Update cmaple to 1.1.0

[BiocondaBot]

Update cmaple: 1.0.0 → 1.1.0

Info	Link or Description
Recipe	recipes/cmaple (click to view/edit other files)
Summary	MAximum Parsimonious Likelihood Estimation in C/C++.
Home	https://github.com/iqtree/cmaple
Releases	https://github.com/iqtree/cmaple/tags
Recipe Maintainer(s)	@corneliusroemer
Author	@iqtree

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This pull request was automatically generated (see docs).

[coderabbitai]

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request involves modifications to the meta.yaml file for the cmaple package. Key changes include an increment in the version number from "1.0.0" to "1.1.0", and an update to the SHA256 checksum to "72079ac3881840ce6a6d45603202a2ab9a399aa8ebaf51fbdcd85337696e4435". Additionally, the build number has been adjusted from 1 to 0. The source URL has been updated to reflect the new version, changing from v1.0.0 to v1.1.0. The summary text has been modified to include a period at the end, and a previous comment regarding ARM builds has been removed. The overall structure, including requirements and about sections, remains unchanged.

The build.sh script has been modified to enhance its functionality, particularly for macOS systems. The conditional check for macOS has been improved, and specific configuration options for CMake have been introduced. The CMake command now includes -DCMAKE_BUILD_TYPE=Release for clarity in build configuration.

Additionally, the deleted CMakeLists.txt file contained various settings for compiling the software, including project name, version, and platform-specific compiler options.

Possibly related PRs

• mashmap: add aarch64 build #51161: The meta.yaml file for the mashmap package was updated, including a version change, similar to the version update in the cmaple package's meta.yaml.
• added arm and aarch64 builds #51184: The meta.yaml file for the mbgc package was modified to include a version update and additional platforms, which parallels the version update in the cmaple package's meta.yaml.
• Update haplomap to 0.1.2 #51305: The meta.yaml file for the haplomap package was updated with a new version and SHA256 checksum, similar to the changes made in the cmaple package's meta.yaml.
• Update mtgrasp to 1.1.8 #51491: The meta.yaml file for the mtgrasp package was updated to reflect a new version and SHA256 checksum, akin to the updates in the cmaple package's meta.yaml.
• Update crabs to 1.0.4 #51645: The meta.yaml file for the crabs package was modified to update the version and SHA256 checksum, similar to the changes in the cmaple package's meta.yaml.
• Update crabs to 1.0.6 #51694: The meta.yaml file for the crabs package was updated with a new version and SHA256 checksum, reflecting similar changes made in the cmaple package's meta.yaml.
• Update pbstarphase to 1.0.0 #51735: The meta.yaml file for the pbstarphase package was updated with a new version and SHA256 checksum, paralleling the changes in the cmaple package's meta.yaml.
• Update pbmm2 to 1.16.0 #51791: The meta.yaml file for the pbmm2 package was updated with a new version and SHA256 checksum, similar to the updates in the cmaple package's meta.yaml.
• Update r-mfassignr to 1.1.2 #51813: The meta.yaml file for the r-mfassignr package was updated with a new version and SHA256 checksum, akin to the changes in the cmaple package's meta.yaml.
• Update aletsch to 1.1.3 #51828: The meta.yaml file for the aletsch package was updated with a new version and SHA256 checksum, similar to the updates in the cmaple package's meta.yaml.
• Update tirmite to 1.1.6 #51842: The meta.yaml file for the tirmite package was updated with a new version and SHA256 checksum, paralleling the changes in the cmaple package's meta.yaml.
• Update gsmap to 1.71.2 #51854: The meta.yaml file for the gsmap package was updated with a new version and SHA256 checksum, similar to the changes in the cmaple package's meta.yaml.

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between fcc1a30 and c193948.

📒 Files selected for processing (3)

• recipes/cmaple/build.sh (2 hunks)
• recipes/cmaple/meta.yaml (3 hunks)
• recipes/cmaple/patch (0 hunks)

💤 Files with no reviewable changes (1)

• recipes/cmaple/patch

🚧 Files skipped from review as they are similar to previous changes (1)

• recipes/cmaple/meta.yaml

🔇 Additional comments (4)

recipes/cmaple/build.sh (4)

11-11: LGTM: Improved shell syntax for Darwin check.

The change to use [[ instead of [ for string comparison is a good improvement. The double bracket syntax provides more robust string comparison and is the preferred modern bash syntax.

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18-20: LGTM: Proper handling of macOS-specific CMake configuration.

The addition of CONFIG_ARGS with -DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER for macOS is a good practice. This prevents potential issues with system frameworks and app bundles interfering with the build process.

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33-38: LGTM: Improved CMake configuration clarity and organization.

The changes improve the CMake configuration by:

1. Explicitly setting build type to Release
2. Better organizing the configuration options
3. Properly incorporating the new CONFIG_ARGS variable

The -Wno-dev -Wno-deprecated --no-warn-unused-cli flags help reduce noise during the build process.

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Line range hint 1-48: Verify the build configuration changes.

Let's verify that these build script changes align with the package update requirements.

✅ Verification successful

Let me analyze the build script changes in the context of the review comment.

The build script changes in recipes/cmaple/build.sh show:

1. AVX flags are being disabled with -mno-avx -mno-avx2 and replaced with specific architecture flags -march=nocona -mtune=haswell
2. CMake build type is set to Release
3. Framework and AppBundle finding is disabled on macOS
4. Proper compiler paths and flags are set
5. Google Test is disabled with -DBUILD_GMOCK=OFF -DINSTALL_GTEST=OFF

These changes are standard build configuration practices for conda-forge/bioconda packages:

• Disabling AVX for broader compatibility (especially for Rosetta2 on Apple Silicon)
• Using Release build type for optimized binaries
• Proper compiler configuration
• Disabling tests to avoid unnecessary dependencies

The build configuration changes are appropriate and follow best practices for conda packages.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the build configuration changes align with upstream

# Check if there are any specific build requirements in the upstream release
gh release view v1.1.0 --repo corneliusroemer/cmaple

# Look for any build-related changes in CMakeLists.txt
rg -A 5 "CMAKE_BUILD_TYPE|CMAKE_FIND_FRAMEWORK|CMAKE_FIND_APPBUNDLE" 

Length of output: 257645

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