Installation
This tutorial demonstrates how to install Pysodb on SOVIew (a spatial omics visualization tool).
Reference tutorials can be found at https://soview-doc.readthedocs.io/en/latest/index.html and https://github.com/TencentAILabHealthcare/pysodb.
Installing softwares and tools
1. The first step is to install Visual Studio Code, Conda and Jupyter notebook in advance.
Reference tutorials presents how to install Visual Studio Code, Conda and Jupyter notebook,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 and https://code.visualstudio.com/docs/datascience/data-science-tutorial.
2. Launch Visual Studio Code and open a terminal window.
Henceforth, various packages or modules will be installed via the command line
Installation SOVIew
3. Select the installation path and open it
[ ]:
cd <path>
4. Create a conda environment
[ ]:
conda create -n <environment_name> python=3.8
5. Activate a conda environment
Run the following command on the terminal to activate the conda environment:
[ ]:
conda activate <environment_name>
6. Clone SOView code
[ ]:
git clone https://github.com/yuanzhiyuan/SOView
If cloning the code fails through git, please download it at https://github.com/yuanzhiyuan/SOView, upload it to the folder created above, and extract it.
7. Open the SOView directory
[ ]:
cd SOView
8. Install SOView package from source code
[ ]:
pip install .
Installation Pysodb
Keep the conda environment active
9. 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.
10. Open the Pysodb directory
[ ]:
cd pysodb
11. 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
[1]:
print('finish!')
finish!