Setting up the environment

This documentation assumes that you are working under a Linux environment with python 3.9 or newer. But the process is almost the same for windows and mac os.

Installation from source

Please note that in order to avoid any conflict between python modules, it is strongly advised that you install cutevariant in its own python virtual environment.

Python 3.9 or newer is required as well as sqlite>=3.32.

# Clone repository
git clone https://github.com/labsquare/cutevariant.git
cd cutevariant
# Create a virtual environement
python3 -m virtualenv venv 
source venv/bin/activate
# Install cutevariant deps in local mode
python -m pip install -e 
# Run cutevariant as module 
python -m cutevariant # or `make run`
# Run test 
python -m pytest tests

Troubleshooting

Wrong Sqlite version on Linux

# Uninstall previous versions of sqlite3 (to avoid conflicts)
sudo apt remove sqlite3
# Download latest sqlite version
wget https://www.sqlite.org/2022/sqlite-autoconf-3380500.tar.gz
# Extract it
tar -xvf sqlite-autoconf-3380500.tar.gz
cd sqlite-autoconf-3380500
./configure
# Run make to build
make
# Run make install, this will put the shared object in /usr/local/lib
sudo make install
# Then add LD_LIBRARY_PATH to your bash profile (either ~/.zshrc, ~/.bashrc, or whatever is your favorite)
echo "export LD_LIBRARY_PATH=/usr/local/lib" >> ~/.zshrc
# Source your shell profile so you don't have to restart it
source ~/.zshrc
#Now just to be sure:
sqlite3 --version
# You should see 3.38 now. If not, this means that the installation went wrong.
# That's it! Now you can install cutevariant, either from PyPI or directly from source