Coptr fix ranges for versions of python and numpy #52019
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Actionable comments posted: 2
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📒 Files selected for processing (1)
recipes/coptr/meta.yaml(2 hunks)
🔇 Additional comments (1)
recipes/coptr/meta.yaml (1)
17-20: Build configuration looks good.
The build number increment and run_exports configuration are appropriate for dependency constraint changes.
| @@ -25,8 +25,8 @@ requirements: | |||
| - pip | |||
| run: | |||
| - bowtie2 >=2.4.1 | |||
| - python >=3.7 | |||
| - numpy >=1.19.1 | |||
| - python >=3.7,<=3.8 | |||
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💡 Codebase verification
🛠️ Refactor suggestion
Let me analyze the output and generate the final response.
Consider updating Python version constraints
The upper bound <=3.8 is overly restrictive. The search results show numerous bioinformatics packages in the repository successfully supporting Python 3.9+ versions. Unless there's a specific dependency requiring Python 3.8, updating the version constraints would:
- Ensure longer-term maintainability as Python 3.8 reaches EOL
- Align with the broader bioconda ecosystem where Python 3.9+ is widely supported
- Enable users to leverage newer Python features and security updates
Suggested change:
- python >=3.7,<3.10 # or even <3.11 after testing🔗 Analysis chain
Consider supporting newer Python versions.
The upper bound <=3.8 seems overly restrictive as Python 3.8 is approaching EOL (October 2024). Many scientific packages support newer Python versions. Unless there's a specific compatibility issue, consider:
- Testing with Python 3.9+ to verify compatibility
- Removing or increasing the upper bound if tests pass
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if package is tested with newer Python versions in other recipes
rg -l "python.*>=3\.[789]" recipes/
Length of output: 18756
| - python >=3.7 | ||
| - numpy >=1.19.1 | ||
| - python >=3.7,<=3.8 | ||
| - numpy >=1.19.1,<=1.24.4 |
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💡 Codebase verification
NumPy version constraint needs updating for compatibility
The current NumPy constraint >=1.19.1,<=1.24.4 is too restrictive and outdated compared to the ecosystem requirements:
- Most packages in the repository require NumPy >=1.25 or >=1.26
- The package depends on scipy
>=1.5.2,<2.0.0, which is compatible with newer NumPy versions - Newer versions of NumPy (1.25+) are stable and widely adopted in the scientific Python ecosystem
Recommendation: Update the NumPy requirement to >=1.19.1,<1.27.0 to maintain compatibility with both older and newer dependencies while ensuring ABI compatibility.
🔗 Analysis chain
Verify NumPy version compatibility with dependencies.
The NumPy constraint >=1.19.1,<=1.24.4 needs verification:
- Check if this range is compatible with the scipy requirement
>=1.5.2,<2.0.0 - Ensure it meets the minimum NumPy version requirements of other dependencies
Let me gather more specific information about the numpy requirements in these packages.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check numpy requirements in related scientific packages
echo "Checking numpy requirements in scipy recipes..."
rg "numpy.*>=.*" recipes/scipy*/meta.yaml
echo "Checking numpy requirements in other scientific packages..."
rg -l "numpy.*>=.*1\.2[5-9]" recipes/
Length of output: 1279
Script:
#!/bin/bash
# Check exact numpy version requirements in the identified packages
echo "Checking exact numpy requirements in packages..."
for pkg in neofox strainy taxmyphage zarp xclone vitap tribal tracegroomer toulligqc syngap superdsm seismic-rna robust-bias-aware pling phabox pgscatalog.calc parm pango-collapse monsda macs3 integron_finder htsinfer gene-trajectory-python crocodeel dimet cpstools circulocov checkqc bx-python b2btools aci
do
echo "=== $pkg ==="
rg "numpy.*>=.*" "recipes/$pkg/meta.yaml" -A 1
done
# Also check for scipy dependency in coptr
echo "=== Checking scipy requirement in coptr ==="
rg "scipy.*>=.*" recipes/coptr/meta.yaml
Length of output: 14431
Describe your pull request here
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