Add JARVIS3 recipe. #51730
Add JARVIS3 recipe. #51730
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mirakaya
commented
Oct 28, 2024
mirakaya
commented
- Add JARVIS3 tool
|
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (3)
recipes/jarvis3/build.sh (1)
1-16: Consider adding logging for build steps.To help with debugging potential build issues, consider adding more verbose output.
Add echo statements for major steps:
+echo "Setting up build environment..." export C_INCLUDE_PATH=$C_INCLUDE_PATH:${PREFIX}/include export LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib +echo "Building JARVIS3..." cd src || exit 1 make CC=$CC CFLAGS="$CFLAGS -fcommon" || exit 1 +echo "Installing JARVIS3..."🧰 Tools
🪛 Shellcheck
[warning] 4-4: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 11-11: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
recipes/jarvis3/meta.yaml (2)
21-24: Consider enhancing test coverage.While the current tests verify basic functionality, consider:
- Adding error case tests (e.g., invalid input)
- Making version check more robust by checking exact output
- Verifying the output file content, not just its existence
Example improvement:
- - JARVIS3 --version 2>&1 | grep "Version 3, Release 7" + - test "$(JARVIS3 --version 2>&1)" = "JARVIS3 Version 3, Release 7"
26-31: Consider enhancing package metadata.While the basic metadata is present, consider adding:
- A more detailed description under
description:field- Reference to the related paper or publication
- Tags to improve package discoverability
Example addition:
description: | JARVIS3 is an improved encoder specifically designed for genomic sequences, providing efficient compression while maintaining sequence integrity. tags: - genomics - compression
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/jarvis3/build.sh (1 hunks)
- recipes/jarvis3/meta.yaml (1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/jarvis3/build.sh
[warning] 4-4: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 11-11: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/jarvis3/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/jarvis3/build.sh (2)
1-3: LGTM: Environment setup looks correct.The environment variables are properly set to include the conda prefix paths.
1-16: Verify JARVIS3 binary architecture compatibility.Since this is a bioconda recipe, we should ensure the binary is built correctly for the target architecture.
🧰 Tools
🪛 Shellcheck
[warning] 4-4: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
[warning] 11-11: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
recipes/jarvis3/meta.yaml (4)
1-5: LGTM! Package metadata follows conda conventions.The package name and version are correctly defined using Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-14: Verify source integrity.The source URL follows the correct pattern, but let's verify the SHA256 checksum matches the GitHub release.
#!/bin/bash # Verify the checksum matches the release curl -sL https://github.com/cobilab/jarvis3/archive/refs/tags/v3.7.tar.gz | sha256sum
16-19: Consider adding runtime dependencies.While build dependencies are correct, please verify if JARVIS3 has any runtime dependencies that should be listed under
run:section.#!/bin/bash # Check for potential runtime dependencies in source rg -l "^\s*#include\s+<[^>]+>" --type c
7-10: Please elaborate on OSX compatibility issues.While the comment indicates issues with clang flags, it would be helpful to:
- Document which specific flags are problematic
- Consider if these flags could be conditionally modified for OSX support
Let's check if other bioconda packages handle similar clang issues:
| mv extra/ ${PREFIX}/bin | ||
| mv JARVIS3.sh ${PREFIX}/bin | ||
| mv JARVIS3 ${PREFIX}/bin |
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Add error checking for file operations.
The installation steps should verify that files exist before moving them.
Apply this diff to add safety checks:
-mv extra/ ${PREFIX}/bin
-mv JARVIS3.sh ${PREFIX}/bin
-mv JARVIS3 ${PREFIX}/bin
+[ -d "extra" ] && mv extra/ ${PREFIX}/bin || exit 1
+[ -f "JARVIS3.sh" ] && mv JARVIS3.sh ${PREFIX}/bin || exit 1
+[ -f "JARVIS3" ] && mv JARVIS3 ${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.
| mv extra/ ${PREFIX}/bin | |
| mv JARVIS3.sh ${PREFIX}/bin | |
| mv JARVIS3 ${PREFIX}/bin | |
| [ -d "extra" ] && mv extra/ ${PREFIX}/bin || exit 1 | |
| [ -f "JARVIS3.sh" ] && mv JARVIS3.sh ${PREFIX}/bin || exit 1 | |
| [ -f "JARVIS3" ] && mv JARVIS3 ${PREFIX}/bin || exit 1 |
recipes/jarvis3/build.sh
Outdated
| cd ${PREFIX}/bin | ||
| sed 's/ \.\// /g; s/\"\.\//"/g' JARVIS3.sh > aux.sh | ||
| rm JARVIS3.sh | ||
| mv aux.sh JARVIS3.sh | ||
| chmod +x JARVIS3.sh | ||
| JARVIS3.sh --install |
There was a problem hiding this comment.
Improve path modification safety and add installation verification.
The path modification process needs better error handling and the installation should be verified.
Apply this diff to improve safety:
-cd ${PREFIX}/bin
-sed 's/ \.\// /g; s/\"\.\//"/g' JARVIS3.sh > aux.sh
-rm JARVIS3.sh
-mv aux.sh JARVIS3.sh
-chmod +x JARVIS3.sh
-JARVIS3.sh --install
+cd ${PREFIX}/bin || exit 1
+if [ -f "JARVIS3.sh" ]; then
+ sed 's/ \.\// /g; s/\"\.\//"/g' JARVIS3.sh > aux.sh || exit 1
+ mv aux.sh JARVIS3.sh || exit 1
+ chmod +x JARVIS3.sh || exit 1
+ if ! ./JARVIS3.sh --install; then
+ echo "JARVIS3 installation failed"
+ exit 1
+ fi
+else
+ echo "JARVIS3.sh not found"
+ 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.
| cd ${PREFIX}/bin | |
| sed 's/ \.\// /g; s/\"\.\//"/g' JARVIS3.sh > aux.sh | |
| rm JARVIS3.sh | |
| mv aux.sh JARVIS3.sh | |
| chmod +x JARVIS3.sh | |
| JARVIS3.sh --install | |
| cd ${PREFIX}/bin || exit 1 | |
| if [ -f "JARVIS3.sh" ]; then | |
| sed 's/ \.\// /g; s/\"\.\//"/g' JARVIS3.sh > aux.sh || exit 1 | |
| mv aux.sh JARVIS3.sh || exit 1 | |
| chmod +x JARVIS3.sh || exit 1 | |
| if ! ./JARVIS3.sh --install; then | |
| echo "JARVIS3 installation failed" | |
| exit 1 | |
| fi | |
| else | |
| echo "JARVIS3.sh not found" | |
| exit 1 | |
| fi |
🧰 Tools
🪛 Shellcheck
[warning] 11-11: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
| cd src | ||
| make CC=$CC CFLAGS="$CFLAGS -fcommon" | ||
| mkdir -p ${PREFIX}/bin | ||
| make |
There was a problem hiding this comment.
Add error handling for directory change and build process.
The build process should fail gracefully if any step fails.
Apply this diff to add error handling:
-cd src
-make CC=$CC CFLAGS="$CFLAGS -fcommon"
-mkdir -p ${PREFIX}/bin
-make
+cd src || exit 1
+make CC=$CC CFLAGS="$CFLAGS -fcommon" || exit 1
+mkdir -p ${PREFIX}/bin || exit 1
+make || exit 1Also, there appears to be a redundant make command. Consider removing the second one.
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| cd src | |
| make CC=$CC CFLAGS="$CFLAGS -fcommon" | |
| mkdir -p ${PREFIX}/bin | |
| make | |
| cd src || exit 1 | |
| make CC=$CC CFLAGS="$CFLAGS -fcommon" || exit 1 | |
| mkdir -p ${PREFIX}/bin || exit 1 | |
| make || exit 1 |
🧰 Tools
🪛 Shellcheck
[warning] 4-4: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
|
@BiocondaBot please add label |
There was a problem hiding this comment.
Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/jarvis3/meta.yaml (1)
7-12: Consider starting build number at 0
The build number is set to 1, but as this appears to be a new recipe, it should typically start at 0. The build number should only be incremented when the package is rebuilt without a version change.
build:
# Passes some invalid flags for clang
skip: True # [osx]
- number: 1
+ number: 0
run_exports:
- {{ pin_subpackage("jarvis3", max_pin="x") }}📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/jarvis3/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/jarvis3/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/jarvis3/meta.yaml (3)
1-5: LGTM: Package metadata follows conda conventions
The package name and version are correctly defined using Jinja2 templating.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
28-33: Enhance package metadata
The summary could be more descriptive to help users understand the tool's purpose and features. Also, let's verify the presence of the LICENSE file in the source repository.
#!/bin/bash
# Description: Verify LICENSE file and gather more detailed description
# Expected: Find LICENSE file and potential description from README
# Check for LICENSE file in the repository
rg -l 'GNU.*General.*Public.*License' || echo "GPL license text not found"
# Look for a better description in README files
rg -i -A 5 'description|overview|about' -g 'README*' || echo "No detailed description found"Consider expanding the summary to include key features and use cases of JARVIS3.
14-16: Verify source integrity
Let's verify that the SHA256 checksum matches the GitHub release tarball.
recipes/jarvis3/meta.yaml
Outdated
| test: | ||
| commands: | ||
| - JARVIS3 --version 2>&1 | grep "Version 3, Release 7" | ||
| - printf ">test_seq\nACGTCGCGCGCGCG\n" > test.fa; JARVIS3.sh -i test.fa | grep "test.fa.tar" |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Improve test robustness
Two suggestions for the test section:
- The version string should use the template variable:
Version {{ version.split('.')[0] }}, Release {{ version.split('.')[1] }} - The test file should be cleaned up after the test
test:
commands:
- - JARVIS3 --version 2>&1 | grep "Version 3, Release 7"
- - printf ">test_seq\nACGTCGCGCGCGCG\n" > test.fa; JARVIS3.sh -i test.fa | grep "test.fa.tar"
+ - JARVIS3 --version 2>&1 | grep "Version {{ version.split('.')[0] }}, Release {{ version.split('.')[1] }}"
+ - |
+ printf ">test_seq\nACGTCGCGCGCGCG\n" > test.fa
+ JARVIS3.sh -i test.fa | grep "test.fa.tar"
+ rm -f test.fa test.fa.tar📝 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.
| test: | |
| commands: | |
| - JARVIS3 --version 2>&1 | grep "Version 3, Release 7" | |
| - printf ">test_seq\nACGTCGCGCGCGCG\n" > test.fa; JARVIS3.sh -i test.fa | grep "test.fa.tar" | |
| test: | |
| commands: | |
| - JARVIS3 --version 2>&1 | grep "Version {{ version.split('.')[0] }}, Release {{ version.split('.')[1] }}" | |
| - | | |
| printf ">test_seq\nACGTCGCGCGCGCG\n" > test.fa | |
| JARVIS3.sh -i test.fa | grep "test.fa.tar" | |
| rm -f test.fa test.fa.tar |
| requirements: | ||
| build: | ||
| - make | ||
| - {{ compiler('c') }} |
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💡 Codebase verification
From analyzing the build.sh and meta.yaml files, I can now generate a final response since I have enough information about the runtime requirements.
Runtime dependencies should be added
The package requires runtime dependencies that are not specified in meta.yaml:
- The
JARVIS3.shshell script is installed and used for execution, indicating a runtime dependency onbash - The test commands show that the package creates and processes files, suggesting filesystem operations
Please add the following under requirements:
run:
- bash🔗 Analysis chain
Verify runtime dependencies
The recipe only specifies build requirements. Please verify if there are any runtime dependencies needed for JARVIS3 to function correctly (e.g., bash for JARVIS3.sh script).
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for potential runtime dependencies
# Look for system calls and library dependencies in the source code
# Search for common system utilities used in shell scripts
rg -l 'command -v|which |#!/.*/(env )?(bash|sh|python|perl|awk|sed)' || echo "No shell scripts found"
# Search for common library includes that might indicate dependencies
ast-grep --pattern '#include <$_>' || echo "No C includes found"
Length of output: 10341
Script:
#!/bin/bash
# Let's check the source repository and build files for runtime dependencies
# Check source files in the recipe directory
ls -la recipes/jarvis3/
# Check if there's a build.sh to understand the installation process
cat recipes/jarvis3/build.sh
# Look for any README or documentation files
fd -t f "README|INSTALL" recipes/jarvis3/
# Check the source code repository if URL is mentioned in meta.yaml
cat recipes/jarvis3/meta.yaml
Length of output: 1584
