggested in previous reviews, which will help with the tool's discoverability.
To address the yamllint warning, remove the extra blank line at the end of the file:
- Genomics - Variant Analysis -🧰 Tools
🪛 yamllint
[warning] 43-43: too many blank lines
(1 > 0) (empty-lines)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/get_mnv/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/get_mnv/meta.yaml
[warning] 43-43: too many blank lines
(1 > 0) (empty-lines)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/get_mnv/meta.yaml (6)
1-7: LGTM: Package and version declaration look good.The use of Jinja2 variables for name, version, and sha256 is a good practice for maintainability. The package name is correctly set to lowercase, and the version is properly defined.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source section is well-defined.The source URL correctly points to a GitHub release, and the use of Jinja2 variables in the URL is appropriate. The inclusion of the sha256 checksum is crucial for package verification.
27-35: LGTM: About section is comprehensive and well-defined.The about section provides all necessary information, including the home page, license (correctly specified as GPL-3.0), summary, description, and relevant URLs. The description clearly explains the tool's purpose and functionality.
1-3: Note on yamllint error: False positive due to Jinja2 templating.The yamllint error reported for line 1 ("syntax error: found character '%' that cannot start any token") can be safely ignored. This is a false positive due to the use of Jinja2 templating, which is standard practice in Bioconda recipes. The
{% set ... %}syntax is correct and should not be changed.🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-43: Overall, the recipe is well-structured and adheres to Bioconda guidelines.The
meta.yamlfile for theget_mnvpackage is comprehensive and provides all necessary information for building, testing, and describing the package. The use of Jinja2 templating, appropriate sections, and correct specification of build requirements demonstrate good practices in recipe creation.Minor suggestions have been made for consistency (translating comments to English) and improvements (enhancing test coverage). These changes, while beneficial, are not critical for the recipe's functionality.
Please address the suggestions at your discretion, particularly focusing on:
- Verifying any potential runtime dependencies
- Enhancing the test section with more comprehensive checks
- Removing the extra blank line at the end of the file
Once these minor points are addressed, the recipe should be ready for inclusion in the Bioconda repository.
🧰 Tools
🪛 yamllint
[warning] 43-43: too many blank lines
(1 > 0) (empty-lines)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
19-21: LGTM: Requirements section is correct, with a suggestion for verification.The Rust compiler is correctly specified as a build requirement.
Please verify if there are any additional runtime dependencies for the
get_mnvtool. If there are none, the current configuration is correct. Otherwise, consider adding them under arun:subsection. To help with this verification, you can run the following command:This script will search for external crate usage in the Rust source files and optionally check the Cargo.toml file for listed dependencies.
recipes/get_mnv/meta.yaml
Outdated
| test: | ||
| commands: | ||
| - get_mnv --help # Asegúrate de que `get_mnv` sea el nombre del binario |
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🛠️ Refactor suggestion
Enhance test coverage and maintain consistency.
While the current test ensures that the get_mnv binary is installed and executable, consider adding more comprehensive tests to verify the tool's functionality.
- Translate the Spanish comment to English for consistency:
- - get_mnv --help # Asegúrate de que `get_mnv` sea el nombre del binario
+ - get_mnv --help # Ensure that `get_mnv` is the correct binary name- Consider adding more test commands to verify key functionalities of the tool. For example:
test:
commands:
- get_mnv --help
- get_mnv --version
- get_mnv --test-data # If there's a test data optionWould you like assistance in generating more comprehensive test commands based on the tool's functionality?
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/get_mnv/meta.yaml (2)
13-26: LGTM: Build section is well-configured, with a minor suggestion.The build configuration is comprehensive and correct. Setting environment variables ensures proper paths, and the use of
run_exportsis good for maintaining version consistency.Consider translating the Spanish comment to English for consistency:
- - {{ pin_subpackage(name, max_pin="x") }} # Asegura que el paquete se versionee correctamente para las dependencias futuras. + - {{ pin_subpackage(name, max_pin="x") }} # Ensures that the package is correctly versioned for future dependencies.
53-59: LGTM: Extra section is well-defined, with a minor formatting suggestion.The extra section correctly specifies the recipe maintainer and includes the suggested categories, which is great for improving the discoverability of the tool.
Remove the extra blank lines at the end of the file to address the yamllint warning:
- Genomics - Variant Analysis - -🧰 Tools
🪛 yamllint
[warning] 59-59: too many blank lines
(1 > 0) (empty-lines)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/get_mnv/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/get_mnv/meta.yaml
[warning] 59-59: 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/get_mnv/meta.yaml (5)
1-7: LGTM: Package and version section is well-defined.The use of Jinja2 templating for name and version, along with the provided SHA256 checksum, follows best practices. The package section is correctly formatted.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source section is correctly configured.The URL is properly formatted for a GitHub release, and the use of templated values ensures consistency with the package section. The SHA256 checksum is correctly referenced.
28-37: LGTM: Requirements section is comprehensive and appropriate.The build and run requirements are well-defined for a Rust project. Including OpenSSL as both a build and runtime dependency is correct, and the inclusion of libgcc for runtime compatibility is a good practice.
43-51: LGTM: About section is comprehensive and well-formatted.The about section provides all necessary information, including home, license, summary, and a clear description of the tool's functionality. The documentation and development URLs are correctly included. The license is correctly specified as GPL-3.0, addressing the issue mentioned in a past review comment.
1-1: Note on static analysis warning.The static analysis tool reports a syntax error for the '%' character on line 1. This is a false positive and can be safely ignored. The '%' character is correctly used here for Jinja2 templating, which is a common practice in Conda recipe files.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
recipes/get_mnv/meta.yaml
Outdated
| test: | ||
| commands: | ||
| - get_mnv --help # Verifica que el binario `get_mnv` se haya instalado correctamente. |
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🛠️ Refactor suggestion
Enhance test coverage and maintain consistency.
While the current test ensures that the get_mnv binary is installed and executable, consider adding more comprehensive tests to verify the tool's functionality.
- Translate the Spanish comment to English for consistency:
- - get_mnv --help # Verifica que el binario `get_mnv` se haya instalado correctamente.
+ - get_mnv --help # Verify that the `get_mnv` binary is installed correctly.- Consider adding more test commands to verify key functionalities of the tool. For example:
test:
commands:
- get_mnv --help
- get_mnv --version
- get_mnv --test-data # If there's a test data optionWould you like assistance in generating more comprehensive test commands based on the tool's functionality?
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/get_mnv/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/get_mnv/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/get_mnv/meta.yaml (6)
1-7: LGTM: Package metadata is well-defined.The package metadata section is correctly structured using Jinja2 variables for name, version, and SHA256 hash. This approach allows for easier updates in the future.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source information is correctly specified.The source section properly defines the URL for the GitHub release and includes the SHA256 hash for verification. The use of variables ensures consistency and ease of updates.
34-50: LGTM: Requirements are comprehensive and well-defined.The requirements section correctly specifies both build and run dependencies. The inclusion of necessary libraries like OpenSSL, Curl, and HTSlib aligns well with the build script's environment variables. This ensures that all required components are available for both building and running the package.
56-64: LGTM: About section is comprehensive and accurate.The about section provides all necessary information, including the home page, license, summary, and a detailed description of the tool's functionality. The license is correctly specified as "GPL-3.0", addressing the typo mentioned in a previous review comment. The documentation and development URLs are also properly included.
66-71: LGTM: Extra section is well-defined with appropriate categories.The extra section correctly specifies the recipe maintainer and includes relevant categories for the tool. The addition of "Genomics" and "Variant Analysis" categories, as suggested in a previous review, will help users find the tool more easily.
52-54: 🛠️ Refactor suggestionEnhance test coverage for better validation.
While the current test ensures that the
get_mnvbinary is installed and executable, consider adding more comprehensive tests to verify the tool's functionality.Consider expanding the test section with additional commands:
test: commands: - get_mnv --help - get_mnv --version - get_mnv --test # If there's a built-in test option # Add a command to run get_mnv with sample input, if possibleThese additional tests will provide better validation of the tool's installation and basic functionality.
recipes/get_mnv/meta.yaml
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| build: | ||
| number: 0 | ||
| script: | | ||
| export LANG=C.UTF-8 | ||
| export LC_ALL=C.UTF-8 | ||
| export RUST_BACKTRACE=1 | ||
| export OPENSSL_NO_VENDOR=1 | ||
| export OPENSSL_DIR=$PREFIX | ||
| export OPENSSL_INCLUDE_DIR=$PREFIX/include | ||
| export OPENSSL_LIB_DIR=$PREFIX/lib | ||
| export CURL_STATIC_SSL=1 | ||
| export CURL_SYS_STATIC=1 | ||
| export CARGO_NET_OFFLINE=true | ||
| export HTS_LIB_DIR=$PREFIX/lib | ||
| export HTS_INCLUDE_DIR=$PREFIX/include | ||
| export HTS_STATIC=1 | ||
| export HTS_SYS_BUNDLED=0 | ||
| cargo install --no-track --locked --verbose --root "${PREFIX}" --path . | ||
| run_exports: | ||
| - {{ pin_subpackage(name, max_pin="x") }} |
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Consider removing CARGO_NET_OFFLINE environment variable.
The build section is well-structured with appropriate environment variable settings for OpenSSL, Curl, and HTSlib. However, there's a potential issue:
The CARGO_NET_OFFLINE=true setting might cause problems during the build process by preventing Cargo from downloading any dependencies. This could lead to build failures if all dependencies are not already available locally.
Consider removing this line or setting it to false:
- export CARGO_NET_OFFLINE=true
+ # export CARGO_NET_OFFLINE=false # Allow Cargo to download dependencies if neededThis change will allow Cargo to download any missing dependencies during the build process.
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| build: | |
| number: 0 | |
| script: | | |
| export LANG=C.UTF-8 | |
| export LC_ALL=C.UTF-8 | |
| export RUST_BACKTRACE=1 | |
| export OPENSSL_NO_VENDOR=1 | |
| export OPENSSL_DIR=$PREFIX | |
| export OPENSSL_INCLUDE_DIR=$PREFIX/include | |
| export OPENSSL_LIB_DIR=$PREFIX/lib | |
| export CURL_STATIC_SSL=1 | |
| export CURL_SYS_STATIC=1 | |
| export CARGO_NET_OFFLINE=true | |
| export HTS_LIB_DIR=$PREFIX/lib | |
| export HTS_INCLUDE_DIR=$PREFIX/include | |
| export HTS_STATIC=1 | |
| export HTS_SYS_BUNDLED=0 | |
| cargo install --no-track --locked --verbose --root "${PREFIX}" --path . | |
| run_exports: | |
| - {{ pin_subpackage(name, max_pin="x") }} | |
| build: | |
| number: 0 | |
| script: | | |
| export LANG=C.UTF-8 | |
| export LC_ALL=C.UTF-8 | |
| export RUST_BACKTRACE=1 | |
| export OPENSSL_NO_VENDOR=1 | |
| export OPENSSL_DIR=$PREFIX | |
| export OPENSSL_INCLUDE_DIR=$PREFIX/include | |
| export OPENSSL_LIB_DIR=$PREFIX/lib | |
| export CURL_STATIC_SSL=1 | |
| export CURL_SYS_STATIC=1 | |
| # export CARGO_NET_OFFLINE=false # Allow Cargo to download dependencies if needed | |
| export HTS_LIB_DIR=$PREFIX/lib | |
| export HTS_INCLUDE_DIR=$PREFIX/include | |
| export HTS_STATIC=1 | |
| export HTS_SYS_BUNDLED=0 | |
| cargo install --no-track --locked --verbose --root "${PREFIX}" --path . | |
| run_exports: | |
| - {{ pin_subpackage(name, max_pin="x") }} |
|
@BiocondaBot please add label |
| - openssl | ||
| - curl | ||
| - pkg-config | ||
| - htslib |
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The libraries should be in 'host', not 'build'
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||
| about: | ||
| home: "https://github.com/PathoGenOmics-Lab/get_mnv" | ||
| license: "GPL-3.0" |
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| license: "GPL-3.0" | |
| license: "GPL-3.0" | |
| license_family: GPL3 |
Co-authored-by: Martin Grigorov <[email protected]>
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Actionable comments posted: 3
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/get_mnv/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/get_mnv/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/get_mnv/meta.yaml (6)
1-7: LGTM: Package information is well-defined.The package name, version, and SHA256 checksum are correctly set using Jinja2 variables. This approach allows for easy updates in the future.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
9-11: LGTM: Source information is correctly specified.The source URL points to the correct GitHub release, and the SHA256 checksum is properly referenced using a Jinja2 variable.
13-32: LGTM: Build section is well-structured with appropriate settings.The build section is correctly configured:
- Build number is set to 0 for a new package.
- Environment variables are properly set for OpenSSL, Curl, and HTSlib.
- The
CARGO_NET_OFFLINEvariable is correctly commented out, addressing a previous review comment.- The cargo install command is correct.
- The
run_exportssection ensures proper versioning in dependencies.
66-71: LGTM: Extra section is well-defined.The extra section provides appropriate information:
- The recipe maintainer is correctly specified.
- The categories (Genomics and Variant Analysis) are relevant and help users find the tool easily.
This section effectively addresses a previous suggestion to add categories.
1-1: Note on yamllint warning: False positive.The yamllint tool reports a syntax error for the '%' character at the beginning of the file. This is a false positive and can be safely ignored. The '%' character is part of the Jinja2 template syntax, which is valid and commonly used in Bioconda recipes for variable substitution and control structures.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-71: Overall assessment: Good recipe with minor improvements needed.The
get_mnvrecipe is well-structured and follows most Bioconda guidelines. To fully comply with best practices and improve the recipe, please address the following key points:
- Restructure the requirements section by moving libraries to a 'host' section and using
{{ pin_compatible() }}in the 'run' section.- Enhance the test section with more comprehensive test commands.
- Update the license specification to "GPL-3.0" and add the license_family.
Once these changes are implemented, the recipe will be in excellent shape for inclusion in the Bioconda repository.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
recipes/get_mnv/meta.yaml
Outdated
| requirements: | ||
| build: | ||
| - {{ compiler('rust') }} | ||
| - openssl | ||
| - curl | ||
| - pkg-config | ||
| - htslib | ||
| - bzip2 | ||
| - xz | ||
| - zlib | ||
| run: | ||
| - openssl | ||
| - curl | ||
| - htslib | ||
| - bzip2 | ||
| - xz | ||
| - zlib |
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🛠️ Refactor suggestion
Refactor suggestion: Adjust requirements section structure.
Consider restructuring the requirements section to better align with Bioconda best practices:
- Move the libraries (openssl, curl, htslib, bzip2, xz, zlib) from the 'build' section to a new 'host' section.
- Keep only the Rust compiler and pkg-config in the 'build' section.
- Adjust the 'run' section to use the
{{ pin_compatible() }}function for the libraries.
Here's a suggested restructure:
requirements:
build:
- {{ compiler('rust') }}
- pkg-config
host:
- openssl
- curl
- htslib
- bzip2
- xz
- zlib
run:
- {{ pin_compatible('openssl') }}
- {{ pin_compatible('curl') }}
- {{ pin_compatible('htslib') }}
- {{ pin_compatible('bzip2') }}
- {{ pin_compatible('xz') }}
- {{ pin_compatible('zlib') }}This structure ensures that the libraries are available at build time and properly pinned at runtime.
recipes/get_mnv/meta.yaml
Outdated
| about: | ||
| home: "https://github.com/PathoGenOmics-Lab/get_mnv" | ||
| license: "GPL-3.0-or-later" | ||
| license_file: LICENSE | ||
| summary: "Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences." | ||
| description: | | ||
| get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data. | ||
| doc_url: "https://github.com/PathoGenOmics-Lab/get_mnv" | ||
| dev_url: "https://github.com/PathoGenOmics-Lab/get_mnv" |
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Update license specification and LGTM for the rest.
The about section provides comprehensive information about the package. However, please update the license specification as per a previous review comment:
- license: "GPL-3.0-or-later"
+ license: "GPL-3.0"
+ license_family: GPL3This change ensures consistency with Bioconda's preferred license specification format.
The rest of the section, including the home page, summary, description, and URLs, is well-defined and informative.
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| about: | |
| home: "https://github.com/PathoGenOmics-Lab/get_mnv" | |
| license: "GPL-3.0-or-later" | |
| license_file: LICENSE | |
| summary: "Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences." | |
| description: | | |
| get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data. | |
| doc_url: "https://github.com/PathoGenOmics-Lab/get_mnv" | |
| dev_url: "https://github.com/PathoGenOmics-Lab/get_mnv" | |
| about: | |
| home: "https://github.com/PathoGenOmics-Lab/get_mnv" | |
| license: "GPL-3.0" | |
| license_family: GPL3 | |
| license_file: LICENSE | |
| summary: "Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences." | |
| description: | | |
| get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data. | |
| doc_url: "https://github.com/PathoGenOmics-Lab/get_mnv" | |
| dev_url: "https://github.com/PathoGenOmics-Lab/get_mnv" |
There was a problem hiding this comment.
Actionable comments posted: 3
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/get_mnv/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/get_mnv/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/get_mnv/meta.yaml (4)
1-11: LGTM: Package and source sections are well-defined.The package name, version, and source URL are correctly specified using Jinja2 variables. The SHA256 checksum is provided for integrity verification. This structure follows Bioconda best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-32: LGTM: Build section is comprehensive and follows best practices.The build section is well-structured with appropriate environment variable settings for OpenSSL, Curl, and HTSlib. The use of
run_exportsensures proper versioning in future dependencies.Good job on commenting out the
CARGO_NET_OFFLINEline. This allows Cargo to download any missing dependencies during the build process if needed.
62-67: LGTM: Extra section is well-defined.The extra section correctly specifies the recipe maintainer and includes relevant categories for the tool. This information will help users find the tool more easily.
1-1: Ignore yamllint false positive.The static analysis tool (yamllint) reports a syntax error for the '%' character. This is a false positive as the '%' is part of valid Jinja2 templating used in Bioconda recipes. No action is required to address this.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
| requirements: | ||
| build: | ||
| - {{ compiler('rust') }} | ||
|
|
||
| host: | ||
| - openssl | ||
| - curl | ||
| - pkg-config | ||
| - htslib | ||
| - bzip2 | ||
| - xz | ||
| - zlib |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add run section with pinned library versions.
The requirements section is well-structured with build and host sections. However, it's missing a run section to specify runtime dependencies. Consider adding a run section with pinned versions of the libraries:
run:
- {{ pin_compatible('openssl') }}
- {{ pin_compatible('curl') }}
- {{ pin_compatible('htslib') }}
- {{ pin_compatible('bzip2') }}
- {{ pin_compatible('xz') }}
- {{ pin_compatible('zlib') }}This ensures that the package uses compatible versions of the libraries at runtime.
| test: | ||
| commands: | ||
| - get_mnv --help |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Enhance test coverage.
While the current test ensures that the get_mnv binary is installed and executable, consider adding more comprehensive tests to verify the tool's functionality. For example:
test:
commands:
- get_mnv --help
- get_mnv --version
- get_mnv --test # If there's a built-in test option
# Add a command to run get_mnv on a small test dataset, if possibleThese additional tests would provide better assurance that the tool is functioning correctly after installation.
Would you like assistance in generating more specific test commands based on the tool's functionality?
recipes/get_mnv/meta.yaml
Outdated
| about: | ||
| home: "https://github.com/PathoGenOmics-Lab/get_mnv" | ||
| license: "GPL-3.0-or-later" | ||
| license_family: GPL3 | ||
| license_file: LICENSE | ||
| summary: "Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences." | ||
| description: | | ||
| get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data. | ||
| doc_url: "https://github.com/PathoGenOmics-Lab/get_mnv" | ||
| dev_url: "https://github.com/PathoGenOmics-Lab/get_mnv" |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Update license specification.
The about section provides comprehensive information about the package. However, please update the license specification as follows:
- license: "GPL-3.0-or-later"
+ license: "GPL-3.0"This change ensures consistency with Bioconda's preferred license specification format. The license_family: GPL3 entry is correct and should be kept.
The rest of the section, including the home page, summary, description, and URLs, is well-defined and informative.
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| about: | |
| home: "https://github.com/PathoGenOmics-Lab/get_mnv" | |
| license: "GPL-3.0-or-later" | |
| license_family: GPL3 | |
| license_file: LICENSE | |
| summary: "Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences." | |
| description: | | |
| get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data. | |
| doc_url: "https://github.com/PathoGenOmics-Lab/get_mnv" | |
| dev_url: "https://github.com/PathoGenOmics-Lab/get_mnv" | |
| about: | |
| home: "https://github.com/PathoGenOmics-Lab/get_mnv" | |
| license: "GPL-3.0" | |
| license_family: GPL3 | |
| license_file: LICENSE | |
| summary: "Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences." | |
| description: | | |
| get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data. | |
| doc_url: "https://github.com/PathoGenOmics-Lab/get_mnv" | |
| dev_url: "https://github.com/PathoGenOmics-Lab/get_mnv" |
|
Anything else is required @martin-g ? |
|
|
||
| about: | ||
| home: "https://github.com/PathoGenOmics-Lab/get_mnv" | ||
| license: "GPL-3.0" |
There was a problem hiding this comment.
| license: "GPL-3.0" | |
| license: "GPL-3.0-or-later" |
Add get_mnv, a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences.
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