Add metalsinglecell

[gingerii]

Add metalsinglecell

Mandatory

Name of the tool: metalsinglecell

Short description: A Metal/MLX GPU implementation of the scanpy/squidpy single-cell analysis stack for Apple Silicon — drop-in replacements for the core scanpy (pp/tl) and squidpy (gr) functions that run on the M-series GPU, plus an out-of-core streaming front-end for datasets larger than memory.

How does the package use scverse data structures (please describe in a few sentences): Every function takes an AnnData object, computes on the GPU, and writes results back to the same slots scanpy/squidpy use (.X, .obsm, .obsp, .var, .uns) with scanpy's copy= semantics, so plotting and downstream tooling are unchanged. The API mirrors the scanpy/squidpy namespaces (pp, tl, gr), making it a drop-in for existing AnnData-based pipelines. The out-of-core path streams an on-disk AnnData-compatible zarr store.

• The code is publicly available under an OSI-approved license
• The package provides versioned releases
• The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
• Automated tests cover essential functions of the package and a reasonable range of inputs and conditions
• Continuous integration (CI) automatically executes these tests on each push or pull request
• The package provides API documentation via a website or README
• The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
• I am an author or maintainer of the tool and agree on listing the package on the scverse website

Notes for reviewers

• License: BSD-3-Clause · PyPI: https://pypi.org/project/metalsinglecell/ · Docs: https://metal-singlecell.readthedocs.io
• Tests: tests/ (CPU lane + self-hosted Metal-GPU lane); CI: .github/workflows/ci.yml (CPU lane on ubuntu + macos, incl. an "installs without mlx on Linux" contract check).
• The GPU backend (mlx) is a Darwin/arm64-only dependency and is lazy-imported, so the package installs and imports on any platform (CI proves this on Linux).