bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Update seismic-rna dependencies #51693

Closed matthewfallan closed 3 days ago

matthewfallan commented 4 days ago

Describe your pull request here


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:
    - ...

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 4 days ago
📝 Walkthrough
📝 Walkthrough
📝 Walkthrough ## Walkthrough This pull request introduces modifications to the `build.sh` script and the `meta.yaml` file for the `seismic-rna` package. In `build.sh`, the order of options in the `set` command is changed from `set -euxo pipefail` to `set -eux -o pipefail`, which does not alter the script's functionality but adjusts the specification of options. Additionally, a formatting issue is noted as there is no newline at the end of the file. In `meta.yaml`, the build number is incremented from `0` to `1`. The `requirements` section sees significant changes: the `pip` dependency is removed, `fastqc` is replaced with `fastp` (with a version constraint of `>=0.23.0`), and both `matplotlib-base` and `cutadapt` dependencies are removed from the `run` requirements. The structure of the file remains unchanged in other sections. ## Possibly related PRs - **#51320**: This PR updates the `seismic-rna` package to version 0.21.0, which is directly related to the main PR that modifies the `build.sh` and `meta.yaml` files for the same package. - **#51493**: This PR updates the `seismic-rna` package to version 0.21.1, which is also directly related to the main PR as it involves changes to the `meta.yaml` file for the same package. ## Suggested labels `please review & merge`, `new version` ## Suggested reviewers - bgruening - adamhospital

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