bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Enforce openjdk 21, part 3/4 (Linx, Neo, Orange, Pave, Peach) #52272

Closed luan-n-nguyen closed 5 days ago

luan-n-nguyen commented 5 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.
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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 5 days ago
📝 Walkthrough ## Walkthrough This pull request includes modifications to the `meta.yaml` files for five different packages: `hmftools-linx`, `hmftools-neo`, `hmftools-orange`, `hmftools-pave`, and `hmftools-peach`. The changes primarily involve updating the version numbers and build numbers for each package. Specifically, the build numbers have been incremented, reflecting new build iterations. Additionally, the run requirements for the `openjdk` dependency have been updated across all packages, changing the constraint from `>=8` to `>=8,<=21`, which restricts the maximum version of OpenJDK that can be utilized. The SHA256 checksums remain unchanged, and other sections of the `meta.yaml` files, such as source URLs, test commands, and metadata, are intact. ## Possibly related PRs - **#51294**: This PR updates the `hmftools-linx` package, which is directly related to the main PR that also modifies the `hmftools-linx` package's `meta.yaml` file. - **#51698**: This PR includes changes to the `hmftools-linx` package, specifically updating the version and build number, which aligns with the changes made in the main PR. - **#51831**: This PR modifies the `hmftools-redux` package to restrict the `openjdk` version, similar to the main PR's update of the `openjdk` requirement in `hmftools-linx`. - **#52122**: This PR also updates the `hmftools-redux` package to set the `openjdk` version constraint, reflecting a similar change to that in the main PR. ## Suggested labels `please review & merge` ## Suggested reviewers - martin-g - adamhospital

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luan-n-nguyen commented 5 days ago

@BiocondaBot please add label