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 hdfm_zarr from GitHub in a Conda environment. Normally we don’t need to install hdmf directly, but until hdmf 3.4.0 is released we need to use the dev version of hdmf.

conda create --name hdmf-zarr-test python=3.9
conda activate hdmf-zarr-test
conda install h5py

git clone --recurse-submodules https://github.com/hdmf-dev/hdmf.git
cd hdmf
pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt -r requirements-opt.txt
pip install -e .
cd ..

git clone https://github.com/hdmf-dev/hdmf-zarr.git
cd hdmf-zarr
pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt
pip install -e .

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