Update homopolish to 0.4.2 #43420
Update homopolish to 0.4.2 #43420
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces updates to the In the requirements section, the The license has changed from "GNU GENERAL PUBLIC LICENSE" to "GPL-3.0-or-later," with the addition of a Possibly related PRs
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/homopolish/meta.yaml(1 hunks)
🔇 Additional comments (5)
recipes/homopolish/meta.yaml (5)
15-17: LGTM! Build configuration follows best practices
- Build number correctly reset to 0 for new version
- noarch: python is appropriate for this package
- Installation flags will help with build debugging
1-59: Overall update looks good!
The version update from 0.4.1 to 0.4.2 is well structured with:
- Appropriate version bump and checksum update
- Enhanced build configuration
- Improved package metadata
- Added scientific identifiers
Once all verification checks pass, this update is ready to merge.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
31-31: Verify new dependency availability and constraints
New dependencies added: python-wget, requests, and fastani. Let's verify their availability in conda channels.
Also applies to: 37-37, 41-41
56-59: Verify DOI validity
Added identifiers enhance package discoverability. Let's verify the DOI exists.
✅ Verification successful
DOI is valid and resolves correctly
Added identifiers enhance package discoverability, and the DOI exists.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify DOI resolves correctly
DOI="10.1186/s13059-021-02282-6"
curl -sI "https://doi.org/$DOI" | grep -q "HTTP/2 200" && echo "DOI verified" || echo "DOI not found"
Length of output: 146
Script:
#!/bin/bash
# Description: Verify DOI resolves correctly by checking HTTP status code
DOI="10.1186/s13059-021-02282-6"
STATUS_CODE=$(curl -o /dev/null -s -w "%{http_code}" "https://doi.org/$DOI")
if [ "$STATUS_CODE" -eq 200 ]; then
echo "DOI verified"
else
echo "DOI not found"
fi
Length of output: 194
Script:
#!/bin/bash
# Description: Verify DOI resolves correctly by accepting HTTP status codes 200 and 302
DOI="10.1186/s13059-021-02282-6"
STATUS_CODE=$(curl -o /dev/null -s -w "%{http_code}" "https://doi.org/$DOI")
if [ "$STATUS_CODE" -eq 200 ] || [ "$STATUS_CODE" -eq 302 ]; then
echo "DOI verified"
else
echo "DOI not found"
fi
Length of output: 214
2-2: Verify source integrity and availability
Let's verify the source tarball exists and its checksum matches.
Also applies to: 10-10
| license: GPL-3.0-or-later | ||
| license_family: GPL3 | ||
| license_file: LICENSE | ||
| summary: "Homopolish is a polish tools" | ||
| summary: "High-quality Nanopore-only genome polisher" |
There was a problem hiding this comment.
💡 Codebase verification
LICENSE file does not contain GPL-3.0 text
- The LICENSE file at LICENSE contains the MIT License instead of GPL-3.0.
🔗 Analysis chain
Verify license file existence and content
License information has been updated to follow SPDX identifiers. Let's verify the LICENSE file.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify LICENSE file exists and contains GPL-3.0 text
# Check if LICENSE file exists and contains GPL-3.0 header
if [ -f "recipes/homopolish/LICENSE" ]; then
grep -i "GNU GENERAL PUBLIC LICENSE" recipes/homopolish/LICENSE && echo "License file verified"
else
echo "LICENSE file not found in recipe directory"
# Check in source repository
curl -s "https://raw.githubusercontent.com/SeaneryChang/homopolish/main/LICENSE" | grep -i "GNU GENERAL PUBLIC LICENSE" && echo "License verified in repository"
fi
Length of output: 349
Script:
#!/bin/bash
# Description: Verify LICENSE file exists and contains GPL-3.0 text
LICENSE_PATH="recipes/homopolish/LICENSE"
REPO_LICENSE_URL="https://raw.githubusercontent.com/SeaneryChang/homopolish/main/LICENSE"
# Function to check LICENSE content
check_license() {
local file="$1"
if grep -iq "GNU GENERAL PUBLIC LICENSE" "$file"; then
echo "LICENSE file verified in recipe directory."
else
echo "LICENSE file in recipe directory does not contain GPL-3.0 text."
fi
}
# Check if LICENSE file exists in recipe directory
if [ -f "$LICENSE_PATH" ]; then
check_license "$LICENSE_PATH"
else
echo "LICENSE file not found in recipe directory."
echo "Attempting to verify LICENSE file from source repository..."
curl -s "$REPO_LICENSE_URL" | grep -iq "GNU GENERAL PUBLIC LICENSE"
if [ $? -eq 0 ]; then
echo "LICENSE file verified in source repository."
else
echo "LICENSE file not verified in source repository."
fi
fi
Length of output: 641
Script:
#!/bin/bash
# Description: Verify LICENSE file exists in common locations and contains GPL-3.0 text
# Define possible LICENSE file paths
LICENSE_PATHS=(
"recipes/homopolish/LICENSE"
"recipes/homopolish/LICENSE.txt"
"recipes/homopolish/docs/LICENSE"
"LICENSE"
"LICENSE.txt"
)
# Define repository LICENSE URL
REPO_LICENSE_URL="https://raw.githubusercontent.com/SeaneryChang/homopolish/main/LICENSE"
# Function to check LICENSE content
check_license() {
local content="$1"
if echo "$content" | grep -iq "GNU GENERAL PUBLIC LICENSE"; then
echo "LICENSE file verified with GPL-3.0 text."
exit 0
else
echo "LICENSE file does not contain GPL-3.0 text."
fi
}
# Iterate over possible LICENSE file paths
for path in "${LICENSE_PATHS[@]}"; do
if [ -f "$path" ]; then
echo "Found LICENSE file at $path."
license_content=$(cat "$path")
check_license "$license_content"
exit 0
fi
done
echo "No LICENSE file found in common locations. Attempting to fetch from source repository..."
repo_license=$(curl -s "$REPO_LICENSE_URL")
if [ -n "$repo_license" ]; then
echo "Fetched LICENSE from source repository."
check_license "$repo_license"
else
echo "Failed to fetch LICENSE from source repository."
exit 1
fi
Length of output: 5174
Update
homopolish: 0.4.1 → 0.4.2recipes/homopolish(click to view/edit other files)@SeaneryChangThis pull request was automatically generated (see docs).