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Installation instructions

This is the installation instruction for the python package PyStemmusScope, which allows for preparing data and running the STEMMUS-SCOPE model. The model source code STEMMUS_SCOPE repository. For model-specific instructions, check the Getting started page.

Note that the latest version of PyStemmusScope is compatible with latest version of STEMMUS-SCOPE model.

Install PyStemmusScope

To install the package, you need to have Python ">=3.9, <3.12" installed. Run the commands below in a terminal (On Windows, use python instead of python3):

python3 -m pip install pystemmusscope

or

Open a jupyter notebook and run the code below in a cell:

!pip install pystemmusscope

On CRIB, you can use the following command to install the package:

python3 -m pip install --user pystemmusscope

Install jupyterlab

Jupyterlab is needed to run notebooks. Run the commands below in a terminal:

python3 -m pip install jupyterlab

Open a terminal, make sure the environment is activated. Then, run jupyter lab:

jupyter lab

JupyterLab will open automatically in your browser. Now, you can run the notebook run_model_on_different_infra.ipynb.

Install WSL [optional]

As the STEMMUS-SCOPE executable only supports Unix-like systems, Windows users cannot run STEMMUS-SCOPE natively. However, users of Windows 10 and newer can use WSL (Windows Subsystem for Linux) to run the model. Check the Microsoft Guide for a compatibility information and for general WSL instructions. If no installation exists, a Ubuntu distribution can be installed using the following commands:

wsl --install

After installation, you can start up the WSL instance and update the default software:

sudo apt update && sudo apt upgrade

You can now set up a python environment using either python's venv, or use Conda/Mamba. Note that the command to run python and pip can be python3 and pip3 by default.

For the rest of the installation instructions simply follow the steps below. Note that it is possible to access files from the Windows filesystem from within WSL, by accessing, e.g., /mnt/c/ instead of C:\. This means that large input data files can be stored on your Windows installation instead of inside the WSL distro. However, WSL does not have write permission. Therefore, output data will be stored within WSL. Make sure that WorkDir in the model config file is set correctly.

Create pystemmusscope conda environment [optional]

If a conda environment is needed, for example, on Snellius, run the commands below in a terminal:

# Download and install Mamba on linux
wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-pypy3-Linux-x86_64.sh
bash Mambaforge-pypy3-Linux-x86_64.sh -b -p ~/mamba

# Update base environment
. ~/mamba/bin/activate
mamba update --name base mamba

# Download environment file
wget https://raw.githubusercontent.com/EcoExtreML/STEMMUS_SCOPE_Processing/main/environment.yml

# Create a conda environment called 'pystemmusscope' with all required dependencies
mamba env create -f environment.yml

# The environment can be activated with
. ~/mamba/bin/activate pystemmusscope