Installation

SPECI is distributed as an open-source Python toolkit. The recommended way to install and run SPECI is via the Conda environment provided in this repository. This ensures that all required dependencies are installed and your setup is fully reproducible.

Setting Up Your Environment

  1. Install Conda (if not already installed)

    Download and install [Anaconda](https://www.anaconda.com/products/distribution) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html) for your operating system.

  2. Clone the SPECI repository

    Open a terminal and run:

    git clone https://github.com/Manting-Mu/OLIGO.git
cd OLIGO

  3. Create the SPECI environment

    Use the provided environment.yml file to set up a new Conda environment with all necessary dependencies:

    conda env create -f environment.yml

  4. Activate the environment

    conda activate speci-env

    (The environment name may differ if you change it in the environment.yml file.)

  5. Launch Jupyter Notebook

    jupyter notebook

    Open the SPECI notebooks (e.g., SPECI.ipynb) or use the scripts in the speci/ folder as needed.

Dependencies

Key dependencies installed include:

  • Python (>= 3.10)

  • JupyterLab / Notebook

  • pandas, numpy, matplotlib

  • openbabel (via conda-forge)

Refer to the environment.yml file for a complete, up-to-date list.

Troubleshooting

If you encounter any issues with installation, please open an issue on the [GitHub repository](https://github.com/Manting-Mu/OLIGO/issues).