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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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salmon: add arm64 build #51788

Closed mencian closed 2 days ago

mencian 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
📝 Walkthrough
📝 Walkthrough ## Walkthrough The pull request introduces modifications to the `build.sh` script and the `meta.yaml` file for the `salmon` package. In `build.sh`, environment variables for `LDFLAGS` and `CFLAGS` have been updated to include library paths and optimization flags, particularly for macOS systems. New compiler flags and CMake parameters have been added, enhancing the build configuration for various dependencies and ensuring compatibility with the Staden library. The `meta.yaml` file sees an increment in the build number from 2 to 3 and includes several new dependencies such as `pkg-config`, `staden_io_lib`, `libgff`, `cereal`, `libiconv`, and `libdeflate`. Additionally, the file has been updated to reflect support for the `osx-arm64` platform and includes a new maintainer. Overall, these changes aim to improve the build process and dependency management for the `salmon` package across different operating systems. ## Possibly related PRs - **#50103**: Related due to modifications in the `meta.yaml` file that include platform-specific dependencies, similar to changes made in the `meta.yaml` of the main PR. - **#50996**: Changes in the `meta.yaml` file to add support for additional platforms, which aligns with the updates in the main PR's `meta.yaml`. - **#50997**: Similar updates to the `meta.yaml` file for platform support, reflecting changes made in the main PR. - **#51067**: The addition of platform support in the `meta.yaml` file is relevant to the changes in the main PR. - **#51098**: The `meta.yaml` updates for platform compatibility are related to the changes in the main PR. - **#51161**: The addition of support for additional platforms in the `meta.yaml` file aligns with the changes in the main PR. - **#51203**: The updates to the `meta.yaml` file for platform support are relevant to the main PR. - **#51221**: Changes in the `meta.yaml` file for platform support are similar to those in the main PR. - **#51267**: The addition of platform support in the `meta.yaml` file is relevant to the changes in the main PR. - **#51281**: The updates to the `meta.yaml` file for platform support are related to the changes in the main PR. - **#51425**: The addition of platform support in the `meta.yaml` file is relevant to the changes in the main PR. - **#51448**: The updates to the `meta.yaml` file for platform support are similar to those in the main PR. - **#51598**: The addition of platform support in the `meta.yaml` file is relevant to the changes in the main PR. - **#51661**: The updates to the `meta.yaml` file for platform support are similar to those in the main PR. - **#51706**: The introduction of a new recipe with platform support in the `meta.yaml` file is relevant to the changes in the main PR. ## Suggested labels `aarch64`
📜 Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
📥 Commits Files that changed from the base of the PR and between ffe9feb3c8d7dac41f0175547ac575dc59d5216e and c6c2b68fdc5af261eb415255c34e6056033ad811.
📒 Files selected for processing (1) * recipes/salmon/build.sh (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1) * recipes/salmon/build.sh

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