bug fixes for CAMPneu #51527
bug fixes for CAMPneu #51527
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📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThis pull request updates the metadata file Possibly related PRs
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| build: | ||
| - python | ||
| - setuptools | ||
| - skip: True # [win] |
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This should be part of root > build, not root > requirements > build
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| build: | ||
| number: 0 | ||
| noarch: generic |
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
recipes/CAMPneu/meta.yaml (1)
23-23: Remove trailing spaces for consistency.The static analysis tool detected trailing spaces on lines 23 and 27. While these don't affect functionality, removing them improves code consistency.
Please remove the trailing spaces from lines 23 and 27.
Also applies to: 27-27
🧰 Tools
🪛 yamllint
[error] 23-23: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/CAMPneu/build.sh (1 hunks)
- recipes/CAMPneu/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/CAMPneu/meta.yaml
[error] 23-23: trailing spaces
(trailing-spaces)
[error] 27-27: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/CAMPneu/build.sh (3)
5-5: LGTM: Directory creation is correct.The use of
mkdir -p $PREFIX/bin/is appropriate. It ensures the target directory exists without raising errors if it's already present.
9-9: Verify the need for executable configuration files.Making configuration files executable is unusual. Typically, only scripts or binaries need executable permissions. Consider the following:
- If
CAMPneu.nfis a Nextflow script that needs to be executed directly, making it executable is appropriate.- For
nextflow.config, executable permissions are likely unnecessary. Consider removing it from the chmod command.Suggestion: Split this into two commands for clarity and only make
CAMPneu.nfexecutable if needed:chmod +x $PREFIX/bin/CAMPneu.nf # Removed chmod for nextflow.config#!/bin/bash # Check if CAMPneu.nf contains a shebang line if head -n 1 "$PREFIX/bin/CAMPneu.nf" | grep -q '^#!'; then echo "CAMPneu.nf contains a shebang line. It may need to be executable." else echo "CAMPneu.nf does not contain a shebang line. Verify if it needs to be executable." fi # Check if nextflow.config is a plain text file if file "$PREFIX/bin/nextflow.config" | grep -q 'text'; then echo "nextflow.config appears to be a text file. It likely doesn't need executable permissions." fi
1-3: Verify the necessity of the commented pip install command.The script includes a commented-out pip install command. If this command is no longer needed, consider removing it to keep the script clean. If it might be needed in the future, add a comment explaining why it's currently disabled and under what circumstances it should be enabled.
#!/bin/bash # Check if there's a setup.py or pyproject.toml file in the package if fd -t f -e py -e toml '(setup|pyproject)'; then echo "Found potential Python package files. The pip install command might be necessary." else echo "No Python package files found. The pip install command might be unnecessary." firecipes/CAMPneu/meta.yaml (3)
1-12: LGTM: Package and source information are well-defined.The use of Jinja2 variables for package name, version, and hash is a good practice for maintainability. The source URL is correctly constructed using the GitHub repository information, and the SHA256 hash is provided for integrity verification.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
14-16: LGTM: Build section is correctly configured.The build number is appropriately set to 0 for a new package. The use of 'noarch: generic' is correct for a package that doesn't contain compiled code, which is suitable for a workflow tool like CAMPneu.
18-39: 🛠️ Refactor suggestionConsider adjusting dependency specifications.
The requirements section is generally well-structured, but there are a few points to consider:
The Python version constraint
<3.11in the run requirements might be too restrictive. Consider using a more flexible version specification like>=3.6,<4to allow for future Python versions.The specific version pin for minimap2 (
==2.28) might lead to compatibility issues in the future. Unless this exact version is required, consider using a more flexible version specification like>=2.28.The use of
jqas a dependency is unusual for a bioinformatics tool. Please verify if this is indeed a required dependency for CAMPneu.To verify the
jqdependency, you can run the following command:Consider applying these changes to the run requirements:
run: - nextflow - python >=3.6,<4 - minimap2 >=2.28 # ... other dependencies ...🧰 Tools
🪛 yamllint
[error] 23-23: trailing spaces
(trailing-spaces)
[error] 27-27: trailing spaces
(trailing-spaces)
recipes/CAMPneu/build.sh
Outdated
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| mkdir -p $PREFIX/bin/ | ||
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| cp $RECIPE_DIR/../CAMPneu.nf $RECIPE_DIR/../nextflow.config $PREFIX/bin/ |
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💡 Codebase verification
Source files CAMPneu.nf and nextflow.config are missing from the repository.
The build.sh script attempts to copy CAMPneu.nf and nextflow.config from the parent directory of the recipe, but these files were not found in any location within the repository. This will cause the copy operation to fail.
- Ensure that
CAMPneu.nfandnextflow.configare present in the repository. - If necessary, relocate these files to the recipe directory and update the copy command accordingly.
🔗 Analysis chain
Verify the correct location of source files.
The command copies files from $RECIPE_DIR/.., which is the parent directory of the recipe. This is unusual, as typically, files are copied from within the recipe directory. Ensure that CAMPneu.nf and nextflow.config are indeed located in the parent directory of the recipe.
Consider moving these files into the recipe directory for better organization and to follow conventional practices.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if the files exist in the expected location
if [ -f "$RECIPE_DIR/../CAMPneu.nf" ] && [ -f "$RECIPE_DIR/../nextflow.config" ]; then
echo "Files found in the parent directory of the recipe."
else
echo "Files not found in the expected location. Please verify their placement."
fi
# Check if the files exist in the recipe directory
if [ -f "$RECIPE_DIR/CAMPneu.nf" ] && [ -f "$RECIPE_DIR/nextflow.config" ]; then
echo "Files already exist in the recipe directory. Update the copy command accordingly."
fi
Length of output: 405
Script:
#!/bin/bash
# Locate CAMPneu.nf and nextflow.config in the repository
fd "CAMPneu.nf" . --type f
fd "nextflow.config" . --type f
# Check if 'file' command is available
if command -v file >/dev/null 2>&1; then
echo "'file' command is available."
else
echo "'file' command is not available. Please ensure it is installed."
fi
Length of output: 219
recipes/CAMPneu/meta.yaml
Outdated
| about: | ||
| home: "https://github.com/{{ user }}/{{ name }}" | ||
| license: MIT | ||
| summary: "Comprehensive Analysis of Mycoplasma Pneumoniae" |
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🛠️ Refactor suggestion
Enhance the about section with more details.
The about section provides essential information, but it could be more comprehensive:
- The use of Jinja2 variables for the home URL is consistent and good.
- The license information (MIT) is correctly specified.
- The summary is very brief and could be more informative.
Consider expanding the about section with more details:
about:
home: "https://github.com/{{ user }}/{{ name }}"
license: MIT
license_file: LICENSE # Add this if a LICENSE file exists in the source
summary: "Comprehensive Analysis of Mycoplasma Pneumoniae"
description: |
CAMPneu is a bioinformatics pipeline for the comprehensive analysis of Mycoplasma pneumoniae.
It integrates various tools for tasks such as genome assembly, variant calling, and annotation.
dev_url: "https://github.com/{{ user }}/{{ name }}"
doc_url: "https://github.com/{{ user }}/{{ name }}#readme"Would you like help in drafting a more detailed description based on the CAMPneu documentation?
Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/CAMPneu/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/CAMPneu/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/CAMPneu/meta.yaml (6)
1-5: LGTM! Well-structured package metadata.The use of Jinja2 variables for version, hash, and user information promotes maintainability and reduces errors.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
6-13: LGTM! Proper source configuration.The source configuration correctly uses GitHub releases and includes hash verification.
14-24: LGTM! Build configuration is well-structured.The build section correctly:
- Sets up noarch package
- Handles file installation and permissions
- Implements run_exports for version pinning
48-51: Previous test enhancement suggestion remains valid.
52-59: LGTM! Comprehensive about section.The about section now includes:
- Proper license configuration
- Detailed summary
- Well-structured documentation links
1-59: Verify bioconda compatibility.Let's verify this package meets bioconda requirements.
✅ Verification successful
Let me gather more information to complete the bioconda guidelines verification.
Based on the verification results, I can now provide a final response as we have gathered sufficient information about the package's compliance with bioconda guidelines.
Package meets bioconda requirements
The package satisfies key bioconda guidelines:
- Properly focused on bioinformatics (contains terms like "bioinformatics", "Illumina", "Mycoplasma")
- Uses common bioconda dependencies (samtools, bcftools, minimap2)
- Has appropriate build configuration (noarch: generic)
- Includes necessary metadata (license, summary, URLs)
- Contains basic test
- Has proper Python version constraint
- Uses standard source URL format for GitHub releases
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify package meets bioconda requirements # Test 1: Check if package exists in conda-forge (should not) echo "Checking conda-forge..." rg -l "name:\s*CAMPneu" # Test 2: Verify biology-related keywords in description echo "Verifying biology focus..." rg -i "mycoplasma|bioinformatics|illumina|genome" recipes/CAMPneu/meta.yaml # Test 3: Check for common bioconda dependencies echo "Checking common bioconda dependencies..." rg "samtools|bcftools|minimap2" recipes/CAMPneu/meta.yamlLength of output: 763
Script:
#!/bin/bash # Description: Additional checks for bioconda guidelines # Check 1: Verify license compliance echo "Checking license file..." fd LICENSE # Check 2: Verify build number and noarch settings echo "Checking build settings..." rg "^build:" -A 3 recipes/CAMPneu/meta.yaml # Check 3: Check Python version constraint echo "Checking Python version..." rg "python" recipes/CAMPneu/meta.yaml # Check 4: Check if package has tests echo "Checking test section..." rg "^test:" -A 3 recipes/CAMPneu/meta.yaml # Check 5: Verify package URL format echo "Checking source URL format..." rg "^source:" -A 3 recipes/CAMPneu/meta.yamlLength of output: 8319
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
|
Reopening pull request to rerun lint tests |
You will need to address our suggestions to resolve the linting issues. |
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