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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Add coptr #51764

Closed ramirobarrantes closed 2 days ago

ramirobarrantes 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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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 ``.
ramirobarrantes commented 2 days ago

@BiocondaBot Please add label

coderabbitai[bot] commented 2 days ago
📝 Walkthrough ## Walkthrough The pull request introduces a new file named `meta.yaml` for the `coptr` software package. This file establishes the package's configuration, setting the name to "coptr" and the version to "1.1.4". It includes a source section with a URL for downloading the package from PyPI and a SHA256 checksum for integrity verification. The build section specifies that the `cli` function from the `coptr.cli` module serves as the main entry point and that the package will be installed using Python's pip without dependencies or build isolation. The requirements section lists the necessary dependencies for both host and runtime environments, including specific versions for Python, setuptools, wheel, pip, numpy, pysam, scipy, and matplotlib-base. Additionally, the test section outlines commands to verify the installation and functionality of the package. Metadata about the package, such as its homepage, summary, licensing information, and maintainers, is also included. ## Possibly related PRs - **#50973**: The `meta.yaml` file for the `pgrc` package also defines package configuration, including dependencies and entry points, similar to the changes made in the `coptr` package's `meta.yaml`. - **#51268**: The `meta.yaml` for the `patchify` package introduces a new package configuration, including dependencies and entry points, akin to the modifications in the `coptr` package's `meta.yaml`. - **#51326**: The `meta.yaml` for the `seqspec` package outlines package configuration, dependencies, and entry points, paralleling the structure and purpose of the `coptr` package's `meta.yaml`. - **#51476**: The `meta.yaml` for the `gene-trajectory-python` package includes similar elements such as package configuration, dependencies, and entry points, reflecting the changes made in the `coptr` package's `meta.yaml`. - **#51618**: The `meta.yaml` for the `mikrokondo-tools` package also defines package configuration, dependencies, and entry points, which aligns with the changes in the `coptr` package's `meta.yaml`. ## Suggested labels `please review & merge` ## Suggested reviewers - martin-g - mencian

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