The tutorials are written as jupyter notebooks - browser based Python kernels to run, document, and visualize code (https://jupyter.org/). If you installed Python using Anaconda, it is possible that jupyter is already installed (check with
jupyter --version - you should see something like
notebook : 6.4.11 in the list that appears). If no list appears, your need to install jupyter notebook first.
Install phenopype` (see installation instructions) and
pip install jupyter notebook).
Download and unpack the github archive containing the data and code.
Open a terminal in the unpacked folder - don’t forget to activate your conda environment (see warning below).
Start the notebooks with
jupyter notebookand click on one of the tutorial files (your browser might give you a security warning - you can ignore it).
Run the code cell by cell inside the browser window (Shift + Enter to run cell and advance).
Make sure you install jupyter notebook to your specific environment (i.e. activate it first using
conda activate pp. If not installed in a specific environment, running
jupyter notebook will fall back on the conda base environment where phenopype may not be installed (this is a common source of confusion).
Below are the read-only html versions of the code contained in the notebooks - to run them yourself, follow the above instructions. If you want to use the notebooks as a blueprint for your own project, you can also save them as a Python script from a running jupyter notebook using
File > Download as > Python (.py).