Installation

Conda must be installed, please follow the instructions and recommendations here.

Users

Create a new environment with colzette installed in there

mamba create -n colzette -c openalea3 -c conda-forge  openalea.colzette
mamba activate colzette

Install colzette in a existing environment

mamba install -c openalea3 -c conda-forge openalea.colzette

(Optional) Test your installation

mamba install -c conda-forge pytest
git clone https://github.com/openalea/colzette.git
cd colzette/test; pytest

Developers

Install From source

Clone the colzette repository

git clone git@github.com:openalea-incubator/colzette.git

After cloning the colzette repo, run the following commands in the colzette/ directory:

# Install dependency with conda
mamba env create -f conda/environment.yml
mamba activate colzette_dev

# (Optional) Test your installation
cd test; pytest

This will create a conda environment with dependencies installed and install colzette in editable state.

Running notebook Examples

you can run the jupyter notebook in doc/examples. First install jupyterlab and òpenalea.widgets

mamba install -c openalea3 -c conda-forge jupyterlab openalea.widgets

then in doc/examples launch jupyter-lab

cd doc/examples
jupyter-lab

Contribute to colzette

You need to create a new branch and update your modifications on this branch. When you’re done you can ask for a pull request so that your branch is merged to the main one.

# Create new branch
git branch name_new_branch
# Check the branches
git branch
# Move to new branch
git switch name_new_branch
# Add updates to new branch
git status
git add your_modifications
git commit -m "your message"
git push -u origin name_new_branch