Add recipe for stxtyper v1.0.25 #51792
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📝 WalkthroughWalkthroughThis pull request introduces two significant changes related to the Secondly, a new metadata file called Possibly related PRs
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Actionable comments posted: 2
📜 Review details
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📒 Files selected for processing (2)
- recipes/stxtyper/build.sh (1 hunks)
- recipes/stxtyper/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/stxtyper/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (1)
recipes/stxtyper/build.sh (1)
1-11: Verify build dependencies in meta.yaml.
The build script assumes the availability of make and a C++ compiler. Ensure these are properly specified in meta.yaml.
Let's check the meta.yaml file for build requirements:
✅ Verification successful
Build dependencies are properly specified in meta.yaml
The meta.yaml file correctly includes both make and {{ compiler('cxx') }} in the build requirements section, which satisfies the build script's dependencies.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if make and compiler are specified in meta.yaml
rg -A 5 "requirements:" recipes/stxtyper/meta.yaml
Length of output: 131
| make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}" | ||
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| make install PREFIX="${PREFIX}" |
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Add error checking and ensure proper installation.
The build and install commands should include error checking and use DESTDIR for staged installations.
Apply these improvements:
-make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}"
+# Ensure CPU_COUNT is set
+export CPU_COUNT=${CPU_COUNT:-1}
+
+# Build with error checking
+if ! make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}"; then
+ echo "Build failed"
+ exit 1
+fi
-make install PREFIX="${PREFIX}"
+# Install with DESTDIR for proper staging
+if ! make install DESTDIR="${PREFIX}" PREFIX=""; then
+ echo "Installation failed"
+ exit 1
+fi📝 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.
| make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}" | |
| make install PREFIX="${PREFIX}" | |
| # Ensure CPU_COUNT is set | |
| export CPU_COUNT=${CPU_COUNT:-1} | |
| # Build with error checking | |
| if ! make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}"; then | |
| echo "Build failed" | |
| exit 1 | |
| fi | |
| # Install with DESTDIR for proper staging | |
| if ! make install DESTDIR="${PREFIX}" PREFIX=""; then | |
| echo "Installation failed" | |
| exit 1 | |
| fi |
| export INCLUDES="-I${PREFIX}/include" | ||
| export LIBPATH="-L${PREFIX}/lib" | ||
| export CXXFLAGS="${CXXFLAGS} -O3" | ||
| export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include" | ||
| export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" |
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🛠️ Refactor suggestion
Consider more robust compiler flag handling.
While the environment setup is generally correct, there are a few suggestions for improvement:
- The -O3 optimization level might be too aggressive and could cause issues on some platforms
- Consider using DESTDIR for staged installations
Here's a more robust approach:
-export INCLUDES="-I${PREFIX}/include"
-export LIBPATH="-L${PREFIX}/lib"
-export CXXFLAGS="${CXXFLAGS} -O3"
-export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include"
-export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+# Use -O2 for better stability
+export CXXFLAGS="${CXXFLAGS} -O2"
+export CPPFLAGS="${CPPFLAGS} -O2 -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"📝 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.
| export INCLUDES="-I${PREFIX}/include" | |
| export LIBPATH="-L${PREFIX}/lib" | |
| export CXXFLAGS="${CXXFLAGS} -O3" | |
| export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include" | |
| export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" | |
| # Use -O2 for better stability | |
| export CXXFLAGS="${CXXFLAGS} -O2" | |
| export CPPFLAGS="${CPPFLAGS} -O2 -I${PREFIX}/include" | |
| export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" |
|
@mencian It looks like this may be a duplicate of the ncbi-stxtyper recipe we are maintaining. Is there something we can improve about the ncbi-stxtyper recipe to meet your needs? |
|
This was a mistake on my part, I've reverted this PR here. |
|
@mencian Thanks! If you are using StxTyper let us know if you have any comments or questions. |
Describe your pull request here
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