Development

Prerequisits

The ${BIOTERM_ROOT_DIRECTORY} contains an additional requirements_dev.txt file for developers. Use

$ pip install -r requirements_dev.txt

after having your virtual environment activated, to install the additional packages required for developing. Then, run

$ pre-commit install  # installs .git/hooks/pre-commit
$ pre-commit install --hook-type pre-push  # installs .git/hooks/pre-push

to set up the git hook scripts stored in .pre-commit-config.yaml in the .git/hooks directory.

Settings

When deploying on a local machine, certain settings need to be adopted to ease the development. This especially concerns the server backend and frontend, which are dockerized for production deployment and The nginx configuration needs to be adopted as well, to point to either the docker container’s host adress or the local machine’s localhost.

In addition, on a local machine self-signed certificates are used and TLS verification needs to be disabled.

Warning

Don’t forget to turn TLS verification back on when deploying for production, as this might get by unnoticed.

Backend

In the docker-compose.yml file, uncomment the ports directive for the timescaledb service:

...
    timescaledb:
        ...
        ports:
        - 5432:5432
...

Also, disable the biotermserverapi service completely by commenting out the whole service and its directives.

Then, change the environment variable POSTGRES_SERVER from timescaledb:5432 to localhost:5432.

Set the environment variable USE_TLS to False.

Warning

FastAPI requires Python 3.9 !

Then, set up a virtual environment and install the required packages located in bioterm/server/backend/requirements.txt:

$ python3.9 -m venv .venv
$ source .venv/bin/activate
$ pip install -r requirements.txt

run

$ sudo docker compose up -d

in bioterm/server/backend to start the PostgreSQL service.

To run the server use the following command in the bioterm root directory:

$ uvicorn bioterm.server.backend.app.main:app --reload --host 0.0.0.0 --port 8001

Frontend

For information regarding frontend development, please refer to webUI.

NGINX

For local development, change the API section configuration as follows:

### API SECTION

server {

    ...

    location / {
        # set $api_upstream http://biotermserverapi:8001;
        # proxy_pass $api_upstream;
        proxy_pass http://host.docker.internal:8001;

        ...

    }
}

Change the APP section as follows:

### APP SECTION

server {

    ...

    location / {
        # set $app_upstream http://bioterm-webui:8081;
        # proxy_pass $app_upstream;
        proxy_pass http://host.docker.internal:8081/;

        ...

    }
}

authentik

Commmitlint

feat: new feature
fix: bug fix
docs: changes to the documentation
style: formatting, missing semi colons, etc; no production code change
refactor: refactoring production code, eg. renaming a variable, moving stuff around
test: adding missing tests, refactoring tests; no production code change
chore: TBD

Coding Style

Please check Coding Style Guide for details.