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Contributing

Welcome

Welcome to the team! The CoronaWhy Geo Task Force is excited to have you be part of this incredible crowd-sourced effort to better understand and synthesize COVID-19-related literature. The main focus of our task force is centered around three goals:

  • Provide high-quality data to complement the literature provided by #task-risk on geographical risk factors for the spread of COVID-19.
  • Extract information to enable compelling visualizations of what is currently happening by #data-viz .
  • Extract important geographic location data from the corpus of scientific papers to help domain experts select the most relevant literature for various topics.

Everyone is welcome to contribute code via pull requests, file issues on GitHub, add to our documentation, or to help out in any other way, and their work will be greatly appreciated! Every little bit helps, and credit will always be given.

If you are interested in getting involved ping @Daniel Robert-Nicoud or @Manuel Alvarez in the CoronaWhy slack team.

We will be communicating primarily through the Slack #task-geo channel. Project management/task delegation will be visible on the team's Trello board (ping @Marie Bjerede to get access to that).

Your hard work is invaluable in making quick, actionable progress on understanding the state of the world with regard to the combatting this terrible pandemic. THANK YOU.

You can contribute in many ways:

Types of Contributions

Report Bugs

Report bugs at the GitHub Issues page.

If you are reporting a bug, please include:

  • Your operating system name and version.
  • Any details about your local setup that might be helpful in troubleshooting.
  • Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.

Write Documentation

task-geo could always use more documentation, whether as part of the official task-geo docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to file an issue at the GitHub Issues page.

If you are proposing a feature:

  • Explain in detail how it would work.
  • Keep the scope as narrow as possible, to make it easier to implement.
  • Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!

Ready to contribute? Here's how to set up task-geo for local development.

  1. Fork the task-geo repo on GitHub.

  2. Clone your fork locally:

    $ git clone [email protected]:your_name_here/task-geo.git

  3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:

    $ mkvirtualenv task-geo
$ cd task-geo/
$ make install-develop

  4. Create a branch for local development:

    $ git checkout -b name-of-your-bugfix-or-feature

    Try to use the naming scheme of prefixing your branch with gh-X where X is the associated issue, such as gh-3-fix-foo-bug. And if you are not developing on your own fork, further prefix the branch with your GitHub username, like githubusername/gh-3-fix-foo-bug.

    Now you can make your changes locally.

  5. While hacking your changes, make sure to cover all your developments with the required unit tests, and that none of the old tests fail as a consequence of your changes. For this, make sure to run the tests suite and check the code coverage:

    $ make lint       # Check code styling
$ make test       # Run the tests
$ make coverage   # Get the coverage report

  6. When you're done making changes, check that your changes pass all the styling checks and tests, including other Python supported versions, using:

    $ make test-all

  7. Make also sure to include the necessary documentation in the code as docstrings following the Google docstrings style. If you want to view how your documentation will look like when it is published, you can generate and view the docs with this command:

    $ make view-docs

  8. Commit your changes and push your branch to GitHub:

    $ git add .
$ git commit -m "Your detailed description of your changes."
$ git push origin name-of-your-bugfix-or-feature

  9. Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

  1. It resolves an open GitHub Issue and contains its reference in the title or the comment. If there is no associated issue, feel free to create one.
  2. Whenever possible, it resolves only one issue. If your PR resolves more than one issue, try to split it in more than one pull request.
  3. The pull request should include unit tests that cover all the changed code
  4. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the documentation in an appropriate place.
  5. The pull request should work for all the supported Python versions. Check the Github Build Status page and make sure that all the checks pass.
  6. If you are working on the task-geo team, please make one of your team mates review your code before submitting the PR.
  7. Have a look at older PR for the same kind of submission, and check that your code is compliant of the comments made to them, and the rationale behind them.

Unit Testing Guidelines

All the Unit Tests should comply with the following requirements:

  1. Unit Tests should be based only in unittest and pytest modules.
  2. The tests that cover a module called task_geo/path/to/a_module.py should be implemented in a separated module called tests/task_geo/path/to/test_a_module.py. Note that the module name has the test_ prefix and is located in a path similar to the one of the tested module, just inside the tests folder.
  3. Each method of the tested module should have at least one associated test method, and each test method should cover only one use case or scenario.
  4. Test case methods should start with the test_ prefix and have descriptive names that indicate which scenario they cover. Names such as test_some_methed_input_none, test_some_method_value_error or test_some_method_timeout are right, but names like test_some_method_1, some_method or test_error are not.
  5. Each test should validate only what the code of the method being tested does, and not cover the behavior of any third party package or tool being used, which is assumed to work properly as far as it is being passed the right values.
  6. Any third party tool that may have any kind of random behavior, such as some Machine Learning models, databases or Web APIs, will be mocked using the mock library, and the only thing that will be tested is that our code passes the right values to them.
  7. Unit tests should not use anything from outside the test and the code being tested. This includes not reading or writing to any file system or database, which will be properly mocked.

Tips

To run a subset of tests:

$ python -m pytest tests.test_task_geo
$ python -m pytest -k 'foo'