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 Compose

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

podman compose up --build

Open http://localhost:8000. The local image runs migrations before starting runserver. Source files and templates are mounted individually so image-built static assets are not hidden by a broad ./app:/app bind mount.

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 prod image target, does not mount source files, sets DJANGO_DEBUG=False, runs migrations once in a short-lived migrate service, and then starts the image default Gunicorn command. 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

# 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>