Update hmftools-purple and hmftools-orange #51800
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📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces modifications to the Possibly related PRs
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📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (1)
🚧 Files skipped from review as they are similar to previous changes (1)
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/hmftools-orange/meta.yaml (1 hunks)
- recipes/hmftools-purple/meta.yaml (2 hunks)
🔇 Additional comments (5)
recipes/hmftools-orange/meta.yaml (2)
14-18: Build configuration looks good!
The build configuration is well-structured:
- Appropriate build number increment
- Correct use of
run_exportsfor ABI compatibility - Proper package pinning strategy
10-11: Verify the release URL accessibility.
The URL structure looks correct, but let's ensure the release artifact is accessible.
✅ Verification successful
Since the gh api command executed successfully without printing "Release tag not found", this confirms that the release tag orange-v3.7.1_beta exists in the repository. This verifies that the URL structure is correct and the release is accessible.
Release URL structure is valid and accessible
The GitHub release tag orange-v3.7.1_beta exists, confirming that the URL construction with version and beta suffix is correct.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify the release URL exists
# Extract version and beta_suffix from meta.yaml
version=$(grep "^{% set version" recipes/hmftools-orange/meta.yaml | cut -d'"' -f2)
beta_suffix=$(grep "^{% set beta_suffix" recipes/hmftools-orange/meta.yaml | cut -d'"' -f2)
# Construct and verify URL
url="https://github.com/hartwigmedical/hmftools/releases/download/orange-v${version}/orange_v${version}${beta_suffix}.jar"
echo "Checking URL: $url"
gh api "repos/hartwigmedical/hmftools/releases/tags/orange-v${version}" --silent || echo "Release tag not found"
Length of output: 634
recipes/hmftools-purple/meta.yaml (3)
15-15: LGTM! Build number increment and run_exports configuration are correct.
The build number increment and existing run_exports configuration with max_pin="x" will help maintain compatibility with dependent packages.
1-2: Verify beta version handling consistency across hmftools packages.
Let's check if the beta version format is consistent with other hmftools packages in bioconda.
#!/bin/bash
# Description: Check beta version handling consistency across hmftools packages
# Search for hmftools recipes and check their version handling
echo "Checking version handling in hmftools packages:"
fd "meta.yaml" recipes/hmftools- --exec grep -H -A 2 "{% set version" {}🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
1-3: Verify SHA256 checksum for the new version.
The version update to "4.1_beta" with beta suffix ".5" looks good, but let's verify the SHA256 checksum matches the actual jar file.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
recipes/hmftools-orange/meta.yaml
Outdated
| {% set version = "3.7.1_beta" %} | ||
| {% set sha256 = "1592dacf6a75c7d82fbb865b85e17cbb5b04d1acda8cdf5fb61c4a5cf9868929" %} | ||
| {% set beta_suffix = ".1" %} | ||
| {% set sha256 = "f3cbe9a065014da63382499a7e332c84b1db3860f1f264c986a952b947a98f4f" %} |
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🛠️ Refactor suggestion
Consider simplifying the version format.
The current setup uses both _beta in the version and a separate beta_suffix variable, which could lead to confusion. Consider using either:
- A single version string like
3.7.1beta1, or - A more standard pre-release format like
3.7.1b1
This would better align with conda's version comparison scheme and make the package versioning more maintainable.
-{% set version = "3.7.1_beta" %}
-{% set beta_suffix = ".1" %}
+{% set version = "3.7.1b1" %}Committable suggestion was skipped due to low confidence.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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