krakentools: alpha_diversity requires scipy #52125
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/krakentools/meta.yaml (1)
22-24: Remove trailing spacesThere are trailing spaces on the following lines:
- Line 22: after
python- Line 24: after
numpyrun: - - python + - python - biopython - - numpy + - numpy - scipy🧰 Tools
🪛 yamllint
[error] 22-22: trailing spaces
(trailing-spaces)
[error] 24-24: trailing spaces
(trailing-spaces)
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📒 Files selected for processing (1)
recipes/krakentools/meta.yaml(2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/krakentools/meta.yaml
[error] 22-22: trailing spaces
(trailing-spaces)
[error] 24-24: trailing spaces
(trailing-spaces)
🔇 Additional comments (4)
recipes/krakentools/meta.yaml (4)
15-15: LGTM: Build number increment is appropriate
The build number increment is correct as we're adding a new dependency (scipy) which requires a rebuild.
46-46: LGTM: Summary update is appropriate
The simplified summary is more focused and follows package metadata best practices by keeping it concise and descriptive.
25-25: Verify scipy version requirements
While adding scipy as a dependency is correct based on the alpha_diversity.py requirement, we should verify if any specific version constraints are needed.
#!/bin/bash
# Check alpha_diversity.py for scipy usage and version requirements
rg -A 5 "from scipy|import scipy"
# Check if there are any scipy version-specific features used
ast-grep --pattern 'from scipy.$_ import $_'45-45: Verify LICENSE file existence
Adding the license file reference is good practice, but let's verify its existence in the source repository.
✅ Verification successful
LICENSE file exists in the source repository
The LICENSE file is present at KrakenTools-1.2/LICENSE in the source tarball, confirming that the license_file reference in meta.yaml is correct.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify LICENSE file in the source tarball
curl -sL https://github.com/jenniferlu717/KrakenTools/archive/v1.2.tar.gz | \
tar tz | grep -i license
Length of output: 262
| run_exports: | ||
| - {{ pin_subpackage("krakentools", max_pin="x.x") }} |
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🛠️ Refactor suggestion
Consider removing run_exports section
Since this is a pure Python package (noarch: python), the run_exports section is unnecessary. This directive is typically used for C/C++ libraries to ensure ABI compatibility, but Python packages don't have the same binary interface concerns.
build:
noarch: python
number: 1
- run_exports:
- - {{ pin_subpackage("krakentools", max_pin="x.x") }}📝 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.
| run_exports: | |
| - {{ pin_subpackage("krakentools", max_pin="x.x") }} |
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@bernt-matthias, thank you for pointing that out. You're right; including the run_exports section can be important for noarch: python packages when enforcing version constraints for downstream dependencies. I appreciate your clarification.
✏️ Learnings added
Learnt from: bernt-matthias
PR: bioconda/bioconda-recipes#52125
File: recipes/krakentools/meta.yaml:16-17
Timestamp: 2024-11-15T09:23:00.586Z
Learning: For `noarch: python` packages, including a `run_exports` section may be necessary to enforce version constraints for downstream dependencies.
Note: Learnings are effective only in the context of similar code segments. To apply general coding guidelines, please configure review instructions. You can manage existing learnings in the app.
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
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Locally tested here galaxyproject/tools-iuc#6553 |
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@BiocondaBot please add label |
https://github.com/jenniferlu717/KrakenTools/blob/d4a2fbe2833c2392a724697c0c97a3014e748474/DiversityTools/alpha_diversity.py#L32
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