Update decom recipe by adding kmtricks dependency #51911
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request updates the Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/decom/meta.yaml (1)
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1-71: Consider updating package documentation.The package has undergone significant changes:
- Moved from pure Python (noarch) to compiled code
- Added new dependencies
- Added run_exports pinning
Consider:
- Updating the package documentation to reflect build requirements
- Adding build instructions to the README
- Documenting system requirements for end users
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📒 Files selected for processing (1)
recipes/decom/meta.yaml(3 hunks)
🔇 Additional comments (3)
recipes/decom/meta.yaml (3)
15-15: LGTM: Build number increment is appropriate.
The build number increment is correct as dependencies have been modified.
43-44: Verify kmtricks version compatibility.
The addition of zlib and kmtricks as runtime dependencies needs verification:
- Is kmtricks >=1.4.0 the minimum compatible version?
- Are there any known compatibility issues with newer versions?
#!/bin/bash
# Check if kmtricks is available in bioconda
conda search -c bioconda kmtricks --info
# Look for version requirements in source code
rg -l "kmtricks" 26-29: Verify build requirements against upstream.
The addition of C++ compiler and build tools suggests this package now includes compiled components. This is a significant change from being a noarch package.
Consider documenting the reason for this architectural change in the PR description.
CamilaDuitama
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/decom/meta.yaml (2)
35-35: Consider updating numpy version constraint.The numpy version constraint
>=1.7is quite old. Consider setting a more recent minimum version to ensure compatibility with modern features and security updates.
75-75: Add newline at end of file.Add a newline character at the end of the file to comply with YAML formatting standards.
- - CamilaDuitama + - CamilaDuitama +🧰 Tools
🪛 yamllint
[error] 75-75: no new line character at the end of file
(new-line-at-end-of-file)
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📒 Files selected for processing (1)
recipes/decom/meta.yaml(3 hunks)
🧰 Additional context used
🪛 yamllint
recipes/decom/meta.yaml
[error] 75-75: no new line character at the end of file
(new-line-at-end-of-file)
🔇 Additional comments (3)
recipes/decom/meta.yaml (3)
14-14: LGTM: Build number increment is appropriate.
The build number increment is correct as dependencies were modified.
42-42: LGTM: kmtricks dependency added as per PR objective.
The addition of kmtricks >=1.4.0 aligns with the PR's purpose and follows Bioconda's versioning guidelines.
30-32: Verify Python version constraints with kmtricks compatibility.
The Python version constraint has been tightened significantly. Let's verify this aligns with kmtricks requirements.
✅ Verification successful
Let me check kmtricks' Python requirements to ensure alignment.
Let me try one more search to specifically look for kmtricks' requirements:
Python version constraints are appropriate
The Python version constraints (>=3.9,<3.13) are well-aligned with the package requirements:
- kmtricks is used as a dependency (>=1.4.0) without specific Python constraints
- The upper bound <3.13 is a good practice to prevent untested Python versions
- The lower bound >=3.9 is reasonable for a modern scientific package
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check kmtricks recipe for Python version requirements
fd -t f "meta.yaml" -x grep -l "kmtricks" {} \; | xargs cat | grep -A 5 "python"
Length of output: 477
Script:
#!/bin/bash
# Check kmtricks package for Python version constraints
fd -t f "meta.yaml" -x grep -l "kmtricks" {} \; -exec dirname {} \; | xargs -I {} find {} -type f -name "meta.yaml" | xargs cat | grep -A 5 "python"
# Also check setup.py/pyproject.toml for any Python version specifications
fd -t f "setup.py|pyproject.toml" | xargs cat | grep -A 5 "python"
Length of output: 2164
Script:
#!/bin/bash
# Search for kmtricks package requirements
rg -A 5 "kmtricks" --type yaml
# Also check if there's any kmtricks documentation or README
fd -t f "README|INSTALL" -e md -e txt | xargs cat | grep -A 5 -B 5 "python"
Length of output: 1963
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EDIT to decom recipe
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