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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Update apply patch to bwamem2 to add ARM support #51771

Open FriederikeHanssen opened 2 days ago

FriederikeHanssen commented 2 days ago

Describe your pull request here

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes. This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe. If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation). Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x) {{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions {{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions {{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning {{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

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coderabbitai[bot] commented 2 days ago

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📥 Commits Reviewing files that changed from the base of the PR and between 7f27cd4450be3cede12780c7fd0385aaab19084b and 938654d130ef51c8c6fe1c3b053cf118e18da281.
📝 Walkthrough
📝 Walkthrough
📝 Walkthrough
📝 Walkthrough
📝 Walkthrough ## Walkthrough The pull request introduces significant modifications to the BWA-MEM2 project, primarily focusing on improving its functionality and structure. A new submodule, `ext/simde`, is added and integrated into the build process through updates to the `Makefile`, which now includes the `CPPFLAGS` definition for `MATE_SORT` and expands the `INCLUDES` path to include headers from the new submodule. The handling of SIMD operations is also updated, replacing direct inclusions of `` and `` with `simde/x86/avx2.h` and `simde/x86/sse4.1.h` for better compatibility across architectures. Several inline functions related to SSE2 operations are removed in favor of SIMD-compatible alternatives. Additionally, method signatures in multiple source files are updated to reflect changes in parameters and internal logic. The code also undergoes formatting changes, including the removal of unnecessary comments and improved error handling practices. ## Changes | File Path | Change Summary | |---------------------------------------------|----------------------------------------------------------------------------------------------------| | `recipes/bwa-mem2/Makefile.patch` | Added new submodule `ext/simde`, updated `CPPFLAGS` for `MATE_SORT`, expanded `INCLUDES` path. | | `src/fastmap.cpp`, `src/bwamem.cpp` | Updated multiple method signatures to change parameters and internal logic; removed inline SSE2 functions. | | `recipes/bwa-mem2/meta.yaml` | Updated version to "2.2.1", incremented build number from 5 to 7, added additional platforms. | ## Possibly related PRs - **#49740**: The changes in the `meta.yaml` file for `kmer-db` include the addition of `additional-platforms: - linux-aarch64 - osx-arm64`, which aligns with the architecture compatibility enhancements in the main PR for `bwa-mem2`. - **#50996**: The `meta.yaml` updates for `tRNAscan-SE` also introduce support for `linux-aarch64` and `osx-arm64`, similar to the architecture support added in the main PR. - **#51120**: The `gxf2bed` package's `meta.yaml` includes new entries for `linux-aarch64` and `osx-arm64`, reflecting the same architectural support focus as seen in the main PR. - **#51121**: The `longreadsum` package's `meta.yaml` adds support for `linux-aarch64` and `osx-arm64`, which is consistent with the architecture enhancements in the main PR. - **#51203**: The `r-cobrar` package's `meta.yaml` updates include support for `linux-aarch64` and `osx-arm64`, paralleling the architecture compatibility changes in the main PR. - **#51370**: The `devider` package's `meta.yaml` introduces support for `linux-aarch64`, aligning with the architecture enhancements in the main PR. - **#51376**: The `gnparser` package's `meta.yaml` adds support for `linux-aarch64` and `osx-arm64`, consistent with the architecture focus of the main PR. - **#51505**: The `diamond` package's `meta.yaml` includes `linux-aarch64` and `osx-arm64` under `additional-platforms`, reflecting the same architectural support as in the main PR. - **#51598**: The `d4binding` package's `meta.yaml` adds support for `linux-aarch64`, which is in line with the architecture enhancements in the main PR. ## Suggested labels `aarch64`, `osx-arm64`, `please review & merge` ## Suggested reviewers - rpetit3

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rpetit3 commented 2 days ago

@biocondabot please fetch artifacts

BiocondaBot commented 2 days ago

No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped.