Cloud-based notebooks are also available:
1. [Structure definition and analysis](https://mybinder.org/v2/gh/Plant-Root-Soil-Interactions-Modelling/CPlantBox/workshop_1111?labpath=tutorial%2Fjupyter%2Fworkshop_11_11_2024%2F1_cplantbox.ipynb)
2. [water flow in CPlantBox](https://mybinder.org/v2/gh/Plant-Root-Soil-Interactions-Modelling/CPlantBox/workshop_1111?labpath=tutorial%2Fjupyter%2Fworkshop_11_11_2024%2F2_water_flux.ipynb)

# build local
## semi-automated CPlantBox (with dumux-rosi) installation via python script (recommended)
### Linux
This installation method requires ubuntu >= 20.04 and python >= 3.7.\
For CPlantBox __without__ the dumux-rosi extension, download the python file "installCPlantBox.py".\
Run
```bash
sudo apt-get update
sudo apt-get upgrade
[ ! -d 'cpbenv' ] && python3 -m venv cpbenv && source cpbenv/bin/activate || source cpbenv/bin/activate
wget https://raw.githubusercontent.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/master/installCPlantBox.py
python3 installCPlantBox.py
```
It will create a "CPB" folder and install inside the dependencies necessary to run CPlantBox.\
For CPlantBox __with__ the dumux-rosi extension, download the python file "installDumuxRosi_Ubuntu.py" (based on the dumux installation file).\
run
```bash
sudo apt-get update
sudo apt-get upgrade
[ ! -d 'cpbenv' ] && python3 -m venv cpbenv && source cpbenv/bin/activate || source cpbenv/bin/activate
wget https://raw.githubusercontent.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/master/installDumuxRosi_Ubuntu.py
python3 installDumuxRosi_Ubuntu.py
```
This will create a "DUMUX" folder and install inside the dependencies necessary to run dumux-rosi.
CPlantBox is setup within the virtual environment 'cpbenv'. \
**Do not forget to reactivate the 'cpbenv' environment when using CPlantBox:**
```bash
source cpbenv/bin/activate
```
This script might work on other linux OS but has not been tested.

### windows
CPlantBox is currently not available on windows.
Some pointers to setup a linux environment on windows are given on the [wiki](https://github.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/wiki/Help-for-windows-users).

## manual linux installation
Clone the repository by running:
```bash
git clone --depth 1 -b master https://github.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox.git
```
Run CMake which configures the CPlantBox libraries by
```bash
cmake . && make
```
in the root folder, and run some Python tutorial examples (see tutorial/latex/PlantBox_RootSytem), e.g
```bash
cd tutorial/examples/python
python3 example1a.py
```

The dependecies are listed in the requirements.txt file.
## Installation on the JSC agrocluster
Refer to the wiki:\
https://github.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/wiki/CPlantBox-on-the-J%C3%BClich-Supercomputer-cluster
# Folder sructure

`/modelparameter` Plant parameter files\
`/src` CPlantBox C++ codes\
`/test` Python tests for all CPlantBox classes\
`/tutorial` learn to use CPlantBox\
`/experimental` Specific applications (in sub-folders). contrary to scripts in `/tutorial`, might not be kept up to date

# Code documentation

Create the documentation by running doxygen in the folder
$ doxygen doxy_config

The documentation will be located in the folder /doc. Compile doc/latex/refman.tex to generate the full doxygen documentation in doc/latex/refman.pdf.

Collaboration diagrams give an overview of the code in folder /docs.

# Examples
Simulation videos availabe in Youtube Channel https://www.youtube.com/channel/UCPK-pFfpK94jiamgwHxX32Q