bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
1.64k stars 3.27k forks source link

Build bindash on osx #51661

Closed mencian closed 6 days ago

mencian commented 6 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.

Bot commands for PR management

Please use the following BiocondaBot commands: Everyone has access to the following BiocondaBot commands, which can be given in a comment:
@BiocondaBot please update Merge the master branch into a PR.
@BiocondaBot please add label Add the please review & merge label.
@BiocondaBot please fetch artifacts Post links to CI-built packages/containers.
You can use this to test packages locally.
Note that the @BiocondaBot please merge command is now depreciated. Please just squash and merge instead. Also, the bot watches for comments from non-members that include `@bioconda/` and will automatically re-post them to notify the addressed ``.
coderabbitai[bot] commented 6 days ago
📝 Walkthrough ## Walkthrough The pull request introduces modifications to the `build.sh` and `meta.yaml` files for the Bindash project. In `build.sh`, environment variables such as `INCLUDES`, `LIBPATH`, and `LDFLAGS` are set to define include and library paths based on the `PREFIX` variable. A conditional block is added to adjust `CONFIG_ARGS` for macOS, disabling certain CMake features. The CMake command is updated to utilize `-S` and `-B` options for source and build directories, alongside additional flags for installation prefix and C++ compiler settings. The `make` command remains mostly unchanged, preserving its verbosity and parallel execution. In `meta.yaml`, the version number is incremented from 2 to 3, and the `run` requirements see the removal of `zlib`. Formatting updates are made to the `home`, `license`, `dev_url`, and `doc_url` fields for consistency, with the addition of a new `doc_url` pointing to the README for the specific version. The `extra` section is updated to include `osx-arm64` in the supported platforms list. ## Possibly related PRs - **#50991**: This PR adds support for `osx-arm64`, which is relevant as the main PR also includes changes to support this platform in the `meta.yaml` file. - **#51176**: This PR updates the `meta.yaml` file to include `osx-arm64` in the additional platforms, similar to the changes made in the main PR. - **#51161**: This PR adds support for `osx-arm64` in the `mashmap` package, aligning with the main PR's focus on enhancing compatibility for this architecture. - **#51505**: This PR adds `osx-arm64` as an additional platform in the `diamond` package, which is consistent with the main PR's updates to support this platform. - **#51515**: This PR also includes updates to the `diamond` package, which shares a focus on enhancing compatibility with `osx-arm64`, similar to the main PR's changes. ## Suggested labels `please review & merge`, `osx-arm64`

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