Codex - Connectome Data Explorer for FlyWire

Description

Codex is a web application for exploring and analyzing neurons and annotations from the FlyWire Whole Brain Connectome.

Setup

Python 3.9 or later is required.

We recommend using an environment manager such as Poetry:

poetry install

Download and initialize the FlyWire connectome data (initially or upon version updates)

poetry run ./scripts/make_data.sh

Run service locally

poetry run ./scripts/run_local.sh

To run in Flask debug mode

poetry run ./scripts/run_local_dev.sh

Navigate to localhost:5000

Testing before posting a PR or merging (please fork - do not create branches in the main repo)

Manual UI testing (Required)

Run service locally and click around in all pages

Unit tests & code coverage (Required)

poetry run ./scripts/run_unit_tests.sh

If test status or coverage percentage change, update the static badges above

Linting / code formatting

poetry run ./scripts/lint.sh