If you don't need the development version of the python-opentree package you can install the version available from the Python Package Index (PyPI) using pip:
pip install opentree
If you want/need the latest version of python-opentree or if you are a developer who wants to install multiple times, you probably want to clone the code from its GitHub repository, and install it locally in a virtual environment.
To do this, first git clone the code from GitHub to your machine:
git clone https://github.com/OpenTreeOfLife/python-opentree.git
Change to its directory with cd:
cd python-opentree
Create a Python 3 virtual environment named env (you only need to ever run this once):
python3 -m venv env
Activate the virtual environment named env (you will want to do this each time you are using the package):
source env/bin/activate
Install the package requirements:
pip install -r requirements.txt
Install the python-opentree package locally:
pip install -e .
You can deactivate the virtual environment by running:
deactivate
If you plan to run the python-opentree example Jupyter notebooks, you will also need to install Jupyter within a Python virtual environment.
First, create a Python virtual environment and activate it, as shown above.
Now, install a Jupyter kernel:
pip install ipykernel
python -m ipykernel install --user --name=opentree
Install Jupyter from PyPI using pip:
pip install jupyter
Finally, open the python-opentree example Jupyter notebooks with:
jupyter notebook docs/notebooks/
You can then install python-opentree within the virtual environment from PyPI or GitHub, following the instructions above.