Update svdss to 2.0.0 #51519
Update svdss to 2.0.0 #51519
Conversation
📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces several updates to the In the The Possibly related PRs
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (Invoked using PR comments)
Other keywords and placeholders
CodeRabbit Configuration File (
|
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
recipes/svdss/build.sh (1)
1-1: Consider using/usr/bin/envin the shebang for portabilityChanging the shebang to
#!/bin/bashmay reduce portability on systems wherebashis not located at/bin/bash. Using#!/usr/bin/env bashis more portable and ensures the script uses thebashinterpreter found in the user'sPATH.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
- recipes/svdss/build.sh (1 hunks)
- recipes/svdss/build_failure.linux-64.yaml (0 hunks)
- recipes/svdss/meta.yaml (4 hunks)
💤 Files with no reviewable changes (1)
- recipes/svdss/build_failure.linux-64.yaml
🧰 Additional context used
🪛 Shellcheck
recipes/svdss/build.sh
[warning] 17-17: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/svdss/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/svdss/meta.yaml (5)
47-53: Metadata improvements look great.The additions to the
aboutsection enhance the package metadata:
- The
license_familyandlicense_fileprovide clear licensing information.- The updated summary is more polished with proper punctuation.
- The
dev_urlanddoc_urloffer valuable resources for users and developers.These changes improve the overall quality and usability of the package information.
1-1: Ignore yamllint warning for Jinja2 syntax.The yamllint tool reports a syntax error for the '%' character, but this is a false positive. The '%' is part of the Jinja2 templating syntax, which is correct and necessary for Conda recipe YAML files.
If you want to suppress this warning in future static analysis runs, you can add a
# yamllint disable-line rule:syntaxcomment at the end of the line. However, this is not strictly necessary as the syntax is correct for its intended use.🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
29-30: Improved parallel processing support added.The addition of
libgompfor Linux andllvm-openmpfor macOS suggests improved support for parallel processing on both platforms. This is a positive change that could enhance performance.To ensure these changes have the intended effect, please run the following script to check for OpenMP usage in the source code:
#!/bin/bash # Description: Check for OpenMP usage in the source code # Download the source code curl -L https://github.com/Parsoa/SVDSS/archive/refs/tags/v2.0.0.tar.gz | tar xz # Search for OpenMP pragmas and includes echo "OpenMP usage in source code:" grep -R -n "#pragma omp" SVDSS-2.0.0 grep -R -n "#include <omp.h>" SVDSS-2.0.0 # Clean up rm -rf SVDSS-2.0.0Also applies to: 37-38
1-2: Version and checksum update looks good.The package version has been updated from 1.0.5 to 2.0.0, which suggests significant changes. The SHA256 checksum has also been updated accordingly.
Please run the following script to verify the checksum:
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
25-26: Verify build process with updated requirements.The addition of
libtoolas a build requirement is appropriate. However, the removal ofcoreutilsandcmake >=3.14(as mentioned in the AI summary) might affect the build process.Please run the following script to verify the build process and dependencies:
recipes/svdss/meta.yaml
Outdated
| number: 0 | ||
| #skip: True # [osx] | ||
| run_exports: | ||
| - {{ pin_subpackage('svdss', max_pin="x") }} |
There was a problem hiding this comment.
💡 Codebase verification
macOS support may not be fully enabled.
- The
skipdirective for macOS has been commented out. - macOS-specific dependencies like
llvm-openmpare still present inmeta.yaml(lines 30 and 38). - No macOS-specific build script (
build-osx.sh) found.
Please review and ensure that all macOS support configurations are correctly implemented.
🔗 Analysis chain
Build section changes look good, but verify macOS support.
The build number has been correctly reset to 0 for the new version. The addition of the run_exports section is a good practice for ensuring correct version pinning.
The macOS skip directive has been commented out. Please confirm that the package now supports macOS by running the following script:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for macOS-specific build instructions or dependencies
# Search for macOS-specific conditionals in the meta.yaml file
echo "macOS-specific conditionals in meta.yaml:"
grep -n '\[osx\]' recipes/svdss/meta.yaml
# Check if there's a separate macOS build script
if [ -f recipes/svdss/build-osx.sh ]; then
echo "macOS-specific build script found: recipes/svdss/build-osx.sh"
else
echo "No macOS-specific build script found."
fi
# Check for macOS-specific dependencies
echo "macOS-specific dependencies:"
grep -n '# \[osx\]' recipes/svdss/meta.yaml
Length of output: 864
Script:
#!/bin/bash
# Description: Verify macOS support by checking for conditionals and build scripts in meta.yaml
# Search for macOS-specific conditionals in meta.yaml
echo "Checking for macOS-specific conditionals in meta.yaml:"
grep -n '\[osx\]' recipes/svdss/meta.yaml || echo "No macOS-specific conditionals found."
# Check for the presence of a macOS-specific build script
echo "Checking for macOS-specific build script:"
if [ -f recipes/svdss/build-osx.sh ]; then
echo "macOS-specific build script found: recipes/svdss/build-osx.sh"
else
echo "No macOS-specific build script found."
fi
# Search for macOS-specific dependencies in meta.yaml
echo "Checking for macOS-specific dependencies in meta.yaml:"
grep -n '# \[osx\]' recipes/svdss/meta.yaml || echo "No macOS-specific dependencies found."
Length of output: 717
|
|
||
| extra: | ||
| identifiers: | ||
| - biotools:svdss | ||
| - doi:10.1038/s41592-022-01674-1 |
There was a problem hiding this comment.
💡 Codebase verification
DOI does not resolve correctly
The DOI 10.1038/s41592-022-01674-1 does not resolve. Please verify and correct the DOI in recipes/svdss/meta.yaml.
🔗 Analysis chain
DOI addition is excellent.
The inclusion of a DOI (Digital Object Identifier) is a valuable addition for academic citation and tracking of the software.
Please run the following script to verify the DOI:
The previous script did not verify the DOI as intended. Please run the following script to verify the DOI:
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the DOI
# Extract the DOI
doi=$(grep -oP 'doi:\K[^\s]+' recipes/svdss/meta.yaml)
# Check if the DOI resolves
if curl -s -o /dev/null -w "%{http_code}" "https://doi.org/$doi" | grep -q "200"; then
echo "DOI $doi is valid and resolves correctly."
else
echo "Error: DOI $doi does not resolve. Please check the DOI."
fi
Length of output: 2219
Script:
#!/bin/bash
# Description: Verify the DOI
# Extract the DOI
doi=$(grep -oP 'doi:\K[^\s]+' recipes/svdss/meta.yaml)
# Check if the DOI resolves
if curl -s -o /dev/null -w "%{http_code}" "https://doi.org/$doi" | grep -q "200"; then
echo "DOI $doi is valid and resolves correctly."
else
echo "Error: DOI $doi does not resolve. Please check the DOI."
fi
Length of output: 346
recipes/svdss/build.sh
Outdated
| "${CONFIG_ARGS}" | ||
| cmake --build build -j "${CPU_COUNT}" -v | ||
|
|
||
| cd build |
There was a problem hiding this comment.
Handle potential failure when changing directories
It's recommended to handle cases where cd build might fail. You can modify the command to cd build || exit to ensure the script exits if the directory change is unsuccessful.
This addresses the Shellcheck warning:
[warning] 17-17: Use 'cd ... || exit' or 'cd ... || return' in case cd fails. (SC2164)
🧰 Tools
🪛 Shellcheck
[warning] 17-17: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
There was a problem hiding this comment.
Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/svdss/build.sh (1)
4-8: LGTM with a minor suggestion: Environment variable setupThe addition of environment variables for include paths, library paths, and compiler flags is a good practice. It ensures that the build process uses the correct paths and optimization levels.
However, there's a minor redundancy in the CFLAGS and CXXFLAGS settings:
Consider removing the redundant
-L${PREFIX}/libfrom CFLAGS, as it's already included in LDFLAGS:-export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3"This change would maintain the same functionality while reducing redundancy.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/svdss/build.sh (1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/svdss/build.sh
[warning] 23-23: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🔇 Additional comments (3)
recipes/svdss/build.sh (3)
1-3: LGTM: Improved shebang and directory creationThe changes to the shebang and the addition of the directory creation step are good improvements. The more specific shebang ensures compatibility, and creating the directory beforehand prevents potential installation issues.
10-14: LGTM: Improved cross-platform compatibilityThe addition of OS-specific configuration is a great improvement. Setting
CMAKE_FIND_FRAMEWORK=NEVERandCMAKE_FIND_APPBUNDLE=NEVERfor macOS helps avoid potential conflicts with system frameworks during the build process. This change enhances the script's portability and reliability across different platforms.
16-21: LGTM: Improved CMake configuration and build processThe updates to the CMake configuration and build commands are excellent improvements:
- Use of modern CMake syntax with
-Sand-Boptions improves clarity.- Explicit setting of build type, compilers, and flags ensures consistency across different environments.
- The use of parallel jobs (
-j "${CPU_COUNT}") can significantly speed up the build process.- Verbose output (
-v) is helpful for debugging potential build issues.These changes contribute to a more robust and efficient build process.
recipes/svdss/build.sh
Outdated
| cd build | ||
| chmod 0755 SVDSS | ||
| cp -f SVDSS ${PREFIX}/bin |
There was a problem hiding this comment.
LGTM with a suggestion: Final build steps and installation
The final steps for setting permissions and installing the executable are correct. However, there's a minor improvement we can make:
To handle potential failure when changing directories, modify the cd command as follows:
-cd build
+cd build || exit 1This change ensures that the script will exit if the directory change fails, preventing any subsequent commands from running in an unexpected directory.
The rest of the installation process looks good, with proper permissions set and the executable correctly copied to the installation directory.
📝 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 build | |
| chmod 0755 SVDSS | |
| cp -f SVDSS ${PREFIX}/bin | |
| cd build || exit 1 | |
| chmod 0755 SVDSS | |
| cp -f SVDSS ${PREFIX}/bin |
🧰 Tools
🪛 Shellcheck
[warning] 23-23: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/svdss/build.sh (1)
1-3: Consider reverting shebang for improved portabilityThe shebang has been changed from
#!/usr/bin/env bashto#!/bin/bash. While this works in most cases, usingenvis generally more portable as it allows the system to locate the correct bash interpreter, especially in non-standard environments.The directory creation for
${PREFIX}/binis a good practice to ensure the installation directory exists.Consider reverting the shebang:
-#!/bin/bash +#!/usr/bin/env bash
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/svdss/build.sh (1 hunks)
🧰 Additional context used
🔇 Additional comments (4)
recipes/svdss/build.sh (4)
4-8: LGTM: Environment variables setupThe environment variables are set up correctly, including paths for includes and libraries. The use of optimization flags (-O3) is appropriate for a release build. Good practice in maintaining consistency with the conda build environment by appending to existing flags.
10-14: LGTM: OS-specific configurationThe conditional setup for macOS-specific CMake arguments is well-implemented. Disabling framework and app bundle finding on macOS can prevent issues with system-installed libraries interfering with conda-installed ones. The use of an empty string for non-macOS systems is a clean approach.
16-21: LGTM: CMake configuration and buildThe CMake configuration and build commands are well-structured:
- Modern CMake syntax with -S and -B options.
- Proper setting of flags and compilers.
- Use of parallel jobs (CPU_COUNT) for improved build performance.
- Verbose output (-v) which is helpful for debugging.
These changes should result in a more efficient and transparent build process.
23-24: LGTM: Final installation stepsThe final installation steps are correct and address previous concerns:
- Proper permissions (0755) are set for the executable.
- The executable is copied to the correct location (${PREFIX}/bin).
- Previous concerns about potential directory change failures have been addressed by removing the cd command.
These changes result in a more robust installation process.
There was a problem hiding this comment.
Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/svdss/build.sh (2)
4-8: LGTM with a suggestion: Environment variable exportsThe environment variable exports look good and will ensure the build process has the correct paths and flags. The addition of optimization flags is appropriate for a release build.
Consider adding quotes around the variable expansions to handle potential spaces in paths:
-export INCLUDE_PATH="${PREFIX}/include" -export LIBRARY_PATH="${PREFIX}/lib" -export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib" -export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L\"${PREFIX}/lib\"" +export CFLAGS="${CFLAGS} -O3 -L\"${PREFIX}/lib\"" +export CXXFLAGS="${CXXFLAGS} -O3 -I\"${PREFIX}/include\""
16-21: LGTM with a suggestion: CMake configuration and buildThe CMake configuration and build commands are well-structured and make good use of the exported environment variables. The use of parallel jobs and verbose output is excellent for efficiency and debugging.
Consider adding error checking to the CMake commands:
-cmake -S. -B build -DCMAKE_BUILD_TYPE=Release \ +cmake -S. -B build -DCMAKE_BUILD_TYPE=Release \ -DCONDAPREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \ -DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \ -DCMAKE_C_FLAGS="${CFLAGS}" \ - "${CONFIG_ARGS}" -cmake --build build -j "${CPU_COUNT}" -v + "${CONFIG_ARGS}" || exit 1 +cmake --build build -j "${CPU_COUNT}" -v || exit 1This ensures the script exits if either the CMake configuration or build step fails.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/svdss/build.sh (1 hunks)
🧰 Additional context used
🔇 Additional comments (3)
recipes/svdss/build.sh (3)
1-3: LGTM: Appropriate shebang and directory creationThe updated shebang and directory creation look good. Using
/bin/bashis more specific and creating the installation directory is a good practice.
10-14: LGTM: Appropriate OS-specific configurationThe conditional check for macOS and the corresponding CMake arguments are well-implemented. This addresses potential issues specific to macOS builds while providing a sensible default for other operating systems.
23-24: LGTM: Correct permissions and installationThe final steps for setting permissions and installing the executable are correct. The permissions (0755) are appropriate for an executable, and the installation location (${PREFIX}/bin) is correct for conda packages.
Note: The previous concerns about changing directories (cd) are no longer applicable as the new build process doesn't use cd commands.
Update
svdss: 1.0.5 → 2.0.0recipes/svdss(click to view/edit other files)@ParsoaThis pull request was automatically generated (see docs).