adding the conda recipes for inmoose tool #51274
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📝 Walkthrough📝 WalkthroughWalkthroughA new metadata file named In the The Possibly related PRs
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recipes/inmoose/meta.yaml (3)
41-53: Review and update test sectionThe test section looks good overall, but there are a few points to consider:
The import tests for
sklearn.clusterandAgglomerativeClustering(lines 49-50) are included, but these modules are not listed in the run requirements. Either add these to the run requirements if they are indeed dependencies, or remove them from the import tests.Consider adding more specific command tests to ensure core functionalities are working. For example, you could add a simple data processing command if the package provides one.
To address these points:
- Align the import tests with the run requirements.
- Add more specific command tests, if applicable. For example:
commands: - inmoose --help - inmoose --version - inmoose some-command --help # Replace with an actual command from the packageWould you like assistance in identifying suitable command tests based on the package documentation?
55-58: Improve package metadata in the about sectionThe about section provides good information, but could be improved:
The
homeURL currently points to the GitHub repository. It would be better to point to the project's homepage or documentation if available. If not, use the root of the GitHub repository instead of the/tree/masterpath.The
licensespecification should be "GPL-3.0" without the word "license".Consider adding a
doc_urlfield pointing to the package's documentation if available.Here's a suggested update:
about: home: https://github.com/epigenelabs/inmoose license: GPL-3.0 license_family: GPL license_file: LICENSE # Add this if a LICENSE file is present in the source summary: 'InMoose is the Integrated Multi Omic Open Source Environment. It is a collection of tools for the analysis of omic data.' doc_url: https://inmoose.readthedocs.io/ # Add this if documentation is availableWould you like assistance in finding the correct documentation URL for the package?
1-64: Summary of review findingsThank you for submitting this recipe for the Inmoose package. Overall, the structure is good, but there are several points that need to be addressed:
- Update the incorrect MD5 checksum and verify version consistency.
- Review and update package requirements, removing duplicates and updating version constraints.
- Align import tests with run requirements in the test section.
- Improve the about section with correct license specification and URLs.
Minor suggestions include removing the
preserve_egg_dirsetting if not needed, and considering additional command tests.Please address these points and feel free to ask if you need any clarification or assistance with the changes. Once updated, I'll be happy to review the changes again.
Would you like me to provide any specific guidance on implementing these changes or clarifying any of the suggestions?
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🔇 Additional comments (3)
recipes/inmoose/meta.yaml (3)
5-11: LGTM: Package and source sections are well-definedThe package and source sections are correctly formatted. Good use of Jinja2 templating for the package name and version. The source URL correctly points to the GitHub release tarball.
60-64: LGTM: Extra section is well-configuredThe extra section is correctly configured to ensure proper Unicode locale settings in containers when using Python 3. The included comment explaining the reason for this configuration is helpful and follows good documentation practices.
13-19: Review build configuration and verify entry pointThe build configuration looks good overall. However, there are two points to consider:
The
preserve_egg_dir: Trueline (16) might not be necessary for most modern Python packages. Consider removing it unless it's specifically required for this package.Please verify that the entry point on line 19 correctly matches the package's actual CLI command structure.
To verify the entry point, you can check the package's documentation or run this command after installation:
This will help ensure that the
root_commandfunction exists in the__master__.pyfile.
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🧹 Outside diff range and nitpick comments (1)
recipes/inmoose/meta.yaml (1)
13-19: Add run_exports and LGTM for the restThe build section looks good overall. Consider adding
run_exportsas suggested in a previous comment:build: noarch: python number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} preserve_egg_dir: True script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - inmoose = inmoose.__master__:root_commandThis addition will help manage dependencies when other packages depend on inmoose.
The rest of the build section, including the entry point, looks correct.
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🔇 Additional comments (2)
recipes/inmoose/meta.yaml (2)
5-7: LGTM: Package section is correctThe package section is correctly implemented, using Jinja2 variables for the name and version.
1-1: Ignore YAML syntax error for Jinja2 templatingThe static analysis tool reported a syntax error for the '%' character at the beginning of the file. This is a false positive. The '%' characters are part of Jinja2 templating syntax, which is commonly used and valid in Conda recipes. You can safely ignore this warning.
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recipes/inmoose/meta.yaml (3)
13-21: LGTM: Build section is well-defined with a minor suggestionThe build section is correctly configured for a noarch Python package. The run_exports section has been added as suggested, which is good for package compatibility.
Consider removing the
preserve_egg_dir: Trueline unless it's specifically required for this package. It's generally not needed for modern Python packages.
23-40: LGTM with suggestions: Requirements section improved but needs version reviewThe requirements section has been improved by separating host and run requirements correctly. The removal of pytest from run requirements addresses a previous comment.
Consider reviewing and potentially updating the version constraints for the run requirements. For example:
- Remove version constraints for stable libraries like numpy, pandas, and matplotlib-base unless specific versions are required.
- Update the biopython constraint to a more recent version if compatible with your package.
This will make the package more flexible and easier to maintain in the long run.
12-12: Minor: Remove trailing spaceThere's a trailing space at the end of line 12. While this doesn't affect functionality, it's good practice to remove it for consistency.
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🔇 Additional comments (6)
recipes/inmoose/meta.yaml (6)
1-7: LGTM: Package and version section looks goodThe package name, version, and SHA256 checksum are correctly defined. The use of Jinja2 variables is appropriate, and the package name is properly lowercased in the package section.
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9-11: LGTM: Source section is correctly updatedThe source URL and SHA256 checksum are properly defined using Jinja2 variables. The changes address previous comments about using the version variable in the URL and switching to SHA256 for improved security.
41-48: LGTM: Test section is appropriately simplifiedThe test section has been improved by simplifying the import tests to focus on top-level package imports. The inclusion of a basic CLI functionality test is good for ensuring the entry point works correctly.
50-55: LGTM: About section is complete and accurateThe about section provides all necessary information, including the correct home URL, updated license information (GPL-3.0-or-later), and a clear summary of the package's functionality. The changes address previous comments about the license specification.
57-61: LGTM: Extra section is correctly configuredThe extra section properly configures the container for extended-base support in Python 3 environments. The included comment provides valuable context for why this configuration is necessary, which is helpful for future maintenance.
1-61: Overall: Good job on addressing previous commentsThe meta.yaml file for the inmoose package looks good overall. Most of the issues raised in previous reviews have been addressed, including:
- Updating to SHA256 checksum
- Correcting the source URL format
- Updating the license information
- Simplifying the test imports
There are only a few minor suggestions for further improvement:
- Consider removing the
preserve_egg_dir: Trueline if not specifically required.- Review and potentially update version constraints in the run requirements.
- Remove the trailing space on line 12.
Great work on implementing the feedback and creating a solid bioconda recipe!
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recipes/inmoose/meta.yaml (2)
9-12: LGTM: Source section is correct, minor formatting issueThe source section looks good:
- The URL correctly uses the version variable, which is great for maintainability.
- The SHA256 checksum is properly referenced.
There's a minor formatting issue: remove the trailing space on line 12.
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20-40: LGTM with minor suggestion: Requirements look good overallThe requirements section is well-structured and addresses previous review comments:
- Host and run requirements are correctly specified.
- Python version requirement is consistent across all sections.
- Run requirements list all necessary dependencies without overly strict version constraints.
- pytest has been removed from run requirements as suggested.
Consider removing the C compiler from the build requirements:
requirements: build: - - {{ compiler('c') }} - python >=3.8 - pipThis is likely unnecessary for a pure Python package and may cause issues on some platforms.
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🔇 Additional comments (5)
recipes/inmoose/meta.yaml (5)
1-7: LGTM: Package metadata looks goodThe package metadata section is well-structured:
- Jinja2 variables are used for version and checksum, which is good for maintainability.
- The SHA256 checksum has been updated as requested in previous reviews.
- The package name is correctly set to lowercase using the
|lowerfilter.🧰 Tools
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13-18: LGTM: Build configuration is correctThe build section is well-configured:
noarch: pythonis appropriate for a pure Python package.- The build number is correctly set to 0 for a new package.
- Run exports are properly configured.
- The build script uses the recommended pip installation method.
42-50: LGTM: Test section is comprehensiveThe test section is well-structured and addresses previous review comments:
- Import tests cover the main package and important submodules.
- Command-line interface tests check for basic functionality (--help and --version).
- Import tests have been simplified as suggested in previous reviews.
52-57: LGTM: About section is complete and accurateThe about section provides all necessary information:
- The home page URL is correct.
- License information has been updated as requested in previous reviews.
- The license file is correctly specified.
- The summary provides a clear and concise description of the package.
1-57: LGTM: Overall recipe structure is correctThe recipe follows the standard conda-forge structure and best practices. All sections are present and well-organized.
Note: The yamllint error about Jinja2 syntax (
found character '%' that cannot start any token) is a false positive and can be safely ignored. This is a common occurrence with conda recipe files due to the use of Jinja2 templating.🧰 Tools
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recipes/inmoose/meta.yaml (3)
22-44: Consider adding version constraints for critical dependenciesThe requirements section is comprehensive, but consider adding version constraints for critical dependencies to ensure compatibility:
requirements: run: - python - numpy >=1.18.0 - scipy >=1.4.0 - pandas >=1.0.0 - scikit-learn >=0.22.0 - matplotlib >=3.1.0 - seaborn >=0.10.0 # Add constraints for other critical dependenciesThis helps maintain consistency across different environments and prevents potential issues with incompatible versions.
Would you like assistance in determining appropriate version constraints for these dependencies?
46-54: LGTM: Test section is adequate with room for improvementThe test section covers essential aspects:
- Import tests for the main package and key submodules.
- Basic CLI functionality tests.
Consider adding a simple functional test to ensure core functionality:
test: imports: - inmoose - inmoose.pycombat - inmoose.consensus_clustering.consensus_clustering commands: - inmoose --help - inmoose --version - python -c "import inmoose; inmoose.some_core_function()" # Replace with an actual core functionWould you like assistance in identifying a core function to test?
12-12: Remove trailing spacesThere are trailing spaces on line 12. Please remove them to improve code cleanliness:
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🔇 Additional comments (4)
recipes/inmoose/meta.yaml (4)
1-11: LGTM: Package and source sections are well-definedThe package and source sections are correctly defined:
- Jinja2 variables are used appropriately for name, version, and SHA256.
- The source URL is correctly formatted with the version variable.
- SHA256 is used for integrity verification, addressing previous comments.
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13-20: LGTM: Build section is well-configuredThe build section is correctly configured:
noarch: pythonis appropriate for a Python package.- Build number is set to 0 for the initial release.
run_exportsis used correctly for dependency pinning.- The build script uses pip for installation, which is standard.
- The entry point for the CLI is properly defined.
56-61: LGTM: About section is complete and accurateThe about section provides all necessary information:
- Home URL is correct.
- License information is complete and accurate.
- License file is specified.
- The summary gives a clear description of the package's purpose.
63-67: LGTM: Extra section addresses potential locale issuesThe extra section correctly configures the container for Python 3:
- It sets
extended-base: truefor Python 3 environments.- The comment explains that this is necessary for click to work properly with Unicode locales.
This configuration helps prevent potential issues related to locale settings in containerized environments.
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recipes/inmoose/meta.yaml (2)
22-44: LGTM: Requirements section looks good with a minor suggestionThe requirements section is well-defined:
- Host requirements correctly include python and pip.
- Run requirements list appropriate Python packages for the inmoose tool.
- Previous concerns about outdated version constraints and the inclusion of pytest have been addressed.
Consider adding version constraints to critical dependencies to ensure compatibility. For example:
run: - python >=3.6 - numpy >=1.17 - pandas >=1.0This helps maintain consistency across different environments.
12-12: Minor: Remove trailing spacesThere are trailing spaces on this line. While this doesn't affect functionality, it's good practice to remove them for consistency.
Remove the trailing spaces from this line.
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🔇 Additional comments (6)
recipes/inmoose/meta.yaml (6)
1-11: LGTM: Package metadata and source sections are well-definedThe package metadata and source sections are correctly defined:
- Jinja2 variables are used for name, version, and SHA256 checksum.
- The source URL correctly uses the version variable.
- SHA256 checksum is used for integrity verification, as previously suggested.
🧰 Tools
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[error] 1-1: syntax error: found character '%' that cannot start any token
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13-20: LGTM: Build section is well-configuredThe build section is correctly configured:
- Package is set as
noarch: python.- Build number is properly set to 0.
- Run exports are correctly defined using
pin_subpackage.- The build script uses pip for installation.
- The CLI entry point is properly defined.
46-54: LGTM: Test section is appropriately definedThe test section has been improved:
- Import tests for the main package and key submodules are included.
- CLI functionality tests (--help and --version) are appropriate.
- The import tests have been simplified as suggested in previous comments.
56-61: LGTM: About section is complete and accurateThe about section provides all necessary information:
- Home page is correctly specified.
- License information has been updated to GPL-3.0-or-later as suggested.
- License family and file are correctly specified.
- The summary provides a clear description of the package.
63-67: LGTM: Extra section correctly configures container environmentThe extra section properly addresses container configuration:
- Extended-base is enabled for Python 3 environments.
- This configuration correctly handles the unicode locale requirement for the click library.
1-67: Overall: Recipe is well-structured and ready for useThis conda recipe for the inmoose package is well-structured and follows conda-forge best practices. All major sections (metadata, build, requirements, test, about, and extra) are correctly defined. Previous review comments have been addressed, including updating to SHA256 checksum, simplifying import tests, and updating license information.
Minor suggestions for improvement include:
- Adding version constraints to critical dependencies in the run requirements.
- Removing trailing spaces on line 12.
These minor issues do not affect the functionality of the recipe. The recipe appears ready for use and should successfully build and package the inmoose tool.
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🧹 Outside diff range and nitpick comments (3)
recipes/inmoose/meta.yaml (3)
9-12: LGTM! Source section is correct, with a minor formatting suggestion.The source section is well-defined:
- The URL correctly uses the Jinja2 version variable.
- The SHA256 checksum is properly referenced.
There's a trailing space on line 12. Consider removing it for cleaner formatting:
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[error] 12-12: trailing spaces
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22-45: LGTM! Requirements section is comprehensive, with a minor suggestion.The requirements section is well-defined:
- Host and run requirements are appropriately separated.
- Run requirements cover a wide range of necessary libraries.
- Version constraints are not overly strict, allowing for flexibility.
- The pytest requirement has been removed from run requirements, addressing a previous comment.
Consider moving
numpyfrom host to run requirements only, as it's not typically needed during the build process for a pure Python package:host: - python - pip - - numpy run: - python - numpy # ... other run requirementsThis change can slightly optimize the build process.
1-68: Overall, the inmoose recipe looks great! 🎉This recipe is well-structured, follows best practices, and addresses previous comments and concerns. The package metadata, source, build, requirements, test, about, and extra sections are all properly configured.
There are only a few minor suggestions for improvement:
- Remove a trailing space in the source section.
- Consider moving
numpyfrom host to run requirements only.These minor issues don't significantly impact the functionality of the package. Great job on creating this Conda recipe!
If you'd like assistance implementing these minor suggestions or have any questions about the review, please don't hesitate to ask. I'm here to help!
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🔇 Additional comments (5)
recipes/inmoose/meta.yaml (5)
1-7: LGTM! Package metadata section looks good.The package metadata section is well-structured and follows best practices:
- Jinja2 variables are correctly used for name, version, and SHA256 checksum.
- The package name is properly set to lowercase.
- The SHA256 checksum is now used instead of MD5, addressing a previous security concern.
🧰 Tools
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[error] 1-1: syntax error: found character '%' that cannot start any token
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13-20: LGTM! Build section is well-defined.The build section is correctly configured:
noarch: pythonis appropriate for a pure Python package.- Build number is correctly set to 0.
- Run exports are properly defined using the
pin_subpackagemacro.- The build script uses pip to install the package.
- The CLI entry point is correctly defined.
47-55: LGTM! Test section is well-structured and comprehensive.The test section is appropriately defined:
- Import tests cover the main package and key submodules.
- Command tests verify basic CLI functionality (--help and --version).
- The import tests have been simplified, addressing previous concerns about unusual imports.
57-62: LGTM! About section is complete and accurate.The about section provides all necessary metadata:
- The home URL is correct.
- License information is complete and accurate (GPL-3.0-or-later).
- The license family and file are correctly specified.
- The summary provides a clear and concise description of the package.
64-68: LGTM! Extra section properly addresses container configuration.The extra section is correctly configured:
- Container settings are provided to ensure Unicode locale compatibility with click and Python 3.
- The use of
extended-base: truefor Python 3 is appropriate to generate the required locale settings.
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recipes/inmoose/meta.yaml (2)
22-44: LGTM with a minor suggestion: Requirements are well-definedThe requirements section is comprehensive and addresses previous comments:
- Host requirements correctly include Python and pip.
- Run requirements list all necessary Python libraries.
- Version constraints are used where needed for compatibility.
Minor suggestion:
Consider adding version constraints to more packages if specific versions are required for compatibility. This can help ensure consistent behavior across different environments.
46-54: LGTM with a suggestion: Test configuration is goodThe test section is well-structured:
- Import tests cover the main package and key submodules.
- CLI functionality tests are included to check basic operation.
Suggestion for improvement:
Consider adding more comprehensive tests, such as:
- Testing additional submodules if they exist.
- Including a simple data processing test to ensure core functionality.
Example:
test: imports: - inmoose - inmoose.pycombat - inmoose.consensus_clustering commands: - inmoose --help - inmoose --version - python -c "import inmoose; inmoose.test_core_functionality()" # Add a core functionality test
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recipes/inmoose/meta.yaml
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🔇 Additional comments (6)
recipes/inmoose/meta.yaml (6)
1-7: LGTM: Package metadata is well-definedThe package metadata section is correctly implemented:
- Jinja2 variables are used for name, version, and SHA256 checksum.
- The package name is properly set to lowercase.
- SHA256 is used for integrity verification, addressing a previous comment.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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9-11: LGTM: Source configuration is correctThe source section is properly configured:
- The URL correctly uses the Jinja2 version variable.
- The SHA256 checksum is properly referenced using the Jinja2 variable.
13-20: LGTM: Build configuration is well-definedThe build section is correctly configured:
noarch: pythonis appropriate for a Python package.- Build number is set to 0 for a new package.
- Run exports are properly configured.
- The build script uses pip for installation.
- The CLI entry point is correctly defined.
56-61: LGTM: About section is complete and accurateThe about section provides all necessary metadata:
- Home URL is correctly specified.
- License information is accurate (GPL-3.0-or-later) and includes the license file.
- The summary provides a clear and concise description of the package.
63-67: LGTM: Extra section is correctly configuredThe extra section is properly set up:
- Container configuration for extended-base is correctly set for Python 3.
- The comment explains the purpose of this configuration (addressing locale issues with click in Python 3 environments).
1-67: Overall: Well-structured Conda recipe for inmooseThis Conda recipe for inmoose is well-structured and follows best practices:
- Package metadata, source, build, requirements, tests, and metadata sections are correctly defined.
- Previous review comments have been addressed, including the use of SHA256 for integrity verification.
- The recipe provides a comprehensive setup for packaging and distributing inmoose.
Minor suggestions for improvement have been made regarding:
- Adding version constraints to more packages in the requirements section if needed.
- Expanding the test section with more comprehensive tests.
Great job on creating this Conda recipe! It's ready for use with these minor considerations.
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[error] 1-1: syntax error: found character '%' that cannot start any token
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recipes/inmoose/meta.yaml (2)
20-42: Consider reviewing version constraints in run requirementsThe requirements section looks good overall:
- Host requirements are correct for a Python package.
- Run requirements are comprehensive and include necessary libraries.
However, consider reviewing the version constraints for some packages. Overly strict constraints might make it difficult to maintain the package in the long term. For example:
- numpy, scipy, pandas: Consider allowing newer versions if compatible.
- biopython: The current version constraint might be outdated.
Would you like assistance in researching compatible version ranges for these packages?
44-52: Consider simplifying the consensus_clustering import testThe test section looks good overall:
- Import tests cover the main package and key submodules.
- Command tests verify basic CLI functionality.
However, the import test for
consensus_clusteringseems overly specific:- inmoose.consensus_clustering.consensus_clusteringConsider simplifying it to:
- inmoose.consensus_clusteringThis change would make the import test more consistent with the others and less likely to break if the internal structure changes.
Would you like me to propose this change?
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recipes/inmoose/meta.yaml (4)
1-7: LGTM: Package metadata is correctly definedThe package metadata section is well-structured:
- Jinja2 variables are used appropriately for name, version, and SHA256 checksum.
- The package name is correctly set to lowercase.
- The version (0.7.2) matches the one mentioned in the PR objectives.
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9-11: LGTM: Source section is correctly configuredThe source section is well-defined:
- The URL correctly uses the Jinja2 version variable for GitHub releases.
- The SHA256 checksum is properly referenced using the Jinja2 variable.
13-18: LGTM: Build section is properly configuredThe build section is well-structured:
noarch: pythonis correctly set for a pure Python package.- Build number is appropriately set to 0 for a new recipe.
- Run exports are correctly configured.
- The build script uses the standard pip install command.
54-65: LGTM: About and extra sections are well-definedThe about and extra sections are correctly configured:
- The license information has been updated as suggested in previous reviews.
- The summary provides a clear and concise description of the package.
- The container configuration for Python 3 is correct and includes a helpful comment explaining its purpose.
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13-19: LGTM with a minor suggestion: Build section is well-configuredThe build section is correctly implemented:
noarch: pythonis appropriate for a pure Python package.- Skip condition ensures compatibility with Python 3.9+.
run_exportswithpin_subpackageis correctly used.- The pip install command includes appropriate flags for reproducibility.
Consider adding a comment explaining the reason for the Python version skip condition, e.g.:
skip: True # [py < 39] # inmoose requires Python 3.9+This will help future maintainers understand the reasoning behind this constraint.
21-44: LGTM with a minor suggestion: Requirements are well-definedThe requirements section is comprehensive and correctly structured:
- Appropriate split between build, host, and run requirements.
- Version constraints are used where necessary.
- Use of
matplotlib-baseinstead ofmatplotlibas suggested in a previous comment.Consider adding comments to explain any strict version constraints, e.g.:
- cython >=3.0.0 # Required for compatibility with recent numpy versions - numpy >=2.0.0 # Needed for specific array operations used in inmooseThis will help future maintainers understand the reasoning behind these constraints.
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recipes/inmoose/meta.yaml
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🔇 Additional comments (6)
recipes/inmoose/meta.yaml (6)
1-7: LGTM: Package metadata is well-definedThe package metadata section is correctly implemented:
- Jinja2 variables are used for name, version, and SHA256 checksum.
- The package name is properly set to lowercase.
- SHA256 checksum is used as recommended in previous comments.
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9-11: LGTM: Source section is correctly implementedThe source section is well-defined:
- The URL correctly uses the Jinja2 version variable.
- SHA256 checksum is properly referenced using the Jinja2 variable.
These changes address previous comments about using Jinja2 variables in the URL and updating to SHA256.
46-54: LGTM: Test section is appropriately definedThe test section is well-structured and covers essential aspects:
- Import tests for the main package and key submodules.
- Command-line interface tests for basic functionality (help and version).
These tests address previous comments about simplifying import tests while still covering crucial functionality.
56-62: LGTM: About section provides comprehensive metadataThe about section is well-defined and includes all necessary information:
- Correct home and dev_url pointing to the GitHub repository.
- Complete license information, addressing previous comments.
- Clear and concise summary of the package's purpose.
This section provides valuable metadata for users and maintainers.
64-68: LGTM: Extra section properly configured for container compatibilityThe extra section is correctly implemented:
- Container configuration for extended-base is included to address Unicode locale issues.
- The comment provides a clear explanation of the configuration's purpose.
This configuration ensures proper functionality of the click library in containerized environments with Python 3.
1-68: Overall: Well-structured and comprehensive conda recipeThis conda recipe for the inmoose package is well-implemented and follows best practices:
- All necessary sections (metadata, source, build, requirements, test, about, and extra) are present and correctly configured.
- Previous review comments have been addressed, including the use of SHA256 checksums, Jinja2 variables, and appropriate license information.
- The recipe provides a clear structure for building and distributing the package.
Minor suggestions for improvement have been made, including:
- Adding a comment to explain the Python version skip condition.
- Including comments to clarify strict version constraints in the requirements section.
These suggestions are optional and do not affect the functionality of the recipe. Great job on creating this conda recipe!
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20-44: Consider reviewing version constraintsThe requirements section has been improved and addresses previous comments. However, consider the following:
Some version constraints might still be too strict or outdated. For example:
cython >=3.0.0: This is a very recent version. Consider if a lower version would suffice.numpy >=2.0.0: This is also a very recent version. Many packages might not be compatible with NumPy 2.0 yet.For packages without version constraints (e.g., scipy, pandas, scikit-learn), consider if adding minimum version requirements would be beneficial for ensuring compatibility.
Would you like assistance in researching more flexible version ranges for these dependencies?
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recipes/inmoose/meta.yaml
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🔇 Additional comments (7)
recipes/inmoose/meta.yaml (7)
1-7: LGTM: Package metadata looks goodThe package metadata section is well-structured and follows best practices:
- Jinja2 variables are correctly used for name, version, and SHA256 checksum.
- The package name is properly set to lowercase.
- The SHA256 checksum has been updated as requested in previous comments.
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9-11: LGTM: Source section is correctly configuredThe source section is well-structured and addresses previous comments:
- The URL correctly uses the Jinja2 version variable.
- The checksum type has been updated to SHA256 and uses the correct Jinja2 variable.
13-18: LGTM: Build section is well-configuredThe build section is correctly set up:
- Build number is appropriately set to 0 for a new recipe.
- Skip condition ensures compatibility with Python 3.9+.
- Run exports are properly configured.
- The build script uses the recommended pip installation method.
46-54: LGTM: Test section looks goodThe test section has been improved and addresses previous comments:
- Import tests have been simplified and focus on top-level package imports.
- Command tests check for basic CLI functionality (--help and --version).
This provides a good balance between thoroughness and simplicity in testing.
56-62: LGTM: About section is complete and accurateThe about section has been updated and looks great:
- License information is correct and complete, addressing previous comments.
- The summary provides a clear and concise description of the package.
- Home and dev_url are correctly set.
64-68: LGTM: Extra section is correctly configuredThe extra section is well set up:
- The container configuration correctly addresses potential locale issues with click and Python 3.
- This follows best practices for ensuring compatibility in containerized environments.
1-68: Overall, the recipe looks great with minor suggestionsThe
meta.yamlfile for theinmoosepackage is well-structured and follows conda packaging best practices. All sections have been improved based on previous comments. The only remaining suggestion is to review and possibly update some version constraints in the requirements section.Great job on addressing the previous comments and creating a solid conda recipe!
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recipes/inmoose/meta.yaml (2)
20-44: LGTM with a minor suggestion: Requirements are well-definedThe requirements section is correctly implemented:
- Build, host, and run requirements are properly separated.
- Version constraints have been updated and seem appropriate.
- pytest has been removed from the run requirements, addressing a previous comment.
- matplotlib-base is used instead of matplotlib, as suggested.
Consider adding a comment explaining the need for the C and C++ compilers in the build section, as it's not immediately obvious why they're required for a Python package.
46-50: Suggestion: Enhance the test sectionThe test section has been simplified as per previous suggestions. However, it could be further improved:
- Add a command to test the CLI functionality:
commands: - inmoose --help - inmoose --version
- Consider adding more comprehensive tests in a separate test script if needed.
Would you like assistance in creating a more comprehensive test script that includes specific imports and functionality tests?
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recipes/inmoose/meta.yaml
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🔇 Additional comments (6)
recipes/inmoose/meta.yaml (6)
1-7: LGTM: Package metadata is well-definedThe package metadata section is correctly implemented:
- Jinja2 variables are used for name, version, and SHA256 checksum.
- The package name is properly set to lowercase.
- SHA256 is used for integrity verification, addressing a previous comment.
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🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
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9-11: LGTM: Source section is correctly implementedThe source section is well-defined:
- The URL correctly uses the Jinja2 version variable.
- The SHA256 checksum is properly referenced using the Jinja2 variable.
These changes address previous comments about using the version variable in the URL and updating to SHA256.
13-18: LGTM: Build section is well-configuredThe build section is correctly implemented:
- Build number is appropriately set to 0.
- The skip condition for Python versions < 3.9 is correct.
- Run exports are properly defined.
- The build script uses the recommended pip installation method.
52-58: LGTM: About section is complete and accurateThe about section is well-defined:
- The home and dev_url are correctly set.
- The license information is complete and correct, addressing a previous comment.
- The summary provides a clear description of the package.
60-64: LGTM: Extra section is correctly configuredThe extra section is properly implemented:
- The container configuration for Python 3 is correct.
- It addresses potential issues with click and Unicode locales in Python 3 environments.
1-64: Overall: Well-implemented conda recipe with minor suggestions for improvementThe conda recipe for inmoose is well-structured and follows best practices. It addresses most of the previous comments and concerns. Here's a summary of the review:
- Package metadata, source, and build sections are correctly implemented.
- Requirements are well-defined and use appropriate version constraints.
- The test section has been simplified but could benefit from adding CLI functionality tests.
- The about section is complete and accurate.
- The extra section correctly configures the container for Python 3 compatibility.
To further improve the recipe:
- Consider adding a comment explaining the need for C and C++ compilers in the build requirements.
- Enhance the test section by adding CLI functionality tests and possibly creating a more comprehensive test script.
These minor improvements will make the recipe even more robust and maintainable.
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Thanks a lot @mencian :) |
Dear All,
It's my first bioconda recipe, so I believe that this will be followed up with comments and updates.
The tool name is Inmoose, it is mainly designed for batch correction of transcriptomic data, however it can also perform further analysis such as differential expression. I need this tool in one of my workflows created on Galaxy platform.
Thanks a lot,
Engy