[biobb_mem] update 5.0.0 #51940
[biobb_mem] update 5.0.0 #51940
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (2)
recipes/biobb_mem/meta.yaml (2)
19-32: Consider optimizing dependency specifications.
setuptoolsis only needed during build time, so it's correctly placed inhostonly.- Consider if
ambertoolsandchapreally need to be in thehostsection if they're not required during build time.
33-38: Consider adding more comprehensive tests.The current test section only verifies that modules can be imported. Consider adding:
- Command-line interface tests if applicable
- Basic functionality tests
- Example data processing tests
Would you like me to help create additional test cases?
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📒 Files selected for processing (1)
recipes/biobb_mem/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/biobb_mem/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/biobb_mem/meta.yaml (2)
1-7: LGTM! Package metadata follows conda packaging best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-18: Verify the dependency pinning strategy.
The run_exports section uses x as max_pin, which means only the major version will be pinned. Given this is a bioinformatics package, consider if stricter version pinning is needed to ensure reproducibility.
✅ Verification successful
The results show that the x max_pin strategy is consistently used across all biobb packages in the ecosystem. This is a deliberate and standardized approach across the entire biobb suite. Let me generate the final response:
Pinning strategy is consistent with biobb ecosystem standards
The current run_exports configuration using max_pin='x' follows the established pattern used consistently across all biobb packages. This standardized approach ensures compatibility and maintainability across the entire biobb suite while still providing adequate version control through major version pinning.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if other biobb packages use similar pinning strategy
rg -l 'pin_subpackage.*max_pin.*x' recipes/biobb_**/meta.yaml
Length of output: 1584
| source: | ||
| url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz | ||
| sha256: 9637a957e8bf41cc8474133d66fa991bf16ac674064f7283a1153df79349e819 | ||
|
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Add the license file path.
The license_file field is empty but the package is Apache licensed. This should point to the LICENSE file in the source distribution.
- license_file: ''
+ license_file: LICENSEAlso applies to: 44-44
| doc_url: '' | ||
| dev_url: '' |
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🛠️ Refactor suggestion
Add documentation and development URLs.
The description mentions readthedocs documentation, but doc_url is empty. Similarly, dev_url should point to the GitHub repository.
- doc_url: ''
- dev_url: ''
+ doc_url: 'http://biobb_analysis.readthedocs.io/en/latest/'
+ dev_url: 'https://github.com/bioexcel/biobb_mem'Committable suggestion skipped: line range outside the PR's diff.
| extra: | ||
| recipe-maintainers: '' |
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Add recipe maintainers.
The recipe-maintainers field is empty. This should list the GitHub usernames of people responsible for maintaining this recipe.
- recipe-maintainers: ''
+ recipe-maintainers:
+ - RubenChMCommittable suggestion skipped: line range outside the PR's diff.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/biobb_mem/meta.yaml (1)
35-41: Consider enhancing test coverage.While the basic import tests are good, consider adding additional test commands to verify CLI tools or example scripts if available.
test: imports: - biobb_mem - biobb_mem.chap - biobb_mem.lipyphilicBB - biobb_mem.ambertools + commands: + - biobb_mem --help # if CLI tools are available
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Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/biobb_mem/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/biobb_mem/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/biobb_mem/meta.yaml (5)
1-7: LGTM! Package metadata is well-structured.
The package name and version are properly defined using Jinja2 variables, following conda packaging best practices.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
12-18: LGTM! Build configuration follows best practices.
The build configuration is well-structured:
- Uses
noarch: pythonfor platform independence - Includes
run_exportsto manage dependency versions - Uses standard pip installation command
47-55: LGTM! Well-documented package information.
The description provides comprehensive information about the package, including its purpose, documentation links, and licensing details.
8-11: Verify the source tarball and checksum.
The source configuration looks correct, but let's verify the tarball exists and the checksum matches.
19-34: Consider version constraints for gromacs and chap.
While most dependencies have version constraints, gromacs and chap are unpinned. This might lead to compatibility issues if these packages introduce breaking changes.
Consider adding version constraints if these packages have known compatibility ranges:
- ambertools >=22.5
- - gromacs
- - chap
+ - gromacs >=VERSION
+ - chap >=VERSION
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/biobb_mem/meta.yaml (1)
35-40: Consider adding runtime tests.While import tests are good, consider adding runtime tests to verify basic functionality. This could include running simple commands or checking version strings.
test: imports: - biobb_mem - biobb_mem.chap - biobb_mem.lipyphilicBB - biobb_mem.ambertools + commands: + - python -c "from biobb_mem import __version__; assert __version__"
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
recipes/biobb_mem/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/biobb_mem/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/biobb_mem/meta.yaml (5)
1-6: LGTM!
The package metadata is correctly defined using Jinja2 variables.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
8-10: LGTM!
The source configuration is correct with proper URL construction and SHA256 checksum.
12-17: LGTM!
The build configuration follows best practices with proper noarch Python package setup and dependency pinning through run_exports.
42-57: Previous review comments are still applicable.
The following issues from the previous review are still valid:
- Missing license_file path
- Missing doc_url and dev_url
59-60: Previous review comment about missing recipe maintainers is still applicable.
recipes/biobb_mem/meta.yaml
Outdated
| requirements: | ||
| host: | ||
| - python >=3.9 | ||
| - setuptools | ||
| - biobb_common ==5.0.0 | ||
| - lipyphilic ==0.10.0 | ||
| - ambertools >=22.5 | ||
| - gromacs ==2018.6 | ||
| - chap | ||
| run: | ||
| - python >=3.9 | ||
| - biobb_common ==5.0.0 | ||
| - lipyphilic ==0.10.0 | ||
| - ambertools >=22.5 | ||
| - gromacs ==2018.6 | ||
| - chap |
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💡 Codebase verification
Update gromacs dependency to match other biobb packages
The current gromacs 2018.6 version in biobb_mem is significantly outdated compared to other biobb packages in the repository:
- biobb_analysis uses gromacs >=2022.2
- biobb_gromacs uses gromacs ==2022.2
Since biobb_mem depends on biobb_common 5.0.0 (latest), it should align with the gromacs versions used by other up-to-date biobb packages. Consider updating to gromacs >=2022.2 to maintain consistency across the biobb ecosystem.
🔗 Analysis chain
Consider updating gromacs dependency.
The recipe pins gromacs to version 2018.6, which is quite old (about 6 years old). Consider updating to a more recent version to benefit from bug fixes, performance improvements, and new features.
Since we cannot directly check conda package versions in the sandbox environment, let me try to verify the gromacs versions through other means.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check available gromacs versions in conda-forge
conda search -c conda-forge gromacs --info
Length of output: 117
Script:
#!/bin/bash
# Search for other gromacs version references in the repository
rg "gromacs.*[0-9]" --type yaml -A 2 -B 2
# Also check if there are any migration or update related files
fd -e yaml -e yml -e md -e txt | xargs rg -l "gromacs"
Length of output: 3251
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