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smalt: add aarch64/arm64 builds #51104

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@martin-g martin-g commented Oct 2, 2024

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Summary by CodeRabbit

  • New Features

    • Updated the build number for the smalt package.
    • Added support for additional platforms: linux-aarch64 and osx-arm64.
    • Introduced a new dependency specification for the smalt subpackage.
  • Bug Fixes

    • Corrected indentation in the requirements section.

@martin-g martin-g added aarch64 Related to adding linux-aarch64 support osx-arm64 Related to adding osx-arm64 support labels Oct 2, 2024
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📥 Commits

Files that changed from the base of the PR and between 956a7ea and 8bb8633.

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request modifies the meta.yaml file for the smalt package. Key changes include an increment in the build number from 2 to 3, the addition of a run_exports key specifying a dependency on the smalt subpackage, and updates to the source section to include a URL and MD5 checksum. The requirements section has a corrected indentation, and a new additional-platforms key is added, listing linux-aarch64 and osx-arm64. Other sections remain unchanged.

Changes

File Change Summary
recipes/smalt/meta.yaml - Build number updated from 2 to 3.
- Added run_exports with dependency on smalt.
- Updated source with URL and MD5 checksum.
- Corrected indentation for - {{ compiler('c') }}.
- Added additional-platforms for linux-aarch64 and osx-arm64.

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Actionable comments posted: 1

🧹 Outside diff range and nitpick comments (2)
recipes/smalt/meta.yaml (2)

6-7: LGTM! Consider using SHA256 instead of MD5.

The addition of the source URL and checksum is correct and matches the package version. However, consider using SHA256 instead of MD5 for improved security, as MD5 is considered cryptographically weak.


Line range hint 14-29: Consider updating Python requirement.

While not part of the current changes, it's worth noting that this package requires Python 2.6 or higher but less than 3. Given that Python 2 is no longer supported, consider updating the package to support Python 3 if possible.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 5ca5963 and 956a7ea.

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

38-40: LGTM! Verify build process for new platforms.

The addition of linux-aarch64 and osx-arm64 platforms aligns with the PR objective. This will allow the package to be built for ARM-based systems, increasing its compatibility.

To ensure the package can be built correctly for these new platforms, please verify:

  1. The build process on these platforms.
  2. Any platform-specific dependencies or configurations needed.

You may want to run test builds on these platforms to confirm everything works as expected.

Comment on lines +10 to +12
number: 3
run_exports:
- {{ pin_subpackage('smalt', max_pin="x.x") }}
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💡 Codebase verification

Based on the search results, it's clear that the changes to the smalt package could potentially impact multiple other packages. Specifically, biotradis, iva, quatradis, and shiver all list smalt as a dependency in their meta.yaml files.

Recommendation: Carefully review the changes made to smalt and consider testing the dependent packages.

Given the widespread use of smalt as a dependency, it's crucial to ensure that the changes made don't introduce any breaking changes or unexpected behavior in the dependent packages. Consider the following steps:

  1. Review the specific changes made to the smalt package.
  2. Test the dependent packages (biotradis, iva, quatradis, and shiver) with the updated smalt version to ensure compatibility.
  3. If possible, communicate with the maintainers of these dependent packages to inform them of the changes and encourage testing.

This approach will help maintain the stability of the ecosystem and prevent potential issues down the line.

🔗 Analysis chain

LGTM! Consider clarifying the run_exports pinning.

The build number increment is correct. The addition of run_exports is a good practice for ensuring compatibility with downstream recipes. However, consider clarifying why the max_pin is set to "x.x". Is this based on the package's versioning scheme or known compatibility issues?

To verify the impact of this change, let's check for any recipes that depend on smalt:


To properly assess the impact of the changes to the smalt package, I need to check if other packages directly depend on it. I'll search for smalt dependencies in the identified meta.yaml files.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for recipes that depend on smalt
# Expected result: List of recipes (if any) that depend on smalt

rg -l 'smalt' recipes/*/meta.yaml

Length of output: 319519


Script:

#!/bin/bash
# Search for smalt dependencies in related meta.yaml files
rg -i "smalt" recipes/shiver/meta.yaml recipes/quatradis/meta.yaml recipes/iva/meta.yaml recipes/biotradis/meta.yaml

Length of output: 372

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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martin-g commented Oct 2, 2024

The ARM64 builds fail with:

Could not solve for environment specs
12:49:06 BIOCONDA INFO (OUT) The following packages are incompatible
12:49:06 BIOCONDA INFO (OUT) ├─ python >=2.6,<3  is installable with the potential options
12:49:06 BIOCONDA INFO (OUT) │  ├─ python 2.7.15 would require
12:49:06 BIOCONDA INFO (OUT) │  │  └─ openssl >=1.1.1a,<1.1.2a , which can be installed;
12:49:06 BIOCONDA INFO (OUT) │  └─ python 2.7.15 would require
12:49:06 BIOCONDA INFO (OUT) │     └─ openssl >=1.0.2p,<1.0.3a , which does not exist (perhaps a missing channel);
12:49:06 BIOCONDA INFO (OUT) └─ samtools is not installable because there are no viable options
12:49:06 BIOCONDA INFO (OUT)    ├─ samtools [1.19.2|1.20] would require
12:49:06 BIOCONDA INFO (OUT)    │  └─ htslib [>=1.19.1,<1.20.0a0 |>=1.20,<1.21.0a0 ] but there are no viable options
12:49:06 BIOCONDA INFO (OUT)    │     ├─ htslib [1.19.1|1.20] would require
12:49:06 BIOCONDA INFO (OUT)    │     │  └─ openssl >=3.2.1,<4.0a0 , which conflicts with any installable versions previously reported;
12:49:06 BIOCONDA INFO (OUT)    │     └─ htslib 1.20 would require
12:49:06 BIOCONDA INFO (OUT)    │        └─ openssl >=3.3.1,<4.0a0 , which conflicts with any installable versions previously reported;
12:49:06 BIOCONDA INFO (OUT)    └─ samtools 1.21 would require
12:49:06 BIOCONDA INFO (OUT)       └─ htslib >=1.21,<1.22.0a0 , which requires
12:49:06 BIOCONDA INFO (OUT)          └─ openssl >=3.3.2,<4.0a0 , which conflicts with any installable versions previously reported

The package needs to be updated to Python 3.x

@martin-g martin-g closed this Oct 2, 2024
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