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0_GitGithub_Workflow.Rmd
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0_GitGithub_Workflow.Rmd
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---
title: "Use GitHub to work with MAgPIE"
subtitle: MAgPIE model development team (magpie@pik-potsdam.de)
date: "`r format(Sys.time(), '%d %B, %Y')`"
author: "Kristine Karstens (karstens@pik-potsdam.de)"
output:
rmarkdown::github_document:
toc: yes
---
# 1 Introduction
MAgPIE is published as open source software on GitHub. Hence we invite all interested people to understand but also develop the code. Since there are various workflows, how to use GitHub for collaborative software development, we want to give some general remarks on our prefered one.
Note the following:
- **Git** is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency (from: https://git-scm.com/ - very good help, documentation, tutorial page for git).
- **GitHub** is an American company (owned by Microsoft) that provides hosting for software development version control using Git. (GitLab, SourceForge and various more are open-source alternatives to GitHub.)
### Learning objectives
The goal of this exercise is to set up MAgPIE for collaborative working. After completion of this exercise, you'll be able to:
1. Fork and update MAgPIE from/with upstream repository.
2. Understand the basic workflow including pull requests and branches.
3. Have heard some very basic git commands and know where to find more help.
# 2 GitHub workflow for magpiemodel
```{r, echo=FALSE, out.width = '100%',fig.align='center'}
knitr::include_graphics("figures/github_workflow.png")
```
Every code development (even bugfixes) will be merged into our main repository under https://github.com/magpiemodel/magpie with the help of so called pull requests. Pull request gives us control over the changes entering our branches. To create a pull request, we use personal or institutional forks. They have to be kept up-to-date with our upstream repository (the original magpiemodel fork).
> **Exercise**: Visit us on https://github.com/magpiemodel/magpie and create your own fork by clicking at 'fork' (at the upper right).
It is basically possible to change the code just using the GitHub interface, but since you want to test and run your code locally you have to clone the repository from your fork anyway. This can be done using the 'https' or 'ssh' adress of your fork together with the `git clone` command (cmd/bash/GUI) at your machine. We recommend to upload an ssh-key and use ssh to connect to GitHub.
> **Exercise**: Visit your fork and clone the repository at your machine.
To keep your fork up-to-date with the upstream repository you can use the GitHub interface. Via `Compare` you are able to check if the upstream is some commits ahead and, if so, merge this new changes into your fork. If you feel familiar with git, you also can do this merging procedure by adding both your fork and the upstream repository as so called 'remotes' to your local repository.
> **Exercise**: Check, if there is anything to merge from the upstream repository into your fork. If so, merge it into your fork.
# 3 Zoo of branches
To start new developments we create feature branches to keep the develop branch clean. In the following figure you can see a simple example for branches and their relationships.
```{r, echo=FALSE, out.width = '100%',fig.align='center'}
knitr::include_graphics("figures/git_branches.png")
```
- The master branch of the upstream repository will be created by the magpiemodel team after accumulation of new developments in the develop branch. Please do not try to create a pull request directly to the master branch when you are not 100% sure, that you have a urgent hotfix.
- The develop branch is the basis for new developments. Create a feature branch at your project fork to start your feature.
- After you have finished your development by creating some commits, you merge your work via a pull request back to the develop branch of the upstream repository. You can merge your changes before into your develop and start a pull request from there or your directly create it from your feature branch.
- The work itself will be done at your local project clone and will be pushed into your project fork. Basic commands for the interaction between your magpie fork and the local working copy can be found in the next section.
# 4 Start to commit yourself
When you start making your first changes to the code at your local copy, we strongly recommend to do a tutorial to get familiar with the basic commands in git. You can also have a look on 'git cheat sheets' like https://about.gitlab.com/images/press/git-cheat-sheet.pdf.
Here we just want to draw your attention to:
- the branching workflow, we kindly ask you to use and
- the various working areas of the git workflow.
```{r, echo=FALSE, out.width = '100%',fig.align='center'}
knitr::include_graphics("figures/git_basics.png")
```
Git wil help you not only to push changes to your remote repositories to version control them, you will also locally control your development steps:
- When you introduce changes at your working directory, you can mark your changes by `git add`-ing them to your 'staging area'.
- After you have collected all your changes for your next commit, you will `git commit` them to your local version history.
- When you `git push` your changes to your remote repository, you will see them finally at your forks GitHub-page.
- Now you can do a `pull request`.
# 5 References to learn more
- https://education.github.com/git-cheat-sheet-education.pdf
- https://git-scm.com/book/en/v2
- https://guides.github.com/activities/hello-world/
- https://www.youtube.com/playlist?list=PLg7s6cbtAD15G8lNyoaYDuKZSKyJrgwB-