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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Update lofreq to add bcftools dependency #51672

Closed natefoo closed 6 days ago

natefoo commented 6 days ago

51417 introduced additional post-2.1.5 development changes to lofreq 2.1.5. These included a new dependency on bcftools, which was not a dependency of the package. Without this dependency the current build of lofreq is broken for all invocations of lofreq call-parallel.

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

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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:
    - ...

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Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
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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) }}

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coderabbitai[bot] commented 6 days ago
📝 Walkthrough ## Walkthrough The pull request introduces changes to the `meta.yaml` file for the `lofreq` package. The build number has been incremented from `13` to `14`, indicating a new build iteration, although the version number remains unchanged at `2.1.5`. A new dependency, `bcftools`, has been added to the `run` requirements, indicating that this tool is now necessary for the package's execution. Additionally, a test command for `bcftools --help` has been included in the `test` section to ensure the functionality of `bcftools` is verified during testing. The other sections of the `meta.yaml` file, including `source`, `about`, and `extra`, remain unchanged, maintaining the overall structure of the file while implementing the specified modifications. ## Possibly related PRs - **#51278**: This PR updates the `bcftools` dependency version in the `harpy` package, which is directly related to the addition of `bcftools` as a required dependency in the main PR for the `lofreq` package. ## Suggested labels `please review & merge` ## Suggested reviewers - mencian - martin-g

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