add pantax #50983
add pantax #50983
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Actionable comments posted: 5
🧹 Outside diff range and nitpick comments (4)
recipes/pantax/build.sh (1)
1-19: Overall script review and suggestions for improvement.The build script covers the installation process for various components of the Pantax package, including Gurobi, VG tools, Pantax scripts, and Fastix. While it provides a good foundation, there are several areas where it could be improved:
- Error Handling: Implement consistent error handling throughout the script, especially for directory changes and critical operations.
- Flexibility: Make the script more adaptable to different Python versions and system configurations.
- Specificity: Be more specific when copying files to avoid including unnecessary items.
- Dependency Checks: Add checks for required tools and dependencies (e.g., Cargo) before attempting to use them.
- Documentation: Consider adding comments to explain the purpose of each major section and any non-obvious operations.
- Cleanup: Ensure temporary files or directories are cleaned up after installation.
These improvements will make the script more robust, maintainable, and less prone to errors during the installation process.
🧰 Tools
🪛 Shellcheck
[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 10-10: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
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[warning] 12-12: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
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[warning] 16-16: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
recipes/pantax/meta.yaml (3)
8-18: LGTM: Sources are well-defined with proper checksums.The source section is well-structured with URLs and SHA256 checksums for each component. The use of specific folders for Gurobi and VG is appropriate.
Consider adding a comment to explain why the Gurobi wheel and VG binary are included as separate sources. This would improve clarity for future maintainers.
🧰 Tools
🪛 yamllint
[error] 12-12: trailing spaces
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45-47: Consider adding more comprehensive tests.The current test command
pantax -his a good basic check to ensure the CLI is accessible. However, to improve the robustness of the package, consider adding more comprehensive tests. For example:
- Check the version:
pantax --version- Run a simple classification task with a small test dataset
- Verify the presence of key dependencies:
python -c "import pandas, numpy, networkx"Adding these tests would help ensure that the core functionality of the package is working as expected after installation.
1-56: Minor: Remove trailing spaces for better code hygiene.The static analysis tool reported several instances of trailing spaces in the YAML file. While these don't affect functionality, removing them improves code cleanliness and adheres to best practices.
Please remove trailing spaces from the following lines:
- Line 12
- Line 13
- Line 14
- Line 16
- Line 17
- Line 23
You can use your text editor's "trim trailing whitespace" feature or a command-line tool like
sedto automatically remove these spaces.🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 12-12: trailing spaces
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[error] 13-13: trailing spaces
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[error] 14-14: trailing spaces
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[error] 23-23: trailing spaces
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📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/pantax/build.sh (1 hunks)
- recipes/pantax/meta.yaml (1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/pantax/build.sh
[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 10-10: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 12-12: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 16-16: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/pantax/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 12-12: trailing spaces
(trailing-spaces)
[error] 13-13: trailing spaces
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[error] 14-14: trailing spaces
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[error] 16-16: trailing spaces
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🔇 Additional comments (5)
recipes/pantax/build.sh (1)
1-5: Verify the macOS installation process.The current implementation for macOS simply copies the entire source directory to the prefix directory. This approach might not be the intended behavior and could potentially include unnecessary files or miss important installation steps.
Please confirm if this is the correct installation process for macOS. If not, consider implementing a more comprehensive installation procedure similar to the one for other operating systems.
recipes/pantax/meta.yaml (4)
1-6: LGTM: Package name and version are well-defined.The use of Jinja2 templating for the package name and version is a good practice. The version number follows semantic versioning, which is appropriate for package management.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
20-23: LGTM: Build section is correctly configured.The build number is appropriately set to 0 for a new package. The use of
run_exportswithpin_subpackageis a good practice for maintaining ABI compatibility. The "x.x" pin allows updates to patch versions, which is generally a safe approach.🧰 Tools
🪛 yamllint
[error] 23-23: trailing spaces
(trailing-spaces)
49-52: LGTM: About section is informative and complete.The about section provides all necessary information: the home page URL, license (GPL-3.0), and a concise summary of the package's functionality. This is excellent for users and maintainers to quickly understand the purpose and terms of use for the package.
54-56: Please clarify the reason for skipping theshould_be_noarch_pythonlint.The
skip-lintssection is used to ignore theshould_be_noarch_pythonlint. While this may be necessary due to the nature of the package (bioinformatics tool with compiled dependencies), it would be helpful to have a comment explaining why this lint is being skipped. This will help future maintainers understand the reasoning behind this decision.Could you please add a comment explaining why the
should_be_noarch_pythonlint is being skipped? This will improve the maintainability of the package.
recipes/pantax/build.sh
Outdated
| mkdir -p ${PREFIX}/bin/tools | ||
| cd ../vg | ||
| cp vg* ${PREFIX}/bin/tools/vg |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve error handling and file copying specificity.
- Add error handling for the
cdcommand:
-cd ../vg
+cd ../vg || exit 1- Consider being more specific when copying files to avoid including unnecessary files:
-cp vg* ${PREFIX}/bin/tools/vg
+cp vg vg_* ${PREFIX}/bin/tools/This assumes that the main executable is named vg and any related files start with vg_. Adjust the pattern as needed for your specific use case.
📝 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.
| mkdir -p ${PREFIX}/bin/tools | |
| cd ../vg | |
| cp vg* ${PREFIX}/bin/tools/vg | |
| mkdir -p ${PREFIX}/bin/tools | |
| cd ../vg || exit 1 | |
| cp vg vg_* ${PREFIX}/bin/tools/ |
🧰 Tools
🪛 Shellcheck
[warning] 10-10: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
recipes/pantax/build.sh
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| cd $SRC_DIR/tools/fastix | ||
| cargo install fastix --root ./ | ||
| cp $SRC_DIR/tools/fastix/bin/fastix ${PREFIX}/bin/tools |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve error handling and add Cargo availability check.
- Add error handling for the
cdcommand:
-cd $SRC_DIR/tools/fastix
+cd $SRC_DIR/tools/fastix || exit 1- Add a check for Cargo availability before attempting to install Fastix:
+if ! command -v cargo &> /dev/null; then
+ echo "Cargo is not installed. Please install Rust and Cargo to build Fastix."
+ exit 1
+fi
cargo install fastix --root ./This change ensures that the script fails gracefully if Cargo is not available on the system.
📝 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.
| cd $SRC_DIR/tools/fastix | |
| cargo install fastix --root ./ | |
| cp $SRC_DIR/tools/fastix/bin/fastix ${PREFIX}/bin/tools | |
| cd $SRC_DIR/tools/fastix || exit 1 | |
| if ! command -v cargo &> /dev/null; then | |
| echo "Cargo is not installed. Please install Rust and Cargo to build Fastix." | |
| exit 1 | |
| fi | |
| cargo install fastix --root ./ | |
| cp $SRC_DIR/tools/fastix/bin/fastix ${PREFIX}/bin/tools |
🧰 Tools
🪛 Shellcheck
[warning] 16-16: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
recipes/pantax/build.sh
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| cd $SRC_DIR/scripts | ||
| chmod +x pantax | ||
| cp $SRC_DIR/scripts/pantax ${PREFIX}/bin | ||
| cp $SRC_DIR/scripts/*py ${PREFIX}/bin |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve error handling and file copying specificity.
- Add error handling for the
cdcommand:
-cd $SRC_DIR/scripts
+cd $SRC_DIR/scripts || exit 1- Consider being more specific when copying Python files to avoid including unnecessary files:
-cp $SRC_DIR/scripts/*py ${PREFIX}/bin
+cp $SRC_DIR/scripts/{file1.py,file2.py,file3.py} ${PREFIX}/binReplace file1.py, file2.py, etc., with the actual names of the Python scripts that need to be copied. This approach ensures that only the necessary files are included in the installation.
Committable suggestion was skipped due to low confidence.
🧰 Tools
🪛 Shellcheck
[warning] 12-12: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
recipes/pantax/build.sh
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| cd gurobi11 | ||
| ${PYTHON} -m pip install gurobipy-11.0.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl | ||
| rm gurobipy-11.0.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve error handling and Python version flexibility.
- Add error handling for the
cdcommand to ensure the script exits if the directory change fails:
-cd gurobi11
+cd gurobi11 || exit 1- Consider using a more flexible approach for the Python wheel file to support different Python versions:
-${PYTHON} -m pip install gurobipy-11.0.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
+${PYTHON} -m pip install gurobipy-11.0.2-cp${PYTHON_VERSION/./}-cp${PYTHON_VERSION/./}-manylinux2014_x86_64.manylinux_2_17_x86_64.whlThis assumes that the PYTHON_VERSION environment variable is available and set correctly.
Committable suggestion was skipped due to low confidence.
🧰 Tools
🪛 Shellcheck
[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
recipes/pantax/meta.yaml
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| requirements: | ||
| build: | ||
| - {{ compiler('rust') }} | ||
| host: | ||
| - python ==3.10 | ||
| - pip | ||
| run: | ||
| - python =3.10 | ||
| - samtools =1.19.2 | ||
| - bcftools =1.19 | ||
| - htslib =1.19.1 | ||
| - pggb =0.5.4 | ||
| - graphaligner =1.0.17 | ||
| - h5py =3.10.0 | ||
| - pandas =2.2.0 | ||
| - tqdm =4.66.1 | ||
| - numpy =1.26.3 | ||
| - networkx =3.2.1 | ||
| - time =1.8 | ||
|
|
There was a problem hiding this comment.
Consider relaxing Python version constraint and review 'time' dependency.
The requirements section is generally well-structured with specific versions for dependencies, which is good for reproducibility. However, there are two points to consider:
-
Python version is strictly pinned to 3.10. Consider allowing a range of Python versions (e.g.,
>=3.10,<3.11) to provide more flexibility for users while maintaining compatibility. -
The 'time' package is listed as a run dependency with version 1.8. This is unusual because 'time' is typically a built-in Python module. Please verify if this is a different 'time' package or if it can be removed from the dependencies.
Please review these points and update the requirements section accordingly.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (4)
recipes/pantax/meta.yaml (4)
20-24: LGTM: Build section is well-defined.The build section is correctly structured with:
- Skip for OSX platforms
- Build number set to 0
- Proper run exports definition
Consider adding a comment explaining why the build is skipped for OSX, for better maintainability. For example:
build: skip: True # [osx] # Pantax is not compatible with OSX due to <reason>🧰 Tools
🪛 yamllint
[error] 24-24: trailing spaces
(trailing-spaces)
46-48: LGTM: Basic test is present. Consider adding more comprehensive tests.The current test command
pantax -hverifies that the pantax CLI is accessible and can display help information, which is a good basic check.Consider adding more comprehensive tests to ensure proper functionality of the package. For example:
- Test a simple classification task with a small sample dataset.
- Verify the output format of the classification results.
- Check if all required dependencies are properly linked and functional.
55-57: LGTM: Lint skip is likely necessary. Consider adding a comment.The 'should_be_noarch_python' lint is skipped, which is probably necessary given the nature of the package (bioinformatics tool with compiled dependencies).
Consider adding a brief comment explaining why this lint is skipped for better maintainability. For example:
extra: skip-lints: - should_be_noarch_python # Pantax requires architecture-specific compiled dependencies
1-57: Minor: Clean up trailing spaces and ignore false positive yamllint warning.The yamllint tool reported several trailing spaces in the file. While these don't affect functionality, removing them improves code style.
Please remove trailing spaces from lines 12, 13, 14, 16, 17, and 24.
Note: The yamllint warning about the '%' character at the beginning of the file is a false positive. This character is part of the Jinja2 templating syntax used in Conda recipes and is correct in this context.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 12-12: trailing spaces
(trailing-spaces)
[error] 13-13: trailing spaces
(trailing-spaces)
[error] 14-14: trailing spaces
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[error] 16-16: trailing spaces
(trailing-spaces)
[error] 17-17: trailing spaces
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[error] 24-24: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/pantax/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/pantax/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 12-12: trailing spaces
(trailing-spaces)
[error] 13-13: trailing spaces
(trailing-spaces)
[error] 14-14: trailing spaces
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[error] 16-16: trailing spaces
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[error] 17-17: trailing spaces
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[error] 24-24: trailing spaces
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🔇 Additional comments (4)
recipes/pantax/meta.yaml (4)
1-6: LGTM: Package name and version are correctly defined.The package name "pantax" and version "1.0.1" are properly set using Jinja2 templating, which is a good practice for Conda recipes.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-18: LGTM: Sources are well-defined with proper versioning and checksums.The source section is correctly structured with:
- Main package source (pantax.tar.gz)
- Gurobi wheel for Python 3.10
- VG binary
Each source has a specific URL and SHA256 checksum, which is excellent for ensuring reproducibility. The use of designated folders for additional sources is also a good practice.
🧰 Tools
🪛 yamllint
[error] 12-12: trailing spaces
(trailing-spaces)
[error] 13-13: trailing spaces
(trailing-spaces)
[error] 14-14: trailing spaces
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[error] 16-16: trailing spaces
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[error] 17-17: trailing spaces
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26-44: Consider relaxing Python version constraint and review 'time' dependency.The requirements section is well-structured with specific versions for dependencies. However, there are two points to consider:
Python version is strictly pinned to 3.10. Consider allowing a range of Python versions (e.g.,
>=3.10,<3.11) to provide more flexibility for users while maintaining compatibility.The 'time' package is listed as a run dependency with version 1.8. This is unusual because 'time' is typically a built-in Python module. Please verify if this is a different 'time' package or if it can be removed from the dependencies.
These issues were previously mentioned in a past review comment. Please review and update the requirements section accordingly.
50-53: LGTM: About section is concise and informative.The about section provides essential information:
- Home page URL
- License (GPL-3.0)
- A brief summary of the package's functionality
This information is sufficient for users to understand the purpose and licensing of the package.
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/pantax/meta.yaml (2)
46-48: LGTM: Basic test is present, but consider adding more comprehensive tests.The current test checks if the CLI is accessible, which is a good start. However, consider adding more comprehensive tests to ensure the functionality of the package. For example:
- Test the import of the Python package (if applicable).
- Run a small example dataset through the main functionality.
- Check the output of a specific subcommand.
1-57: Minor: Remove trailing spaces for better code cleanliness.The static analysis tool reported several instances of trailing spaces. While these don't affect functionality, removing them improves code cleanliness. Consider using an editor with a trailing space removal feature or running a command to remove them.
You can use the following command to remove trailing spaces:
sed -i 's/[[:space:]]*$//' recipes/pantax/meta.yamlNote: The syntax error reported for the Jinja2 templating appears to be a false positive and can be ignored.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 12-12: trailing spaces
(trailing-spaces)
[error] 13-13: trailing spaces
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[error] 14-14: trailing spaces
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[error] 16-16: trailing spaces
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[error] 17-17: trailing spaces
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[error] 24-24: trailing spaces
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[error] 37-37: trailing spaces
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[error] 38-38: trailing spaces
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📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/pantax/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/pantax/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 12-12: trailing spaces
(trailing-spaces)
[error] 13-13: trailing spaces
(trailing-spaces)
[error] 14-14: trailing spaces
(trailing-spaces)
[error] 16-16: trailing spaces
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[error] 17-17: trailing spaces
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[error] 24-24: trailing spaces
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[error] 37-37: trailing spaces
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[error] 38-38: trailing spaces
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🔇 Additional comments (6)
recipes/pantax/meta.yaml (6)
1-6: LGTM: Package and version section looks good.The package name and version are correctly defined using Jinja2 templating, which is a good practice for maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
20-24: LGTM: Build section is well-defined, but verify OSX skip.The build section correctly specifies the build number and uses
run_exportsfor version consistency. However, the OSX build is skipped.Please confirm that skipping the OSX build is intentional and necessary for this package. You may want to check if there are any OS-specific dependencies or incompatibilities that justify this decision.
🧰 Tools
🪛 yamllint
[error] 24-24: trailing spaces
(trailing-spaces)
26-44: Consider relaxing Python version constraint and review 'time' dependency.The requirements section is well-structured with specific versions for dependencies, which is good for reproducibility. However, there are two points to consider:
Python version is strictly pinned to 3.10. Consider allowing a range of Python versions (e.g.,
>=3.10,<3.11) to provide more flexibility for users while maintaining compatibility.The 'time' package is listed as a run dependency with version 1.8. This is unusual because 'time' is typically a built-in Python module. Please verify if this is a different 'time' package or if it can be removed from the dependencies.
These points were raised in a previous review comment. Please address them if they haven't been resolved.
🧰 Tools
🪛 yamllint
[error] 37-37: trailing spaces
(trailing-spaces)
[error] 38-38: trailing spaces
(trailing-spaces)
50-53: LGTM: About section is complete and accurate.The about section provides all necessary information including the home page, license (GPL-3.0), and a concise summary of the package's functionality.
55-57: LGTM: Extra section is present, but verify the lint skip.The extra section correctly specifies a lint to skip. This aligns with the earlier decision to skip OSX builds, suggesting that the package is not architecture-independent.
Please confirm that skipping the 'should_be_noarch_python' lint is necessary for this package. This decision should be consistent with the package's architecture dependencies and the reason for skipping OSX builds.
8-18: LGTM: Source section is well-defined, but verify the multiple sources approach.The source section correctly specifies URLs and SHA256 checksums for the main package, Gurobi wheel, and VG binary. This approach ensures reproducibility and security. However, the use of multiple sources is somewhat unusual.
Please confirm that this multiple sources approach is necessary for the package and aligns with Bioconda best practices. You may want to run the following command to check if similar packages use this approach:
🧰 Tools
🪛 yamllint
[error] 12-12: trailing spaces
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[error] 13-13: trailing spaces
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[error] 14-14: trailing spaces
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
Docker image(s) built:
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Actionable comments posted: 4
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/pantax/build.sh (1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/pantax/build.sh
[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 11-11: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 15-15: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 21-21: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🔇 Additional comments (1)
recipes/pantax/build.sh (1)
21-23:⚠️ Potential issueImprove error handling and add Cargo availability check.
- Add error handling for the
cdcommand:-cd $SRC_DIR/tools/fastix +cd $SRC_DIR/tools/fastix || exit 1
- Add a check for Cargo availability before attempting to install Fastix:
+if ! command -v cargo &> /dev/null; then + echo "Cargo is not installed. Please install Rust and Cargo to build Fastix." + exit 1 +fi cargo install fastix --root ./This change ensures that the script fails gracefully if Cargo is not available on the system.
Likely invalid or redundant comment.
🧰 Tools
🪛 Shellcheck
[warning] 21-21: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
recipes/pantax/build.sh
Outdated
| mkdir -p ${PREFIX}/bin/tools | ||
| cd ${PREFIX}/vg | ||
| cp vg* ${PREFIX}/bin/tools/vg | ||
| chmod +x ${PREFIX}/bin/tools/vg |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve error handling and file copying specificity.
- Add error handling for the
cdcommand:
-cd ${PREFIX}/vg
+cd ${PREFIX}/vg || exit 1- Consider being more specific when copying files to avoid including unnecessary files:
-cp vg* ${PREFIX}/bin/tools/vg
+cp vg vg_* ${PREFIX}/bin/tools/This assumes that the main executable is named vg and any related files start with vg_. Adjust the pattern as needed for your specific use case.
📝 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.
| mkdir -p ${PREFIX}/bin/tools | |
| cd ${PREFIX}/vg | |
| cp vg* ${PREFIX}/bin/tools/vg | |
| chmod +x ${PREFIX}/bin/tools/vg | |
| mkdir -p ${PREFIX}/bin/tools | |
| cd ${PREFIX}/vg || exit 1 | |
| cp vg vg_* ${PREFIX}/bin/tools/ | |
| chmod +x ${PREFIX}/bin/tools/vg |
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🪛 Shellcheck
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recipes/pantax/build.sh
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| cd $SRC_DIR/scripts | ||
| chmod +x pantax | ||
| chmod +x data_preprocessing | ||
| cp $SRC_DIR/scripts/pantax $SRC_DIR/scripts/data_preprocessing ${PREFIX}/bin | ||
| cp $SRC_DIR/scripts/*py ${PREFIX}/bin |
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🛠️ Refactor suggestion
Improve error handling and file copying specificity.
- Add error handling for the
cdcommand:
-cd $SRC_DIR/scripts
+cd $SRC_DIR/scripts || exit 1- Consider being more specific when copying Python files to avoid including unnecessary files:
-cp $SRC_DIR/scripts/*py ${PREFIX}/bin
+cp $SRC_DIR/scripts/{pantax.py,data_preprocessing.py} ${PREFIX}/binReplace pantax.py and data_preprocessing.py with the actual names of the Python scripts that need to be copied. This approach ensures that only the necessary files are included in the installation.
Committable suggestion was skipped due to low confidence.
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recipes/pantax/build.sh
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| cd ${PREFIX}/gurobi11 | ||
| ${PYTHON} -m pip install gurobipy-11.0.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl | ||
| rm gurobipy-11.0.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
There was a problem hiding this comment.
Improve error handling and Python version flexibility.
- Add error handling for the
cdcommand:
-cd ${PREFIX}/gurobi11
+cd ${PREFIX}/gurobi11 || exit 1- Make the Python wheel installation more flexible:
-${PYTHON} -m pip install gurobipy-11.0.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
+${PYTHON} -m pip install gurobipy-11.0.2-cp${PYTHON_VERSION/./}-cp${PYTHON_VERSION/./}-manylinux2014_x86_64.manylinux_2_17_x86_64.whlThis assumes that the PYTHON_VERSION environment variable is available and set correctly. If it's not, you may need to extract it from ${PYTHON} or set it explicitly.
Committable suggestion was skipped due to low confidence.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (4)
recipes/pantax/meta.yaml (4)
8-18: LGTM: Source section is well-defined, but consider adding comments for clarity.The source section correctly specifies multiple sources with their respective URLs and SHA256 checksums. This is good for security and reproducibility. However, to improve clarity, consider adding comments explaining the purpose of each source, especially for the Gurobi wheel and VG binary.
For example:
source: - url: https://github.com/LuoGroup2023/PanTax/releases/download/v{{ version }}/{{ name }}.tar.gz sha256: c14a46b41f580cf39ad502049d267cd31bbfd4dc05028215cc669c0e52f58ce7 # Main pantax package - url: https://files.pythonhosted.org/packages/07/0f/6039cf6e22f9cbec57cdedff103949e4856c18fd2cb714bc70cdc8b52941/gurobipy-11.0.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl sha256: 164e72462c2f1a705fcec73acc060aa639e745827bfe877714ff7b2ccabc5237 folder: gurobi11 # Gurobi optimization library wheel - url: https://github.com/vgteam/vg/releases/download/v1.52.0/vg sha256: 07776b51aa6494b45982e4134eb84005ddc743e81c67e61fa52bff211d81777c folder: vg # Variation graph toolkit binaryThis addition would make the purpose of each source more evident to maintainers and contributors.
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26-44: Consider relaxing the Python version constraint.The requirements section is well-structured with specific versions for dependencies, which is excellent for reproducibility. However, the Python version is strictly pinned to 3.10. Consider allowing a range of Python versions (e.g.,
>=3.10,<3.11) to provide more flexibility for users while maintaining compatibility.For example:
host: - python >=3.10,<3.11 - pip run: - python >=3.10,<3.11This change would allow for minor version updates of Python 3.10 while ensuring compatibility with the Gurobi wheel.
The rest of the requirements look good, with appropriate versions specified for all dependencies.
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46-48: LGTM: Basic test present. Consider adding more comprehensive tests.The current test ensures that the
pantaxcommand is available and can be executed, which is a good basic check. However, to improve the robustness of the package, consider adding more comprehensive tests. For example:
Check the version of the installed package:
- pantax --versionRun a simple analysis on a small test dataset (if possible):
- pantax --test-dataVerify the presence of key dependencies:
- python -c "import pandas; import numpy; import networkx"These additional tests would provide more confidence in the correct installation and functionality of the package.
1-57: Minor: Remove trailing spaces for better code style.The static analysis tool detected trailing spaces on several lines (12, 13, 14, 16, 17, 24, 37, 38). While these don't affect functionality, removing them would improve code style and consistency. Consider using an editor with a trailing space removal feature or running a cleanup script to address this.
Note: The syntax error reported for the Jinja2 templating can be safely ignored as it's valid in the context of a Conda recipe.
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recipes/pantax/meta.yaml
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🔇 Additional comments (4)
recipes/pantax/meta.yaml (4)
1-6: LGTM: Package and version section looks good.The package name and version are correctly defined using Jinja2 templating, which is a good practice for maintainability.
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20-24: LGTM: Build section is well-configured.The build section is correctly configured:
- Skipping the build for OSX is noted and likely intentional.
- The build number is appropriately set to 0 for the initial release.
- The run_exports section ensures proper pinning in dependent packages, using Jinja2 templating for maintainability.
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50-53: LGTM: About section is concise and informative.The about section provides all necessary information:
- The home URL is correctly specified.
- The license (GPL-3.0) is clearly stated, which is crucial for open-source software.
- The summary succinctly describes the package's purpose.
This section effectively communicates the essential details about the package.
55-57: LGTM: Extra section correctly specifies lint skip.The extra section appropriately specifies skipping the "should_be_noarch_python" lint. This is correct given that the package includes architecture-specific binaries (such as the VG binary), making it not suitable for a noarch package.
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recipes/pantax/build.sh
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recipes/pantax/meta.yaml
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| - url: https://github.com/vgteam/vg/releases/download/v1.52.0/vg | ||
| sha256: 07776b51aa6494b45982e4134eb84005ddc743e81c67e61fa52bff211d81777c | ||
| folder: vg |
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Can you instead require VG in the requirements section?
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This is impossible. The requirement PGGB works with vg 1.40, but I need updated versions (vg 1.52) in other parts of my codes.
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https://anaconda.org/bioconda/vg provides a newer version
recipes/pantax/meta.yaml
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| - url: https://github.com/LuoGroup2023/PanTax/releases/download/v{{ version }}/{{ name }}.tar.gz | ||
| sha256: c14a46b41f580cf39ad502049d267cd31bbfd4dc05028215cc669c0e52f58ce7 | ||
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| - url: https://files.pythonhosted.org/packages/07/0f/6039cf6e22f9cbec57cdedff103949e4856c18fd2cb714bc70cdc8b52941/gurobipy-11.0.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
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Please require this as a dependency and do not pip install them
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Gurobipy can be install with conda install gurobi::gurobi and pip. But I don't know how to set channels gurobi to install it.
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You can use only dependencies from conda-forge and bioconda channels. You cannot install from third-party channels and/or Pip
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
Docker image(s) built:
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Co-authored-by: Martin Grigorov <[email protected]>
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (4)
recipes/pantax/meta.yaml (4)
20-24: Consider supporting OSX builds.The build section is generally well-configured:
- The build number is correctly set to 0.
- The run_exports section is properly used to pin the subpackage.
However, the package is currently skipped for OSX builds. If possible, consider supporting OSX to increase the package's availability across different platforms.
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26-31: Consider relaxing the Python version constraint.The build requirements are generally well-defined:
- The inclusion of the Rust compiler is appropriate if the package contains Rust code.
- pip is correctly included in the host requirements for installing Python packages during the build process.
However, the Python version is strictly pinned to 3.10. Consider allowing a range of Python versions (e.g.,
>=3.10,<3.11) to provide more flexibility for users while maintaining compatibility.
1-57: Clean up trailing spaces.The static analysis tool reported several instances of trailing spaces in the YAML file. While these don't affect functionality, removing them improves code cleanliness. Consider using an editor with a trailing space removal feature or running a cleanup script to address this.
You can use the following command to remove trailing spaces:
sed -i 's/[[:space:]]*$//' recipes/pantax/meta.yaml🧰 Tools
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1-57: Summary: Well-structured package with areas for improvementOverall, the
meta.yamlfile for the pantax package is well-structured and provides a good foundation. However, there are several areas where improvements could be made:
Dependency Management: Consider relaxing version constraints where appropriate, especially for Python and some of the bioinformatics tools. This will improve maintainability and flexibility.
Build Process: The inclusion of pre-built binaries (Gurobi wheel and VG) may pose compatibility and security risks. Consider alternative approaches, such as building from source or using conda-forge packages.
Test Coverage: Enhance the test suite to provide more comprehensive coverage of the package's functionality.
Platform Support: If possible, consider adding support for OSX builds to increase the package's availability.
Code Cleanliness: Remove trailing spaces throughout the file for better maintainability.
These improvements will enhance the package's robustness, maintainability, and user-friendliness. Please address these points and feel free to ask for clarification or assistance on any of the suggested changes.
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recipes/pantax/meta.yaml
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🔇 Additional comments (4)
recipes/pantax/meta.yaml (4)
1-6: LGTM: Package metadata is well-defined.The package name and version are correctly set using Jinja2 variables, which is a good practice for maintainability. The version number follows semantic versioning.
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50-53: LGTM: About section is well-defined.The about section provides all necessary information:
- The home URL correctly points to the GitHub repository.
- The license is properly specified as GPL-3.0-or-later.
- The summary is concise and informative, clearly describing the package's functionality.
55-57: Clarify the need to skip the noarch Python lint.The package is set to skip the "should_be_noarch_python" lint, which suggests it contains architecture-specific components. This is consistent with the inclusion of pre-built binaries in the source section.
However, it's worth considering if this skip is necessary:
- Could the architecture-specific components be separated into a different package?
- Is it possible to build these components from source instead of including pre-built binaries?
Please clarify why the package cannot be noarch Python. If possible, consider refactoring to make it architecture-independent, as this could simplify distribution and installation.
8-18: Review the source section for potential issues.While the source section is comprehensive, there are a few concerns:
- The inclusion of pre-built binaries (Gurobi wheel and VG) might pose compatibility issues across different systems.
- Downloading the VG binary directly from GitHub releases could be a security risk. Consider packaging VG separately or using a more controlled distribution method.
- The use of a specific Python wheel for Gurobi (cp310) limits the package to Python 3.10, which may reduce flexibility.
To ensure the VG binary is compatible and secure, please run the following script:
Consider refactoring this section to improve compatibility and security.
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recipes/pantax/meta.yaml
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| run: | ||
| - python =3.10 | ||
| - samtools =1.19.2 | ||
| - bcftools =1.19 | ||
| - htslib =1.19.1 | ||
| - pggb =0.5.4 | ||
| - graphaligner =1.0.17 | ||
| - h5py =3.10.0 | ||
| - pandas =2.2.0 | ||
| - tqdm =4.66.1 | ||
| - numpy =1.26.3 | ||
| - networkx =3.2.1 | ||
| - pyarrow =14.0.2 |
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🛠️ Refactor suggestion
Review dependency version constraints.
The run requirements section is comprehensive, but there are some points to consider:
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The Python version is strictly pinned to 3.10, which limits flexibility. Consider allowing a range of compatible Python versions.
-
Many dependencies have very specific version requirements. While this ensures reproducibility, it may make updates challenging. Consider using version ranges (e.g.,
>=1.19.2,<1.20) for dependencies that are likely to remain compatible across minor versions. -
For bioinformatics tools like samtools, bcftools, and htslib, consider if such strict version pinning is necessary. These tools often maintain backwards compatibility, so allowing minor version updates might be beneficial.
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Verify if all listed dependencies are directly required by pantax. Remove any that are indirect dependencies to keep the requirements list focused.
Consider relaxing version constraints where appropriate to improve maintainability while preserving compatibility.
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@BiocondaBot please add label |
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@martin-g Could you please take some time to review and merge it? Thank you so much. |
recipes/pantax/build.sh
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| cp -rf $SRC_DIR $PREFIX | ||
| else | ||
| cd ${SRC_DIR}/gurobi11 | ||
| ${PYTHON} -m pip install gurobipy-11.0.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
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I think it is not allowed to install dependencies with Pip like this.
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Where does it install it, by the way ? It looks like it is no inside $PREFIX
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Why? Are there any rules that restrict this installation behavior? I have already installed the artifact locally and tested it sucessfully, and PanTax is works well. Gurobipy, as a Python package, should be installed in the /path/to/env/lib/python3.10/site-packages/gurobipy. ${PREFIX} should be /path/to/env/bin，so it will certainly not be installed there.
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About the question of vg version. I use vg version 1.52 instead of newer version to ensure the robustness and reproducibility of our tool. All my experiments are run on this version. In addition, I have a dependency PGGB. PGGB depends on vg version 1.40. Therefore, I cannot directly add vg to the dependency, otherwise the vg version 1.40 will be overwritten by the new version of vg.
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| - url: https://github.com/LuoGroup2023/PanTax/releases/download/v{{ version }}/{{ name }}.tar.gz | ||
| sha256: c14a46b41f580cf39ad502049d267cd31bbfd4dc05028215cc669c0e52f58ce7 | ||
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There was a problem hiding this comment.
You can use only dependencies from conda-forge and bioconda channels. You cannot install from third-party channels and/or Pip
recipes/pantax/meta.yaml
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| - url: https://github.com/vgteam/vg/releases/download/v1.52.0/vg | ||
| sha256: 07776b51aa6494b45982e4134eb84005ddc743e81c67e61fa52bff211d81777c | ||
| folder: vg |
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https://anaconda.org/bioconda/vg provides a newer version
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Actionable comments posted: 6
🧹 Outside diff range and nitpick comments (1)
recipes/pantax/meta.yaml (1)
8-10: LGTM: Source section is well-defined, with a minor formatting suggestion.The source URL and SHA256 checksum are correctly specified, which is excellent for reproducibility. However, there's a minor formatting issue:
Remove the trailing space at the end of line 9:
- - url: https://github.com/LuoGroup2023/PanTax/releases/download/v{{ version }}/{{ name }}.tar.gz + - url: https://github.com/LuoGroup2023/PanTax/releases/download/v{{ version }}/{{ name }}.tar.gz
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recipes/pantax/build.sh
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🔇 Additional comments (5)
recipes/pantax/meta.yaml (5)
1-6: LGTM: Package section is well-defined.The package name and version are correctly defined using Jinja2 templating, which is a good practice for maintainability.
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12-16: LGTM: Build section is well-defined, with a minor formatting suggestion and a verification request.The build section is correctly configured with the macOS skip and run_exports. However, there are two points to address:
- Remove the trailing space at the end of line 16:
- - {{ pin_subpackage(name, max_pin="x.x") }} + - {{ pin_subpackage(name, max_pin="x.x") }}
- Confirm that skipping the build for macOS is intentional and necessary. If it's due to known compatibility issues, consider adding a comment explaining the reason for future reference.
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43-46: LGTM: About section is well-defined.The about section provides all necessary information concisely. The use of the SPDX identifier for the license is correct and follows best practices.
48-50: Clarify the reason for skipping the 'should_be_noarch_python' lint.The extra section skips the 'should_be_noarch_python' lint, which suggests that the package is not architecture-independent. However, this seems to contradict the use of Python as the main language.
Please clarify the reason for skipping this lint. Is it due to the Rust compiler requirement or other architecture-specific dependencies? If so, consider adding a comment explaining the rationale to improve maintainability.
18-38: 🛠️ Refactor suggestion
⚠️ Potential issueReview dependency versions and formatting in the requirements section.
The requirements section is comprehensive, but there are several points to consider:
- The Python version is strictly pinned to 3.10. Consider allowing a range of compatible Python versions for better flexibility:
host: - python >=3.10,<3.11 run: - python >=3.10,<3.11
- The 'vg' package doesn't have a version specified. This could lead to compatibility issues. Consider pinning it to a specific version:
- vg =1.52.0 # Replace with the appropriate version
Remove trailing spaces from lines 31 and 33.
Consider using version ranges for some dependencies to allow for minor updates while maintaining compatibility. For example:
- samtools >=1.19.2,<1.20 - bcftools >=1.19,<1.20 - htslib >=1.19.1,<1.20
- Confirm that all listed dependencies are directly required by pantax. Remove any that are indirect dependencies to keep the requirements list focused.
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@BiocondaBot please fetch artifacts |
|
Package(s) built are ready for inspection:
Docker image(s) built:
|
Co-authored-by: Martin Grigorov <[email protected]>
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🪛 yamllint
recipes/pantax/meta.yaml
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🔇 Additional comments (4)
recipes/pantax/meta.yaml (4)
1-10: LGTM: Package and source information are well-defined.The use of Jinja2 variables for the package name and version is a good practice for maintainability. The source URL is correctly formatted, and the SHA256 checksum is provided for integrity verification.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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43-48: LGTM: About section is well-defined.The about section provides comprehensive information including the home URL, license details (using the correct SPDX identifier), and a concise summary of the package's functionality. This follows best practices for Conda recipe metadata.
50-52: Clarify the need to skip 'should_be_noarch_python' lint.The
should_be_noarch_pythonlint is being skipped, which suggests that this package is not architecture-independent. However, given that the package appears to be primarily Python-based, this raises a question:
- Is there a specific reason why this package cannot be
noarch: python?
- If it's due to the Rust components or other architecture-specific dependencies, it would be helpful to document this reasoning as a comment in the recipe.
If there are no architecture-specific components, consider removing this skip-lint and making the package
noarch: python. Otherwise, please add a comment explaining the rationale for skipping this lint.
1-52: Overall, the recipe is well-structured with minor improvements suggested.The
meta.yamlfile for thepantaxpackage follows the general structure of a Conda recipe and includes all necessary sections. Here's a summary of the review:
- Package and source information are well-defined.
- The build section could benefit from reviewing the
pin_subpackagedirective.- Requirements section could be improved by relaxing some version constraints.
- Test section could be expanded for more comprehensive coverage.
- About section is complete and follows best practices.
- The skip-lint in the extra section needs clarification.
Additionally, there are a few trailing spaces that should be removed (lines 16, 31, 33, and 37).
These suggested improvements will enhance the maintainability and flexibility of the recipe while ensuring it remains functional and follows Conda packaging best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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[error] 16-16: trailing spaces
(trailing-spaces)
[error] 31-31: trailing spaces
(trailing-spaces)
recipes/pantax/meta.yaml
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| build: | ||
| skip: True # [osx] | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage(name, max_pin="x.x") }} |
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🛠️ Refactor suggestion
Review pin_subpackage directive and remove trailing space.
The build section is generally well-defined. However, consider the following points:
- The
pin_subpackagedirective uses"x.x", which might be too strict for a 1.x version. For version 1.x, using"x"is typically sufficient unless you expect API breaks in minor versions. - There's a trailing space on line 16 that should be removed.
Consider updating the run_exports section as follows:
run_exports:
- {{ pin_subpackage(name, max_pin="x") }}This change allows for minor version updates while still maintaining compatibility.
🧰 Tools
🪛 yamllint
[error] 16-16: trailing spaces
(trailing-spaces)
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Actionable comments posted: 7
🧹 Outside diff range and nitpick comments (2)
recipes/pantax/meta.yaml (2)
12-16: Remove trailing space and consider clarifying OSX skip reason.The build section looks good overall:
- The use of
run_exportswithpin_subpackageis good for dependency management.- Consider adding a comment explaining why the build is skipped for OSX.
Please remove the trailing space on line 16:
- - {{ pin_subpackage(name, max_pin="x") }} + - {{ pin_subpackage(name, max_pin="x") }}🧰 Tools
🪛 yamllint
[error] 16-16: trailing spaces
(trailing-spaces)
50-52: Consider adding a comment for skip-lints.The use of
skip-lintsto ignore 'should_be_noarch_python' is noted. This aligns with the earlier OSX build skip, suggesting that the package might be architecture-specific.Consider adding a brief comment explaining why this lint is being skipped. For example:
extra: skip-lints: - should_be_noarch_python # Package contains architecture-specific componentsThis will help future maintainers understand the reasoning behind this decision.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/pantax/build.sh (1 hunks)
- recipes/pantax/meta.yaml (1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/pantax/build.sh
[warning] 6-6: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 12-12: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/pantax/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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[error] 16-16: trailing spaces
(trailing-spaces)
[error] 31-31: trailing spaces
(trailing-spaces)
🔇 Additional comments (2)
recipes/pantax/meta.yaml (2)
1-10: LGTM: Package and source sections are well-defined.The package and source sections are correctly structured:
- Good use of Jinja2 variables for maintainability.
- Proper URL structure for GitHub release.
- SHA256 checksum is provided for integrity verification.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
43-48: LGTM: About section is complete and accurate.The about section contains all necessary information:
- Home URL is provided.
- License information is complete and correct (GPL-3.0-or-later).
- LICENSE file is specified.
- Summary provides a clear description of the package's functionality.
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
Docker image(s) built:
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| #!/usr/bin/env bash | |||
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| if [ "$(uname)" == "Darwin" ]; then | |||
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The meta.yaml says to skip OSX
Describe your pull request here
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