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CONTRIBUTING.md

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Contributing

Note: every project (i.e., subdirectories) also contains additional contribution information relevant to the specific sub-project.

Local setup

Before you begin with setting up your local development environment, ensure that you have the following list of tools installed:

After making sure that you have all the required dependencies take the following steps to setup your local environment:

  1. Clone this repository by running git clone [email protected]:hpi-dhc/PharMe.git or git clone https://github.com/hpi-dhc/PharMe.git in your terminal
  2. If you use VSCode, Open the workspace ./pharme.code-workspace in VSCode. You can find this workspace in the project root.

    Note: You will most likely be prompted by VSCode to install some extensions and get packages. Please confirm these two actions.

  3. From the root of the project, run yarn bootstrap in order to set up pre-commit linting via Husky. This is used primarily to enforce the conventional-commit style

Selecting an issue

Visit the issues page and look for an interesting problem you want to solve.

Once you have selected an issue to work on, assign yourself to that issue so we don't end up with two people doing the same thing.

Working on stuff

Note: This project enforces a conventional commit style. We highly encourage you to familiarize yourself with this format of commit messaging in order to result in more readable, meaningful commit messages (not only for tools such as auto-changelog-generators, but also your fellow contributors!)

To avoid conflicts with other contributors, create a new branch and switch to that branch. You could name your branch according to this pattern: issue/<id>-<lowercase-issue-title-with-dashes> (e.g., issue/3-contribution-guide).

Work on your code. Repeat:

  • Implement your changes
  • Commit your changes
  • Push to the repo

Debugging

If you wish to debug, simply go to the 'Run and Debug' section of the vscode activity bar (Ctrl+Shift+D), select the project you would like to debug and hit the green play button.

It's working

When you're done, file a pull request. We will take a look at your code and once all checks pass, your code can get merged 🥳

Dual remote repository setup

This repository exists in two versions: (1) the public version on GitHub, and (2) a private ("study") version that is being specifically adapted for a study involving PharMe on a privately hosted GitHub at Icahn School of Medicine at Mount Sinai.

The study version should always extend the public version (i.e., changes affecting both versions should be made in the public repository and merged to the Sinai repository). This process currently needs to be done manually.

To be able to manage changes accross versions, we keep both remotes in one local repository. To support multipe users for the different remote repositories, we use git-worktree. To setup the two remotes with git-worktree run the following commands:

  • In your PharMe repository, add the Sinai remote: git remote add sinai https://github.mountsinai.org/HPIMS/pharme_project
  • Fetch from the new remote: git fetch sinai
  • Checkout the Sinai main branch as a working tree: git worktree add --track -b Sinai-PharMe ../Sinai-PharMe sinai/main
  • Change directories to the newly created working tree: cd ../Sinai-PharMe
  • Enable different Git configurations per worktree: git config extensions.worktreeConfig true
  • Configure the Git user to match the Sinai GitHub credentials
    • git config --worktree user.name "YOUR-USERNAME"
    • git config --worktree user.email "[email protected]"
  • Configure the push behavior to be able to push directly to a differently named upstream branch: git config --worktree push.default upstream