bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Enforce openjdk 21, part 4/4 (Purple, Sage, Sigs, Virusinterpreter) #52274

Open luan-n-nguyen opened 1 day ago

luan-n-nguyen commented 1 day 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 1 day ago
📝 Walkthrough ## Walkthrough This pull request introduces modifications to the `meta.yaml` files for multiple `hmftools` packages. The changes include updates to version numbers and build numbers across the packages. Specifically, the `hmftools-purple` package's build number is increased from 2 to 3, and its OpenJDK requirement is revised to a version range of `>=8,<=21`. The `hmftools-sage` package sees its version updated to "4.0_beta.3" and its build number incremented from 3 to 4, with a similar OpenJDK requirement adjustment. The `hmftools-sigs` package's build number is updated from 0 to 1, along with a change in the OpenJDK requirement to `>=8,<=21`. Lastly, the `hmftools-virus-interpreter` package has its version set to "3.7_beta," its build number increased from 0 to 1, and the OpenJDK requirement adjusted to the same version range. The source URLs and other metadata remain unchanged across these packages. ## Possibly related PRs - **#51294**: Updates the `hmftools-purple` package's `meta.yaml` file, modifying the `openjdk` requirement to `>=8,<=21`. - **#51698**: Similar to the main PR, this PR updates the `hmftools-purple` package's `meta.yaml` file to specify the `openjdk` requirement as `>=8,<=21`. - **#51800**: Modifies the `hmftools-purple` package's `meta.yaml` file, changing the `openjdk` requirement to `>=8,<=21`. - **#52122**: Updates the `hmftools-redux` package's `meta.yaml` file to set the `openjdk` requirement to `>=8,<=21`. ## Suggested labels `please review & merge` ## Suggested reviewers - martin-g - mencian

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luan-n-nguyen commented 1 day ago

@BiocondaBot please add label

bgruening commented 1 day ago

@luan-n-nguyen can you remind me please why this is needed? Is JDK22+ breaking things?