Update biobb_dna to 5.0.0 #51602
Update biobb_dna to 5.0.0 #51602
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📝 WalkthroughWalkthroughThe pull request involves an update to the Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/biobb_dna/meta.yaml (1)
Based on the current findings and PyPI version information from the previous script, I can now provide a final response about the dependency versions:
Dependencies need updates for biobb_dna 5.0.0
The current dependency specifications need updates:
biobb_common ==4.2.0should be updated to==5.0.0since:
- A new major version (5.0.0) is available
- This is a companion package and should match the major version of biobb_dna
curves ==3.0.2appears incorrect as:
- PyPI shows latest version is 0.1.4
- The version number format suggests this may be from a different source
- The package description in meta.yaml refers to "Curves+" which may be different from the PyPI package
The other dependencies can remain as they are since they use minimum version constraints and the current versions are still compatible:
pandas >=1.3.0(latest 2.2.3)scikit-learn >=0.24.2(latest 1.5.2)🔗 Analysis chain
Line range hint
22-28: Verify dependency compatibility with new major version.The package has specific version requirements:
- biobb_common ==4.2.0 (exact pin)
- curves ==3.0.2 (exact pin)
- pandas >=1.3.0
- scikit-learn >=0.24.2
Let's verify if these versions are still appropriate for biobb_dna 5.0.0.
Also applies to: 30-34
Let me analyze the dependencies and versions to verify compatibility. I'll generate additional scripts to check the codebase for any version-specific code or compatibility requirements.
This will help us understand any specific version requirements or compatibility constraints in the codebase. Let me analyze the results before making a final recommendation about the dependency versions.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check if dependencies versions are up-to-date # Expected: Latest versions of dependencies and any compatibility notes # Check latest versions on PyPI echo "Checking latest versions:" for pkg in biobb_common curves pandas scikit-learn; do echo "$pkg: $(curl -s https://pypi.org/pypi/$pkg/json | jq -r '.info.version')" done # Check if setup.py or pyproject.toml has different requirements fd -t f "setup.py|pyproject.toml" | xargs catLength of output: 42862
Script:
#!/bin/bash # Check for version-specific imports or usage of biobb_common and curves rg -A 3 "from biobb_common" rg -A 3 "import biobb_common" # Check for any specific version requirements in the codebase rg -i "biobb_common.*version" rg -i "curves.*version" # Look for any compatibility notes or version requirements in docs fd -t f "README.md|CHANGELOG|HISTORY" | xargs catLength of output: 4600
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/biobb_dna/meta.yaml (1 hunks)
🧰 Additional context used
🔇 Additional comments (2)
recipes/biobb_dna/meta.yaml (2)
Line range hint
13-17: Build configuration looks appropriate.The build configuration is correct:
- noarch: python is appropriate as it's a pure Python package
- run_exports with x-pin is suitable for a Python library
- build script using pip is standard
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
10-10: Verify SHA256 checksum authenticity.The SHA256 checksum has been updated. Let's verify it matches the source package.
| @@ -1,13 +1,13 @@ | |||
| {% set name = "biobb_dna" %} | |||
| {% set version = "4.2.4" %} | |||
| {% set version = "5.0.0" %} | |||
There was a problem hiding this comment.
💡 Codebase verification
Based on the search results, I can now provide a final response regarding the version update implications:
Version update compatibility needs attention
The version bump from 4.2.4 to 5.0.0 requires careful consideration as:
- Most biobb packages in the ecosystem are currently using biobb_common ==4.2.0
- Only a few packages (biobb_cmip, biobb_chemistry, biobb_analysis, biobb_amber) have been updated to use biobb_common ==5.0.0
- This major version update could break compatibility with packages still depending on version 4.2.0
Action items:
- The following packages need version updates to maintain compatibility:
- biobb_haddock
- biobb_flexserv
- biobb_vs
- biobb_structure_utils
- biobb_pmx
- biobb_pdb_tools
- biobb_ml
- biobb_gromacs
- biobb_pytorch
- biobb_io
- biobb_cp2k
- biobb_model
- biobb_godmd
- biobb_flexdyn
🔗 Analysis chain
Verify the major version update implications.
This is a major version bump from 4.2.4 to 5.0.0, which typically indicates breaking changes.
Let's verify the changelog and release notes:
Let me try a different approach to verify the version update implications by checking the package's repository directly.
This will help us:
- Find any changelog information in markdown files
- Check package configuration files for version details
- Cross-reference biobb_common dependency usage in other recipes to ensure version compatibility
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Fetch and examine the release notes for breaking changes
# Expected: Release notes or changelog entries for version 5.0.0
# Check if there's a CHANGELOG.md in the package
gh release view v5.0.0 -R bioexcel/biobb_dna || echo "No release notes found"
Length of output: 282
Script:
#!/bin/bash
# Search for changelog or release notes in the repository
fd -t f -e md "CHANGELOG|HISTORY|RELEASE" -X cat {}
# Also check the package's setup.py or pyproject.toml for version info
fd -t f "setup.py|pyproject.toml" -X cat {}
# Check biobb_common dependency version in other recipes
rg "biobb_common" recipes/ -A 2 -B 2
Length of output: 54983
Update
biobb_dna: 4.2.4 → 5.0.0recipes/biobb_dna(click to view/edit other files)This pull request was automatically generated (see docs).