Git workflow¶

This step-by-step git approach is a your safe haven on working with git. When you stick to these guidelines, you will be succesfully using the ‘Github workflow’ we apply for the COVID 19 model. The master branch is holy to us and should be on all time a working, up-to-date representation of the functionalities!

This workflow flow assumes you have forked the COVID repository of Biomath (called upstream by default) to your own Github account (called origin by default) and cloned your own version to your computer.

Before I start working¶

STEP 1: Update the master branch on my PC to make sure it is aligned with the remote master (upstream):
```
  git checkout master
  git pull upstream master
```
STEP 2: Choose your option:
- OPTION 2A: I already have a branch I want to continue working on: Switch to existing topic branch:
```
  git checkout name_existing_branch
  git fetch upstream
  git merge upstream/master
```
  (Note: Normally you are the only working on your branch. In the rare case someone updated your branch, update your branch with the remote adjustments: git merge upstream/name_existing_branch)
- OPTION 2B: I’ll make a new branch to work with: Create a new topic branch from master(!):
```
  git checkout master
  git checkout -b name_new_branch
```

While editing¶

STEP 3.x: adapt in tex, code,… (multiple times)

New files added
```
  git add .
```

Adaptation

  git commit -am "clear and understandable message about edits"

Edits on branch ready¶

STEP 4: Pull request to add your changes to the current master. Choose your option:
- OPTION 2A CHOSEN:
```
  git push origin name_existing_branch
```
- OPTION 2B CHOSEN:
```
  git push origin name_new_branch
```
STEP 5: Code review!

Go to your repo online and click the New pull request block or click the link in the message in the terminal. This will guide you to the Biomath github repo to make the pull request. You and collaborators can make comments about the edits and review the code.

If everything is ok, click the Merge pull request, followed by confirm merge. Delete the online branch, since obsolete.

You’re work is now tracked and added to master! Congratulations.

If the code can’t be merged automatically (provided by a message online), go to STEP 7.

STEP 6: Update local master and remove local merged branch

  git checkout master
  git pull upstream master
  git branch -d name_merged_branch

Pull request can not be merged¶

STEP 7: master has changed and there are conflicts: update your working branch with rebase

  git checkout name_existing_branch
  git fetch origin
  git merge upstream/master
  # fix conflicts local
  git add file_with_conflict
  git commit file_with_conflict
  git push origin name_existing_branch