[biobb_amber] update 5.0.0 #51430
[biobb_amber] update 5.0.0 #51430
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📝 WalkthroughWalkthroughThe pull request introduces modifications to the Possibly related PRs
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Actionable comments posted: 1
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (1)
- recipes/biobb_amber/meta.yaml (2 hunks)
🧰 Additional context used
🔇 Additional comments (5)
recipes/biobb_amber/meta.yaml (5)
2-2: Version update looks good.The package version has been correctly updated to 5.0.0, which is consistent with the PR title and indicates a major version update.
23-23: biobb_common dependency updated correctly.The biobb_common dependency has been updated to version 5.0.0, which is consistent with the main package version update. This change is applied correctly in both the
hostandrunrequirements.Also applies to: 27-27
Line range hint
1-28: Overall assessment: Changes look good with some points to verify.The updates to the
meta.yamlfile for biobb_amber 5.0.0 are consistent and appear to be correct. The main changes include:
- Updating the package version to 5.0.0
- Updating the SHA256 checksum
- Adding an upper bound to the Python version constraint
- Updating the biobb_common dependency to 5.0.0
- Specifying an exact version for the ambertools dependency
These changes are applied consistently throughout the file. However, please verify the following:
- The correctness of the new SHA256 checksum
- The rationale behind the Python version upper bound
- The specific version requirement for ambertools
Once these points are clarified or confirmed, the changes can be considered ready for merging.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
21-21: Python version constraint updated with upper bound.The Python version constraint has been updated to
>=3.8,<3.11, adding an upper bound to prevent potential compatibility issues with newer Python versions. This change is applied consistently in both thehostandrunrequirements.Consider the following:
- Is there a specific reason for excluding Python 3.11 and above?
- Are there plans to test and support newer Python versions in the future?
To check the latest Python version supported by the dependencies, you can run:
#!/bin/bash # Check the latest Python version supported by biobb_common and ambertools conda search biobb_common==5.0.0 ambertools==22.5.0 pythonThis will help ensure that the Python version constraint aligns with the dependencies' requirements.
Also applies to: 26-26
10-10: SHA256 checksum updated correctly.The SHA256 checksum has been updated to match the new version of the package. This is crucial for ensuring the integrity of the downloaded package.
To verify the checksum, you can run the following command:
Compare the output with the checksum in the meta.yaml file to ensure they match.
| - biobb_common ==4.2.0 | ||
| - ambertools >=22.0 | ||
| - biobb_common ==5.0.0 | ||
| - ambertools ==22.5.0 |
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💡 Codebase verification
Inconsistent ambertools version constraints across recipes.
The ambertools dependency is specified as ==22.5.0 in recipes/biobb_amber/meta.yaml while other recipes use >=22.0. This inconsistency may lead to compatibility issues or reduced flexibility.
🔗 Analysis chain
ambertools dependency updated to specific version.
The ambertools dependency has been updated from >=22.0 to ==22.5.0. This change ensures consistency but may limit flexibility for users.
Please confirm:
- Is version 22.5.0 of ambertools specifically required for compatibility with biobb_amber 5.0.0?
- Would it be possible to use a more flexible version constraint (e.g.,
>=22.5.0,<23.0) to allow for minor updates?
To check the available versions of ambertools, you can run:
This will help ensure that the specified version is appropriate and available.
Also applies to: 28-28
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check available versions of ambertools
conda search ambertools
Length of output: 98
Script:
#!/bin/bash
# Check available versions of ambertools using pip
pip index versions ambertools
Length of output: 102
Script:
#!/bin/bash
# Search for all occurrences of 'ambertools' in the codebase
rg 'ambertools'
Length of output: 587
Describe your pull request here
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