Update biobb_amber to 5.0.2 #51653
Update biobb_amber to 5.0.2 #51653
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📝 WalkthroughWalkthroughThe pull request involves an update to the Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/biobb_amber/meta.yaml (2)
Line range hint
44-48: Documentation links need updating.There's a syntax error in the description field's documentation link. The extra parenthesis and bracket should be removed.
- description: "Biobb_amber is a BioBB category for AMBER MD package. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: http://biobb_amber.readthedocs.io/en/latest/)](http://biobb_amber.readthedocs.io/en/latest/" + description: "Biobb_amber is a BioBB category for AMBER MD package. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: http://biobb_amber.readthedocs.io/en/latest/"🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
Line range hint
42-43: Missing license file specification.The
license_filefield is empty but the package is Apache licensed. This should be specified.license: Apache Software License license_family: APACHE - license_file: '' + license_file: LICENSE🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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📒 Files selected for processing (1)
- recipes/biobb_amber/meta.yaml (1 hunks)
🔇 Additional comments (3)
recipes/biobb_amber/meta.yaml (3)
Line range hint
22-29: Verify dependency compatibility.The package maintains its dependencies:
- biobb_common ==5.0.0
- ambertools ==22.5.0
- Python >=3.8,<3.11
Let's verify if these versions are compatible with the new version.
#!/bin/bash # Description: Check if dependencies exist in conda-forge/bioconda # Expected: All dependencies should be available echo "Checking conda-forge/bioconda for dependencies..." conda search biobb_common==5.0.0 -c conda-forge -c bioconda || echo "biobb_common 5.0.0 not found" conda search ambertools==22.5.0 -c conda-forge -c bioconda || echo "ambertools 22.5.0 not found"🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
2-2: Verify version bump authenticity.Let's verify that this version exists in the upstream repository and PyPI.
✅ Verification successful
Let me gather more information about the package release by checking the repository tags and commits.
Version 5.0.2 is verified and available in both PyPI and GitHub tags
The version bump to 5.0.2 is legitimate as:
- Version 5.0.2 exists in PyPI releases
- Git tag
v5.0.2is present in the upstream repository (bioexcel/biobb_amber)🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify version exists in PyPI and matches upstream # Expected: Version 5.0.2 should exist in PyPI and match the GitHub release # Check PyPI version echo "Checking PyPI version..." curl -s https://pypi.org/pypi/biobb_amber/json | jq -r '.releases | keys[]' | grep "5.0.2" || echo "Version not found in PyPI" # Check GitHub releases echo "Checking GitHub releases..." gh release list --repo bioexcel/biobb_amber | grep "5.0.2" || echo "Version not found in GitHub releases"Length of output: 362
Script:
#!/bin/bash # Check git tags and commits for version 5.0.2 echo "Checking git tags..." git ls-remote --tags https://github.com/bioexcel/biobb_amber.git | grep "5.0.2" echo -e "\nChecking recent commits..." git ls-remote --heads https://github.com/bioexcel/biobb_amber.git main | cut -f1 | xargs -I{} curl -s "https://api.github.com/repos/bioexcel/biobb_amber/commits/{}" | jq -r '.commit.message' | head -n 5Length of output: 523
10-10: Verify SHA256 checksum authenticity.Let's verify the SHA256 matches the PyPI source distribution.
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Closing in favor of #51649. |
Update
biobb_amber: 5.0.0 → 5.0.2recipes/biobb_amber(click to view/edit other files)This pull request was automatically generated (see docs).