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Install pre-commit hooks

We use pre-commit.com to run a set of standard pre-commit hooks. You can install these as follows:

cd taxonium
pip install pre-commit
pre-commit install

For front-end development

cd taxonium_component
yarn install
yarn storybook

This should bring up a development server showing Taxonium.

Linking taxonium_data_handling

A small amount of front-end code comes from the taxonium_data_handling repo. If you need to work on this code then you can "link" the taxonium_data_handling to the web client repo.

cd taxonium_data_handling
yarn install
yarn link
cd ../taxonium_component
yarn link taxonium_data_handling

For back-end development

cd taxonium_backend
yarn install
node server.js --data-file tfci.jsonl.gz

This will launch the backend server on port 8000, from a small tree file. (Though sometimes this checked in tree file gets out of date in terms of format, you can also use the latest full public tree: https://cov2tree.nyc3.cdn.digitaloceanspaces.com/latest_public.jsonl.gz but this will need more RAM).

Linking taxonium_data_handling

A small amount of backend code comes from the taxonium_data_handling repo. If you need to work on this code then you can "link" the taxonium_data_handling to the backend repo.

cd taxonium_data_handling
yarn install
yarn link
cd ../taxonium_backend
yarn link taxonium_data_handling

Codespaces

We do a lot of development for the client side version in GitHub Codespaces. There is no reason that you have to do that, but the devcontainer set up means you can easily if you so wish.