Installation

For Users

Install hdmf-zarr from PyPI

pip install hdmf-zarr

Install hdmf-zarr from conda-forge

conda install -c conda-forge hdmf-zarr

For Developers

Install hdmf-zarr from GitHub

The following illustrates how to install both hdmf and hdmf_zarr from GitHub in a Conda environment, with all of the optional, testing, and documentation dependencies for hdmf-zarr. Normally, we don’t need to install hdmf directly, but it is often useful to use the dev branch of the hdmf GitHub repository.

conda create --name hdmf-zarr-dev python=3.14
conda activate hdmf-zarr-dev

git clone --recurse-submodules https://github.com/hdmf-dev/hdmf.git
cd hdmf
pip install -e ".[all]"
cd ..

git clone https://github.com/hdmf-dev/hdmf-zarr.git
cd hdmf-zarr
pip install -e ".[all]"

Note

Depending on versions, it is possible that when installing hdmf-zarr, that pip will install HDMF directly from PyPI instead of using the development version of HDMF that is already installed. In that case call pip uninstall hdmf and go to the hdmf directory and run pip install -e . again