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CellCounter

CircleCI Coverage Status

Cellcounter Django app to count cells for haematological blood film analysis. Cellcounter is deployed at cellcountr.com.

Running Locally

Clone the repository:

git clone ...

Create a virtual environment:

virtualenv -p python3 .env
source .env/bin/activate
pip install --upgrade pip
pip install -r requirements.txt

(if you don't have virtualenv, then sudo pip install virtualenv) (if you don't have pip, then sudo easy_install pip)

Update your database:

python manage.py migrate

Run the Django webserver locally, setting the DEBUG environment variable:

export DEBUG=True
export ALLOWED_HOSTS="127.0.0.1"
python manage.py runserver

Testing

To run the test suite locally, you also need the test requirements in your virtualenv:

pip install -r test-requirements.txt

export TEST=True
python manage.py test

To install npm from source for JavaScript testing:

curl https://nodejs.org/dist/node-latest.tar.gz | tar xvz
cd node-v*
./configure --prefix=$VIRTUAL_ENV
make install

npm ci

export DEBUG=True; export ALLOWED_HOSTS="127.0.0.1"
./test_integration

To run the test suite via docker:

docker build --target test -t cellcountr/cellcountr_test:latest .

docker run cellcountr/cellcountr_test:latest python manage.py test

Deployment

To create the docker volume to store the media files:

sudo mkdir -p /var/www/mediafiles
docker volume create --driver local --opt type=none --opt device=/var/www/mediafiles --opt o=bind media_volume

To build and run the docker image:

cp env.dev.example env.dev
edit env.dev
docker compose build

docker compose up -d

docker compose exec web python manage.py migrate --no-input

To stop the docker image:

docker compose down -v