Installation#

Three ways to install, depending on whether you just want the regrender command or an editable developer checkout:

  • Option 1 — one-shot uv tool (no clone, no env): just use the CLI. Recommended for end users.

  • Option 2 — uv virtual environment: editable checkout for development.

  • Option 3 — conda environment: editable checkout for development.

Prerequisites#

  • Python 3.12 or higher

  • Git (for Options 2 and 3)

Option 1 — One-shot install with uv (no environment)#

If you just want to run the regrender command, install it as a uv tool straight from GitHub — no cloning, no virtual environment to manage:

uv tool install git+https://github.com/ytsimon2004/regrender.git

This installs regrender into an isolated environment and puts it on your PATH. Upgrade or remove it later with:

uv tool upgrade regrender
uv tool uninstall regrender

Note

If regrender is not found after install, run uv tool update-shell (then restart your shell) to add uv’s tool directory to your PATH.

Option 2 — uv virtual environment (development)#

For an editable checkout. uv is a fast Python package installer and resolver — install it first if you don’t have it.

# Clone
git clone https://github.com/ytsimon2004/regrender.git
cd regrender

# Create and activate a virtual environment
uv venv
source .venv/bin/activate         # Linux/macOS
.venv\Scripts\activate            # Windows

# Install in editable mode
uv pip install -e .

Option 3 — conda environment (development)#

If you prefer conda for environment management:

# Clone
git clone https://github.com/ytsimon2004/regrender.git
cd regrender

# Create and activate a conda environment
conda create -n regrender python=3.12 -y
conda activate regrender

# Install in editable mode
pip install -e .

Verification#

After any of the above, verify that regrender is available:

regrender --help

Download the atlas#

regrender uses the Allen CCF atlas, which BrainGlobe/neuralib fetches automatically the first time you run register, roi, or probe (this may take a few minutes). To pull it ahead of time so the first real command doesn’t stall:

regrender setup

This fetches the 10 µm Allen mouse atlas (what regrender is built around). It’s a no-op if the atlas is already cached.