bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
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Add recipe for stxtyper v1.0.25 #51792

Closed mencian closed 2 days ago

mencian commented 2 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.

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coderabbitai[bot] commented 2 days ago
📝 Walkthrough ## Walkthrough This pull request introduces two significant changes related to the `stxtyper` package within the `recipes/stxtyper/` directory. Firstly, a new shell script file named `build.sh` has been added. This script is intended to streamline the build process by setting various environment variables, including `INCLUDES`, `LIBPATH`, `CXXFLAGS`, `CPPFLAGS`, and `LDFLAGS`, which are essential for the compilation of the software. The script utilizes the `make` command with parallel execution to optimize build time and subsequently installs the built package into a specified directory. Secondly, a new metadata file called `meta.yaml` has been created for the `stxtyper` package. This file outlines the package's configuration details, including its name, version, SHA256 checksum, source URL, build and run requirements, and a test command to verify installation. The `meta.yaml` file serves to manage dependencies and encapsulates all necessary information for building, running, and testing the `stxtyper` package. ## Possibly related PRs - **#51485**: This PR updates the `ncbi-stxtyper` package to version 1.0.25, which is directly related to the main PR that introduces a new build script for the `stxtyper` package, indicating a connection in terms of package management and versioning. ## Suggested labels `please review & merge`, `new version`

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evolarjun commented 1 day ago

@mencian It looks like this may be a duplicate of the ncbi-stxtyper recipe we are maintaining. Is there something we can improve about the ncbi-stxtyper recipe to meet your needs?

mencian commented 1 day ago

This was a mistake on my part, I've reverted this PR here.

evolarjun commented 1 day ago

@mencian Thanks! If you are using StxTyper let us know if you have any comments or questions.