Installation

The installation scenarios depending on your setup.

Use Case 1: Google Colab (No Local GPU)

For users who want to try StomataPy without installing anything locally:

Open In Colab

Use Case 2: Windows with NVIDIA GPU

For local Windows installation with GPU acceleration:

Install with UV:

# Clone repository
git clone https://github.com/Alias-z/StomataPy.git
cd StomataPy

# Install basic dependencies
uv venv venv --python 3.10
uv sync --link-mode=copy

# Install PyTorch with CUDA
uv pip install torch==2.1.1+cu118 torchvision==0.16.1+cu118 torchaudio==2.1.1+cu118 --extra-index-url https://download.pytorch.org/whl/cu118

# Install OpenMMLab dependencies
uv run -m mim install mmengine==0.10.4 mmcv==2.1.0 mmpretrain --trusted-host download.openmmlab.com --find-links https://download.openmmlab.com/mmcv/dist/cu118/torch2.1.0/index.html

# Install submodules
uv pip install -e ./sam-hq -e ./mmsegmentation -e ./mmdetection --no-build-isolation

# Install xformers for inference acceleration
uv pip install xformers==0.0.23

Use Case 3: Linux Server with NVIDIA GPU

For headless server deployment:

# Clone repository
git clone https://github.com/Alias-z/StomataPy.git
cd StomataPy

# Build and run with Docker (choose more GPUs for training)
docker build -t stomatapy .
docker run --gpus '"device=0,1,2,3"' -v $(pwd)/data:/workspace/data stomatapy