Installation

This tutorial demonstrates how to install Pysodb on a method which use for spatial data integration.

Using stagate as an example, install Pysodb in its installation environment.

Reference tutorials presents can be found at https://github.com/QIFEIDKN/STAGATE_pyG and https://github.com/TencentAILabHealthcare/pysodb.

Installing softwares and tools

1. The first step is to install Visual Studio Code, Conda, Jupyter notebook and CUDA in advance.

Reference tutorials presents how to install Visual Studio Code, Conda, Jupyter notebook and CUDA, respectively. And they can be found at https://code.visualstudio.com/Docs/setup/setup-overview, https://code.visualstudio.com/docs/python/environments#_activating-an-environment-in-the-terminal, https://code.visualstudio.com/docs/datascience/data-science-tutorial and https://developer.nvidia.com/cuda-downloads.

STAGATE’s tensorflow version is based on version 1.15.0. Officials have stopped updating TensorFlow1 and now many algorithms are more developed based on TensorFlow2, STAGATE_pyG will be selected and demonstrated for installation in this tutorial.

Since STAGATE_pyG is based on pyG (PyTorch Geometric) framework, it requires GPUs on a device and need to install CUDA tool. A tutorials is available at https://developer.nvidia.com/cuda-downloads.

2. Launch Visual Studio Code and open a terminal window.

Henceforth, various packages or modules will be installed via the command line

Installation STAGATE_pyG

3. Select the installation path and open it

cd <path>

4. Clone STAGATE_pyG code

git clone https://github.com/QIFEIDKN/STAGATE_pyG.git

If cloning the code fails through git, please download it at https://github.com/QIFEIDKN/STAGATE_pyG, upload it to the folder created above, and extract it.

5. Open the STAGATE_pyG directory

cd STAGATE_pyG

6. Create a conda environment

conda create -n <environment_name> python=3.8

7. Activate a conda environment

Run the following command on the terminal to activate the conda environment:

conda activate <environment_name>

8. Install torch with CUDA

eg. pip install torch==1.13.0+cu117 -f https://download.pytorch.org/whl/cu117/torch_stable.html

pip install torch==<torch_version>+<cuda_version> -f https://download.pytorch.org/whl/<cuda_version>/torch_stable.html

9. Install PyTorch Geometric

Install a PyTorch Geometric according to the version of pytorch and CUDA, system. Select the package and copy a run command to run on your terminal. https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html

eg. pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv torch_geometric -f https://data.pyg.org/whl/torch-1.13.0+cu117.html

10. Install other python packages from requirement.txt

pip install -r requirement.txt

11. Install palettable package

pip install palettable

12. Install harmonypy package

pip install harmonypy

Installation Pysodb

Keep the conda environment active

13. Clone Pysodb code

git clone https://github.com/TencentAILabHealthcare/pysodb.git

If cloning the code fails through git, please download it at https://github.com/TencentAILabHealthcare/pysodb, upload it to the folder created above, and extract it.

14. Open the Pysodb directory

cd pysodb

15. Install a Pysodb package from source code

python setup.py install

If “error: urllib3 2.0.0a3 is installed but urllib3<1.27,>=1.21.1 is required by {‘requests’}” appears, users can execute the following commands,respectively.

pip install 'urllib3>=1.21.1,<1.27'
python setup.py install

print('finish！')

finish！