Add FMSI #51277
Add FMSI #51277
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces several updates to the The Changes to the Suggested labels
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (7)
recipes/fmsi/build.sh (1)
1-5: Overall, the build script is well-structured but could benefit from enhanced error handling.The script successfully accomplishes its main goals of building and installing the FMSI package. It follows Conda conventions and uses appropriate commands. However, implementing the suggested improvements for quoting, error handling, and existence checking will make the script more robust and reliable, especially in different environments or when debugging build issues.
Consider adding logging or echo statements at key points in the script (e.g., before and after the make command, and during installation) to provide more visibility into the build process. This can be helpful for troubleshooting in CI/CD pipelines or when users encounter issues.
recipes/fmsi/meta.yaml (6)
4-10: LGTM: Package and source information are correctly defined.The package name, version, source URL, and SHA256 checksum are all properly set. The use of Jinja2 variables for version and checksum in the URL and sha256 fields is a good practice.
Consider adding a
license_familyfield in theaboutsection to make it easier for users to filter packages based on license compatibility.
12-15: LGTM: Build section is correctly configured.The build number is properly set to 0 for a new package. The use of
run_exportswithpin_subpackageis a good practice for managing package dependencies.Consider adding a
skipcondition if the package is not intended to be built on certain platforms. For example:build: number: 0 skip: True # [win] run_exports: - {{ pin_subpackage('fmsi', max_pin="x.x") }}This would skip building on Windows if the package is not compatible.
18-27: LGTM: Requirements are well-defined.The build, host, and run requirements are appropriately specified. The use of
{{ compiler('cxx') }}and{{ compiler('c') }}is the correct way to specify C++ and C compilers in conda-forge recipes.Consider pinning the zlib version in the run requirements to ensure compatibility:
run: - zlib - {{ pin_compatible('zlib') }}This helps maintain consistency across different environments.
29-31: LGTM: Test command is provided.The test command checks for the presence and basic functionality of the 'fmsi' command, which is good.
Consider adding more comprehensive tests if possible. For example:
test: commands: - fmsi -h 2>&1 | grep "FMSI" - fmsi --version - test -f $PREFIX/bin/fmsi # [unix] - if not exist %LIBRARY_BIN%\\fmsi.exe exit 1 # [win]This would also check the version output and verify the presence of the executable file.
33-37: LGTM: About section provides essential metadata.The about section includes the necessary information such as the home URL, license type, license file, and a summary of the package's functionality.
Consider adding the following fields to provide more information to users:
- Add a
license_familyfield:license_family: MIT- Include a
doc_urlif documentation is available:doc_url: https://github.com/OndrejSladky/fmsi/blob/master/README.md- Add a
dev_urlpointing to the repository for development:dev_url: https://github.com/OndrejSladky/fmsiThese additions would provide users with more resources and make the package more discoverable.
38-38: Minor: Remove extra blank lines at the end of the file.There are extra blank lines at the end of the file. Consider removing them to adhere to YAML style guidelines.
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- recipes/fmsi/build.sh (1 hunks)
- recipes/fmsi/meta.yaml (1 hunks)
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recipes/fmsi/meta.yaml
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🔇 Additional comments (2)
recipes/fmsi/build.sh (1)
1-1: LGTM: Correct shebang for a bash script.The shebang
#!/bin/bashis appropriate for a bash script and ensures portability across different Unix-like systems.recipes/fmsi/meta.yaml (1)
1-2: LGTM: Version and checksum are correctly defined.The use of Jinja2 variables for version and checksum is a good practice for maintainability.
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recipes/fmsi/build.sh
Outdated
| install -d "${PREFIX}/bin" | ||
| install fmsi "${PREFIX}/bin/" |
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🛠️ Refactor suggestion
Enhance installation process with existence check.
The installation commands are generally good, using the install command and following Conda conventions with ${PREFIX}. However, consider adding a check for the existence of the fmsi executable before attempting to install it.
Here's an improved version of the installation commands:
install -d "${PREFIX}/bin"
-install fmsi "${PREFIX}/bin/"
+if [ -f fmsi ]; then
+ install fmsi "${PREFIX}/bin/"
+else
+ echo "Error: fmsi executable not found" >&2
+ exit 1
+fiThis change ensures that the fmsi executable exists before attempting to install it, providing better error handling and feedback if the build process fails to produce the executable.
📝 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 "${PREFIX}/bin" | |
| install fmsi "${PREFIX}/bin/" | |
| install -d "${PREFIX}/bin" | |
| if [ -f fmsi ]; then | |
| install fmsi "${PREFIX}/bin/" | |
| else | |
| echo "Error: fmsi executable not found" >&2 | |
| exit 1 | |
| fi |
recipes/fmsi/build.sh
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| @@ -0,0 +1,5 @@ | |||
| #!/bin/bash | |||
|
|
|||
| make CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" | |||
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🛠️ Refactor suggestion
Enhance the make command for robustness.
While the current make command is functional, consider the following improvements:
- Quote the entire value of CXX to handle potential spaces in paths.
- Add error handling to ensure the build process succeeds before proceeding.
Here's an improved version of the make command:
-make CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}"
+make CXX="${CXX}" CXXFLAGS="${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" || exit 1This change separates CXX from the flags and adds error handling. If the make command fails, the script will exit with a non-zero status.
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| make CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" | |
| make CXX="${CXX}" CXXFLAGS="${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" || exit 1 |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/fmsi/meta.yaml (3)
12-17: LGTM: Build section is correctly configured. Consider removing extra blank line.The build number and run exports are properly set. The pinning strategy for run exports is correct.
Consider removing the extra blank line at line 17 to maintain consistent formatting:
run_exports: - {{ pin_subpackage('fmsi', max_pin="x.x") }} - requirements:
29-31: LGTM: Basic test is provided. Consider adding more comprehensive tests.The current test checks for the presence and basic functionality of the 'fmsi' command. This is a good start, but consider adding more comprehensive tests if possible.
If feasible, consider adding tests that:
- Check for specific expected output or behavior.
- Verify the functionality with sample input data.
- Test different command-line options.
These additional tests would provide more confidence in the package's functionality.
38-38: Minor: Remove extra blank line at the end of the file.To adhere to YAML best practices, remove the extra blank line at the end of the file.
summary: FMSI - memory efficient k-mer set index based on masked superstrings and Burrows-Wheeler transform -🧰 Tools
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📒 Files selected for processing (1)
- recipes/fmsi/meta.yaml (1 hunks)
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🪛 yamllint
recipes/fmsi/meta.yaml
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🔇 Additional comments (6)
recipes/fmsi/meta.yaml (6)
1-2: LGTM: Version and checksum are correctly defined.The use of Jinja2 variables for version and SHA256 checksum is a good practice for maintainability.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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4-6: LGTM: Package metadata is correctly defined.The package name is set to "fmsi", and the version uses the Jinja2 variable, ensuring consistency with the earlier definition.
8-10: LGTM: Source information is correctly defined.The source URL is properly formatted with the version variable, and the SHA256 checksum is correctly referenced using the Jinja2 variable.
18-27: LGTM: Requirements are correctly specified.The build, host, and run requirements are appropriately defined for a C++ project. The use of Jinja2 variables for compilers and the inclusion of zlib in both host and run requirements are correct practices.
33-37: LGTM: About section is comprehensive and accurate.The about section provides all necessary metadata, including the home URL, license information (MIT, as mentioned in the PR objectives), and a concise summary of the tool's functionality.
1-38: Overall: The meta.yaml file is well-structured and follows Conda packaging best practices.The file includes all necessary sections for a Conda package and is correctly configured. The use of Jinja2 variables, appropriate pinning strategies, and comprehensive metadata demonstrate good packaging practices. The minor formatting suggestions provided earlier will further improve the file's consistency.
Great job on creating this package configuration!
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (4)
recipes/fmsi/meta.yaml (4)
12-15: LGTM: Build section is correct. Consider adding skip directive.The build number and run_exports section are correctly defined. The use of pin_subpackage with max_pin="x.x" is a good practice for ensuring compatibility.
Consider adding a
skipdirective to specify which platforms this package can be built on. For example:build: number: 0 skip: True # [win] run_exports: - {{ pin_subpackage('fmsi', max_pin="x.x") }}This would skip building on Windows if the package is not compatible with that platform.
18-30: LGTM: Requirements updated correctly. Consider pinning sdsl-lite version.The addition of sdsl-lite to build, host, and run requirements is consistent with the PR objectives. The existing requirements are maintained correctly.
Consider pinning the version of sdsl-lite to ensure reproducibility. For example:
requirements: build: - sdsl-lite {{ sdsl_lite_version }} host: - sdsl-lite {{ sdsl_lite_version }} run: - sdsl-lite {{ sdsl_lite_version }}Where
{{ sdsl_lite_version }}is a Jinja2 variable defined at the top of the file with the specific version of sdsl-lite you want to use.
36-40: LGTM: About section is comprehensive. Consider adding more metadata.The about section provides essential information including the home URL, license type, license file, and a brief summary of the tool's functionality.
Consider adding more metadata to improve discoverability and provide more information to users. For example:
about: home: https://github.com/OndrejSladky/fmsi/ license: MIT license_file: LICENSE summary: FMSI - memory efficient k-mer set index based on masked superstrings and Burrows-Wheeler transform description: | FMSI is a tool for indexing k-mer sets with masked superstrings. It provides a memory-efficient solution for handling large-scale genomic data analysis tasks. dev_url: https://github.com/OndrejSladky/fmsi/ doc_url: https://github.com/OndrejSladky/fmsi/blob/master/README.md
41-41: Minor: Remove extra blank lines at the end of the file.There are extra blank lines at the end of the file. Consider removing them to adhere to YAML style guidelines.
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[warning] 41-41: too many blank lines
(1 > 0) (empty-lines)
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📒 Files selected for processing (2)
- recipes/fmsi/build.sh (1 hunks)
- recipes/fmsi/meta.yaml (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/fmsi/build.sh
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recipes/fmsi/meta.yaml
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🔇 Additional comments (3)
recipes/fmsi/meta.yaml (3)
1-2: LGTM: Version and checksum updated correctly.The version has been updated to "0.2.4" and the SHA256 checksum has been updated accordingly. This is consistent with the PR objectives and follows best practices for Conda recipes.
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4-10: LGTM: Package and source information updated correctly.The package name, version, and source URL have been updated correctly. The use of Jinja2 variables for version and SHA256 checksum is appropriate and follows best practices.
32-34: LGTM: Test command is appropriate.The test command checks if the
fmsicommand is available and outputs the expected string. This is a basic but sufficient test to ensure the package is installed correctly.
|
Hello, I have been trying to get FMSI to bioconda, but currently I struggle with how to correctly set up the recipe with SDSL-lite as a dependency. FMSI compiled via Next, I tried to get inspired by other recipes which use SDSL-lite as a dependency (namely hypo), but I was unable to get this working (see the last CI run) and unfortunately I do not know how this could be fixed. Would it be possible to ask someone for help with getting this resolved? I am pinging @bioconda/core as in the instructions. Thank you very much! Ondrej |
|
Reposting for @OndrejSladky to enable pings (courtesy of the BiocondaBot):
I have been trying to get FMSI to bioconda, but currently I struggle with how to correctly set up the recipe with SDSL-lite as a dependency. FMSI compiled via Next, I tried to get inspired by other recipes which use SDSL-lite as a dependency (namely hypo), but I was unable to get this working (see the last CI run) and unfortunately I do not know how this could be fixed. Would it be possible to ask someone for help with getting this resolved? I am pinging @bioconda/core as in the instructions. Thank you very much! Ondrej |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/fmsi/meta.yaml (2)
17-26: LGTM: Requirements updated with sdsl-liteThe addition of sdsl-lite to both host and run requirements is correct and aligns with the PR objectives. This should address the dependency issues mentioned in the PR comments.
Consider adding a version constraint for sdsl-lite to ensure compatibility:
host: - sdsl-lite >=2.1.1 run: - sdsl-lite >=2.1.1This helps maintain consistency across different environments and prevents potential issues with future incompatible versions.
28-30: Consider enhancing the test sectionWhile the current test command verifies the basic functionality of the fmsi command, it might be beneficial to add more comprehensive tests.
Consider adding the following improvements:
- Test for the correct version number:
- fmsi --version | grep "{{ version }}"- Test a basic functionality of the tool (if possible with a small example):
- fmsi [example_command] [example_input] | grep [expected_output]These additional tests would provide more confidence in the correct installation and functionality of the package.
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- recipes/fmsi/build.sh (1 hunks)
- recipes/fmsi/meta.yaml (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/fmsi/build.sh
🧰 Additional context used
🪛 yamllint
recipes/fmsi/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (5)
recipes/fmsi/meta.yaml (5)
1-10: LGTM: Package metadata updated correctlyThe package version has been updated to 0.2.4, and the corresponding SHA256 checksum and source URL have been updated accordingly. These changes are consistent with the PR objectives.
🧰 Tools
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[error] 1-1: syntax error: found character '%' that cannot start any token
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12-15: LGTM: Build section is correctThe build number is set to 0, which is appropriate for a new version. The run_exports section is correctly configured to pin the subpackage version, ensuring compatibility for downstream dependencies.
32-39: LGTM: About section is comprehensiveThe about section provides all necessary information including home page, license details, summary, development URL, and documentation URL. The use of templating for the documentation URL ensures it always points to the correct version.
1-2: Note on yamllint warning: False positiveThe yamllint tool reported a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' is part of the Jinja2 templating syntax, which is valid and commonly used in Conda recipe files. No action is required to address this warning.
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41-44: Verify the relevance of the added DOI identifiersThe addition of DOI identifiers is valuable for academic citation and tracking. However, it's important to ensure that these DOIs are directly related to the FMSI project.
Please confirm that both DOIs (10.1101/2024.03.06.583483 and 10.1101/2023.02.01.526717) are directly related to the FMSI project. You can verify this by checking the content of these DOIs:
If both DOIs are confirmed to be directly related to FMSI, no further action is needed. If not, please remove any unrelated DOIs.
✅ Verification successful
DOI Relevance Confirmed
The added DOIs are directly related to the FMSI project based on their titles:
- 10.1101/2024.03.06.583483: Function-Assigned Masked Superstrings as a Versatile and Compact Data Type for k-Mer Sets | bioRxiv
- 10.1101/2023.02.01.526717: Masked superstrings as a unified framework for textual k-mer set representations | bioRxiv
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The following scripts were executed for the analysis:
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#!/bin/bash # Fetch and display the titles of the DOIs echo "DOI: 10.1101/2024.03.06.583483" curl -sL "https://doi.org/10.1101/2024.03.06.583483" | grep -oP '<title>\K(.*)(?=</title>)' | head -n 1 echo "DOI: 10.1101/2023.02.01.526717" curl -sL "https://doi.org/10.1101/2023.02.01.526717" | grep -oP '<title>\K(.*)(?=</title>)' | head -n 1Length of output: 540
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (4)
recipes/fmsi/0001-Makefile.patch (1)
16-16: Improved library path configuration with a minor suggestionThe change to the
LIBSvariable is good. Adding-L${PREFIX}/libensures that the linker can find the required libraries in the Conda environment. The use of+=instead of=is also beneficial as it allows for appending to existingLIBSvalues.Consider moving
-L${PREFIX}/libto the beginning of theLIBSvariable to ensure it takes precedence:-LIBS+= -lz -lsdsl -ldivsufsort -ldivsufsort64 -L${PREFIX}/lib +LIBS+= -L${PREFIX}/lib -lz -lsdsl -ldivsufsort -ldivsufsort64This change ensures that the Conda environment's libraries are prioritized during linking.
Also applies to: 17-17
recipes/fmsi/meta.yaml (3)
19-28: LGTM: Requirements updated, consider adding build dependencyThe addition of sdsl-lite as a dependency in both host and run sections is correct and consistent with the PR objectives. However, consider adding sdsl-lite to the build section as well, as it might be required during the build process.
requirements: build: - make - cmake - {{ compiler('cxx') }} + - sdsl-lite host: - zlib - sdsl-lite run: - sdsl-liteThis ensures that sdsl-lite is available during all stages of the package creation process.
30-32: Consider adding a test for sdsl-lite integrationWhile the existing test command checks for the basic functionality of FMSI, it might be beneficial to add a test that verifies the integration with the newly added sdsl-lite dependency. This could help ensure that the package is built and linked correctly with all its dependencies.
1-2: Note on yamllint warning: False positiveThe yamllint tool reports a syntax error for the '%' character at the beginning of the file. This is a false positive as the '%' is part of the Jinja2 templating syntax, which is commonly used in Conda recipe files.
If you want to suppress this warning in future linting, you can add a
# yamllint disable-line rule:syntaxcomment at the beginning of the file or configure yamllint to ignore Jinja2 syntax in YAML files.🧰 Tools
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[error] 1-1: syntax error: found character '%' that cannot start any token
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📒 Files selected for processing (4)
- recipes/fmsi/0001-Makefile.patch (1 hunks)
- recipes/fmsi/0002-version.patch (1 hunks)
- recipes/fmsi/build.sh (1 hunks)
- recipes/fmsi/meta.yaml (1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/fmsi/0002-version.patch
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/fmsi/build.sh
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recipes/fmsi/meta.yaml
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🔇 Additional comments (8)
recipes/fmsi/0001-Makefile.patch (4)
7-7: Improved compiler selection flexibilityThe change from hardcoded
g++to${CXX}allows for more flexible compiler selection, which is a good practice in Conda recipes. This change respects the environment's compiler setting and aligns with Conda build practices.Also applies to: 11-11
9-9: Improved binary installation pathThe change from a relative path
../fmsito${PREFIX}/bin/fmsiis a good practice in Conda recipes. It ensures that the binary is installed in the correct location within the Conda environment, making the installation more robust and consistent with Conda's file structure.Also applies to: 13-13
10-10: Improved include path configurationThe change from
.to${PREFIX}for theINCLUDES-PATHvariable is a good practice in Conda recipes. It ensures that the correct include paths are used, making the build process more robust and consistent across different Conda environments.Also applies to: 14-14
25-25: Improved sdsl-lite installation configurationThe change in the sdsl-lite build configuration from a relative path
../..to${PREFIX}for theCMAKE_INSTALL_PREFIXis excellent. This ensures that sdsl-lite is installed in the correct location within the Conda environment, maintaining consistency with other changes in the Makefile and adhering to Conda best practices.Also applies to: 26-26
recipes/fmsi/meta.yaml (4)
1-6: LGTM: Package metadata updated correctlyThe package version has been updated to 0.2.4, and the SHA256 checksum has been updated accordingly. These changes are consistent with the PR objectives.
🧰 Tools
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14-17: LGTM: Build section is correctThe build number is set to 0, which is appropriate for a new version. The run_exports section with pin_subpackage for 'fmsi' ensures proper version pinning for downstream dependencies.
34-46: LGTM: Metadata updated with new identifiersThe addition of two new DOI identifiers in the extra section is a welcome improvement. This provides more information about the project and its associated research. The rest of the metadata, including license and summary information, remains accurate and up-to-date.
8-13: LGTM: Source URL updated, verify patch filesThe source URL has been correctly updated to use the new version. However, please ensure that the listed patch files (0001-Makefile.patch and 0002-version.patch) are still applicable and necessary for this new version.
✅ Verification successful
Verified: Patch files exist and are correct
Both
0001-Makefile.patchand0002-version.patchare present and contain the expected modifications. No further action is required.🏁 Scripts executed
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#!/bin/bash # Description: Verify the existence and content of patch files # Test: Check if patch files exist if [ -f recipes/fmsi/0001-Makefile.patch ] && [ -f recipes/fmsi/0002-version.patch ]; then echo "Patch files exist." # Display the content of patch files echo "Content of 0001-Makefile.patch:" cat recipes/fmsi/0001-Makefile.patch echo "Content of 0002-version.patch:" cat recipes/fmsi/0002-version.patch else echo "One or both patch files are missing." fiLength of output: 1534
| @@ -1,10 +1,10 @@ | ||
| .PHONY: all clean | ||
| -CXX= g++ | ||
| -CXXFLAGS= -g -Wall -Wno-unused-function -std=c++17 -O2 |
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💡 Codebase verification
Build environment missing 'make' command
The build verification could not be performed because the make command is not installed in the current environment. Please ensure that make is available to proceed with the build and validate the optimization level change.
🔗 Analysis chain
Verify impact of increased optimization level
The optimization level has been changed from -O2 to -O3. While this can potentially improve performance, it may also increase compile time and binary size. Additionally, more aggressive optimizations might lead to unexpected behavior in some cases.
Please ensure that:
- The increased optimization level doesn't introduce any bugs or unexpected behavior.
- The performance improvement justifies the potential increase in compile time and binary size.
You can use the following script to compare build times and binary sizes:
Also applies to: 12-12
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Compare build times and binary sizes for -O2 and -O3 optimization levels
# Function to build and measure
build_and_measure() {
local opt_level=$1
echo "Building with $opt_level..."
start_time=$(date +%s)
make clean && CXXFLAGS="-g -Wall -Wno-unused-function -std=c++17 $opt_level" make
end_time=$(date +%s)
build_time=$((end_time - start_time))
binary_size=$(du -h ${PREFIX}/bin/fmsi | cut -f1)
echo "Build time: $build_time seconds"
echo "Binary size: $binary_size"
}
echo "Testing with -O2:"
build_and_measure "-O2"
echo "Testing with -O3:"
build_and_measure "-O3"
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Length of output: 1807
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@coderabbitai For future reference, the make command should be installed in the build section of meta.yaml and is listed in this recipe.
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@mencian Thank you for the clarification. You're correct that make is included in the build section of meta.yaml and is listed in this recipe. I'll consider this in future analyses.
(^_^)
✏️ Learnings added
Learnt from: mencian
PR: bioconda/bioconda-recipes#51277
File: recipes/fmsi/0001-Makefile.patch:8-8
Timestamp: 2024-10-16T01:05:46.764Z
Learning: In Bioconda recipes, the `make` command is included in the `build` section of `meta.yaml` and is part of the recipe.
Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (2)
recipes/fmsi/build.sh (1)
5-8: LGTM: Proper environment variable setup with a minor suggestion.The environment variables are set up correctly, using
${PREFIX}consistently and appending toLDFLAGSrather than overwriting it. The addition of the-O3optimization flag toCXXFLAGSis appropriate for a release build.Consider explicitly handling
CPPFLAGSsimilar to howLDFLAGSis handled:export CPPFLAGS="${CPPFLAGS} ${INCLUDES}"This ensures that any pre-existing
CPPFLAGSare preserved while adding the necessary include paths.recipes/fmsi/meta.yaml (1)
31-33: Consider adding more comprehensive tests.The current test command verifies that the
fmsiexecutable is installed and runs without errors. However, it might be beneficial to add more comprehensive tests to ensure the functionality of the package.Consider adding tests that:
- Check the version number of the installed package.
- Verify the presence of key files or libraries.
- Run a simple operation using the
fmsicommand.For example, you could add:
commands: - fmsi -h 2>&1 | grep "FMSI" - fmsi --version | grep "{{ version }}" - test -f $PREFIX/bin/fmsi
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/fmsi/build.sh (1 hunks)
- recipes/fmsi/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/fmsi/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (8)
recipes/fmsi/build.sh (3)
1-3: LGTM: Proper script setup and directory creation.The script starts with the correct shebang line and creates the installation directory using best practices. The use of
${PREFIX}follows Conda conventions.
16-18: 🛠️ Refactor suggestionEnhance make command robustness and error handling.
The make command correctly uses environment variables and includes parallel build options. However, it can be improved for robustness and error handling.
Consider applying the following changes:
- Quote the
CXXvariable to handle potential spaces in paths.- Add error handling to ensure the build process succeeds before proceeding.
-make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" \ - CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" \ - -j"${CPU_COUNT}" +make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" \ + CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" \ + -j"${CPU_COUNT}" || exit 1This change adds error handling. If the make command fails, the script will exit with a non-zero status, preventing further execution in case of build failures.
20-20:⚠️ Potential issueAdd missing installation step and enhance error handling.
The current line sets permissions for the fmsi executable, but there's no command to actually install it to
${PREFIX}/bin. Additionally, we should add a check for the existence of the executable before attempting to install it.Please add the installation command and an existence check. Here's a suggested implementation:
if [ -f fmsi ]; then install -m 755 fmsi "${PREFIX}/bin/" else echo "Error: fmsi executable not found" >&2 exit 1 fiThis change ensures that:
- The
fmsiexecutable exists before attempting to install it.- The executable is properly installed to
${PREFIX}/bin/.- The correct permissions (755) are set during installation.
- An error message is displayed and the script exits if the executable is not found.
recipes/fmsi/meta.yaml (5)
15-18: Build section looks good.The build number is correctly set to 0 for the new version. The
run_exportssection is properly configured to pin thefmsisubpackage, which is a good practice for ensuring consistency in dependent packages.
35-42: About section is well-documented.The about section provides comprehensive information about the package, including home page, license details, and a summary of the package's functionality. The inclusion of dev_url and doc_url with proper versioning is a good practice.
20-29: Requirements updated correctly. Verify sdsl-lite dependency.The addition of
sdsl-liteas a dependency in both host and run environments is consistent with the PR objectives and comments. This should address the compilation issues mentioned in the PR comments.To ensure that the
sdsl-litedependency is correctly specified and available, please run the following command:#!/bin/bash # Check if sdsl-lite is available in the bioconda channel conda search sdsl-lite -c biocondaIf the command doesn't return any results, you may need to add sdsl-lite to the bioconda channel or specify a different channel for this dependency.
44-47: DOI identifiers added. Verify their accuracy.The addition of DOI identifiers is valuable for academic citation and tracking. This is consistent with the PR objectives.
Please verify that these DOIs are correct and relevant to the FMSI project. You can check them using the following commands:
#!/bin/bash # Verify DOIs echo "Checking DOI: 10.1101/2024.03.06.583483" curl -sI "https://doi.org/10.1101/2024.03.06.583483" | grep -i "location:" echo "---" echo "Checking DOI: 10.1101/2023.02.01.526717" curl -sI "https://doi.org/10.1101/2023.02.01.526717" | grep -i "location:"Ensure that the returned URLs are relevant to the FMSI project.
1-2: Version update looks good. Verify SHA256 checksum.The package version has been correctly updated to 0.2.4. This is consistent with the PR objectives.
Please ensure that the SHA256 checksum is correct for the new version. You can verify it using the following command:
Compare the output with the checksum in the meta.yaml file.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
| if [[ `uname` == "Darwin" ]]; then | ||
| export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" | ||
| else | ||
| export CXXFLAGS="${CXXFLAGS}" | ||
| fi |
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🛠️ Refactor suggestion
Simplify OS-specific CXXFLAGS adjustment.
The OS check for Darwin and the addition of the -D_LIBCPP_DISABLE_AVAILABILITY flag for macOS is correct. However, the else clause is unnecessary.
Consider simplifying this section by removing the else clause:
if [[ `uname` == "Darwin" ]]; then
export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
-else
- export CXXFLAGS="${CXXFLAGS}"
fiThis change removes the redundant reassignment of CXXFLAGS to itself, making the script more concise without changing its behavior.
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| if [[ `uname` == "Darwin" ]]; then | |
| export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" | |
| else | |
| export CXXFLAGS="${CXXFLAGS}" | |
| fi | |
| if [[ `uname` == "Darwin" ]]; then | |
| export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" | |
| fi |
| source: | ||
| url: https://github.com/OndrejSladky/fmsi/archive/v{{ version }}.tar.gz | ||
| sha256: {{ sha256 }} | ||
| patches: | ||
| - 0001-Makefile.patch | ||
| - 0002-version.patch |
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💡 Codebase verification
Patch files contain unexpected content.
The files recipes/fmsi/0001-Makefile.patch and recipes/fmsi/0002-version.patch appear to contain scripts for checking DOIs rather than the expected code modifications. Please verify that these patch files include the intended changes for version 0.2.4.
🔗 Analysis chain
Source URL updated correctly. Verify patches.
The source URL has been correctly updated to reflect the new version 0.2.4.
Two patches are being applied during the build process. Please ensure that these patches are still necessary and compatible with the new version:
Review the output to confirm that the patches are still relevant for version 0.2.4.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check the content of the patch files
cat recipes/fmsi/0001-Makefile.patch
echo "---"
cat recipes/fmsi/0002-version.patch
Length of output: 471
This add a recipe for FMSI for indexing k-mer sets with masked superstrings.
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