murthylab/codex

Explore the FlyWire Connectome

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
poetry shell

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

./scripts/make_data.sh

Run service locally

./scripts/run_local.sh

To run in Flask debug mode

./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)

./scripts/run_unit_tests.sh

Linting / code formatting

./scripts/lint.sh