Update chopper for M3s

[wdecoster]

This PR adds some changes to make this work on mac M3s, based on wdecoster/chopper#40

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[coderabbitai]

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request modifies the meta.yaml file for the chopper package, updating the version number from 0.9.0 to 1 and changing the build number from 0 to 1. New fields are added under the about section, including dev_url, doc_url, and notes, which provide links to the development repository, documentation, and a note about native support for Apple Silicon processors. The existing fields in the about section remain unchanged.

Possibly related PRs

• tracs: add aarch64/arm64 builds #50103: The changes in the meta.yaml file for the tracs package include an update to the version and build number, similar to the updates made in the meta.yaml file for the chopper package in the main PR.
• perl-convert-binary-c: add aarch64/arm64 build #51107: The perl-convert-binary-c package's meta.yaml file also sees a version and build number update, paralleling the changes made in the chopper package's meta.yaml.
• gxf2bed: add aarch64/arm64 builds #51120: The gxf2bed package's meta.yaml file includes a build number increment and additional platforms, which aligns with the modifications in the chopper package's meta.yaml.
• longreadsum: add aarch64/arm64 builds #51121: The longreadsum package's meta.yaml file features a build number increment and additional platforms, similar to the changes in the chopper package.
• r-cobrar: add aarch64/arm64 builds #51203: The r-cobrar package's meta.yaml file has a build number increment and additional platforms, reflecting the updates made in the chopper package's meta.yaml.
• devider: add aarch64/arm64 builds #51370: The gnparser package's meta.yaml file includes a build number increment and additional platforms, which is consistent with the changes in the chopper package.
• d4binding: add aarch64/arm64 builds #51598: The d4binding package's meta.yaml file features a build number increment and additional platforms, paralleling the modifications in the chopper package's meta.yaml.
• Build kmer-jellyfish for other platforms #51683: The kmer-jellyfish package's meta.yaml file includes a build number increment and additional platforms, similar to the updates made in the chopper package's meta.yaml.

Suggested labels

osx-arm64

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📥 Commits

Files that changed from the base of the PR and between f27565a and 546cd82.

📒 Files selected for processing (1)

• recipes/chopper/meta.yaml (2 hunks)

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

• recipes/chopper/meta.yaml

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[coderabbitai]

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (2)

recipes/chopper/meta.yaml (2)

11-15: Consider removing redundant skip condition

The skip: false # [not (linux-64 or osx)] condition is redundant with the explicit platforms list below it. The platforms list is a clearer way to specify supported platforms.

-  skip: false # [not (linux-64 or osx)]

---

48-48: Consider linking to more comprehensive documentation

The doc_url currently points to the README. Consider creating and linking to more comprehensive documentation, especially given the new platform support.

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📥 Commits

Files that changed from the base of the PR and between f83e9c7 and 4c3ad1e.

📒 Files selected for processing (1)

• recipes/chopper/meta.yaml (2 hunks)

🔇 Additional comments (1)

recipes/chopper/meta.yaml (1)

Line range hint 35-37: Verify the need for clang as a runtime dependency

The package includes clang as a runtime dependency, which is unusual. Typically, clang is only needed during build time for Rust packages. Please verify if this is intentionally required at runtime.

[coderabbitai]

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)

recipes/chopper/meta.yaml (1)

42-45: Documentation and metadata additions look good.

The added URLs and notes provide valuable information about the package's capabilities and resources.

Consider expanding the notes to include specific version requirements or limitations, if any:

  notes: |
-    includes native support for Apple Silicon (M1/M2/M3) processors
+    includes native support for Apple Silicon (M1/M2/M3) processors since version X.X.X

📜 Review details

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📥 Commits

Files that changed from the base of the PR and between 4c3ad1e and f27565a.

📒 Files selected for processing (1)

• recipes/chopper/meta.yaml (2 hunks)

🔇 Additional comments (2)

recipes/chopper/meta.yaml (2)

9-10: Build configuration is well structured.

The use of run_exports with appropriate pinning helps prevent API/ABI breakage, following best practices.

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47-50: Platform support changes look good.

The addition of ARM platforms (linux-aarch64 and osx-arm64) aligns with the PR objective of enabling M3 support.

Let's verify the build requirements are sufficient for ARM platforms:

[wdecoster]

@martin-g the test now failed, could you identify why?

[martin-g]

The Linux ARM64 build fails due to:

 error[E0606]: casting `&*mut minimap2_sys::mm_idx_t` as `*const minimap2_sys::mm_idx_t` is invalid�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT)    --> /opt/conda/conda-bld/chopper_1730197518455/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimap2-0.1.20+minimap2.2.28/src/lib.rs:834:25�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT)     |�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT) 834 |                         self.idx.as_ref().unwrap() as *const mm_idx_t,�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT)     |                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT) �[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT) error[E0606]: casting `&*mut minimap2_sys::mm_idx_t` as `*const minimap2_sys::mm_idx_t` is invalid�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT)    --> /opt/conda/conda-bld/chopper_1730197518455/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimap2-0.1.20+minimap2.2.28/src/lib.rs:974:41�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT)     |�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT) 974 | ...                   &self.idx.unwrap() as *const mm_idx_t,�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT)     |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT) �[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT) error[E0606]: casting `&*mut minimap2_sys::mm_idx_t` as `*const minimap2_sys::mm_idx_t` is invalid�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT)     --> /opt/conda/conda-bld/chopper_1730197518455/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimap2-0.1.20+minimap2.2.28/src/lib.rs:1021:41�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT)      |�[0m
10:28:15 �[32mBIOCONDA INFO�[0m (OUT) 1021 | ...                   &self.idx.unwrap() as *const mm_idx_t,�[0m

i.e. the minimap2 crate uses SSE intrinsics. I will remove the ARM64 platforms.