Neurotoxicology MEA

Python

Examples use uv, but plain pip can be used.

# Create/activate a virtual environment and install dependencies
cd app
uv python install 3.14
uv venv --python 3.14 
source .venv/bin/activate
uv pip install -r requirements/dev.txt

NodeJS

cd app/frontend
npm install
# Live update tailwindcss:
npm run dev

Django

cd app
python manage.py migrate
python manage.py createsuperuser
python manage.py runserver

Podman/Docker Compose

The default Compose file runs the local development image with Django's development server and a PostgreSQL container:

# Optional: override the local admin/admin defaults.
cp .env.example .env
podman compose up --build
# Or: docker compose up --build

Open http://localhost:8000. The local image runs migrations before starting runserver. It also creates the superuser configured by the DJANGO_SUPERUSER_* variables when that username does not exist. Source files and templates are mounted individually so image-built static assets are not hidden by a broad ./app:/app bind mount.

Compose uses admin for both DJANGO_SUPERUSER_USERNAME and DJANGO_SUPERUSER_PASSWORD when they are unset or empty. Values supplied by the shell or .env override these local defaults. DJANGO_SUPERUSER_EMAIL is optional. Direct image starts must provide the required username and password. Any existing active staff superuser is left unchanged. In case of an existing non-superuser with the configured username, startup fails.

Media files are stored in a named volume mounted at /app/media. This is where Django stores uploaded ingest files. The development Compose stack uses the ntx_dev project name, so its database and media volumes are isolated from the production image test setup.

To test the production image locally, use the standalone docker-compose.prod.yaml:

podman compose -f docker-compose.prod.yaml up --build

This uses the cloud image target, does not mount source files, sets DJANGO_DEBUG=False, and runs migrations and the superuser command in the web container before starting Gunicorn. It uses the ntx_prod_local project name to keep database and media volumes separate from dev.

Ingest

For example, using the example data:

cd app
source .venv/bin/activate
python manage.py import_axion_folder ../data
# Replace existing experiments instead of raising IngestionError:
python manage.py import_axion_folder --replace-existing ../data/ENDpoiNTs
# Control conditions default to DMSO; override if needed:
python manage.py import_axion_folder ../data/ENDpoiNTs --control-chemical Water

Development

# Update Python requirements
# Use uv instead of plain pip
uv pip compile requirements/base.in --universal --output-file requirements/base.txt
uv pip compile requirements/dev.in --universal --output-file requirements/dev.txt
uv pip compile requirements/prod.in --universal --output-file requirements/prod.txt

# Use Ruff linter
ruff check

# Use Ruff formatter
ruff format

# Use Pyright type checking
pyright

# Run the tests from the app dir
# for pytest to discover the configuration
cd app
pytest

# Run Django management commands with activated venv:
cd app
python manage.py <command>