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Update regenie to 4.0 #52002

Merged
merged 1 commit into from
Nov 7, 2024
Merged

Update regenie to 4.0 #52002

merged 1 commit into from
Nov 7, 2024

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Update regenie: 3.64.0

install with bioconda Conda

Info Link or Description
Recipe recipes/regenie (click to view/edit other files)
Summary Regenie is a C++ program for whole genome regression modelling of large genome-wide association studies (GWAS).
Home https://rgcgithub.github.io/regenie/
Releases https://github.com/rgcgithub/regenie/tags
Recipe Maintainer(s) @matuskosut, @joellembatchou
Author @rgcgithub

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Nov 7, 2024
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coderabbitai bot commented Nov 7, 2024

📝 Walkthrough

Walkthrough

The pull request involves updates to the meta.yaml file for the regenie package. The version number is changed from "3.6" to "4.0", and the SHA256 checksum is updated to "8f678d55bccf18ab70680637aca3cfd737060b3da291c803f3016d2ac3a07ccf". The source URL is modified to reflect the new version, pointing to the tarball for version 4.0. Additionally, there is an update to the patch for version 3.6, while previous patches remain commented out. The build, host, and runtime requirements have not been altered, indicating that the dependencies for building and running the package are unchanged. The test commands and metadata, including the package's homepage, license, and summary, also remain consistent with previous versions.

Possibly related PRs

  • Update regenie to 3.6 #50468: The changes in this PR involve updating the meta.yaml file for the regenie package, specifically changing the version and SHA256 checksum, which is directly related to the version update in the main PR.

Suggested reviewers

  • joellembatchou

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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 3765eb5 and ef4af24.

📒 Files selected for processing (1)
  • recipes/regenie/meta.yaml (1 hunks)
🔇 Additional comments (2)
recipes/regenie/meta.yaml (2)

Line range hint 31-31: Review patch compatibility with v4.0.

The patch 0015-update-cmakelist.txt-for-v3.6.patch is specifically designed for v3.6. Applying this patch to v4.0 might cause compatibility issues since this is a major version upgrade. Please verify if:

  1. This patch is still necessary for v4.0
  2. The patch applies cleanly to v4.0
  3. A new version-specific patch should be created instead
#!/bin/bash
# Description: Check if the v3.6 patch applies cleanly to v4.0
# Expected: Should show if there are any conflicts

# Download v4.0 source
curl -sL https://github.com/rgcgithub/regenie/archive/v4.0.tar.gz | tar xz

# Check if the patch applies cleanly (assuming patch is in patches directory)
cd regenie-4.0
patch -p1 --dry-run < ../recipes/regenie/patches/0015-update-cmakelist.txt-for-v3.6.patch
🧰 Tools
🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)


Line range hint 35-57: Verify dependency requirements for v4.0.

Please ensure that:

  1. All dependencies are still compatible with v4.0
  2. No new dependencies were introduced in v4.0
  3. The specific version constraints (e.g., boost-cpp 1.74, mkl >=2020.4) are still appropriate
#!/bin/bash
# Description: Check for any dependency changes in v4.0
# Expected: Should show any new or modified dependencies in CMakeLists.txt

# Search for dependency-related changes in CMakeLists.txt
rg -i "find_package|find_library|requires" regenie-4.0/CMakeLists.txt

# Check if README mentions any new dependencies
rg -i "requirement|depend" regenie-4.0/README.md
🧰 Tools
🪛 yamllint

[error] 1-1: syntax error: found character '%' that cannot start any token

(syntax)

Comment on lines +2 to +3
{% set version = "4.0" %}
{% set sha256 = "8f678d55bccf18ab70680637aca3cfd737060b3da291c803f3016d2ac3a07ccf" %}
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💡 Codebase verification

Patch 0015 needs to be removed for v4.0

The patch 0015-update-cmakelist.txt-for-v3.6.patch was specifically designed for v3.6 and should not be applied to v4.0 as:

  • The patch header explicitly states it's for v3.6: "update cmakelist file for v3.6"
  • v4.0 is a major version update that likely includes its own CMake build system improvements
  • Applying v3.6-specific patches to v4.0 could lead to build failures or unexpected behavior
🔗 Analysis chain

Verify SHA256 checksum against the official release.

Let's confirm the checksum matches the official v4.0 release tarball.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify SHA256 checksum of the source tarball matches the recipe
# Expected: Should output the same checksum as specified in meta.yaml

# Download the tarball and calculate its checksum
curl -sL https://github.com/rgcgithub/regenie/archive/v4.0.tar.gz | sha256sum

Length of output: 399


Script:

#!/bin/bash
# Let's verify the recipe content and source URL pattern first
cat recipes/regenie/meta.yaml

# Then check if there's an official release on GitHub
gh release view rgcgithub/regenie/v4.0 --json assets,tagName,url

Length of output: 2326


Script:

#!/bin/bash
# Let's check if the repository and release exist with correct casing
gh repo view rgcgithub/regenie

# Also check for any releases to verify the correct repository name
gh release list --repo rgcgithub/regenie

# Alternatively, let's check if it's under a different organization
gh repo search "regenie" --owner RGCGITHUB --json nameWithOwner,url

Length of output: 10682


Script:

#!/bin/bash
# Let's verify the checksum of the v4.0 release tarball now that we confirmed it exists
curl -sL https://github.com/rgcgithub/regenie/archive/refs/tags/v4.0.tar.gz | sha256sum

# Also check if the patch is still needed for v4.0
cat recipes/regenie/patches/0015-update-cmakelist.txt-for-v3.6.patch

Length of output: 13941

@martin-g martin-g merged commit 0d50fcf into master Nov 7, 2024
6 checks passed
@martin-g martin-g deleted the bump/regenie branch November 7, 2024 19:41
This was referenced Nov 12, 2024
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2 participants