Installation

1. Install Python

To get started, download and install Anaconda with Python 3. Anaconda is a scientific python distribution which comes with the most common scientific Python packages already built in.

You can test if the installation was successfull by opening a terminal and typing this command:

conda --version

If conda is not recognized, use the anaconda prompt (e.g. through the Anaconda Navigator OR add the path to your Anaconda installation directory (e.g. C:\Anaconda3\Library\bin) to your environmental variables. Further help can be found here:

If you prefer an “Rstudio-like” environment, you can use Phenopype from a Python Integrated Development Environment (IDE). My favorite IDE is Spyder (https://www.spyder-ide.org/), but any other IDE will work too (a slightly outdated overview can be found here). Phenopype can of course also be run from the command line using python.

2. Install phenopype

You can install phenopype using pip, and run it with spyder:

pip install phenopype

However, to have fuller control over your python packages and to not mess up existing Python installation, I recommend to create a virtual environment using conda:

conda create -n "pp" python=3.7 spyder

Important

Adding spyder behind the installation command will install Spyder to the new environment you have just created, otherwise it will be loaded from conda base environment where Phenopype may not be installed.

Now activate the virtual environment and install Phenopype using pip:

conda activate pp
pip install phenopype

You can now use Phenopype by typing spyder or python into the command line. If you are unsure to proceed, consult the tutorials.

2.1 Update Phenopype

For regular major and minor releases:

pip install phenopype -U

2.2 Install hotfixes

To install bug fixes for a current installation:

pip install https://github.com/mluerig/phenopype/archive/fix.zip -U

2.3 Install developmental version

To update to the latest unreleased version of Phenopype:

pip install https://github.com/mluerig/phenopype/archive/latest.zip -U

Important

Any modifications to the python environments or Spyder, should only be done using conda, but modifications to phenopype, its dependencies or other python packages should only be done using pip. Mixing the two installers may break your python enviroment.

3. Choose a text editor

The high throughout method in Phenopype currently requires a text editor to be installed that does not lock the file - read about file locking here.

Important

Your OS needs to know how to handle .yaml files. Make sure that the default app to open these files is set as one of the edtiors that you selected.

For Windows, notepad works. However, I recommend Notepad++, which supports syntax highlighting and has many other useful features: https://notepad-plus-plus.org/downloads/ Make sure that Windows “knows” how to open “.yaml” files: you double click a file, and nothing happens, you need to right click, go to “open with”, and select a text editor as the default application for this file ending.

For Linux Vim or Nano (are already installed on most Linux distributions), and for MacOS, Nano or brackets could work http://brackets.io/.

[More information about this will follow soon]