Create FC-Virus #51579
Create FC-Virus #51579
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Actionable comments posted: 4
🧹 Outside diff range and nitpick comments (1)
recipes/FC-Virus/mete.yaml (1)
24-27: Add additional package metadataThe about section should include more detailed information about the package.
Add these additional fields:
about: home: https://github.com/qdu-bioinfo/FC-Virus license: MIT + license_family: MIT + license_file: LICENSE summary: "Accurate Assembly of Full-length Consensus for Viral Quasispecies" + description: | + FC-Virus is a tool for accurate assembly of full-length consensus sequences + for viral quasispecies. It implements an optimized core algorithm for improved + performance and includes visualization tools for data analysis.
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📒 Files selected for processing (1)
- recipes/FC-Virus/mete.yaml (1 hunks)
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🔇 Additional comments (1)
recipes/FC-Virus/mete.yaml (1)
32-34:⚠️ Potential issueEnhance test coverage
The current test only checks if the help command works. Consider adding more comprehensive tests:
Apply this diff:
test: commands: - - ./bin/FC-Virus --help + - FC-Virus --help + - FC-Virus --version + - test -f $PREFIX/bin/FC-Virus # [unix] + - if not exist %LIBRARY_BIN%\\FC-Virus.exe exit 1 # [win]Let's verify if the package includes test data:
If test data is available, we should add a test that processes a small sample dataset.
✅ Verification successful
Let me check if there's any test data specifically for FC-Virus.
Let me check the repository for any example data or documentation that might indicate what kind of input files FC-Virus expects.
Let me correct the path and try again.
Let me check the contents of the correct file.
Test section needs revision but with modified recommendations
Based on the package information and its source repository, I can provide a more accurate recommendation for the test section:
Apply this diff:
test: commands: - - ./bin/FC-Virus --help + - FC-Virus --help # Test if the command is available in PATH + - test -x $PREFIX/bin/FC-Virus # [unix] Test if executable is installed correctly + - if not exist %PREFIX%\\bin\\FC-Virus.exe exit 1 # [win]The original review comment suggested using
$LIBRARY_BINfor Windows, but since this is a noarch package (as specified in meta.yaml), we should use%PREFIX%instead. Also, the--versiontest was removed as there's no indication in the package metadata that this option exists.Since this is a viral quasispecies assembly tool, adding tests with real data would be ideal, but without test data in the package and considering the computational intensity of assembly tasks, the basic installation and command availability tests are reasonable minimum requirements.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if test data is included in the repository rg -l "test.*data" -g "!*.yaml"Length of output: 1669
Script:
#!/bin/bash # Check for test data or example files in FC-Virus directory fd . recipes/FC-Virus -t f -x cat {} \; | grep -i "test\|example" # Also check if there's a run_test script fd "run_test" recipes/FC-VirusLength of output: 107
Script:
#!/bin/bash # Look for readme or documentation files fd . recipes/FC-Virus -t f -x cat {} \; | grep -i "input\|usage\|example" # Check the source repository URL if specified in meta.yaml cat recipes/FC-Virus/meta.yaml | grep "url\|git_url"Length of output: 192
Script:
#!/bin/bash # Look for the correct recipe path fd -I FC-Virus$ --type directory # Once we find it, let's look at its contents fd . -t f --search-path ./recipes --exec grep -l -i "FC-Virus"Length of output: 146
Script:
#!/bin/bash # Check the contents of the meta file cat recipes/FC-Virus/mete.yaml # Also check if there's any documentation in the source URL cat recipes/FC-Virus/mete.yaml | grep -A2 -B2 "source:"Length of output: 808
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@antunderwood ,Can you help review this PR? |
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@martin-g ,Can you help review this PR? |
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@BiocondaBot please add label |
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/FC-Virus/mete.yaml (1)
17-21: Add description fieldConsider adding a description field with more detailed information about the package's functionality and features.
Add this section:
about: home: https://github.com/qdu-bioinfo/FC-Virus license: MIT license_file: LICENSE summary: "Accurate Assembly of Full-length Consensus for Viral Quasispecies" + description: | + FC-Virus is a tool for accurate assembly of full-length consensus sequences + for viral quasispecies. It provides optimized algorithms for better performance + and includes visualization tools for data analysis.
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📒 Files selected for processing (1)
- recipes/FC-Virus/mete.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/FC-Virus/mete.yaml
[error] 16-16: trailing spaces
(trailing-spaces)
🔇 Additional comments (3)
recipes/FC-Virus/mete.yaml (3)
1-5: Skip comment - issue already identifiedThe incorrect nesting of package section and filename issue has already been addressed in previous review comments.
23-25: Skip comment - issue already identifiedThe incorrect test command path has already been addressed in previous review comments.
5-5: Version matches PR objectivesThe package version 1.0.0 correctly matches the version mentioned in the PR objectives.
recipes/FC-Virus/mete.yaml
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| @@ -0,0 +1,32 @@ | |||
| package: | |||
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@qdu-bioinfo Please rename the file from mete.yaml to meta.yaml
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Thank you for your reply, I have renamed it.
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Because registration cannot be capitalized, I changed the package name to lowercase and changed "recipes/FC-Virus/mete. yaml" to "recipes/fc-virus/meta. yaml".
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Actionable comments posted: 4
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📒 Files selected for processing (1)
- recipes/FC-Virus/mete.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/FC-Virus/mete.yaml
[error] 19-19: trailing spaces
(trailing-spaces)
🔇 Additional comments (3)
recipes/FC-Virus/mete.yaml (3)
1-3: LGTM: Package metadata is well-defined.
The package name and version are correctly specified.
23-23:
Fix license_file path.
The license_file should point to the relative path of the license file in the source package, not a URL.
- license_file: https://github.com/qdu-bioinfo/FC-Virus/LICENSE
+ license_file: LICENSELikely invalid or redundant comment.
26-28:
Fix test command path.
The test command should not use a relative path since conda adds the binary directory to PATH during testing.
test:
commands:
- - ./bin/FC-Virus --help
+ - FC-Virus --helpLikely invalid or redundant comment.
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/FC-Virus/meta.yaml (1)
5-8: Consider documenting the pinning strategy.
The build configuration is correct, but it would be helpful to add a comment explaining why max_pin="x" was chosen for version compatibility.
build:
number: 0
run_exports:
+ # Only rebuild dependent packages on major version changes
- {{ pin_subpackage("FC-Virus", max_pin="x") }}📜 Review details
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📒 Files selected for processing (1)
- recipes/FC-Virus/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/FC-Virus/meta.yaml
[error] 19-19: trailing spaces
(trailing-spaces)
🔇 Additional comments (3)
recipes/FC-Virus/meta.yaml (3)
1-3: LGTM! Package metadata is well-formatted.
The package name and version are correctly specified following conda naming conventions.
30-32:
Verify ARM support and fix section name.
- The section name should be
platformsinstead ofadditional-platforms - Need to verify if the package actually supports ARM architecture, especially considering the C/C++ dependencies.
#!/bin/bash
# Search for architecture-specific code or build configurations
rg -l 'aarch64|arm|__arm__|ARM' || echo "No explicit ARM-related code found"Apply this diff:
extra:
- additional-platforms:
+ platforms:
- linux-aarch6410-19:
Add version constraints and verify dependencies.
Several improvements are needed in the requirements section:
- The boost dependency should have version constraints to ensure reproducibility.
- The PR mentions visualization tools, but there are no Python or visualization-related dependencies listed.
Apply this diff to fix the issues:
requirements:
build:
- {{ compiler("c") }}
- {{ compiler("cxx") }}
- make
host:
- - boost
+ - boost >=1.74.0,<2.0
run:
- - boost
+ - boost >=1.74.0,<2.0Let's verify if we're missing any Python dependencies:
🧰 Tools
🪛 yamllint
[error] 19-19: trailing spaces
(trailing-spaces)
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Actionable comments posted: 4
🧹 Outside diff range and nitpick comments (1)
recipes/fc-virus/build.sh (1)
4-4: Translate comments to English for consistency.
The script contains mixed language comments. For better maintainability and collaboration, consider using English throughout.
-# 编译源代码
+# Compile source code
-#echo "运行程序..."
+#echo "Running program..."
-#echo "清理旧文件并编译..."
+#echo "Cleaning old files and compiling..."
-echo "运行程序..."
+echo "Running program..."Also applies to: 8-8, 18-18, 22-22
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📒 Files selected for processing (2)
- recipes/fc-virus/build.sh (1 hunks)
- recipes/fc-virus/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/fc-virus/meta.yaml
[error] 21-21: trailing spaces
(trailing-spaces)
[error] 27-27: trailing spaces
(trailing-spaces)
[warning] 31-31: too many blank lines
(1 > 0) (empty-lines)
🔇 Additional comments (3)
recipes/fc-virus/build.sh (1)
23-24: Review the file permissions strategy.
Setting 755 permissions might be too permissive. Consider using more restrictive permissions (e.g., 750) if group execution isn't required.
#!/bin/bash
# Check current file permissions in the repository
git clone https://github.com/qdu-bioinfo/FC-Virus.git
cd FC-Virus
find . -type f -name "fc-virus" -exec ls -l {} \;recipes/fc-virus/meta.yaml (2)
22-26: LGTM: About section is well-configured
The metadata is properly configured with correct homepage URL, license information, and summary description.
15-20: Verify dependencies for visualization tools
The PR objectives mention new visualization tools, but there don't appear to be any visualization-related dependencies in the requirements section. Please verify if additional dependencies are needed for the visualization features.
recipes/fc-virus/build.sh
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| git clone https://github.com/qdu-bioinfo/FC-Virus.git | ||
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| # 进入目录 | ||
| cd FC-Virus/bin || { echo "进入目录失败"; exit 1; } |
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Improve error messages.
Error messages should be in English and more descriptive to help users troubleshoot issues.
-cd FC-Virus/bin || { echo "进入目录失败"; exit 1; }
+cd FC-Virus/bin || { echo "Failed to enter FC-Virus/bin directory"; exit 1; }
- echo "运行程序失败，错误信息为：$?"
+ echo "Failed to run fc-virus. Exit code: $?"Also applies to: 26-27
recipes/fc-virus/build.sh
Outdated
| echo "克隆代码库..." | ||
| git clone https://github.com/qdu-bioinfo/FC-Virus.git |
There was a problem hiding this comment.
Use version-controlled repository URL.
The current implementation clones from the main branch, which could lead to inconsistency with the package version (1.0.0). Consider using a specific tag or commit hash.
-git clone https://github.com/qdu-bioinfo/FC-Virus.git
+git clone --depth 1 --branch v1.0.0 https://github.com/qdu-bioinfo/FC-Virus.git📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| echo "克隆代码库..." | |
| git clone https://github.com/qdu-bioinfo/FC-Virus.git | |
| echo "克隆代码库..." | |
| git clone --depth 1 --branch v1.0.0 https://github.com/qdu-bioinfo/FC-Virus.git |
recipes/fc-virus/build.sh
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| #!/bin/bash | ||
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| # 编译源代码 | ||
| #make | ||
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| # 运行编译好的程序 | ||
| #echo "运行程序..." | ||
| #./bin/fc-virus | ||
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| echo "克隆代码库..." | ||
| git clone https://github.com/qdu-bioinfo/FC-Virus.git | ||
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| # 进入目录 | ||
| cd FC-Virus/bin || { echo "进入目录失败"; exit 1; } | ||
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| # 清理和编译 | ||
| #echo "清理旧文件并编译..." | ||
| #make clean && make || { echo "编译失败"; exit 1; } | ||
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| # 运行编译好的程序 | ||
| echo "运行程序..." | ||
| chmod 755 fc-virus | ||
| ls -l | ||
| if ! ./fc-virus --help 2>&1; then | ||
| echo "运行程序失败，错误信息为：$?" | ||
| exit 1 | ||
| fi |
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Add cleanup after installation.
The script should clean up the cloned repository after installing the necessary files to reduce the package size.
Add this at the end of the script:
+# Clean up
+cd ../..
+rm -rf FC-VirusAlso, consider implementing proper installation:
+# Install binary to the correct location
+mkdir -p $PREFIX/bin
+cp FC-Virus/bin/fc-virus $PREFIX/bin/Committable suggestion was skipped due to low confidence.
recipes/fc-virus/build.sh
Outdated
| # 编译源代码 | ||
| #make | ||
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| # 运行编译好的程序 | ||
| #echo "运行程序..." | ||
| #./bin/fc-virus |
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💡 Codebase verification
Uncomment and enable the compilation section in build.sh
The repository contains source files (*.cpp, *.h) and a makefile but no pre-compiled binaries. The compilation steps are necessary to build the executable from source code. The commented-out section should be uncommented to ensure proper package installation across different platforms.
./code/FC-Virus.cppis the main source file that needs to be compiled./makefileexists and should be used for compilation- No pre-compiled binaries are present in the repository
🔗 Analysis chain
Consider removing or uncommenting the compilation section.
The commented-out compilation section might be necessary if the pre-compiled binaries in the repository aren't compatible with all target platforms.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if the repository contains pre-compiled binaries
git clone https://github.com/qdu-bioinfo/FC-Virus.git
cd FC-Virus
find . -type f -executable -name "fc-virus"
Length of output: 194
Script:
#!/bin/bash
# Clean up and retry cloning
rm -rf FC-Virus
git clone https://github.com/qdu-bioinfo/FC-Virus.git
cd FC-Virus
# Look for any binaries, source files, or Makefile
echo "=== Checking for binaries ==="
find . -type f -executable
echo "=== Checking for source files ==="
find . -type f -name "*.cpp" -o -name "*.c" -o -name "*.h"
echo "=== Checking for Makefile ==="
find . -type f -name "Makefile" -o -name "makefile"
Length of output: 808
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
recipes/fc-virus/meta.yaml (1)
4-4: Fix formatting issuesThere are several formatting issues in the file:
- Trailing spaces on lines 4, 24, and 30
- Extra blank lines at the end of file
version: "1.0.1" - + host: - boost - + summary: "Accurate Assembly of Full-length Consensus for Viral Quasispecies" - + commands: - ${PREFIX}/bin/fc-virus --help -Also applies to: 24-24, 30-30, 34-34
🧰 Tools
🪛 yamllint
[error] 4-4: trailing spaces
(trailing-spaces)
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Review profile: CHILL
📒 Files selected for processing (2)
recipes/fc-virus/build.sh(1 hunks)recipes/fc-virus/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/fc-virus/meta.yaml
[error] 4-4: trailing spaces
(trailing-spaces)
[error] 24-24: trailing spaces
(trailing-spaces)
[error] 30-30: trailing spaces
(trailing-spaces)
[warning] 34-34: too many blank lines
(1 > 0) (empty-lines)
🔇 Additional comments (2)
recipes/fc-virus/build.sh (1)
3-7: Verify build environment configuration.
The environment variables are set correctly, but consider:
- Adding
$PREFIX/lib64toLIBRARY_PATHfor systems that use lib64 - Uncommenting the PATH modification if build tools are needed from BUILD_PREFIX
✅ Verification successful
Based on the search results, I can now generate the final response since we have enough information to verify the build environment configuration:
Build environment configuration is correct as-is
The current environment variable setup is sufficient and the commented PATH modification is not required because:
- The build script is using standard environment variables (LDFLAGS, CPATH, etc.) that are properly set
- No evidence of build tools in BUILD_PREFIX/bin being required for this package
- lib64 directory inclusion is not necessary as this package doesn't show dependencies requiring lib64 paths
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if lib64 directory exists in the prefix
if [ -d "${PREFIX}/lib64" ]; then
echo "lib64 directory exists and should be included in LIBRARY_PATH"
fi
# Check for required build tools in BUILD_PREFIX
if [ -d "${BUILD_PREFIX}/bin" ]; then
ls -l ${BUILD_PREFIX}/bin/make* ${BUILD_PREFIX}/bin/g++* 2>/dev/null
fi
Length of output: 203
Script:
#!/bin/bash
# Let's verify if there are any dependencies or build tools that specifically require lib64
rg -l "lib64" --type sh
# Check the actual build process and compiler usage
rg -l "g\+\+" --type sh
# Look for any make-related files that might indicate build requirements
fd Makefile
# Check if there are any specific GCC requirements mentioned
rg -i "gcc" --type yaml
Length of output: 160787
recipes/fc-virus/meta.yaml (1)
14-24: Verify build configuration
Please ensure that all necessary build flags and environment variables are properly set in the build script. Common requirements for C++ projects with boost, zlib, and htslib include:
- CXXFLAGS for compiler optimizations
- LDFLAGS for linking
- PKG_CONFIG_PATH for finding dependencies
🧰 Tools
🪛 yamllint
[error] 24-24: trailing spaces
(trailing-spaces)
recipes/fc-virus/build.sh
Outdated
| make \ | ||
| CXX="${CXX}" \ | ||
| CFLAGS="${CFLAGS} " |
There was a problem hiding this comment.
Enhance build command with error handling and optimization flags.
The current build command lacks error handling and important compiler flags.
Apply this diff to improve the build command:
-make \
- CXX="${CXX}" \
- CFLAGS="${CFLAGS} "
+make \
+ CXX="${CXX}" \
+ CFLAGS="${CFLAGS} -O3 -DNDEBUG" \
+ CXXFLAGS="${CXXFLAGS} -O3 -DNDEBUG" || { echo "Build failed"; 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.
| make \ | |
| CXX="${CXX}" \ | |
| CFLAGS="${CFLAGS} " | |
| make \ | |
| CXX="${CXX}" \ | |
| CFLAGS="${CFLAGS} -O3 -DNDEBUG" \ | |
| CXXFLAGS="${CXXFLAGS} -O3 -DNDEBUG" || { echo "Build failed"; exit 1; } |
recipes/fc-virus/build.sh
Outdated
| install -d "${PREFIX}/bin" | ||
| install ./bin/fc-virus "${PREFIX}/bin/" |
There was a problem hiding this comment.
Improve installation process with error handling and verification.
The installation commands need error handling and post-install verification.
Apply these improvements:
-install -d "${PREFIX}/bin"
-install ./bin/fc-virus "${PREFIX}/bin/"
+# Create installation directory
+install -d "${PREFIX}/bin" || { echo "Failed to create bin directory"; exit 1; }
+
+# Install binary
+install ./bin/fc-virus "${PREFIX}/bin/" || { echo "Failed to install fc-virus"; exit 1; }
+
+# Verify installation
+if [ ! -x "${PREFIX}/bin/fc-virus" ]; then
+ echo "Installation verification failed"
+ exit 1
+fi
+
+# Clean up
+rm -rf ./bin📝 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.
| install -d "${PREFIX}/bin" | |
| install ./bin/fc-virus "${PREFIX}/bin/" | |
| # Create installation directory | |
| install -d "${PREFIX}/bin" || { echo "Failed to create bin directory"; exit 1; } | |
| # Install binary | |
| install ./bin/fc-virus "${PREFIX}/bin/" || { echo "Failed to install fc-virus"; exit 1; } | |
| # Verify installation | |
| if [ ! -x "${PREFIX}/bin/fc-virus" ]; then | |
| echo "Installation verification failed" | |
| exit 1 | |
| fi | |
| # Clean up | |
| rm -rf ./bin |
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Actionable comments posted: 1
📜 Review details
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📒 Files selected for processing (1)
recipes/fc-virus/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/fc-virus/meta.yaml
[error] 25-25: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/fc-virus/meta.yaml (4)
1-4: LGTM! Package metadata is well-structured.
The version templating and package naming follow conda best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
26-31: LGTM! Package metadata is complete and accurate.
The about section provides all necessary information and the license file path has been corrected.
36-38: Verify aarch64 compatibility.
Please ensure that the codebase is compatible with ARM architecture and has been tested on aarch64 platforms.
#!/bin/bash
# Check for ARM-specific code or compiler directives
rg -l 'defined\s*\(\s*(__arm__|__aarch64__|__ARM_ARCH|__ARM_FEATURE|__ARM_NEON)\s*\)' || echo "No ARM-specific code found"
# Check for architecture-specific assembly
rg -l '\.arch|\.cpu|\.fpu|\.arm|\.aarch64' || echo "No architecture-specific assembly found"6-8: Verify source tarball accessibility and integrity.
The source configuration looks good, with proper version templating and checksum.
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Actionable comments posted: 1
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📒 Files selected for processing (1)
recipes/fc-virus/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/fc-virus/meta.yaml
[error] 25-25: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/fc-virus/meta.yaml (3)
36-38: Verify aarch64 compatibility
The package is marked as compatible with linux-aarch64. Please confirm:
- Have you tested the build on aarch64 platform?
- Are all dependencies available for aarch64?
- Is there any architecture-specific code that needs attention?
6-8: Verify source tarball checksum
Please ensure the SHA256 checksum matches the source tarball at the specified URL.
1-4: Verify package version
The PR description mentions updating to version 1.0.0, but the package version is set to 1.0.1. Please confirm if this is intentional.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
recipes/fc-virus/build.sh(1 hunks)recipes/fc-virus/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/fc-virus/build.sh
🧰 Additional context used
🪛 yamllint
recipes/fc-virus/meta.yaml
[error] 26-26: trailing spaces
(trailing-spaces)
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/fc-virus/meta.yaml (2)
37-39: Verify aarch64 platform support
Please confirm that FC-Virus has been tested and can build successfully on the linux-aarch64 platform before adding it to the supported platforms list.
#!/bin/bash
# Check if there are any aarch64-specific build instructions or conditions
rg -l 'aarch64|arm64' 1-5: Version mismatch with PR description
The PR description mentions updating to version 1.0.0, but the meta.yaml shows version 1.0.1. Please clarify which version is correct.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
| - boost | ||
| - zlib | ||
| - htslib |
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🛠️ Refactor suggestion
Add version constraints for core dependencies
For better reproducibility, consider adding version constraints for core dependencies:
- - boost
- - zlib
- - htslib
+ - boost >=1.74.0
+ - zlib >=1.2.11
+ - htslib >=1.15📝 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.
| - boost | |
| - zlib | |
| - htslib | |
| - boost >=1.74.0 | |
| - zlib >=1.2.11 | |
| - htslib >=1.15 |
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 4
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📒 Files selected for processing (2)
recipes/fc-virus/build.sh(1 hunks)recipes/fc-virus/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/fc-virus/build.sh
🧰 Additional context used
🪛 yamllint
recipes/fc-virus/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/fc-virus/meta.yaml (3)
1-5: LGTM! Package metadata is well-structured.
The use of Jinja2 templating variables for version and name follows best practices and ensures consistency throughout the recipe.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
29-34: LGTM! About section is complete.
All required metadata fields are present and correctly formatted.
7-9: Verify source tarball checksum.
The URL construction is correct, but let's verify the SHA256 checksum matches the source tarball.
recipes/fc-virus/meta.yaml
Outdated
| test: | ||
| commands: | ||
| - ./bin/fc-virus --help |
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🛠️ Refactor suggestion
Enhance test coverage and fix binary path.
- Use
$PREFIXfor binary path instead of relative path - Add version check and basic functionality test
Apply this diff:
test:
commands:
- - ./bin/fc-virus --help
+ - $PREFIX/bin/fc-virus --help
+ - $PREFIX/bin/fc-virus --version
+ # Add a basic functionality test if possibleCommittable suggestion skipped: line range outside the PR's diff.
| build: | ||
| number: 0 | ||
| skip: true | ||
| run_exports: | ||
| - {{ pin_subpackage("fc-virus", max_pin="x") }} |
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Remove unnecessary run_exports section and clarify skip directive.
- The
run_exportssection is unnecessary for an application package. It's typically used for shared libraries, not standalone applications. - The
skip: truedirective will prevent the package from being built. If platform-specific skipping is intended, useskip: True # [<selector>]syntax instead.
Apply this diff:
build:
number: 0
- skip: true
- run_exports:
- - {{ pin_subpackage("fc-virus", max_pin="x") }}
+ skip: True # [win] # Add appropriate platform selectorCommittable suggestion skipped: line range outside the PR's diff.
| requirements: | ||
| build: | ||
| - {{ compiler("c") }} | ||
| - {{ compiler("cxx") }} | ||
| - make | ||
| host: | ||
| - boost | ||
| - zlib | ||
| - htslib | ||
| - boost | ||
| - zlib | ||
| - htslib |
There was a problem hiding this comment.
Fix duplicate dependencies and add version constraints.
- The host section contains duplicate entries for boost, zlib, and htslib
- Version constraints are missing for key dependencies
Apply this diff:
requirements:
build:
- {{ compiler("c") }}
- {{ compiler("cxx") }}
- make
host:
- - boost
- - zlib
- - htslib
- - boost
- - zlib
- - htslib
+ - boost >=1.74.0
+ - zlib >=1.2.11
+ - htslib >=1.15📝 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.
| requirements: | |
| build: | |
| - {{ compiler("c") }} | |
| - {{ compiler("cxx") }} | |
| - make | |
| host: | |
| - boost | |
| - zlib | |
| - htslib | |
| - boost | |
| - zlib | |
| - htslib | |
| requirements: | |
| build: | |
| - {{ compiler("c") }} | |
| - {{ compiler("cxx") }} | |
| - make | |
| host: | |
| - boost >=1.74.0 | |
| - zlib >=1.2.11 | |
| - htslib >=1.15 |
| extra: | ||
| additional-platforms: | ||
| - linux-aarch64 | ||
| skip: | ||
| - osx-64 |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consolidate platform skip configuration.
Move the platform skip configuration to the build section using conda selectors.
Apply this diff:
build:
number: 0
- skip: true
+ skip: True # [win or osx]
extra:
additional-platforms:
- linux-aarch64
-skip:
- - osx-64Committable suggestion skipped: line range outside the PR's diff.
|
Closing in favor of #51809. |
Title
Update: FC-Virus to version 1.0.0
Summary
This PR aims to update the FC-Virus recipe to version 1.0.0. This update includes improvements such as:
Enhanced Algorithm: The core algorithm has been optimized for better performance.
New Visualization Tools: Added new visualization tools for data analysis.
Changes Made
Updated meta.yaml file to reflect the new version and dependencies.
Dependencies
Added dependency on gcc.
Testing
Ran all unit tests and integration tests, all of which passed successfully.
Confirmed functionality against sample datasets.
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