add meta #51349
add meta #51349
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces two primary components: a new shell script named The Possibly related PRs
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (8)
recipes/meta/conda_build_config.yaml (1)
9-9: Add a newline at the end of the file.To adhere to best practices and resolve the static analysis warning, please add a newline character at the end of the file.
Apply this change:
python: - 3.8 - 3.9 - 3.10 - - 3.11 + - 3.11 +🧰 Tools
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[error] 9-9: no new line character at the end of file
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recipes/meta/build.sh (3)
7-11: Directory setup looks good, with a minor suggestion.The directory structure creation is well-organized. However, there's a small improvement we can make:
Consider adding error handling to the
cdcommand on line 11:-cd $SRC_DIR/build +cd $SRC_DIR/build || exit 1This change ensures the script exits if the directory change fails, preventing potential issues in subsequent steps.
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[warning] 11-11: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
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22-24: Build and install steps look good, with a suggestion for improvement.The build, install, and cleanup process is concise and effective. However, we can enhance it with error checking:
Consider adding error checking to the build and install steps:
-cmake --build . --config Release -cmake --install . +cmake --build . --config Release || exit 1 +cmake --install . || exit 1This change ensures the script exits if either the build or install step fails, preventing potential issues with incomplete or failed installations.
26-28: MeTA package installation looks good, with a minor suggestion.The package installation step is well-structured, using the correct Python interpreter and appropriate pip options. However, there's a small improvement we can make:
Consider adding error handling to the
cdcommand on line 27:-cd ${SRC_DIR} +cd ${SRC_DIR} || exit 1This change ensures the script exits if the directory change fails, preventing potential issues with the pip installation step.
Additionally, it might be beneficial to add error checking to the pip install command:
-${PYTHON} -m pip install . --no-deps -vv +${PYTHON} -m pip install . --no-deps -vv || exit 1This ensures the script exits if the pip installation fails.
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[warning] 27-27: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
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recipes/meta/meta.yaml (4)
13-15: Document reason for skipping Windows buildsThe build configuration looks good. However, it would be helpful to document the reason for skipping Windows builds. Consider adding a comment explaining why the package is not compatible with Windows, if that's the case.
build: number: 0 - skip: true # [win] + skip: true # [win] # Package is not compatible with Windows due to [reason]
81-92: LGTM with a minor suggestionThe about section is well-structured and informative. It provides clear information about the package's purpose and licensing.
As a minor suggestion, consider adding a
doc_urlfield pointing to any available documentation, if it exists. This can help users find more detailed information about using the package.about: home: https://github.com/bagari/meta license: BSD-3-Clause license_file: LICENSE.txt summary: 'Medial Tractography Analysis (MeTA)' description: | MeTA is a workflow implemented to minimize microstructural heterogeneity in diffusion MRI (dMRI) metrics by extracting and parcellating the core volume along the bundle length in the voxel-space directly while effectively preserving bundle shape and efficiently capturing the regional variation within and along white matter (WM) bundles. dev_url: https://github.com/bagari/meta + doc_url: https://github.com/bagari/meta/wiki # If documentation exists🧰 Tools
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94-96: Consider adding additional maintainersThe extra section correctly lists a recipe maintainer, which is crucial for package management. However, to improve the bus factor and ensure long-term maintenance:
- Consider adding additional maintainers if there are other contributors to the project who could help maintain the package.
- If this is part of a larger project or organization, you might want to add the organization as a maintainer as well.
extra: recipe-maintainers: - bagari + # Consider adding additional maintainers here + # - organization-name
87-91: Remove trailing spacesThere are trailing spaces at the end of lines in the description. While these don't affect functionality, removing them improves code cleanliness.
- MeTA is a workflow implemented to minimize microstructural heterogeneity - in diffusion MRI (dMRI) metrics by extracting and parcellating the core - volume along the bundle length in the voxel-space directly while effectively - preserving bundle shape and efficiently capturing the regional variation - within and along white matter (WM) bundles. + MeTA is a workflow implemented to minimize microstructural heterogeneity + in diffusion MRI (dMRI) metrics by extracting and parcellating the core + volume along the bundle length in the voxel-space directly while effectively + preserving bundle shape and efficiently capturing the regional variation + within and along white matter (WM) bundles.🧰 Tools
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[error] 88-88: trailing spaces
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📒 Files selected for processing (3)
- recipes/meta/build.sh (1 hunks)
- recipes/meta/conda_build_config.yaml (1 hunks)
- recipes/meta/meta.yaml (1 hunks)
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🪛 Shellcheck
recipes/meta/build.sh
[warning] 11-11: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
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[warning] 27-27: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
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recipes/meta/conda_build_config.yaml
[error] 9-9: no new line character at the end of file
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recipes/meta/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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[error] 88-88: trailing spaces
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🔇 Additional comments (5)
recipes/meta/conda_build_config.yaml (1)
1-9: LGTM! The conda build configuration looks good.The
build_variantsection correctly specifies different build options for Linux (osmesa) and macOS (qt). Thepythonsection includes all the required versions (3.8 to 3.11) as mentioned in the PR objectives. This configuration will allow for flexible building across different operating systems and Python versions.🧰 Tools
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[error] 9-9: no new line character at the end of file
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recipes/meta/build.sh (3)
1-6: LGTM: Environment setup looks good.The initial environment setup is well-structured. Unsetting potentially conflicting variables and setting up CMAKE_INSTALL_RPATH and CMAKE_BUILD_WITH_INSTALL_RPATH are good practices for ensuring a clean and portable build.
13-20: CMake configuration is well-structured and comprehensive.The CMake configuration covers all necessary aspects:
- Correct build type (Release) for a package
- Proper installation prefix
- C++ standard specification
- Appropriate module and prefix paths
- Consistent use of RPATH settings
This configuration should result in a well-organized and portable build.
1-28: Overall, the build script is well-structured and follows good practices.The script effectively sets up the environment, configures CMake, builds the project, and installs the package. It's designed to work within a conda build system and includes necessary steps for a clean and portable build.
A few minor suggestions have been made to improve error handling, which would make the script more robust. These include adding checks after directory changes and critical operations like building and installing.
Great job on creating a comprehensive build script for the MeTA package!
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[warning] 11-11: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
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[warning] 27-27: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
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recipes/meta/meta.yaml (1)
17-70: 🛠️ Refactor suggestionConsider optimizing dependency specifications and clarify build variants
The requirements section is comprehensive, which is good for reproducibility. However, consider the following suggestions:
- Some dependencies are repeated across build, host, and run sections. Consider using the
{{ pin_compatible() }}function to reduce repetition and ensure consistency. For example:host: - boost {{ boost }} run: - {{ pin_compatible('boost', max_pin='x.x') }}
The use of
{{ build_variant }}suggests multiple build configurations. Please clarify what these variants are and consider documenting them in a comment.The
libexpatdependency is specified twice with different version constraints. This might lead to conflicts. Consider consolidating these into a single, more specific constraint.✅ Verification successful
Build variant is correctly defined
The
build_variantis properly defined inconda_build_config.yaml, ensuring that the placeholders inmeta.yamlare correctly resolved.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if build_variant is defined elsewhere in the recipe rg "build_variant:" conda_build_config.yaml || echo "build_variant not found in conda_build_config.yaml"Length of output: 218
Script:
#!/bin/bash # Search for all occurrences of 'build_variant' in the codebase rg "build_variant"Length of output: 571
Script:
#!/bin/bash # Display the contents of 'conda_build_config.yaml' to verify 'build_variant' definition cat recipes/meta/conda_build_config.yamlLength of output: 146
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
recipes/meta/meta.yaml (1)
90-92: Consider adding more maintainersCurrently, there's only one recipe maintainer listed. While this is acceptable, it's generally a good practice to have multiple maintainers to ensure continued support and maintenance of the package.
Consider reaching out to other contributors or team members who are familiar with this package and adding them as co-maintainers.
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- recipes/meta/build.sh (1 hunks)
- recipes/meta/conda_build_config.yaml (1 hunks)
- recipes/meta/meta.yaml (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (2)
- recipes/meta/build.sh
- recipes/meta/conda_build_config.yaml
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recipes/meta/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (3)
recipes/meta/meta.yaml (3)
13-15: Build configuration looks goodThe build number is correctly set to 0 for a new package, and the Windows build is skipped with a clear explanation in the comment.
80-88: About section is well-documentedThe about section provides comprehensive information about the package, including its purpose, license, and relevant URLs. This is excellent for user understanding and package discoverability.
1-1: Ignore yamllint error for Jinja2 syntaxThe 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 commonly used in conda recipes.
No action is needed. The syntax is correct for a conda recipe.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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Updated test section with real test example.
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🧹 Outside diff range and nitpick comments (3)
recipes/meta/meta.yaml (3)
13-16: Enhance the Windows skip commentConsider adding a tracking issue number or milestone for Windows support.
- skip: true # [win] # Windows support will be added in next release. + skip: true # [win] # Windows support planned for v1.1.0 (see: <issue_url>)
81-90: Consider adding additional metadataThe about section is well-structured, but consider adding:
license_family: BSDkeywordsfield for better package discoverabilityreferencesfield with relevant publications
91-93: Consider adding co-maintainersHaving multiple maintainers helps ensure long-term package maintenance. Consider adding co-maintainers who are familiar with the codebase.
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recipes/meta/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (2)
recipes/meta/meta.yaml (2)
1-12: LGTM: Package metadata is well-structuredThe package metadata section follows Conda packaging best practices with proper use of Jinja2 templating.
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72-79: Reference existing test improvement suggestionsThe test section could benefit from the improvements suggested in the previous review.
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🧹 Outside diff range and nitpick comments (1)
recipes/meta/meta.yaml (1)
13-15: Enhance skip comment documentationConsider expanding the skip comment to include technical reasons or specific Windows limitations:
- skip: true # [win] # Windows support will be added in next release. + skip: true # [win] # Windows support pending: requires MSVC toolchain compatibility and DLL export fixes (planned for next release)
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recipes/meta/meta.yaml
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🔇 Additional comments (2)
recipes/meta/meta.yaml (2)
1-11: LGTM: Package metadata is well-structuredThe package metadata section follows conda-forge best practices with proper use of Jinja2 templating.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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81-93: LGTM: Package metadata is comprehensiveThe about section provides complete information including license, description, and documentation links.
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recipes/meta/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (3)
recipes/meta/meta.yaml (3)
1-16: LGTM! Well-structured package metadata.The package metadata is properly defined with version pinning and SHA256 verification. The Windows skip note is helpful for tracking future platform support.
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47-67: LGTM! Comprehensive runtime dependencies.The run requirements section includes all necessary dependencies with appropriate version constraints.
79-91: LGTM! Well-documented package metadata.The about section provides comprehensive information about the package, including license, documentation, and description.
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recipes/meta/meta.yaml (1)
Learnt from: bagari PR: bioconda/bioconda-recipes#51349 File: recipes/meta/meta.yaml:68-77 Timestamp: 2024-10-26T03:32:06.828Z Learning: The `meta` package does not contain `meta.core` or `meta.utils` modules.
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recipes/meta/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (6)
recipes/meta/meta.yaml (6)
1-8: LGTM! Package metadata is well-structured.The package metadata section follows conda-forge best practices using Jinja2 variables.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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9-12: LGTM! Source configuration is properly defined.The source URL and checksum are correctly specified.
68-77: LGTM! Test section is comprehensive.The test section includes both import tests and command tests with proper output verification.
89-91: LGTM! Maintainer information is correctly specified.The recipe maintainer matches the GitHub repository owner.
13-16: LGTM! Build settings are appropriate.The build settings are correctly configured, and the comment about future Windows support is helpful.
Let's verify if there are any open issues about Windows support:
#!/bin/bash # Check for Windows-related issues in the repository gh issue list -R bagari/meta --search "windows in:title,body" --json number,title,state
79-88: LGTM! Package metadata is complete.The about section provides comprehensive information about the package.
Let's verify the license file:
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🧹 Outside diff range and nitpick comments (2)
recipes/meta/meta.yaml (2)
19-35: Fix inconsistent version constraint formatting.The version constraints have inconsistent spacing. Some use spaces around operators (
>= 1.14.2, < 1.14.3.0a0) while others don't (=1.82).Apply this diff to maintain consistent formatting:
- - boost = 1.82 - - hdf5 >= 1.14.2, < 1.14.3.0a0 - - vtk-base >=9.2.6,<9.3.0{{ build_variant }} + - boost == 1.82 + - hdf5 >=1.14.2,<1.14.3.0a0 + - vtk-base >=9.2.6,<9.3.0{{ build_variant }}
58-66: Consider adding minimum version constraints for Python packages.Python packages like numpy, pandas, etc., should have minimum version constraints to ensure compatibility while maintaining flexibility.
Consider adding minimum version constraints:
- numpy - nibabel - pandas - pyvista - scipy - tqdm - tslearn - dipy + # Add minimum version constraints, for example: + # - numpy >=1.20 + # - pandas >=1.3 + # - scipy >=1.7
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- recipes/meta/meta.yaml (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
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📓 Learnings (1)
recipes/meta/meta.yaml (1)
Learnt from: bagari PR: bioconda/bioconda-recipes#51349 File: recipes/meta/meta.yaml:68-77 Timestamp: 2024-10-26T03:32:06.828Z Learning: The `meta` package does not contain `meta.core` or `meta.utils` modules.
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recipes/meta/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (3)
recipes/meta/meta.yaml (3)
1-18: LGTM! Well-structured package metadata.The package metadata is properly configured with version pinning and security measures in place. The informative comment about Windows support is helpful for future reference.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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70-79: LGTM! Comprehensive test configuration.The test section includes:
- Source files for testing
- Package import verification
- Command tests with output validation
81-93: LGTM! Complete package metadata.The about section provides comprehensive information including license, documentation URLs, and a clear description of the package's purpose.
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🧹 Outside diff range and nitpick comments (2)
recipes/meta/meta.yaml (2)
20-20: Consider adding a tracking issue for Windows supportThe comment indicates Windows support will be added in the next release. Consider adding a GitHub issue number for tracking this feature.
- skip: true # [win] # Windows support will be added in next release. + skip: true # [win] # Windows support tracked in issue #<number>
64-70: Consider adding version constraints for Python packagesWhile the core dependencies have specific version constraints, some Python packages in the run section lack version constraints. This could lead to compatibility issues.
Consider adding minimum version constraints for critical dependencies:
- - nibabel - - pandas - - pyvista - - scipy - - tqdm - - tslearn - - dipy + - nibabel >=3.0.0 + - pandas >=1.0.0 + - pyvista >=0.34.0 + - scipy >=1.7.0 + - tqdm >=4.0.0 + - tslearn >=0.5.0 + - dipy >=1.5.0
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recipes/meta/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/meta/meta.yaml (1)
85-97: Package metadata is well-documentedThe about section provides comprehensive information including license, documentation links, and a clear description of the package's purpose.
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recipes/meta/meta.yaml (1)
Learnt from: bagari PR: bioconda/bioconda-recipes#51349 File: recipes/meta/meta.yaml:68-77 Timestamp: 2024-10-26T03:32:06.828Z Learning: The `meta` package does not contain `meta.core` or `meta.utils` modules.
🪛 yamllint
recipes/meta/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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🔇 Additional comments (4)
recipes/meta/meta.yaml (4)
1-15: LGTM! Well-structured package metadata and source configuration.The package metadata and source configuration follow conda-forge conventions with proper versioning and integrity checks.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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16-21: LGTM! Clear build configuration with future Windows support planned.The build configuration is well-structured with appropriate version pinning through run_exports.
72-81: LGTM! Comprehensive test configuration.The test section includes:
- Source files for testing
- Package import verification
- Command-line tool testing with output validation
83-95: LGTM! Well-documented package metadata.The about section provides comprehensive information including license, documentation links, and a clear description of the package's purpose.
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recipes/meta/meta.yaml (1)
Learnt from: bagari PR: bioconda/bioconda-recipes#51349 File: recipes/meta/meta.yaml:68-77 Timestamp: 2024-10-26T03:32:06.828Z Learning: The `meta` package does not contain `meta.core` or `meta.utils` modules.
🪛 yamllint
recipes/meta/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/meta/meta.yaml (4)
1-14: LGTM! Package metadata and source configuration look good.The package metadata and source configuration follow best practices with proper version pinning, SHA256 verification, and platform-specific build variants.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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16-21: Please clarify Windows support timeline.The comment indicates Windows support will be added in the next release. Consider adding a GitHub issue to track this enhancement for better visibility.
Would you like me to help create a GitHub issue to track Windows support implementation?
72-81: LGTM! Test configuration is comprehensive.The test section includes:
- Source files for functional testing
- Basic import verification
- Command-line functionality tests with output verification
83-97: LGTM! Package metadata is well-documented.The about section provides comprehensive information including license, documentation links, and a clear description of the package's purpose.
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Thank you so much, @martin-g and @mencian. Do you know when the package will appear on https://anaconda.org/bioconda/repo? I tried |
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It seems there was a PR check failure: https://github.com/bioconda/bioconda-recipes/actions/runs/11566537250/job/32195443196#step:7:44 |
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@martin-g @mencian I'm not sure if this https://github.com/bioconda/bioconda-recipes/actions/runs/11566537250/job/32195443196#step:7:44 It might be for #51670 |
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See #33333 (comment) |
MeTA, which stands for Medial Tractography Analysis, is a workflow designed to minimize brain microstructural heterogeneity in diffusion MRI (dMRI) metrics by extracting and parcellating the core volume along the length of white matter bundles in voxel-space, directly preserving bundle shape while efficiently capturing regional variation within and along the bundles. MeTA is applied to the study of human brain diseases and the genetic architecture of white matter, providing valuable insights into both neurodegenerative conditions and the structural components of brain connectivity.
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