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CONTRIBUTING.md

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Collaborative Development

Prerequisites

Workflow

The workflow for contributing to this project has been inspired by the workflow described by Vincent Driessen.

Step 1: Describe the issue on GitHub

Create an issue in the GitHub repository. The issue title describes the problem you will address. This is an important step as it forces one to think about the "issue".

Step 2: Solve the issue locally

0. Get the latest version of the develop branch
git checkout develop
git pull
1. Create a new (local) branch
git checkout -b feature-1314-my-feature

Naming convention for branches: type-issue-nr-short-description

type

  • master / main / stable - includes the current stable version
  • dev - includes all current developments
  • feature - includes the feature that will be implemented
  • hotfix - includes small improvements before an release, should be branched from a release branch
  • release - includes the current version to be released

The majority of the development will be done in feature branches.

issue-nr

The issueNumber should be taken from Step 1. Do not use the "#".

short-description

Describe shortly what the branch is about. Avoid long and short descriptive names for branches, 2-4 words are optimal.

Other hints:

  • Separate words with - (minus)
  • Avoid using capital letters
  • Do not put your name to the branch name, it's a collaborative project
  • Branch names should be precise and informative

Examples of branch names : feature-42-add-new-ontology-class or feature-911-branch-naming-convention

2. Start editing the files
  • Divide your feature into small logical units
  • Start to write the documentation or a docstring
  • Don't rush, have the commit messages in mind
3. Commit your changes
git commit filename.md
3.2 Fix your latest commit message

You want to improve your latest commit message? Your latest commit is not pushed yet? Edit the commit message of your latest commit

git commit --amend
4. Push your local branch on the remote server origin

If your branch does not exist on the remote server yet, use:

git push --set-upstream origin feature-1314-my-feature

Then push regularly with:

git push

Step 3: Run tests locally

To run tests locally,

  1. create virtualenv in root folder of repo
python -m venv venv

  1. Activate virtualenv

    Linux:

    . venv/bin/activate

    Windows:

    . venv/Scripts/activate

  2. Install requirements

pip install -r requirements.txt
  1. Integration/unit tests 
    pytest
    And for a complete run in different environments: 
    tox -v
  2. Linting tests 
    flake8
    and 
    pylint
    You can fix the linting errors either manually or with the packages autopep8 or black for example.

Step 4: Submit a pull request (PR)

Follow the steps of the GitHub help to create the PR. Please note that you PR should be directed from your branch (for example myfeature) towards the branch dev.

Add a line Fix #<number of the issue created in Step 2.0> in the description of your PR, so that when it is merged, it automatically closes the issue once your code gets merged into the default branch of your repository. Here is a list of other keywords you can use to automatically close the issues

Step 5: Setup continuous integration

To have the test run automatically everytime you push to a pull request you can add the bash commands under # command to run tests of the .travis.yml file. For this you need to have an account by Travis and link your repo to their service. Soon GitHub action might take care of this directly within GitHub.

In the .travis.yml file are many options commented out, you can have very complexe schemes to test on many different python versions etc. For more information look at Travis doc for python.

If a Python interpreter version is missing:

Linux (Ubuntu):

sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt-get update
# Install only missing interpreters:
sudo apt-get install python3.6
sudo apt-get install python3.7