From 58966b6527fe63bbfa364671343d2c3a8bc6cc94 Mon Sep 17 00:00:00 2001 From: Maarten de Vries Date: Mon, 23 Mar 2026 13:16:48 -0400 Subject: [PATCH] Update installation docs to recommend uv pip over conda Conda installations of rapids-singlecell cause dependency conflicts (cupy vs cupy-cuda12x). Using uv pip avoids this issue. Closes #3 Co-Authored-By: Claude Opus 4.6 (1M context) --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index aeb6551..75b1856 100644 --- a/README.md +++ b/README.md @@ -40,18 +40,18 @@ Please refer to the [documentation][link-docs]. ## Installation -You need to have Python 3.11 or newer and a CUDA-capable GPU. We recommend installing in a [conda](https://docs.conda.io/en/latest/miniconda.html) environment with RAPIDS pre-installed. +You need to have Python 3.11 or newer and a CUDA-capable GPU. -1. Install the latest release on PyPI: +We recommend installing [rapids-singlecell](https://rapids-singlecell.readthedocs.io/en/latest/Installation.html) and `scib-rapids` using `uv pip` rather than conda, as conda often causes dependency conflicts (e.g. `cupy` vs `cupy-cuda12x`). ```bash -pip install scib-rapids +uv pip install rapids-singlecell scib-rapids ``` -2. Install the latest development version: +Alternatively, install the latest development version: ```bash -pip install git+https://github.com/maarten-devries/scib-rapids.git@main +uv pip install rapids-singlecell git+https://github.com/maarten-devries/scib-rapids.git@main ``` ## Release notes