scverse/rapids-singlecell/docs

Claude Code and agent skill by scverse/rapids-singlecell

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Checking that the SKILL.md file is still in the repository.

Install

npx vskill@latest install scverse/rapids-singlecell/docs

SKILL.md

(agent-skill)=

Agent skill

Every release ships a version-matched, model-neutral analysis skill for coding agents. It teaches the agent the rapids-singlecell API and current best practices.

{warning}
The agent skill is new and experimental.
Its content, installer, and commands may change substantially between releases.

1. Install the skill

Copy the bundled skill into your agent's personal skill directory:

``{tab-set}
bash
rapids-singlecell-install-skills --agent claude
Installs to $CLAUDE_CONFIG_DIR/skills/ (default ~/.claude/skills/).
`
bash
rapids-singlecell-install-skills --agent codex
Installs to $CODEX_HOME/skills/ (default ~/.codex/skills/).
`
bash
rapids-singlecell-install-skills --agent claude-science
Installs into the active organization from ~/.claude-science/active-org.json.
`
bash
rapids-singlecell-install-skills --agent agents
# or any custom location
rapids-singlecell-install-skills --dest /other/skills/rapids-singlecell
--agent agents installs to ~/.agents/skills/.
`
OptionEffect
--checkCompare the installed copy with the bundle in the active package
--forceReplace a differing copy, e.g. after upgrading rapids-singlecell
--print-pathPrint the location of the bundled skill
The agent looks up the installed API with python -m rapids_singlecell_skills.api, so run it in the same environment as rapids-singlecell.
2. Check the GPU environment
Before starting Jupyter, verify RMM, GPU/CUDA execution, the RSC import, native extensions, and a representative RSC kernel:
bash
rapids-singlecell-check-kernel
rapids-singlecell-check-kernel --mode managed  # planned oversubscription
The preflight is disposable, so configure RMM again at the start of the notebook or script.
Bootstrap from a standalone skill
`{tip}
If the agent only has the skill but RSC is not installed yet, create a fresh environment
from the matching definition on `main`
([CUDA 13](https://github.com/scverse/rapids_singlecell/blob/main/conda/rsc_rapids_26.10_cuda13.yml),
[CUDA 12](https://github.com/scverse/rapids_singlecell/blob/main/conda/rsc_rapids_26.10_cuda12.yml)):
 
CONDA_CHANNEL_PRIORITY=flexible mamba env create --name rsc \   --file /path/to/rsc_rapids_26.10_cuda13.yml
Security
  • Security scanPassed, 95 of 100Pattern checks on the skill's files.
  • Model reviewPassed
See the full security report
Quality evaluation
  • Task evaluationNot runNo evaluation yet. Run one in Skill Studio.
See evaluation results
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