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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Update pyopenms to 3.2.0 #51753

Closed BioGeek closed 2 days ago

BioGeek commented 2 days ago

Update pyopenms to 3.2.0, continuation of #51014

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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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 2 days ago
📝 Walkthrough
📝 Walkthrough ## Walkthrough This pull request includes several changes related to the `pyopenms` package. The file `build_failure.linux-64.yaml` has been deleted, which contained metadata about a previous build failure, including specific dependencies and errors encountered during the build process. The `conda_build_config.yaml` file has been updated to support Python version `3.12.*` and includes a new entry for `cpython`, along with an additional NumPy version `1.26.*`. The `meta.yaml` file has undergone significant updates, changing the package version from `3.1.0` to `3.2.0`, updating the source URL to a hardcoded link, and modifying the MD5 checksum. Additionally, several dependencies have been updated, including `libopenms` and `qt-main`, along with the introduction of new dependencies `eigen` and `icu`. These changes collectively enhance the versioning and dependency management of the `pyopenms` package. ## Possibly related PRs - **#51331**: This PR updates the `libopenms` dependency in the `openms-meta/meta.yaml` file, which is relevant to the changes in the main PR that involve the `pyopenms` package and its dependencies, particularly `libopenms`. - **#51121**: This PR introduces builds for the `longreadsum` package targeting the aarch64/arm64 architecture, which may relate to the dependency management and build configurations discussed in the main PR regarding `pyopenms`. - **#51054**: This PR updates the `k8/meta.yaml` file to allow Python versions 3.8 and later, which is relevant as it also deals with dependency management similar to the changes in the main PR. - **#51346**: This PR updates the `cenote-taker3` package, which includes changes to dependencies and versioning, similar to the updates made in the main PR for `pyopenms`. - **#51528**: This PR updates the `biobb_cp2k` package, which includes changes to dependencies and versioning, aligning with the dependency updates in the main PR for `pyopenms`. ## Suggested labels `please review & merge`, `new version`, `autobump` ## Suggested reviewers - mencian
📜 Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
📥 Commits Files that changed from the base of the PR and between 7b5175d17616475750ebea8830acb8d1fe87c0d2 and d8645223c5b4d7a4491b70f956fb5b962ff1f581.
📒 Files selected for processing (1) * recipes/pyopenms/meta.yaml (4 hunks)
🚧 Files skipped from review as they are similar to previous changes (1) * recipes/pyopenms/meta.yaml

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bgruening commented 2 days ago

Thanks!

jonasscheid commented 2 days ago

Thank you!!