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Use openjdk <=21 for hmftools-redux #52122

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merged 1 commit into from
Nov 15, 2024

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coderabbitai bot commented Nov 15, 2024

📝 Walkthrough

Walkthrough

The pull request modifies the meta.yaml file for the hmftools-redux package. It updates the versioning information by incrementing the build number from 5 to 6. Additionally, the requirements section has been revised to specify a more restrictive version range for the openjdk dependency, changing it from >=8 to >=8,<=21. All other sections of the meta.yaml file, including package, source, run_exports, test, and about, remain unchanged.

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please review & merge

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Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 5c572ed and fd8657e.

📒 Files selected for processing (1)
  • recipes/hmftools-redux/meta.yaml (1 hunks)
🔇 Additional comments (1)
recipes/hmftools-redux/meta.yaml (1)

15-15: LGTM: Build number increment is appropriate

The build number increment follows best practices for package updates without version changes.

run_exports:
- {{ pin_subpackage('hmftools-redux', max_pin="x.x") }}

requirements:
run:
- openjdk >=8
- openjdk >=8,<=21
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💡 Codebase verification

Java version constraint needs adjustment

Based on the upstream source code and recent commits, the Java version constraint should be adjusted. The upstream project explicitly sets Java 11 as the target version in its parent pom.xml (<java.version>11</java.version>), and there's a recent commit "INFRA-541 Redux: Use openjdk 11" specifically for this tool.

  • The current constraint >=8,<=21 should be changed to >=11,<=21 to align with the upstream requirements.
🔗 Analysis chain

Verify Java version compatibility with upstream

The addition of the upper bound <=21 for OpenJDK is a good practice to prevent potential compatibility issues with future Java versions. However, let's verify this constraint against upstream requirements.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify Java version compatibility with upstream project

# Check if there are any Java version requirements mentioned in the upstream repository
gh api repos/hartwigmedical/hmftools/contents/redux/README.md 2>/dev/null | jq -r '.content' | base64 -d | grep -i "java" || true
gh api repos/hartwigmedical/hmftools/contents/redux/pom.xml 2>/dev/null | jq -r '.content' | base64 -d | grep -i "<java.version>" || true

# Check for any Java version related issues or discussions
gh api search/issues -X GET -f q="repo:hartwigmedical/hmftools java version redux" | jq '.items[] | select(.title | test("(?i)java|jdk")) | {title: .title, url: .html_url}'

Length of output: 562


Script:

#!/bin/bash
# Let's try a different approach using direct GitHub API calls and processing the response differently

# Check pom.xml for Java version
gh api repos/hartwigmedical/hmftools/contents/redux/pom.xml | jq -r '.download_url' | xargs curl -s | grep -i "<java.version>"

# Check README.md for Java requirements
gh api repos/hartwigmedical/hmftools/contents/redux/README.md | jq -r '.download_url' | xargs curl -s | grep -i "java"

# Check for maven compiler plugin configuration which often specifies Java version
gh api repos/hartwigmedical/hmftools/contents/redux/pom.xml | jq -r '.download_url' | xargs curl -s | grep -A 5 -B 5 "maven-compiler-plugin"

Length of output: 835


Script:

#!/bin/bash
# Let's check the parent pom.xml for Java version properties
gh api repos/hartwigmedical/hmftools/contents/pom.xml | jq -r '.download_url' | xargs curl -s | grep -A 2 -B 2 "maven.compiler\|java.version"

# Also check if there are any recent commits mentioning Java version changes
gh api repos/hartwigmedical/hmftools/commits --paginate | jq -r '.[] | select(.commit.message | test("(?i)java|jdk")) | {message: .commit.message, date: .commit.author.date}'

Length of output: 15343

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@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
noarch hmftools-redux-1.0_beta-hdfd78af_6.tar.bz2 noarch.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>

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