Installation

Prerequisites

• Conda Package Manager: We recommend using Conda to manage the environment due to dependencies that may not be available via pip.

Installation Steps

For macOS and Ubuntu

1. Clone the Repository

   git clone https://github.com/ucl-cssb/MIMIC.git
   cd MIMIC
   

2. Create the Conda Environment

   conda env create -f environment.yml
   

3. Activate the Environment

   conda activate mimic_env
   

4. Install the Package

   pip install -e .
   

5. Run the Code

   Refer to the Usage section below for instructions on how to run the code.

For Windows

1. Clone the Repository

   git clone https://github.com/ucl-cssb/MIMIC.git
   cd MIMIC
   

2. Create the Conda Environment for Windows

   On Windows, use the environment_windows.yml file:

   conda env create -f environment_windows.yml
   

3. Activate the Environment

   conda activate mimic_env
   

4. Install the Package

   pip install -e .
   

5. Run the Code

   Refer to the Usage section below for instructions on how to run the code.

Alternative Installation Using Pip Only

If you prefer to use pip without Conda, you can install the package and its dependencies by compiling requirements.in into requirements.txt:

# Step 1: Compile requirements.txt from requirements.in
pip install pip-tools
pip-compile requirements.in

# Step 2: Install dependencies
pip install -r requirements.txt
pip install -e .

Note: This method may not install all dependencies correctly, especially if there are packages that are only available via Conda. We recommend using the Conda installation method for full functionality.

Compilers

A g++ compiler is required for the PyMC3 package.