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CryoSiam Installation Guide

This guide walks you through installing CryoSiam in a clean and reproducible way using Conda.
The recommended setup supports full support of GPU execution via PyTorch.

If you are new to Conda or Python environments, don't worry, each step is explained.

Requirements

  • Python 3.8 or newer
  • Conda (Miniforge or Anaconda)
  • An NVIDIA GPU with CUDA 11.8+ for GPU acceleration

Step 1: Create the environment

CryoSiam uses a predefined Conda environment to ensure that all dependencies (including PyTorch) are installed with compatible versions. If you don't have Conda installed, please follow the guide from here.

Run the following command to create the environment:

conda env create -f https://github.com/frosinastojanovska/cryosiam/blob/main/environment.yml

Once the environment is created, activate it: 

conda activate cryosiam

Step 2: Install cryosiam

With the Conda environment activated, clone the CryoSiam repository:

git clone https://github.com/frosinastojanovska/cryosiam.git
cd cryosiam

Install CryoSiam into the active environment: 

pip install --no-deps .

The --no-deps flag ensures that dependencies provided by Conda are used instead of reinstalling them with pip.

Step 3: Verify the installation

To confirm that CryoSiam was installed correctly, run:

cryosiam --version
If the command runs without errors, the installation was successful.

To check that PyTorch is installed correctly and can detect your GPU:

import torch
print(torch.cuda.is_available())  # Should return True if GPU is available

This should print True if a compatible GPU is available and the Pytorch for GPU was installed.

Troubleshooting

  • CUDA errors: Make sure your system has the correct NVIDIA drivers and CUDA version.
  • Missing packages: Make sure the Conda environment is activated before installing or running CryoSiam.
  • Dependency conflicts: Always install CryoSiam in a fresh Conda environment.

Don't Have Conda Installed?

If you do not have Conda yet, we recommend one of the following options.

Miniforge is a minimal installer for Conda that uses conda-forge by default.

Linux / macOS:

# Download and install Miniforge
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh

Windows:

  1. Download the latest installer from:
    https://github.com/conda-forge/miniforge/releases

  2. Run the .exe installer and follow the setup.

Option 2: Install Anaconda (full distribution)

Anaconda includes Conda, Python, and hundreds of data scientific packages.

Download from: https://www.anaconda.com/products/distribution

After installing Miniforge or Anaconda, return to the main Conda installation steps above.

Need Help?

If you run into issues, feel free to open an issue on the CryoSiam GitHub repository.