Update pdivas recipe #52089
Update pdivas recipe #52089
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📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces two main changes to the Second, the Possibly related PRs
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Actionable comments posted: 3
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
recipes/pdivas/LICENSE(1 hunks)recipes/pdivas/meta.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/pdivas/LICENSE
🔇 Additional comments (4)
recipes/pdivas/meta.yaml (4)
15-19: LGTM! Good addition of run_exports
The addition of run_exports with exact pinning is a good practice for ensuring API stability, which aligns with the project guidelines.
36-39: LGTM! Good test coverage
The addition of pip check helps verify dependency compatibility, and the test configuration properly validates both imports and CLI functionality.
27-30: Verify dependency version constraints
Please verify:
- Are the minimum version requirements for pandas, numpy, and cyvcf2 aligned with the package's needs?
- Why is scikit-learn pinned to exactly 1.0.2? This strict pinning might cause dependency conflicts.
#!/bin/bash
# Check for potential dependency conflicts
gh api graphql -f query='
{
securityVulnerabilities(first: 5, ecosystem: PIP, package: "scikit-learn", package: "1.0.2") {
nodes {
advisory {
summary
severity
}
}
}
}'2-6: Verify version consistency
The version has been bumped to 1.2.0, which matches the source URL. However, let's verify this is the latest version available.
✅ Verification successful
Build configuration is correct.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if 1.2.0 is the latest version on PyPI
curl -s https://pypi.org/pypi/pdivas/json | jq -r '.info.version'
Length of output: 497
Script:
#!/bin/bash
# Fetch the latest version of pdivas from PyPI
curl -s https://pypi.org/pypi/pdivas/json | jq -r '.info.version'
# Verify if the fetched version matches 1.2.0
fetched_version=$(curl -s https://pypi.org/pypi/pdivas/json | jq -r '.info.version')
expected_version="1.2.0"
if [ "$fetched_version" == "$expected_version" ]; then
echo "Version is up-to-date."
else
echo "Version mismatch: Expected $expected_version, but found $fetched_version."
fi
Length of output: 268
Script:
#!/bin/bash
# Extract the source URL from meta.yaml
source_url=$(grep '^ url:' recipes/pdivas/meta.yaml | awk '{print $2}' | tr -d '"')
# Extract the expected version
expected_version="1.2.0"
# Check if the version is present in the source URL
if echo "$source_url" | grep -q "$expected_version"; then
echo "Source URL is consistent with version $expected_version."
else
echo "Source URL does not match the expected version $expected_version."
fi
Length of output: 489
Script:
#!/bin/bash
# Extract the build section from meta.yaml
build_section=$(awk '/^build:/,/^requirements:/ {print}' recipes/pdivas/meta.yaml)
# Display the build section
echo "$build_section"
# Check for build number (assuming build number is specified)
build_number=$(echo "$build_section" | grep 'number:' | awk '{print $2}')
if [ -z "$build_number" ]; then
echo "No build number specified."
else
echo "Build number: $build_number"
# Optionally, verify if build number follows expected increment
# This requires knowledge of the previous build number
fi
# Check for build dependencies
build_dependencies=$(echo "$build_section" | grep 'run:' | awk '{print $2}')
if [ -z "$build_dependencies" ]; then
echo "No build dependencies specified."
else
echo "Build dependencies: $build_dependencies"
fi
Length of output: 1439
Script:
#!/bin/bash
# Retrieve the build number from the previous version of meta.yaml
# Get the previous commit that modified meta.yaml
previous_commit=$(git log -2 --pretty=format:"%H" recipes/pdivas/meta.yaml | tail -n1)
if [ -z "$previous_commit" ]; then
echo "No previous commit found for meta.yaml."
exit 1
fi
# Extract the build number from the previous meta.yaml
previous_build_number=$(git show $previous_commit:recipes/pdivas/meta.yaml | grep '^ number:' | awk '{print $2}')
if [ -z "$previous_build_number" ]; then
echo "No build number found in the previous meta.yaml."
else
echo "Previous build number: $previous_build_number"
fi
Length of output: 401
recipes/pdivas/meta.yaml
Outdated
| url: https://files.pythonhosted.org/packages/fc/7e/281e2053ea00eae24162211af598c247d3c5e4fb2c0d043e24c2e19897e6/pdivas-1.2.0.tar.gz | ||
| sha256: 4a2234564557622c5bd2213478956c4a4858ba6768251d24ee43a4fc7550f721 |
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🛠️ Refactor suggestion
Use templated PyPI URL for better maintainability
The direct PyPI URL should be replaced with the templated version for better maintainability.
- url: https://files.pythonhosted.org/packages/fc/7e/281e2053ea00eae24162211af598c247d3c5e4fb2c0d043e24c2e19897e6/pdivas-1.2.0.tar.gz
+ url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"📝 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.
| url: https://files.pythonhosted.org/packages/fc/7e/281e2053ea00eae24162211af598c247d3c5e4fb2c0d043e24c2e19897e6/pdivas-1.2.0.tar.gz | |
| sha256: 4a2234564557622c5bd2213478956c4a4858ba6768251d24ee43a4fc7550f721 | |
| url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" | |
| sha256: 4a2234564557622c5bd2213478956c4a4858ba6768251d24ee43a4fc7550f721 |
|
@BiocondaBot please add label I updated the recipe to work. |
recipes/pdivas/meta.yaml
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| source: | ||
| url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" | ||
| sha256: ca33dc31ecfa9c505105a25146ea8efcdddb1a13cc1ac990c29561cc911d74b9 | ||
| url: https://files.pythonhosted.org/packages/fc/7e/281e2053ea00eae24162211af598c247d3c5e4fb2c0d043e24c2e19897e6/pdivas-1.2.0.tar.gz |
There was a problem hiding this comment.
Can you use the old URL-template?
recipes/pdivas/meta.yaml
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| extra: | ||
| recipe-maintainers: | ||
| - shiro-kur | ||
| - AddYourGitHubIdHere |
recipes/pdivas/meta.yaml
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| license_family: OTHER | ||
| home: http://github.com/account/repository | ||
| summary: 'PDIVAS: Pathogenicity predictor of Deep-Intronic Variants causing Aberrant Splicing' | ||
| license: 'MIT' | ||
| license_file: |
There was a problem hiding this comment.
| license_file: | |
| license_file: LICENSE |
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