2. Installing phenopype

2.1. Initial installation

Activate your virtual environment:

mamba activate <NAME>                           # <NAME> == chosen name, e.g. "pp-env"

Install phenopype to your environment using pip (pip is the standard package manager for Python):

pip install phenopype

That’s it - happy phenopyping! You can now use phenopype, e.g. by typing:

python
import phenopype as pp

You can also use phenopype interactively (recommended), e.g. using a code editor like Spyder or vscode, or from a jupyter notebook - see the tutorials-section for more details.

Warning

Always remember to activate your environment before running phenopype from Python, Spyder or a jupyter notebook.

2.2. Install the plugins package

To install the phenopype-plugins package, simply do:

pip install phenopype-plugins

More detail information can be found at <https://github.com/phenopype/phenopype-plugins>`_

2.3. Installing updates

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

pip install phenopype -U

2.4. Installing from dev branch

You can install phenopype directly from the latest commit developmental branch to test experimental features and new implementations.

Warning

This is generally not recommended and should only be done if you know what you’re doing, or if you have been contacted by the phenopype developers.

pip install https://github.com/phenopype/phenopype/archive/dev.zip

2.5. 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"