Installation¶
scVelo requires Python 3.6 or later. We recommend to use Miniconda.
PyPI¶
Install scVelo from PyPI using:
pip install -U scvelo
-U
is short for --upgrade
.
If you get a Permission denied
error, use pip install -U scvelo --user
instead.
Development Version¶
To work with the latest development version, install from GitHub using:
pip install git+https://github.com/theislab/scvelo@develop
or:
git clone https://github.com/theislab/scvelo && cd scvelo
git checkout --track origin/develop
pip install -e .
-e
is short for --editable
and links the package to the original cloned
location such that pulled changes are also reflected in the environment.
To contribute to scVelo, cd
into the cloned directory and
install the latest packages required for development together with the pre-commit hooks:
pip install -e ".[dev]"
pre-commit install
Dependencies¶
Parts of scVelo (directed PAGA and Louvain modularity) require (optional):
pip install python-igraph louvain
Using fast neighbor search via hnswlib further requires (optional):
pip install pybind11 hnswlib
Jupyter Notebook¶
To run the tutorials in a notebook locally, please install:
conda install notebook
and run jupyter notebook
in the terminal. If you get the error Not a directory: 'xdg-settings'
,
use jupyter notebook --no-browser
instead and open the url manually (or use this
bugfix).
If you run into issues, do not hesitate to approach us or raise a GitHub issue.