Installation

Installation#

We recommend installing MoleCool inside a dedicated virtual environment to avoid dependency conflicts. You can create a virtual environment with e.g. the popular tool virtualenv or with conda.

Note

The module requires at least python 3.8. However, python <=3.10 is recommended.

Creating a virtual environment#

# Create a virtual environment
virtualenv -p python3.10 .venv

# Activate the virtual environment
source .venv/bin/activate

# Create a virtual environment
python -m virtualenv -p python3.10 .venv

# Activate the virtual environment using:
# - Command Prompt / cmd.exe
.\.venv\Scripts\activate.bat

# - PowerShell
.\.venv\Scripts\Activate.ps1

# Create a new conda environment with Python 3.10 (recommended)
conda create -n venv python=3.10

# Activate the environment
conda activate venv

Installing MoleCool#

Once your virtual environment is active (or your conda env is activated), install MoleCool using one of the following methods.

The easiest way is to install the latest stable release from PyPI. This will install the version that has been officially released and tested.

python -m pip install --upgrade pip
pip install MoleCool

Using conda a stable release via conda-forge can be installed via:

conda install -c conda-forge MoleCool

This requires git to be installed which is used to download the latest development version of the module from GitHub initiating a local copy of the repository.

git clone https://www.github.com/LangenGroup/MoleCool
cd MoleCool
python -m pip install --upgrade pip
pip install .

Contributing#

How to contribute in the package’s development

GitHub

If you want to contribute to the code development hosted on GitHub, manually clone the latest development version using git (see above) and install the module along with optional dependencies for devopment or documentation by using the dev and doc extras.

pip install -e .[dev,doc]

Adding the -e flag enables editable mode, which allows you to modify the source code and immediately test changes without repeatedly running pip install ..

Important

Do not import the package (import MoleCool) from the repository’s parent folder (as current working directory) if it has the same name as the package (MoleCool). Doing so can confuse Python, as it may mistake the repository folder for the package itself.

Verifying the installation#

To ensure that MoleCool has been installed correctly, run the provided example suite:

python -m MoleCool.run_examples

This will run a set of fast example scripts included with the package and verify that your installation is working correctly.

Note

By adding the flag -h, you can display the help message along with a list of all runnable examples. Additionally, there are longer example scripts designed to be run on a compute (HPC) server for optimal performance. These scripts also allow you to specify whether the generated plots should be saved to files or displayed directly.

All available example scripts are presented in a well-organized, readable, and documented format in the Examples section.

Quickstart#

from MoleCool import System

system = System(load_constants='138BaF')
system.levels.add_all_levels(v_max=0)

system.levels.print_properties()
Contents