Installation

Important

Our tool could be installed on Linux/Windows with Python3.8.

Attention

When installing Stereopy <= 1.0.0, please use conda install stereopy or conda install stereopy==1.0.0 commands. Because a third-party package removed its historical versions which would lead to an installation failure.

Anaconda

We strongly recommend your operation in an isolated conda environment, so firstly run:

conda create --name st python=3.8  # The env name could be set arbitrarily, not only st.

Then get into the environment you build:

conda activate st

Use the installation command with conda:

conda install stereopy -c stereopy -c grst -c numba -c conda-forge -c bioconda -c fastai

PyPI

The same beginning as conda part:

conda create --name st python=3.8

conda activate st

Use PyPI run:

pip install stereopy

Development Version

The same beginning as conda part:

conda create --name st python=3.8

conda activate st

Use the latest version of dev branch on Github, you need to clone the repository and enter the directory:

git clone -b dev https://github.com/STOmics/stereopy.git

cd stereopy

pip install -r requirements.txt

python setup.py install

Troubleshooting

Possible installation failed due to some factors:

Version of Python

Make sure you are working on Python3.8.

Conflicts of dependencies

Find out packages that lead to failures, then create a new requirements.txt of them and run:

pip install -r requirements.txt