Installation¶

Protomix is written in Python 3 and distributed as a PyPI package.

Virtual environments (recommended)¶

We recommend installing Protomix inside a virtual environment (venv, conda, etc.) to ensure a clean and isolated environment for your dependencies.

To create a virtual environment named protomix with venv:

python3 -m venv protomix
source protomix/bin/activate

Or with conda:

conda create -n protomix
conda activate protomix

The latest stable Protomix version can then be installed using pip:

python3 -m pip install protomix

User installation¶

If you are not using virtual environments, we recommend doing a user installation with pip:

python3 -m pip install --user protomix

On Linux, this will place the Python module under $HOME/.local/lib/python3.X/site-packages, where X should be substituted for the minor version of your Python distribution. During the installation, an executable called protomix is built and placed under $HOME/.local/bin. In order for your Protomix installation to function properly, these paths must (if not already present) be appended to the correct environment variables:

export PATH=$PATH:$HOME/.local/bin
# Do not forget to substitute X for your Python minor version
export PYTHONPATH=$PYTHONPATH:$HOME/.local/lib/python3.X/site-packages

To check that the installation was successful, calling the protomix executable without any arguments should result in usage instructions being printed. During the installation, you may see a large number of dependencies being installed by pip. Protomix includes various packages necessary for NMR data processing.

Development version¶

To install the development version of Protomix, clone the source code from the repository and install it with pip:

git clone https://github.com/yourusername/protomix.git
cd protomix
python3 -m pip install --user .

Experimental features¶

After acquiring the source code, experimental features can be installed from their own development branches:

git checkout [branch_name]
cd protomix
python3 -m pip install --user .

Warning

Experimental features that are in development may produce inaccurate results. Use at your own risk!