Installing and running PlantSimEngine

• Installing and running PlantSimEngine
• • Installing Julia
  • Installing VSCode
  • Installing PlantSimEngine and its dependencies
  • • Julia environments
    • Running an environment
    • Companion packages
    • Using the example models
  • Running a test simulation
  • Environments in VSCode

This page is meant to help along people newer to Julia. If you are quite accustomed to Julia, installing PlantSimEngine should be par for the course, and you can move on to the next section, or read about PlantSimEngine's Key Concepts.

Installing Julia

The direct download link can be found here, and some additional pointers in the official manual.

Installing VSCode

You can get by using a REPL, but if writing a larger piece of software you may prefer using an IDE. PlantSimEngine is developed using VSCode, which you can install by following instruction on this page. A documentation section specific to using Julia in VSCode can be found here.

Installing PlantSimEngine and its dependencies

Julia environments

Julia package management is done via the Pkg.jl package. You can find more in-depth sections detailing its usage, and working with Julia environments in its documentation

If you find this page insufficient to get started, this tutorial explains in detail the subtleties of Julia environments.

Running an environment

Once your environment is set up, you can launch a command prompt and type julia. This will launch Julia, and you should see julia> in the command prompt.

You can always type ? from there to enter help mode, and type the name of a function or language feature you wish to know more about.

You can find out which directory you are in by typing pwd() in a Julia session.

Handling environments and dependencies is done in Julia through a specific Package called Pkg, which comes with the base install. You can either call Pkg features the same way you would for another package, or enter Pkg mode by typing ], which will change the display from julia> to something like (@v1.11) pkg>, indicating your current environment (in this case, the default julia environment, which we don't recommend bloating).

Once in Pkg mode, you can choose to create an environment by typing activate path/to/environment.

You can then add packages that have been added to Julia's online global registry by typing add packagename and you can remove them by typing remove packagename. Typing status or st will indicate what your current environment is comprised of. To update packages in need of updating (a ^ symbol will display next to their name), type update… or up.

If you are editing/developing a package or using one locally, typing develop path/to/package source/ (or dev path/to/package/source) will cause your environment to use that version instead of the registered one.

Typing instantiate will download all the packages declared in the manifest file (if it exists) of an environment.

For instance, PlantSimEngine has a test folder used in development. If you wanted to run tests, you would type ] then activate ../path/to/PlantSimEngine/test then instantiate and then you would be ready to run some scripts.

So if you wish to use PlantSimEngine, you can enter Pkg mode (]), choose an environment folder, then activate that environment with activate ../path/to/your_environment, add PlantSimEngine to it with add PlantSimEngine then download the package and its dependencies with instantiate.

Companion packages

You'll also, for most of our examples, need PlantMeteo. For several multi-scale simulations, you'll need MultiScaleTreeGraph.

Some of the weather data examples make use of the CSV package, some output data is manipulated as a DataFrame, which is part of the DataFrames package.

Using the example models

Example models are exported as a distinct submodule of PlantSimEngine, meaning they aren't part of the main API. You can use them by typing:

using PlantSimEngine.Examples

Running a test simulation

Assuming you've setup you're environement, correctly added PlantMeteo and PlantSimEngine to that environment, and downloaded everything with instantiate, you'll be able to run a test example in your REPL by typing line-by-line:

using PlantSimEngine, PlantMeteo
using PlantSimEngine.Examples
meteo = Atmosphere(T = 20.0, Wind = 1.0, Rh = 0.65, Ri_PAR_f = 500.0)
leaf = ModelList(Beer(0.5), status = (LAI = 2.0,))
out_sim = run!(leaf, meteo)

TimeStepTable{Status{(:LAI, :aPPFD), Tuple{...}(1 x 2):
╭─────┬─────────┬─────────╮
│ Row │     LAI │   aPPFD │
│     │ Float64 │ Float64 │
├─────┼─────────┼─────────┤
│   1 │     2.0 │  1444.4 │
╰─────┴─────────┴─────────╯

Environments in VSCode

There is detailed documentation explaining how to make use of Julia with VSCode with one section indicating how to handle environments in VSCode: https://www.julia-vscode.org/docs/stable/userguide/env/