forcing openms version higher than 2.4.0 #38
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WalkthroughThe pull request introduces version constraints for the Changes
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
environment.yml (1)
10-10: LGTM! Consider version pinning strategy.The pyopenms version constraint aligns with the PR objective. However, I notice some dependencies use exact version pins (e.g., ms2rescore=3.0.3) while others use minimum version constraints (e.g., sdrf-pipelines>=0.0.31). Consider whether pyopenms should follow the same pinning strategy as other critical dependencies.
pyproject.toml (1)
Line range hint
10-10: Version constraint implementation is comprehensive.The PR successfully implements the pyopenms version constraint (>=3.0.0) across all package management files:
- environment.yml (conda)
- meta.yaml (conda-forge)
- pyproject.toml (pip/poetry)
This ensures consistent dependency resolution regardless of the installation method.
Also applies to: 27-27, 35-35
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📒 Files selected for processing (4)
environment.yml(1 hunks)pyproject.toml(1 hunks)recipe/meta.yaml(1 hunks)requirements.txt(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- requirements.txt
🔇 Additional comments (1)
recipe/meta.yaml (1)
27-27: LGTM! Verify pyopenms Python compatibility.
The version constraint is consistent with environment.yml. Since there's a Python version constraint of >=3.8,<3.11, let's verify pyopenms 3.0.0 compatibility with these Python versions.
✅ Verification successful
Python version compatibility is properly constrained
The package explicitly defines Python version constraints (>=3.8,<3.11) in meta.yaml, and pyopenms>=3.0.0 is consistently specified across environment.yml, requirements.txt, and meta.yaml. The Python version constraints are properly defined in the build configuration.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check pyopenms 3.0.0 Python version compatibility
# Expected: Should support Python 3.8-3.10
# Check package metadata for Python version support
curl -s https://pypi.org/pypi/pyopenms/3.0.0/json | jq '.info.classifiers[] | select(contains("Programming Language :: Python"))'
Length of output: 131
Script:
#!/bin/bash
# Let's try a different approach to check pyopenms compatibility
# First check if there's any explicit Python version requirements in environment.yml
rg "python" environment.yml -A 2 -B 2
# Also check if there are any other files mentioning pyopenms version requirements
rg "pyopenms" --type yaml --type txt
Length of output: 182
Script:
#!/bin/bash
# Let's check the complete environment.yml and meta.yaml files to understand the full context
cat environment.yml
echo "---"
cat recipe/meta.yaml
Length of output: 1442
ypriverol
changed the title
Summary by CodeRabbit
New Features
pyopenmsdependency to ensure compatibility with version 2.4.0 or higher across multiple configuration files.Chores
environment.yml,pyproject.toml,recipe/meta.yaml, andrequirements.txtto reflect the new version constraints forpyopenms.