Installing phenopype#

(These instructions are valid across operating systems, and use mamba instead of conda).

Initial installation#

Open a terminal. Then create a virtual environment with mamba. Using such environments will give you full control over which Python packages are installed, and reduces the change of package related issues. Note that phenopype requires Python v3.7, which needs to be explicitly specified. For example, for an environment named “pp”, type:

mamba create -n "pp" python=3.7

You can now activate your environment. This needs to be done every time you are using phenopype:

conda activate pp

Now install phenopype to the environment using pip (pip is the package installer for Python):

pip install phenopype


If you prefer an “Rstudio-like” environment, you can use Phenopype from a Python Integrated Development Environment (IDE), such as Spyder. Spyder needs to be installed with mamba directly to the environment you created before. Using the example from above:

conda activate pp
mamba install spyder -c conda-forge

Once installed, you can run Spyder by typing spyder

That’s it - happy phenopyping! You can now use phenopype by after loading python or spyder from the terminal. You can also use phenopype from a jupyter notebook - for more details, give the tutorials a try. Always remember to activate your environment.

Installing updates#

For regular major and minor releases, use the -U flag with pip:

pip install phenopype -U

Installing past versions#

Major releases are not backwards compatible, so if you have existing phenopype projects that were created with a previous version you need to download that specific version. You can tell pip to do so, for example, for version 1.0.0:

pip install "phenopype==1.0.0"

Or, for the latest phenopype version that is still 1.x.x:

pip install "phenopype < 2"