Gene_Drive

User Installation

pip install Gene_Drive --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple

Pre-requisites

• Python 3.9 x64

Development Environment Setup

When setting up your environment for the first time, you can use the following instructions

Local Setup

1. Clone the business logic/UI repository:

   > git clone https://github.com/InstituteforDiseaseModeling/dash-gene-drive

2. Clone the data repository: Then clone the repo.

   > git clone https://github.com/InstituteforDiseaseModeling/dash-gene-drive-data

3. Create a virtualenv. On Windows, please use venv to create the environment python -m venv dash-gene-drive On Unix(Mac/Linux) you can use venv or virtualenv
4. Activate the virtualenv
5. Set environment variables DATA_DIR = path/to/dash-gene-drive-data ENVIRONMENT = development
6. If you are on windows, run pip install py-make --upgrade --force-reinstall
7. Then run python ./.dev_scripts/bootstrap.py. This will install all the tools.
8. Run the app

python main.py

Development Tips

There is a Makefile file available for most common development tasks. Here is a list of commands

clean       -   Clean up temproary files
setup-dev   -   Set up packages in dev mode 

On Windows, you can use pymake instead of make

Container Setup

using built in development server

docker-compose -f docker-compose.yml build
docker-compose -f docker-compose.yml up

using gunicorn

docker-compose -f docker-compose.staging.yml build
docker-compose -f docker-compose.staging.yml up