Virtual Plant Laboratory @ FSPM 2023

This repository contains the tutorials that were followed during the FSPM 2023 conference as a Jupyter notebook.

These tutorials here are also available at the offical website of the VPLverse virtualplantlab.org and at VPLTutorials.The main difference with respect to the tutorials in this repository is that a single notebook is used here, in order to avoid starting a new Julia session for each tutorial.

Setup

Follow these steps to setup the environment to run the tutorials locally:

• Install Julia on your machine (version 1.8.5).

• Run Julia within a terminal and run the following code to install the dependencies:

using Pkg
pkg"add https://github.com/AleMorales/VPL.git; precompile"
pkg"add https://github.com/AleMorales/Ecophys.jl.git; precompile"
pkg"add https://github.com/AleMorales/Sky.jl.git; precompile"
pkg"add Distributions"
pkg"add Plots"
pkg"add FastGaussQuadrature"

• Add suport for Jupyter notebooks (replace "4" with the number of threads you want to use in your machine).

pkg"add IJulia"
using IJulia
installkernel("Julia (multi-threaded)", env=Dict("JULIA_NUM_THREADS"=>"4"))

• Download the notebook from this repository.

• In the same terminal, run the following code to start the Jupyter notebook server. Replace "dir" with the path where the notebook is located:

notebook(dir="dir")

• The notebook will open in the brower. Make sure to select the multithreaded kernel.