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Rebuild muse recipe #52155
Rebuild muse recipe #52155
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces modifications to the In the Possibly related PRs
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🚧 Files skipped from review as they are similar to previous changes (2)
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/muse/version.patch (1)
8-29
: Consider using a command-line argument parsing libraryThe current approach to command-line argument handling, while functional, could benefit from using a dedicated argument parsing library. This would provide:
- Standardized help messages
- Automatic version flag handling
- Better error handling
- Easier addition of new options in the future
Consider using libraries like
boost::program_options
orCLI11
which are well-suited for C++ applications.recipes/muse/fix-install_muse.sh.patch (2)
Line range hint
2-19
: Consider using conda-build's compiler infrastructureThe OS-specific compiler selection might override conda-build's compiler infrastructure. Instead of setting
TOOL
directly, consider:
- Using
${CC}
and${CXX}
environment variables which are properly set by conda-build- Falling back to OS-specific defaults only if these aren't set
-if [[ `uname` == "Darwin" ]]; then - export TOOL=clang -else - export TOOL=gcc -fi +# Use conda-build's compiler if available, otherwise fall back to OS defaults +if [ -z "${CC}" ]; then + if [[ `uname` == "Darwin" ]]; then + export CC=clang + export CXX=clang++ + else + export CC=gcc + export CXX=g++ + fi +fi +export TOOL=$(basename ${CC})
19-27
: Use PREFIX variable for consistencyThe bootstrap command uses
$(pwd)
for prefix while other commands use${PREFIX}
. For consistency and to ensure proper installation paths:-./bootstrap.sh --with-toolset="${TOOL}" --prefix="$(pwd)" +./bootstrap.sh --with-toolset="${TOOL}" --prefix="${PREFIX}"
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
recipes/muse/fix-install_muse.sh.patch
(4 hunks)recipes/muse/meta.yaml
(2 hunks)recipes/muse/version.patch
(1 hunks)
🔇 Additional comments (10)
recipes/muse/version.patch (4)
2-3
: LGTM: Appropriate file permission adjustment
Removing executable permissions from source files is a good security practice.
11-21
: LGTM: Improved code formatting
The indentation changes enhance code readability while maintaining the original logic.
30-31
: LGTM: Improved control flow
Moving the return statement outside the conditional blocks improves code structure and ensures consistent return behavior.
22-25
: Verify Version string initialization and consider flag consolidation
While the version flag implementation is functionally correct, consider:
- The code assumes
Version
is properly initialized. Verify this variable is always defined. - Consider using only
--version
as the standard flag, as having both--version
and--v
might be confusing.
recipes/muse/meta.yaml (3)
21-21
: LGTM: Build number increment is appropriate
The build number increment is correct as there are recipe changes (new patch and platform support).
63-64
: Verify dependency availability for linux-aarch64
Before enabling aarch64 support, we need to ensure all dependencies are available for this architecture.
#!/bin/bash
# Description: Verify critical dependencies are available for linux-aarch64
# Check if key dependencies have aarch64 builds
DEPS=("boost" "libcurl" "icu" "bzip2" "xz" "zlib")
echo "Checking dependencies for linux-aarch64:"
for dep in "${DEPS[@]}"; do
# Search for conda packages with aarch64 builds
conda search --json "$dep" | jq '.[] | select(.platform == "linux-aarch64" or .platform == "noarch") | {name, version, platform}'
done
# Check if there are any architecture-specific build flags
rg "aarch64|arm64" recipes/muse/
Consider adding CI tests for the aarch64 platform to ensure compatibility.
15-15
: Verify the version.patch file
The addition of version support is good practice. However, let's verify the patch file exists and follows conda-forge/bioconda guidelines.
✅ Verification successful
Let me try another verification approach to check the patch file.
Patch file looks good and follows proper conventions
The version.patch file:
- Exists and has proper permissions
- Follows standard patch format with correct diff headers
- Makes a clean modification to add
--version
support - Contains proper context lines and clean indentation fixes
- Implements version display in a standard way using
--version
and--v
flags
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the version.patch file exists and follows guidelines
# Check if patch file exists
if ! fd "version.patch" recipes/muse/; then
echo "Error: version.patch not found"
exit 1
fi
# Check patch format
rg -U "^diff|^index|^\+\+\+|^---" recipes/muse/version.patch
# Check if patch applies cleanly (look for fuzz/offset warnings)
rg "Hunk.*fuzz|offset" recipes/muse/version.patch
Length of output: 1603
Script:
#!/bin/bash
# Let's check if the patch file exists and examine its contents
ls -l recipes/muse/version.patch
cat recipes/muse/version.patch
Length of output: 1038
recipes/muse/fix-install_muse.sh.patch (3)
Line range hint 30-48
: LGTM! Good improvements to gperftools build
The changes improve the build configuration by:
- Using proper prefix paths
- Implementing parallel builds with CPU_COUNT
- Updating to a newer, stable version
89-91
: LGTM! Proper cleanup implementation
The cleanup section properly removes all temporary build artifacts and directories.
Line range hint 49-88
: Verify libcurl dependencies in meta.yaml
The addition of --enable-libcurl
will require curl development libraries. Please ensure these dependencies are properly declared in meta.yaml.
Describe your pull request here
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add label
command.@bioconda/core
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Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports
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run_exports
section like this:with
...
being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}
{{ pin_subpackage("myrecipe", max_pin="x.x") }}
{{ pin_subpackage("myrecipe", max_pin="x.x") }}
(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}
(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}
while replacing
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with eithername
if aname|lower
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