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| name | spateo-env-setup |
| description | Set up Spateo runtime environment — choose conda or uv |
Configure a reproducible Python environment for Spateo spatial transcriptomics skills. Supports both conda (full dependency resolution) and uv (fast, lightweight).
bash skills/00_env_setup/setup.sh
Script detects available tools and prompts you to choose between conda and uv. If only one is installed, it auto-selects.
conda env create -f skills/00_env_setup/environment.yml
conda activate spateo
Best for:
# Option A: from requirements.txt (fastest)
uv venv .venv-spateo --python 3.10
source .venv-spateo/bin/activate
uv pip install -r skills/00_env_setup/uv_requirements.txt
# Option B: from pyproject.toml (locked resolution)
uv sync --project skills/00_env_setup/uv_pyproject.toml
Best for:
| File | Manager | Description |
|---|---|---|
environment.yml | conda | Full conda-forge spec with pip fallback for spateo-release |
uv_requirements.txt | uv/pip | Flat requirements, version ranges for Python 3.10 |
uv_pyproject.toml | uv | pyproject.toml with [tool.uv] config and git sources |
python -c "import spateo; print(f'spateo: {spateo.__version__}')"
python -c "import pyvista; print(f'pyvista: {pyvista.__version__}')"
python -c "import scanpy; print(f'scanpy: {scanpy.__version__}')"
| Problem | Fix |
|---|---|
numpy version conflict | Install numpy>=1.21,<1.24 first |
vtk build failure | Use conda: conda install -c conda-forge vtk |
pyvista headless | export PYVISTA_OFF_SCREEN=true |
| POT library missing | conda: conda install -c conda-forge pot |
dynamo-release not on PyPI | conda: conda install -c conda-forge dynamo-release |
| uv too old | uv self update |