Update revbayes to v1.2.4 #52069
Update revbayes to v1.2.4 #52069
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request includes significant updates to the In the Possibly related PRs
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🧰 Additional context used🪛 yamllintrecipes/revbayes/meta.yaml[error] 1-1: syntax error: found character '%' that cannot start any token (syntax) 🔇 Additional comments (6)recipes/revbayes/meta.yaml (6)
The build number reset is appropriate for a version bump, and the addition of
Good improvements to the metadata section:
The source URL format has been updated to use the more explicit #!/bin/bash
# Verify source URL and checksum
URL="https://github.com/revbayes/revbayes/archive/refs/tags/v1.2.4.tar.gz"
echo "Checking URL accessibility..."
curl -sI "$URL" | head -n 1
echo "Verifying checksum..."
curl -sL "$URL" | sha256sum
The recipe now includes osx-arm64 platform support. Please ensure that RevBayes 1.2.4 has been tested on Apple Silicon hardware. #!/bin/bash
# Search for arm64 related discussions or issues
gh api graphql -f query='
{
search(query: "repo:revbayes/revbayes arm64 apple silicon m1", type: ISSUE, first: 10) {
nodes {
... on Issue {
title
url
state
}
}
}
}'
The minimum boost-cpp version has been increased from 1.60 to 1.71. Please ensure this is the minimum required version for RevBayes 1.2.4.
The version update from 1.0.13 to 1.2.4 represents a significant change. Please ensure there are no breaking changes that could affect downstream dependencies. ✅ Verification successfulVersion bump is safe from dependency perspective No downstream packages depend on revbayes in the bioconda repository, so the version update from 1.0.13 to 1.2.4 poses no risk of breaking other packages. 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Search for downstream dependencies that might be affected
gh api graphql -f query='
{
search(query: "repo:bioconda/bioconda-recipes path:recipes depends revbayes", type: CODE, first: 100) {
nodes {
... on TextMatch {
fragment
file {
path
}
}
}
}
}'
Length of output: 1264 Script: #!/bin/bash
# Search for recipes that depend on revbayes
rg --files-with-matches 'depends:\s*revbayes' recipes/
Length of output: 56 Script: #!/bin/bash
# Search for recipes that have revbayes as a dependency in build or run requirements
rg -l -e '^- revbayes' recipes/requirements/*
Length of output: 112 Script: #!/bin/bash
# Search for any occurrence of revbayes in all meta.yaml files within recipes/
rg 'revbayes' recipes/**/*.yaml
Length of output: 342942 🧰 Tools🪛 yamllint[error] 1-1: syntax error: found character '%' that cannot start any token (syntax) Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/revbayes/build.sh (1)
20-45: Consider refactoring build configurations to reduce duplicationThe MPI and non-MPI build configurations share most of their cmake arguments. Consider extracting common build configuration into a function to improve maintainability.
Example refactor:
build_revbayes() { local mpi_enabled=$1 ./build.sh -mpi ${mpi_enabled} -help2yml true \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_PREFIX_PATH="${PREFIX}" \ -DCMAKE_CXX_COMPILER="${CXX}" \ -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ -boost_root "${PREFIX}" \ -j "${CPU_COUNT}" \ "${CONFIG_ARGS}" } # Usage: build_revbayes true # For MPI build_revbayes false # For non-MPIrecipes/revbayes/meta.yaml (1)
35-37: Consider enhancing test coverageWhile the basic help command tests are good, consider adding more comprehensive tests to verify functionality.
Consider adding:
- Version check tests
- Basic analysis tests with sample data
- MPI functionality tests
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Review profile: CHILL
📒 Files selected for processing (2)
recipes/revbayes/build.sh(1 hunks)recipes/revbayes/meta.yaml(1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/revbayes/build.sh
[warning] 9-9: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/revbayes/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (8)
recipes/revbayes/build.sh (3)
20-30: MPI build configuration is well structured
The build configuration is comprehensive with proper:
- CMAKE flags for release build
- Compiler and dependency paths
- Parallel build support
- Binary permissions
34-50: Non-MPI build configuration mirrors MPI version appropriately
The build process maintains consistency with the MPI version while properly managing build directories and artifacts. Good practice to clean up build directories between and after builds.
3-6: Environment setup looks good with a note on optimization level
The environment variables are properly configured using conda's PREFIX variable. The -O3 optimization level is appropriate for scientific computing software like RevBayes, but ensure it has been tested thoroughly as it can sometimes lead to numerical precision differences.
✅ Verification successful
No known numerical precision issues found with -O3 optimization
The use of the -O3 optimization level in CXXFLAGS does not conflict with any documented precision requirements in the README.md.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if there are any known numerical precision issues with -O3 for RevBayes
rg -i "precision|accuracy" README.md || echo "No explicit mentions of precision requirements found"
Length of output: 153
recipes/revbayes/meta.yaml (5)
1-2: LGTM! Good use of Jinja2 variables
The version update to 1.2.4 matches the PR objectives, and using variables for name and version follows best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-15: LGTM! Good use of run_exports
The build number reset and run_exports configuration are appropriate for version management and ABI compatibility.
24-32: Verify boost-cpp version compatibility
The boost-cpp version requirement has been increased significantly (from 1.60 to 1.71). Let's verify this requirement.
#!/bin/bash
# Search for boost version requirements in the source
rg -i "boost.*1\.71"
# Check CMake files for boost requirements
fd -e cmake -x cat {} \; | rg -i "boost.*version"The OS-specific OpenMP dependencies look correct:
- llvm-openmp for macOS
- libgomp for Linux
40-58: LGTM! Comprehensive metadata updates
Excellent additions:
- Clear license specification
- Development and documentation URLs
- Biotools and DOI identifiers
- ARM architecture support
#!/bin/bash
# Check if ARM support is configured in build system
fd -e cmake -x cat {} \; | rg -i "aarch64|arm64"9-10: Verify SHA256 checksum for the source tarball
The URL format update to use refs/tags is good. Let's verify the SHA256 checksum.
| mkdir -p $PREFIX/bin | ||
| cd projects/cmake | ||
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| if [ ! -d build ]; then | ||
| mkdir build | ||
| if [[ `uname` == "Darwin" ]]; then | ||
| export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" | ||
| else | ||
| export CONFIG_ARGS="" |
There was a problem hiding this comment.
Add error handling for directory navigation
While the platform-specific configuration is well-implemented, the cd command should include error handling to prevent silent failures.
Apply this diff to add error handling:
mkdir -p $PREFIX/bin
-cd projects/cmake
+cd projects/cmake || exit 1📝 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.
| mkdir -p $PREFIX/bin | |
| cd projects/cmake | |
| if [ ! -d build ]; then | |
| mkdir build | |
| if [[ `uname` == "Darwin" ]]; then | |
| export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" | |
| else | |
| export CONFIG_ARGS="" | |
| mkdir -p $PREFIX/bin | |
| cd projects/cmake || exit 1 | |
| if [[ `uname` == "Darwin" ]]; then | |
| export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" | |
| else | |
| export CONFIG_ARGS="" |
🧰 Tools
🪛 Shellcheck
[warning] 9-9: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
There was a problem hiding this comment.
Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (2)
recipes/revbayes/build.sh (2)
3-5: Consider consolidating compiler flags and adding CXXFLAGSWhile the current environment setup is functional, consider consolidating related flags and adding CXXFLAGS for completeness:
export INCLUDES="-I${PREFIX}/include" export LIBPATH="-L${PREFIX}/lib" -export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} ${LIBPATH}" +export CXXFLAGS="${CXXFLAGS} ${INCLUDES}"
47-47: Consider more comprehensive cleanupThe final cleanup could be more thorough to ensure a clean build environment:
-rm -rf build +# Cleanup all build artifacts +rm -rf build build-mpi CMakeCache.txt CMakeFiles/
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (1)
recipes/revbayes/build.sh(1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/revbayes/build.sh
[warning] 8-8: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🔇 Additional comments (2)
recipes/revbayes/build.sh (2)
7-9: Previous review comment about directory navigation is still applicable
🧰 Tools
🪛 Shellcheck
[warning] 8-8: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
10-14: LGTM! Platform-specific configuration is well implemented
The conditional check uses proper bash syntax and the Darwin-specific configuration correctly handles framework/bundle issues.
| ./build.sh -mpi false -help2yml true \ | ||
| -DCMAKE_BUILD_TYPE=Release \ | ||
| -DCMAKE_PREFIX_PATH="${PREFIX}" \ | ||
| -DCMAKE_CXX_COMPILER="${CXX}" \ | ||
| -boost_root "${PREFIX}" \ | ||
| -j "${CPU_COUNT}" \ | ||
| "${CONFIG_ARGS}" | ||
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| make | ||
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| cd .. | ||
| mkdir -p $PREFIX/bin | ||
| mv rb $PREFIX/bin | ||
| chmod 0755 rb rb-help2yml | ||
| mv rb rb-help2yml $PREFIX/bin/ |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add error handling for non-MPI build commands
Similar to the MPI build section, add error handling:
-./build.sh -mpi false -help2yml true \
+./build.sh -mpi false -help2yml true \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_PREFIX_PATH="${PREFIX}" \
-DCMAKE_CXX_COMPILER="${CXX}" \
-boost_root "${PREFIX}" \
-j "${CPU_COUNT}" \
- "${CONFIG_ARGS}"
+ "${CONFIG_ARGS}" || exit 1
-chmod 0755 rb rb-help2yml
-mv rb rb-help2yml $PREFIX/bin/
+chmod 0755 rb rb-help2yml || exit 1
+mv rb rb-help2yml $PREFIX/bin/ || exit 1📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| ./build.sh -mpi false -help2yml true \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -DCMAKE_PREFIX_PATH="${PREFIX}" \ | |
| -DCMAKE_CXX_COMPILER="${CXX}" \ | |
| -boost_root "${PREFIX}" \ | |
| -j "${CPU_COUNT}" \ | |
| "${CONFIG_ARGS}" | |
| make | |
| cd .. | |
| mkdir -p $PREFIX/bin | |
| mv rb $PREFIX/bin | |
| chmod 0755 rb rb-help2yml | |
| mv rb rb-help2yml $PREFIX/bin/ | |
| ./build.sh -mpi false -help2yml true \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -DCMAKE_PREFIX_PATH="${PREFIX}" \ | |
| -DCMAKE_CXX_COMPILER="${CXX}" \ | |
| -boost_root "${PREFIX}" \ | |
| -j "${CPU_COUNT}" \ | |
| "${CONFIG_ARGS}" || exit 1 | |
| chmod 0755 rb rb-help2yml || exit 1 | |
| mv rb rb-help2yml $PREFIX/bin/ || exit 1 |
| ./build.sh -mpi true -help2yml true \ | ||
| -DCMAKE_BUILD_TYPE=Release \ | ||
| -DCMAKE_PREFIX_PATH="${PREFIX}" \ | ||
| -DCMAKE_CXX_COMPILER="${CXX}" \ | ||
| -boost_root "${PREFIX}" \ | ||
| -j "${CPU_COUNT}" \ | ||
| "${CONFIG_ARGS}" | ||
|
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| # If cmake finds a boost version compiled with cmake, it always links to it unless both | ||
| # Boost_NO_SYSTEM_PATHS=ON and Boost_NO_BOOST_CMAKE=ON (probably a bug in cmake) | ||
| cmake -DCMAKE_PREFIX_PATH=$PREFIX \ | ||
| -DBOOST_ROOT=$PREFIX \ | ||
| -DBoost_NO_SYSTEM_PATHS=ON \ | ||
| -DBoost_NO_BOOST_CMAKE=ON \ | ||
| . | ||
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| make | ||
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| cd .. | ||
| mkdir -p $PREFIX/bin | ||
| mv rb $PREFIX/bin/rb-mpi | ||
| chmod 0755 rb-mpi rb-mpi-help2yml | ||
| mv rb-mpi rb-mpi-help2yml $PREFIX/bin/ |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Add error handling for build commands
While the build configuration is comprehensive, consider adding error handling to catch build failures:
-./build.sh -mpi true -help2yml true \
+./build.sh -mpi true -help2yml true \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_PREFIX_PATH="${PREFIX}" \
-DCMAKE_CXX_COMPILER="${CXX}" \
-boost_root "${PREFIX}" \
-j "${CPU_COUNT}" \
- "${CONFIG_ARGS}"
+ "${CONFIG_ARGS}" || exit 1
-chmod 0755 rb-mpi rb-mpi-help2yml
-mv rb-mpi rb-mpi-help2yml $PREFIX/bin/
+chmod 0755 rb-mpi rb-mpi-help2yml || exit 1
+mv rb-mpi rb-mpi-help2yml $PREFIX/bin/ || exit 1📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| ./build.sh -mpi true -help2yml true \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -DCMAKE_PREFIX_PATH="${PREFIX}" \ | |
| -DCMAKE_CXX_COMPILER="${CXX}" \ | |
| -boost_root "${PREFIX}" \ | |
| -j "${CPU_COUNT}" \ | |
| "${CONFIG_ARGS}" | |
| # If cmake finds a boost version compiled with cmake, it always links to it unless both | |
| # Boost_NO_SYSTEM_PATHS=ON and Boost_NO_BOOST_CMAKE=ON (probably a bug in cmake) | |
| cmake -DCMAKE_PREFIX_PATH=$PREFIX \ | |
| -DBOOST_ROOT=$PREFIX \ | |
| -DBoost_NO_SYSTEM_PATHS=ON \ | |
| -DBoost_NO_BOOST_CMAKE=ON \ | |
| . | |
| make | |
| cd .. | |
| mkdir -p $PREFIX/bin | |
| mv rb $PREFIX/bin/rb-mpi | |
| chmod 0755 rb-mpi rb-mpi-help2yml | |
| mv rb-mpi rb-mpi-help2yml $PREFIX/bin/ | |
| ./build.sh -mpi true -help2yml true \ | |
| -DCMAKE_BUILD_TYPE=Release \ | |
| -DCMAKE_PREFIX_PATH="${PREFIX}" \ | |
| -DCMAKE_CXX_COMPILER="${CXX}" \ | |
| -boost_root "${PREFIX}" \ | |
| -j "${CPU_COUNT}" \ | |
| "${CONFIG_ARGS}" || exit 1 | |
| chmod 0755 rb-mpi rb-mpi-help2yml || exit 1 | |
| mv rb-mpi rb-mpi-help2yml $PREFIX/bin/ || exit 1 |
| #!/bin/bash | ||
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| export INCLUDES="-I${PREFIX}/include" | ||
| export LIBPATH="-L${PREFIX}/lib" | ||
| export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" | ||
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| mkdir -p $PREFIX/bin | ||
| cd projects/cmake | ||
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| if [ ! -d build ]; then | ||
| mkdir build | ||
| if [[ `uname` == "Darwin" ]]; then | ||
| export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" | ||
| else | ||
| export CONFIG_ARGS="" | ||
| fi | ||
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| ./generate_version_number.sh | ||
| mv GitVersion.cpp ../../src/revlanguage/utils/ | ||
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| # MPI version | ||
| ./regenerate.sh -mpi true | ||
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| cd build | ||
| ./build.sh -mpi true -help2yml true \ | ||
| -DCMAKE_BUILD_TYPE=Release \ | ||
| -DCMAKE_PREFIX_PATH="${PREFIX}" \ | ||
| -DCMAKE_CXX_COMPILER="${CXX}" \ | ||
| -boost_root "${PREFIX}" \ | ||
| -j "${CPU_COUNT}" \ | ||
| "${CONFIG_ARGS}" | ||
|
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| # If cmake finds a boost version compiled with cmake, it always links to it unless both | ||
| # Boost_NO_SYSTEM_PATHS=ON and Boost_NO_BOOST_CMAKE=ON (probably a bug in cmake) | ||
| cmake -DCMAKE_PREFIX_PATH=$PREFIX \ | ||
| -DBOOST_ROOT=$PREFIX \ | ||
| -DBoost_NO_SYSTEM_PATHS=ON \ | ||
| -DBoost_NO_BOOST_CMAKE=ON \ | ||
| . | ||
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| make | ||
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| cd .. | ||
| mkdir -p $PREFIX/bin | ||
| mv rb $PREFIX/bin/rb-mpi | ||
| chmod 0755 rb-mpi rb-mpi-help2yml | ||
| mv rb-mpi rb-mpi-help2yml $PREFIX/bin/ | ||
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| # Non-mpi version | ||
| rm -rf build | ||
| mkdir build | ||
| rm -rf build-mpi | ||
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| ./regenerate.sh | ||
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| cd build | ||
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| # If cmake finds a boost version compiled with cmake, it always links to it unless both | ||
| # Boost_NO_SYSTEM_PATHS=ON and Boost_NO_BOOST_CMAKE=ON (probably a bug in cmake) | ||
| cmake -DCMAKE_PREFIX_PATH=$PREFIX \ | ||
| -DBOOST_ROOT=$PREFIX \ | ||
| -DBoost_NO_SYSTEM_PATHS=ON \ | ||
| -DBoost_NO_BOOST_CMAKE=ON \ | ||
| . | ||
| ./build.sh -mpi false -help2yml true \ | ||
| -DCMAKE_BUILD_TYPE=Release \ | ||
| -DCMAKE_PREFIX_PATH="${PREFIX}" \ | ||
| -DCMAKE_CXX_COMPILER="${CXX}" \ | ||
| -boost_root "${PREFIX}" \ | ||
| -j "${CPU_COUNT}" \ | ||
| "${CONFIG_ARGS}" | ||
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| make | ||
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| cd .. | ||
| mkdir -p $PREFIX/bin | ||
| mv rb $PREFIX/bin | ||
| chmod 0755 rb rb-help2yml | ||
| mv rb rb-help2yml $PREFIX/bin/ | ||
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| rm -rf build |
There was a problem hiding this comment.
💡 Codebase verification
Missing Boost Dependency and CMake Version Specification
boost-cppis not listed inmeta.yamldependencies.cmake_minimum_requiredis not specified inCMakeLists.txt.
🔗 Analysis chain
Verify build dependencies and version compatibility
Since this is an update to RevBayes v1.2.4, let's ensure all required dependencies are available and the build process is compatible.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify build dependencies and version compatibility
# Check if meta.yaml exists and contains correct version
if [ -f "../meta.yaml" ]; then
echo "Checking meta.yaml for version and dependencies..."
cat "../meta.yaml"
fi
# Check if boost version meets minimum requirement
echo "Checking boost version requirement..."
if [ -f "../meta.yaml" ]; then
grep "boost-cpp" "../meta.yaml"
fi
# Check for CMake minimum version requirement
echo "Checking CMake version requirement..."
if [ -f "CMakeLists.txt" ]; then
grep "cmake_minimum_required" "CMakeLists.txt"
fi
Length of output: 249
🧰 Tools
🪛 Shellcheck
[warning] 8-8: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
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