[biobb_pmx] update 5.0.0 #52246
[biobb_pmx] update 5.0.0 #52246
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces updates to the Possibly related PRs
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🔇 Additional comments (6)recipes/biobb_pmx/meta.yaml (6)Line range hint The build configuration is well-structured with:
🧰 Tools🪛 yamllint[error] 1-1: syntax error: found character '%' that cannot start any token (syntax)
The version number in the description has been properly updated to match the package version.
Let's ensure the SHA256 checksum matches the source package from PyPI.
The version change from 4.2.1 to 5.0.0 is a major version bump. This typically indicates breaking changes, which is supported by the increased Python version requirement (>=3.9) and updated dependencies. Let's verify the changelog or release notes: ✅ Verification successfulMajor version bump appears justified The version bump to 5.0.0 aligns with semantic versioning principles based on the following evidence:
🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Check for changelog or release notes in the source repository
curl -s "https://raw.githubusercontent.com/bioexcel/biobb_pmx/master/CHANGELOG.md" || \
curl -s "https://raw.githubusercontent.com/bioexcel/biobb_pmx/master/CHANGES.md" || \
curl -s "https://raw.githubusercontent.com/bioexcel/biobb_pmx/v5.0.0/CHANGELOG.md"
Length of output: 97 Script: #!/bin/bash
# Let's check the source URL from meta.yaml and try to find release information
cat recipes/biobb_pmx/meta.yaml | grep -A2 "source:"
# Also check if there's any GitHub releases info
gh release view v5.0.0 --repo bioexcel/biobb_pmx 2>/dev/null || true
Length of output: 291 Script: #!/bin/bash
# Let's examine the requirements changes in meta.yaml to verify if the major version bump is justified
cat recipes/biobb_pmx/meta.yaml | grep -A15 "requirements:"
# Also check if there's a previous version of this recipe to compare
git show HEAD~1:recipes/biobb_pmx/meta.yaml 2>/dev/null | grep -A15 "requirements:" || true
Length of output: 691 Script: #!/bin/bash
# Let's check if there are any older versions to compare with
git log --oneline recipes/biobb_pmx/meta.yaml | head -n 5
# And get the content of an older version to see the actual changes
git show $(git log --oneline recipes/biobb_pmx/meta.yaml | sed -n '2p' | cut -d' ' -f1):recipes/biobb_pmx/meta.yaml | grep -A2 "version =" || true
Length of output: 0
The Python requirement has been increased from >=3.8 to >=3.9. This is a breaking change that needs justification. ✅ Verification successfulLet me gather more information about Python version requirements across the codebase. Let me check for any changes or dependencies that might justify the Python version bump. Let me check for any dependency changes or updates that might require Python 3.9. Based on the gathered information, I can now provide the final response: Python version bump is justified by dependency requirements The Python version requirement increase to >=3.9 is driven by biobb_common v5.0.0, which is a direct dependency that requires Python >=3.9.0. This is a coordinated update across the biobb ecosystem, as evidenced by multiple biobb packages (biobb_analysis, biobb_chemistry, biobb_gromacs, etc.) that have also moved to Python >=3.9 and biobb_common 5.0.0. 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Check if any specific Python 3.9 features are used in the package
curl -s "https://raw.githubusercontent.com/bioexcel/biobb_pmx/v5.0.0/setup.py" | grep -i "python_requires"
Length of output: 133 Script: #!/bin/bash
# Check for Python 3.9 specific features in the codebase
rg -l "match.*case"
# Check for any version-related comments or documentation
fd README.md | xargs rg -i "python.*3\.9"
fd CHANGELOG.md | xargs rg -i "python.*3\.9"
# Check dependencies' Python requirements
cat recipes/biobb_pmx/meta.yaml | rg "python.*>="
Length of output: 66656 Script: #!/bin/bash
# Check for changes in dependencies or requirements
fd CHANGELOG.md | xargs rg -i "3\.9"
# Check setup.py for any version-specific requirements
fd setup.py | xargs rg -i "python.*3\.9"
# Check for any Python 3.9-specific features in the source code
fd .py$ | xargs rg -l "match.*case|removeprefix|removesuffix|zoneinfo|graphlib"
Length of output: 100403 Script: #!/bin/bash
# Check for dependency version changes
cat recipes/biobb_pmx/meta.yaml | rg "biobb_common"
# Check if biobb_common requires Python 3.9
fd "biobb_common" | xargs rg -i "python.*3\.9"
# Check for any recent changes in dependencies
fd CHANGELOG.md | xargs rg -i "python.*3\.9|biobb_common"
Length of output: 70294
Please provide justification for:
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