add files for equirep #51972
add files for equirep #51972
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces two new files related to the The second file, Possibly related PRs
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (2)
recipes/EquiRep/meta.yaml (2)
23-25: Enhance test coverageThe current test only verifies that the binary exists. Consider adding:
- Help command test:
EquiRep --help- Version test:
EquiRep --version- Test with example data if available
33-38: Consider adding co-maintainersHaving multiple maintainers helps ensure long-term recipe maintenance. Consider adding co-maintainers, especially if there are other contributors to the EquiRep project.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/EquiRep/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/EquiRep/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/EquiRep/meta.yaml (3)
12-15: LGTM! Good use of run_exports
The pin_subpackage configuration will help prevent ABI breakage in downstream dependencies.
1-6: 🛠️ Refactor suggestion
Ensure consistent package naming across the recipe
The package name is defined as lowercase "equirep" but the source URL and run_exports use "EquiRep". This inconsistency could cause issues. Consider using lowercase consistently throughout the recipe.
-{% set name = "equirep" %}
+{% set name = "EquiRep" %}Likely invalid or redundant comment.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: Verify source availability and checksum
Please ensure that:
- The GitHub release URL is publicly accessible
- The SHA256 checksum matches the source tarball
recipes/EquiRep/meta.yaml
Outdated
| about: | ||
| home: "https://github.com/Shao-Group/EquiRep" | ||
| license: BSD-3-Clause | ||
| license_file: LICENSE | ||
| summary: "EquiRep is tool to identify tandem repeats." |
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🛠️ Refactor suggestion
Fix grammar in summary and clarify biological relevance
- The summary has a grammatical error: "is tool" should be "is a tool"
- Please expand the summary to clarify the biological relevance of tandem repeats analysis, as Bioconda is specifically for bioinformatics tools.
- summary: "EquiRep is tool to identify tandem repeats."
+ summary: "A bioinformatics tool for identifying tandem repeats in genomic sequences."📝 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.
| about: | |
| home: "https://github.com/Shao-Group/EquiRep" | |
| license: BSD-3-Clause | |
| license_file: LICENSE | |
| summary: "EquiRep is tool to identify tandem repeats." | |
| about: | |
| home: "https://github.com/Shao-Group/EquiRep" | |
| license: BSD-3-Clause | |
| license_file: LICENSE | |
| summary: "A bioinformatics tool for identifying tandem repeats in genomic sequences." |
recipes/EquiRep/meta.yaml
Outdated
| requirements: | ||
| build: | ||
| - make | ||
| - {{ compiler('c') }} | ||
| - {{ compiler('cxx') }} |
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💡 Codebase verification
Based on the analysis of the source code and build files, I can now provide a response regarding the runtime dependencies for EquiRep.
Add runtime dependencies for the compiled binary
The recipe needs the following runtime dependencies:
libgcc-ng- Core system library that the compiled C++ binary links againstlibstdc++- C++ standard libraryzlib- Required for compression support (linked via -lz)
🔗 Analysis chain
Verify runtime dependencies
The recipe only specifies build requirements. Please verify if any runtime dependencies are needed, such as:
- Core system libraries that the compiled binary links against
- Any runtime dependencies mentioned in the project's documentation
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if there's any documentation about dependencies in the source
curl -sL "https://raw.githubusercontent.com/Shao-Group/EquiRep/main/README.md" | grep -i "depend\|require"
Length of output: 106
Script:
#!/bin/bash
# Let's check the source code for potential library dependencies
# Look for #include statements in source files
echo "=== Checking C/C++ includes ==="
fd -e cpp -e c -e h --exec rg -l "#include" {} \; | while read -r file; do
echo "=== In $file ==="
rg "#include" "$file"
done
# Check for shared library linkage in Makefile
echo -e "\n=== Checking Makefile for library linkage ==="
fd Makefile --exec cat {}
Length of output: 160681
Script:
#!/bin/bash
# Let's check for library dependencies in the source code and build files
# Look for library dependencies in source files
echo "=== Checking source files for library dependencies ==="
fd -e cpp -e c -e h --exec rg -l "^#include|^#pragma|LIBS|LDFLAGS" {} \; | while read -r file; do
echo "=== In $file ==="
rg "^#include|^#pragma|LIBS|LDFLAGS" "$file"
done
# Check for linker flags and library dependencies in build files
echo -e "\n=== Checking build files for library dependencies ==="
fd "CMakeLists.txt|Makefile|\.pro$" --exec rg -l "LIBS|LDFLAGS|target_link_libraries|find_package" {} \; | while read -r file; do
echo "=== In $file ==="
rg "LIBS|LDFLAGS|target_link_libraries|find_package" "$file"
done
Length of output: 21348
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Actionable comments posted: 2
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (2)
recipes/equirep/build.sh(1 hunks)recipes/equirep/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/equirep/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (1)
recipes/equirep/build.sh (1)
1-6: Consider adding build verification and documentation.
As this is a Bioconda package:
- Consider adding a basic test after installation to verify the build:
# Add after make install $PREFIX/bin/EquiRep --version || true
- Add a comment block at the top of the script documenting build requirements and any special considerations.
Let's verify if this package follows Bioconda's biological software requirement:
recipes/equirep/build.sh
Outdated
| ./configure | ||
| make |
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Complete the build and installation process.
The current build commands are insufficient for proper Conda package creation:
- Configure needs to specify installation prefix
- Make should utilize parallel builds
- Missing installation step
Apply these changes:
-./configure
-make
+./configure --prefix="${PREFIX}"
+make -j${CPU_COUNT}
+make install📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| ./configure | |
| make | |
| ./configure --prefix="${PREFIX}" | |
| make -j${CPU_COUNT} | |
| make install |
| #!/bin/bash | ||
|
|
||
| set -xe |
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Add required Conda build environment setup.
The build script needs to incorporate Conda-specific environment variables and error handling:
Apply these changes:
#!/bin/bash
-set -xe
+set -euo pipefail
+
+# Conda build environment setup
+export CFLAGS="${CFLAGS} -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CPATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| #!/bin/bash | |
| set -xe | |
| #!/bin/bash | |
| set -euo pipefail | |
| # Conda build environment setup | |
| export CFLAGS="${CFLAGS} -I${PREFIX}/include" | |
| export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" | |
| export CPATH="${PREFIX}/include" | |
| export LIBRARY_PATH="${PREFIX}/lib" |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/equirep/meta.yaml (2)
16-17: Remove extra blank lineThere's an unnecessary blank line after the build section.
run_exports: - {{ pin_subpackage('equirep', max_pin="x") }} - requirements:
31-31: Fix grammar in summary and enhance descriptionThe summary contains a grammatical error ("is tool") and could be more descriptive.
- summary: "EquiRep is tool to identify tandem repeats." + summary: "EquiRep is a tool for identifying tandem repeats in genomic sequences."
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/equirep/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/equirep/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/equirep/meta.yaml (3)
33-38: LGTM!
The extra section correctly specifies additional platforms and maintainer information.
18-21: Consider adding host and run requirements sections
The recipe only specifies build requirements. Consider if any runtime dependencies are needed for the package to function correctly.
#!/bin/bash
# Check source code for potential runtime dependencies
curl -sL "https://github.com/Shao-Group/EquiRep/releases/download/v1.0.0/EquiRep-1.0.0.tar.gz" | \
tar xz --to-stdout | \
rg -i "include\s+[<\"].*[>\"]" | \
sort -u8-10: Verify source URL and checksum
Let's verify the release exists and the checksum is correct.
| test: | ||
| commands: | ||
| - EquiRep |
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🛠️ Refactor suggestion
Enhance test coverage
The current test only verifies that the executable runs. Consider adding:
- Version check command (
EquiRep --version) - Help command test (
EquiRep --help) - Test with example data if available
test:
commands:
- EquiRep
+ - EquiRep --version
+ - EquiRep --helpCommittable suggestion skipped: line range outside the PR's diff.
|
@BiocondaBot please add label |
Describe your pull request here
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
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(see here for the rationale and comprehensive explanation).Add a
run_exportssection 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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