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CONTRIBUTING.md

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Language translations

If you would like to contribute to CoVizu by providing a page translation in another language, thank you!

  • To get started, make a copy of index.html and add a two-letter language code suffix to the basename, e.g., index-fr.html.

  • We have moved all text elements into a single file index.html so that contributors do not have to search through the various JavaScript files for content to translate. In order for this to work, we have had to create a JSON object at the top of the <head> section of index.html. This maps keywords, e.g., number_cases, to the language-specific replacement, e.g., "nombre de cas". A translation should be provided for every keyword in this JSON.

  • Please check through the following HTML elements for content to translate:

    • <label> elements
    • <option> elements within <select> inputs
    • title tags within <div> and <span> elements
    • text enclosed in <div> and <span> elements
    • header elements, e.g., <h3>

  • There are several help texts to translate that are enclosed in <p> tags in the bottom half of the index.html document.

    • Text enclosed in the title tag of a <span> element must be written in a single line (no line breaks) to render properly.
    • Please leave the GISAID Acknowledgements statement: "We gratefully acknowledge all the Authors" in its original English.

Development environment

Development of CoVizu is primarily being carried out on workstations and servers running Ubuntu 16.04+. However, we have also run the system on desktop computers running macOS 10.13. Most web development is tested in Google Chrome.

Coding style

Python

  • Use four spaces to indent, and other conventions described in the PEP8 style guide. It is easier to use a Python-aware IDE like PyCharm or Atom to automate this for you.

  • Organize your code into functions to facilitate testing and so that methods can be called from other scripts.

  • Isolate the main loop of your code under if __name__ == '__main__' to be executed only if the script is being run at the top level (from the command line).

  • Try to use argparse to provide help documentation for command line execution.

  • Use lowercase with underscores to separate words for function and variable names. Do not use camel-case.

  • Every function should open with a docstring. If the function is very brief with a small number of self-explanatory arguments, then a one-line docstring is fine. Otherwise, use a multi-line docstring. Use :param varname: description entries to document arguments. Use :return: type, description entries to document return values.

Committing your code

  • Do not push commits to the master branch. All development should be tracked in the dev branch and then merged into master after it has been tested.
  • If you are trying to implement something new that can potentially break parts of the code that other developers may be working on, then create a new branch and merge it into dev after you have finished building and testing the code.
  • Please try to write concise and informative commit messages.

Front-end Testing

  • Front-end testing is carried out using Cypress.
  • For the purposes of this project, Cypress needs to be installed via direct download. An installation guide can be found here.
  • The baseUrl is currently set as "http://127.0.0.1:8001/. Changes to it can be made in Cypress.json.

Semantic Versioning

We follow semantic versioning specifications.

The version number (MAJOR.MINOR.PATCH) consist of the:

  • MAJOR version - For changes that break backward compatibility. For example, modifying the JSON data structure required for running the front-end of CoVizu
  • MINOR version - For backwards compatible features additions and other minor changes such as modifying documentation
  • PATCH version - For backwards compatible bug fixes

When opening a pull request, please specify the type of change (major, minor or patch) in the title. e.g patch: bug fixes for the search interface.