Update ucsc-wigtobigwig to 472 #51702
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📝 WalkthroughWalkthroughThis pull request includes several modifications across multiple files related to the Possibly related PRs
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Actionable comments posted: 1
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📒 Files selected for processing (4)
- recipes/ucsc-wigtobigwig/build.sh (1 hunks)
- recipes/ucsc-wigtobigwig/htmshell.patch (0 hunks)
- recipes/ucsc-wigtobigwig/include.macos.patch (1 hunks)
- recipes/ucsc-wigtobigwig/meta.yaml (3 hunks)
💤 Files with no reviewable changes (1)
- recipes/ucsc-wigtobigwig/htmshell.patch
🔇 Additional comments (9)
recipes/ucsc-wigtobigwig/build.sh (2)
12-12: LGTM: Consistent optimization flagsAdding
-O3to CXXFLAGS brings C++ optimization in line with the C optimization level, ensuring consistent compiler optimization across the codebase.
20-21: LGTM: Improved binary installationThe change from
cp + chmodtochmod + mvis a good improvement because:
- Setting permissions before moving is slightly safer
- Using
mvis more atomic thancprecipes/ucsc-wigtobigwig/include.macos.patch (3)
7-8: LGTM: Include path addition follows conda build best practices.The addition of
${PREFIX}/includetoHG_INCis the correct approach for conda builds, ensuring that the compiler can find headers installed by build dependencies.
15-16: LGTM: Consistent include path configuration.The change to
KENT_INCmaintains consistency with the previous modification in common.mk, ensuring uniform header discovery across the build.
23-24: Verify Python version compatibility.Removing the Python 2.7 requirement makes the script more flexible, but we should ensure it doesn't use Python 2.7-specific features that might break in Python 3.
✅ Verification successful
Let me analyze the results and generate a final response.
The search results show that the script
expMatrixToBarchartBedis being modified from Python 2.7 to Python 3 compatibility. Looking at the results:
The
2to3.patchfile shows only one Python 2 to 3 compatibility change: replacingiteritems()withitems()for dictionary iteration.No other Python 2.x specific patterns like
unicode(),basestring, orraw_input()were found in the script.The change is part of a larger set of Python 2 to 3 compatibility updates across many UCSC tools, suggesting this is a coordinated effort to modernize the codebase.
Python 2 to 3 compatibility verified - only minor dictionary iteration change needed.
The script appears to be Python 3 compatible with just the dictionary iteration method update, which is a safe and straightforward change. No other Python 2.x specific features were found that would cause compatibility issues.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for Python 2.7 specific syntax in the script # Look for common Python 2.x patterns like print statements without parentheses, # unicode literals, etc. # Search for Python 2.x specific syntax echo "Checking for Python 2.x specific patterns..." rg -l "print [^(]" || true rg "unicode\(" || true rg "basestring" || true rg "raw_input\(" || true # Look for the actual script content to verify its Python compatibility echo "Retrieving script content for manual review..." rg -A 10 "expMatrixToBarchartBed" || trueLength of output: 204889
recipes/ucsc-wigtobigwig/meta.yaml (4)
45-49: LGTM! URL improvements and version-specific documentation.The changes improve URL formatting and add version-specific documentation links. The use of version templating in
doc_urlis particularly good as it ensures documentation matches the package version.
31-31:⚠️ Potential issueConsider zlib runtime dependency.
The addition of
clangdevfor macOS builds is good. However, I notice that whilezlibis a host requirement, it's not listed in run requirements. This might cause runtime issues if the compiled binary dynamically links against zlib.#!/bin/bash # Description: Check if zlib is used in the source code # Expected: Find references to zlib usage that might indicate dynamic linking rg -i 'zlib|compress' kent/src/utils/wigToBigWig/Consider adding this diff if the binary requires zlib at runtime:
run: - libpng - libuuid - mysql-connector-c - libopenssl-static + - zlib
14-15: Verify existence of include.macos.patch file.The patch is correctly conditioned for macOS, but let's verify its existence.
✅ Verification successful
Both patch files exist and are properly configured
The verification confirms that both patch files are present in the recipe directory:
include.patch(1241 bytes) for Linuxinclude.macos.patch(1223 bytes) for macOS🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check if the macOS patch file exists # Expected: File should exist in the recipe directory fd --type f "include.macos.patch" recipes/ucsc-wigtobigwig/Length of output: 213
Script:
#!/bin/bash # Let's check if both patch files exist in the recipe directory ls -la recipes/ucsc-wigtobigwig/include*patch # Also check the contents of the recipe directory to understand the context better ls -la recipes/ucsc-wigtobigwig/Length of output: 823
3-4: Verify SHA256 checksum for version 472.Let's verify that the SHA256 checksum matches the source archive.
| -#!/usr/bin/env python2.7 | ||
| +#!/usr/bin/env python | ||
| # expMatrixToBarchartBed | ||
| """ | ||
| Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. |
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🛠️ Refactor suggestion
Consider adding explicit Python version compatibility handling.
Since this script is part of a bioinformatics tool, it's recommended to:
- Add explicit version checking at runtime
- Include compatibility imports if needed
- Document supported Python versions in the script's docstring
Example addition:
#!/usr/bin/env python
import sys
if sys.version_info[0] < 3:
from __future__ import print_function, division
# Version check
min_python = (2, 7)
if sys.version_info[:2] < min_python:
sys.exit("Python %s.%s or later is required." % min_python)
# expMatrixToBarchartBed
"""
Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
Supported Python versions: 2.7+, 3.x
"""
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