Isabl Docs

Contributing Guide

⏱ tutorial time: 20 minutes
This tutorial will help you set up a full Development environment with all components of the isabl infrastructure.
📘 Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given. isabl could always use more documentation, whether as part of the README, in doc-strings, or even on the web in blog posts articles, and such. Also, bet you've read the Zen Of Python.

Isabl API

  1. 1.
    Clone locally:
    git clone [email protected]:papaemmelab/isabl_api.git
    cd api
  2. 2.
    Build containers:
    docker-compose build
  3. 3.
    Run tests using tox:
    docker-compose run --rm django tox
    Or run pytest, pylint or pydocstyle individually:
    docker-compose run --rm django pytest --ds example.settings --cov=isabl_api
    docker-compose run --rm django pylint isabl_api
    docker-compose run --rm django pydocstyle isabl_api

Create a superuser

Create a superuser with username and password set to admin (we will need it later):
docker-compose run --rm django python migrate
docker-compose run --rm django python createsuperuser --email [email protected] --username admin

Start the backend

docker-compose up
Now you can login in the frontend at http://localhost:8000 (there won't be much to see). An easy way to create objects is to run the client tests.

Coverage report

Since tests were run inside a container, we need to combine the coverages to see the html report:
alias opencov="mv .coverage .coverage.tmp && coverage combine && coverage html && open htmlcov/index.html"
pip install coverage && opencov

Isabl CLI

  1. 1.
    Clone locally:
    git clone [email protected]:papaemmelab/isabl_cli.git
    cd cli
  2. 2.
    Install with pip, it is strongly recommended to install in a virtual environment:
    pip install -r requirements.txt
  3. 3.
    Run tests using tox, make sure you created the admin user:
    Or run pytest, pylint or pydocstyle individually:
    py.test tests/ --cov=isabl_cli -s
    pylint isabl_cli
    pydocstyle isabl_cli
Note: if your changes depend on a particular branch of Isabl API, make sure both Isabl CLI and Isabl API branches are called the same so that the travis configuration can pick that up.

Isabl Web

  1. 1.
    Clone locally:
    git clone [email protected]:papaemmelab/isabl_web.git
    cd web
  2. 2.
    Install yarn:
    brew install yarn --without-node
  3. 3.
    Install dependencies:
    yarn install
  4. 4.
    Start the react development server:
    yarn serve
    Important! export FRONTEND_URL=localhost:8080 before running docker-compose up in the api repository, note that the port may vary.


Simply create a PR in github:
git clone [email protected]:isabl/docs.git

Contribute with Github

  1. 1.
    Create a branch for local development and get ready to make changes locally:
    git pull
    git checkout -b name-of-your-bugfix-or-feature
  2. 2.
    Commit your changes and push your branch to GitHub (see the emoji reference):
    git add .
    git config commit.template .gitmessage
    git commit -m ":emoji: your short and nice description"
    git push origin name-of-your-bugfix-or-feature
  3. 3.
    Create a test in:
  4. 4.
    Submit a pull request through the GitHub website.

Formatting projects

Python Projects are formatted with black. Is required for api, cli and apps, simply run:
pip install black && black .
Project web is formatted following the Vue style guide. For this one, simply run:
yarn lint

Bumping version of PyPi

Following the semantic versioning guidelines and update the VERSION file before creating a PR, for instance:
echo v0.1.0 > isabl_api/VERSION
git add isabl_api/VERSION
git commit -m ":gem: bump to version 0.1.0"

Emoji reference

We use emojis to quickly categorize commits and pull requests. These are some common type of changes we use but feel free to ignore the conventions:
type of change
new feature
bug fix
changes to documentation
formatting no code change
refactoring production code
adding/editing test logic
no production code change
bump to new version
Tip: To insert an emoji in mac type control+cmd+space. Alternative, type the emoji's name within two semicolons (e.g. :rocket:).