Installation

This library can be installed using uv.

Quick install

If you don’t have uv, install it first:

curl -LsSf https://astral.sh/uv/install.sh | sh

Then create an environment and install:

uv venv --python 3.10 dynamoEnv
source dynamoEnv/bin/activate
uv pip install --upgrade -e "git+https://github.com/ubcbraincircuits/pyDynamo#egg=pydynamo_brain&subdirectory=pydynamo_brain"
uv pip install pyNeuroTrace

Note for GPU users: uv installs the CPU-only build of PyTorch by default. To use a CUDA-enabled build, install torch manually before the above, e.g. for CUDA 12.1:

uv pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cu121

Once installed, run with:

pydynamo_brain

or optionally pass a file to open directly:

pydynamo_brain path/to/my/file.dyn.gz

Updating

To update to the latest version, re-run the install command:

uv pip install --upgrade -e "git+https://github.com/ubcbraincircuits/pyDynamo#egg=pydynamo_brain&subdirectory=pydynamo_brain"