For Developers

Local dev

Install in developer mode.

# Clone project repo (or your own fork)
git clone git@github.com:dib-lab/oxli.git && cd oxli

# Create conda dev environment
mamba env create -f environment.yml -n oxli

# Install in development mode
pip install -e '.[test]'

# Checkout new branch
git checkout -b dev_new_feature

# Edit src/lib.rs
# Go make some changes to the rust library.

# Check formatting
cargo fmt

# Build and install python module
maturin develop

# Run tests
pytest src/python/tests/

Developing with GitPod

You can open a ready to go development environment on GitPod using this link. You will need to create a GitPod account.

To test the oxli python API on GitPod, open a Jupyter Lab session with these options.

# Launch Jupyter Lab 
jupyter lab --NotebookApp.allow_origin='*' \
    --NotebookApp.allow_remote_access=True \
    --NotebookApp.token='' \
    --NotebookApp.password='' \
    --no-browser \
    --port=8888