Update biobb_pmx to 5.0.0 #52245
Update biobb_pmx to 5.0.0 #52245
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/biobb_pmx/meta.yaml (2)
Line range hint
41-41: Update version in package descriptionThe description section still references the old version:
v4.2.1 Jan 2024 ReleaseThis should be updated to reflect the new version 5.0.0.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
Dependencies need to be updated to match biobb_pmx 5.0.0 requirements
The dependencies in meta.yaml need to be updated to match the requirements of biobb_pmx 5.0.0:
- biobb_common should be updated from 4.2.0 to 5.0.0
- pmx_biobb remains at 4.1.3
🔗 Analysis chain
Line range hint
23-29: Verify dependency compatibility with version 5.0.0The dependencies are pinned to specific versions:
- biobb_common ==4.2.0
- pmx_biobb ==4.1.3
Given this is a major version update, please verify if these dependencies need to be updated to support version 5.0.0.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if there are newer versions of dependencies curl -s https://pypi.org/pypi/biobb_common/json | jq '.info.version' curl -s https://pypi.org/pypi/pmx_biobb/json | jq '.info.version' # Check dependency requirements in the new version curl -s https://pypi.org/pypi/biobb_pmx/5.0.0/json | jq '.info.requires_dist'Length of output: 278
🧰 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_pmx/meta.yaml(1 hunks)
🔇 Additional comments (1)
recipes/biobb_pmx/meta.yaml (1)
10-10: Verify SHA256 checksum
Please verify that the new SHA256 checksum matches the source package.
| @@ -1,13 +1,13 @@ | |||
| {% set name = "biobb_pmx" %} | |||
| {% set version = "4.2.1" %} | |||
| {% set version = "5.0.0" %} | |||
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💡 Codebase verification
Update dependencies and description for biobb_pmx 5.0.0
The verification reveals several issues that need attention:
- The
biobb_commondependency is pinned to 4.2.0, but version 5.0.0 is available on PyPI - The package description still mentions "v4.2.1 Jan 2024 Release"
- Given the major version bump and the availability of a new major version of
biobb_common, the dependencies should be reviewed
Please:
- Update
biobb_commondependency to version 5.0.0 - Update the description to reflect the current version (5.0.0)
- Consider if
pmx_biobb ==4.1.3is compatible with the new major versions
🔗 Analysis chain
Verify breaking changes in version 5.0.0
This is a major version bump from 4.2.1 to 5.0.0, which typically indicates breaking changes. Please ensure that:
- Breaking changes are documented
- Downstream dependencies are compatible
Let me try to gather more information about the version changes through different sources.
Let me try one more verification to check the dependencies and their versions across releases.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check release notes and changelog for breaking changes
gh api repos/bioexcel/biobb_pmx/releases/tags/v5.0.0 --jq '.body'
# Check reverse dependencies that might be affected
rg -l "biobb_pmx" recipes/
Length of output: 278
Script:
#!/bin/bash
# Check PyPI for release information
curl -s https://pypi.org/pypi/biobb-pmx/json | jq -r '.info.description'
# Check repository for changelog or release information
fd -t f -e md -e rst "CHANGELOG|HISTORY|RELEASE" -i
# Check commit history for version bump commit message
git log --grep="5.0.0" --pretty=format:"%s%n%b" -i
# Check meta.yaml history for previous version
git log -p recipes/biobb_pmx/meta.yaml | grep -A 1 "set version"
Length of output: 5920
Script:
#!/bin/bash
# Check current dependencies in meta.yaml
cat recipes/biobb_pmx/meta.yaml
# Check if biobb_common and pmx_biobb have newer versions
curl -s https://pypi.org/pypi/biobb-common/json | jq -r '.info.version'
curl -s https://pypi.org/pypi/pmx-biobb/json | jq -r '.info.version'
Length of output: 3201
Update
biobb_pmx: 4.2.1 → 5.0.0recipes/biobb_pmx(click to view/edit other files)This pull request was automatically generated (see docs).