Developer install¶
Short version¶
If you have conda and poetry installed you can install it all with the following commands.
From the root folder of the timagetk repository:
cd timagetk
conda env create -n timagetk_dev --file conda/env/timagetk_dev.yaml
conda activate timagetk_dev
poetry install --all-extras
python -m pip install -e ../ctrl/.
python -m pip install -e ../visu_core/.
Note
The poetry install --all-extras command is equivalent to python -m pip install -e .[codecs,doc,nb,test].
This will also need to install ctrl & visu_core from our Gitlab.
Have a look at the detailed section to clone and install their sources.
Third-party - PlantSeg¶
To use the PlantSeg package with a CUDA GPU:
conda install -c gnomon -c conda-forge -c pytorch -c nvidia plantseg pytorch-cuda=11.7 gcc=12
To use the PlantSeg package for CPU:
conda install -c gnomon -c conda-forge -c pytorch plantseg cpuonly
Detailed version¶
Clone the sources¶
We have to clone timagetk sources, but we also need to clone sources for ctrl & visu_core.
From the folder where you want to clone the sources, e.g. ~/Projects/:
git clone https://gitlab.inria.fr/mosaic/timagetk.git --branch develop
git clone https://gitlab.inria.fr/mosaic/work-in-progress/ctrl.git --branch develop
git clone https://gitlab.inria.fr/mosaic/work-in-progress/visu_core.git --branch develop
Initialize a conda environment¶
From the root folder of the timagetk repository:
cd timagetk
conda env create -n timagetk_dev --file conda/env/timagetk_dev.yaml
This will create a conda environment named timagetk_dev and install the required dependencies available as conda packages.
Note
This should install the required packages from morpheme, if not: conda install vt vt-python -c morpheme -c conda-forge.
Install the sources¶
We now may install the sources that we cloned earlier.
Note
The -e option allows accessing modifications to source code without the need to re-install.
Install ctrl sources¶
To install ctrl from the sources with pip, simply run:
conda activate timagetk_dev
python -m pip install -e ../ctrl/.
Install visu_core sources¶
To install visu_core from the sources with pip, simply run:
conda activate timagetk_dev
python -m pip install -e ../visu_core/.
Install timagetk sources¶
To install timagetk from the sources, and the documentation and test requirements, with pip, simply run:
conda activate timagetk_dev
python -m pip install -e .[all]
Note
This should install the packages required to generate the sphinx documentation, if not run: python -m pip install -e .[doc].
This should install the packages required to perform tests, if not run: python -m pip install -e .[test].