Merge branch 'develop' into 'master'

Regular merge of develop

See merge request !76

2020/2020-03-30_basicGitTraining/slides/best_practices.md

+# Best practices
+
+* `pull` before `push`
+* Work on your <font color="red">own</font> branch (in your own fork), and **not** on `master` and **not** on `develop`
+* Do **not push** to `master`, but **submit a Merge Request (MR)**
+* Get your code **reviewed** by your peers (submit a MR!)
+* Submit a MR **often**!
+* `clone` a repository, do not download the `.zip` file.
+* Do **not** combine `git` commands
+   ```bash
+   $ git commit -am "myMessage" # do not do this
+   ```
+* Stage only 1 file at once using
+   ```bash
+   $ git add myFile.md
+   ```
+* Commit **only a few files** at once (after multiple separate `git add` commands)
+* `Push` often - avoid conflicts
+
+Remember: **A `push` a day keeps conflicts away!**

2020/2020-03-30_basicGitTraining/slides/branches.md

+# Development scheme
+
+
+Generally, in a repository, there are guidelines for contributing.
+
+<div class="fragment">
+
+A common development scheme is dual with a:
+
+- **development** version of the code on `develop`
+- **stable** version of the code on `master`
+
+
+A **version** of the code is referred to as a **branch**.
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+<font color="red">In the practice repository, the development branch is called `develop`!</font>
+
+<div class="fragment">
+
+![bulb](slides/img/bulb.png) Use this dual development scheme for your own repositories!
+
+
+
+# Branches
+
+A **version** of the code (i.e., a **branch**) is made up of a sequence of code changes.
+
+<div class="fragment">
+
+These individual code changes are called **commits**.
+
+
+For instance, the `master` and `develop` branches can be represented as a timeline:
+<img src="slides/img/branch-master.png" class="branch-master" height="500em"/>
+
+
+
+# Switch between branches
+
+List all branches of the repository with
+```bash
+$ git branch -a
+```
+
+Exit by typing `q`. The branch with the * is the current branch.
+
+<div class="fragment">
+
+Checkout another branch
+```bash
+$ git checkout <branchName>
+```
+
+<div class="fragment">
+
+You can switch to the `develop` branch with
+```bash
+$ git checkout develop
+```
+If the local branch does not exist but the remote does, it is created automatically.
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+
+# Create your own version
+
+Assume that you want to work on a file:
+
+<div class="fragment">
+
+<font color="red">Create a new **branch**!</font>
+
+```bash
+$ git checkout -b myBranch
+```
+The `-b` flag creates the branch. Locally, you have your own version now:
+<img src="slides/img/branch-create.png" class="branch-create" height="500em"/>
+
+
+
+
+Push your version to your fork:
+```bash
+$ git push origin myBranch
+```
+
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px">

2020/2020-03-30_basicGitTraining/slides/cloneRepo.md

+# How do I start working on a repository?
+
+You have to `clone` it first:
+
+```bash
+$ git clone ssh://git@git-r3lab-server.uni.lu:8022/<groupName>/myRepo.git myRepo
+```
+
+If you did not configure your SSH key, clone using HTTPS:
+```bash
+$ git clone https://git-r3lab.uni.lu/<groupName>/myRepo.git myRepo
+```
+
+You will be prompted to enter your credentials.

2020/2020-03-30_basicGitTraining/slides/configuration.md

+# How to configure `git`?
+
+```bash
+$ git config --global user.name "Firstname Lastname"
+$ git config --global user.email "first.last@uni.lu"
+```
+
+Test whether your username and email have been registered
+
+```bash
+$ git config --list
+```
+
+This should list the configuration with `user.name` and `user.email`.
+
+Exit by typing `q`.
+
+
+
+# What is an SSH key?
+
+An SSH key is a secure access credential.
+
+**Principle**: <br><br>
+Communicate **securely** with Github/Gitlab **without** entering the username/password.
+
+
+
+# How do I get and set my SSH key?
+
+Check if you already have an SSH key:
+
+```bash
+$ ls -al ~/.ssh
+```
+
+If there are 2 files named `id_rsa`, you have an SSH key.
+
+If you don’t have yet an SSH key, you have to generate one:
+```bash
+$ ssh-keygen -t rsa # -b 4096
+```
+
+If you set a password to your key (recommended), add it to the `ssh-agent`:
+```bash
+$ eval "$(ssh-agent -s)"
+$ ssh-add -K ~/.ssh/id_rsa
+```
+
+Then, add the SSH key to Github/Gitlab.
+
+<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file

2020/2020-03-30_basicGitTraining/slides/essential_commands.md

+# The 5 essential commands
+
+
+**Yes**, you only need 5 commands!
+
+`pull, status, add, commit, push`
+
+or in other words (remember these!):
+```bash
+$ git pull <remote> <branch>
+$ git status
+$ git add myFile.md # example
+$ git commit -m "myMessage" # example
+$ git push <remote> <branch>
+```
+
+
+
+# Pull the latest version of an existing branch
+
+Pull the latest revision on branch `myBranch`:
+```bash
+$ git pull origin myBranch
+# Already up to date
+```
+
+<div class="fragment">
+
+Verify its `status` with:
+```bash
+$ git status
+```
+
+
+
+# Modify a file
+
+Copy the file `template.md` in the folder `attendees` and rename it with your firstname:
+
+```bash
+$ cd attendees
+$ cp firstnameLastname.md myName.md
+```
+
+Then, make your changes with your favorite editor!
+
+
+
+# Add your file to the stage
+
+First, check the repository status
+```bash
+$ git status
+# uncommitted changes (displayed in red)
+```
+
+
+<div class="fragment">
+
+Now, add the file (bring it on stage)
+```bash
+$ git add myName.md # replace myName
+$ git status
+# returns the same as before, generally in green (means staged)
+```
+
+<div class="fragment">
+
+**ADVANCED**: If there have been more changes after the file has been added, you can see your changes in the terminal
+```bash
+$ git diff
+```
+exit with `q`
+
+
+
+# Add a commit message
+
+```bash
+$ git commit -m "Add the profile of <myName>"
+$ git status
+```
+
+
+
+# Push your file to your fork
+
+```bash
+$ git push origin myBranch
+```
+
+<div class="fragment">
+
+**ADVANCED**: see the log of all the commits (and your last one) in the terminal
+```bash
+$ git log
+```
+exit by typing `q`.
\ No newline at end of file

2020/2020-03-30_basicGitTraining/slides/forks.md

+# What is a `fork`?
+
+<center>
+<img src="slides/img/fork.jpg" class="as-is" height="500em"/>
+</center>
+<!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
+
+
+
+# Not really ...
+
+<center>
+<img src="slides/img/fork-crossed.png" class="as-is" height="500em"/>
+</center>
+
+
+
+# What is a `fork`?
+
+- In general, when contributing to a repository, you only have **read** access.
+- In other words, you can only **pull** (unless it is your own repository or access has been granted).
+- In general, you **cannot write** changes. In other words, you do not have **push** access.
+- You have to work on your **own copy**.
+- In other words, you have to work on your own <font color="red">**fork**</font>.
+
+
+
+# How to get a fork?
+
+Browse to the original repository and click on the button `Fork`:
+
+![Fork the repo](https://help.github.com/assets/images/help/repository/fork_button.jpg)
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+
+# Time to practice!
+
+Fork the practice repository: <br><br>
+https://git-r3lab.uni.lu/R3/school/git/basic-practice-pages<br><br>
+
+
+Then, clone your fork to your home directory!
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+```bash
+$ git clone ssh://git@git-r3lab-server.uni.lu:8022/<yourName>/basic-practice-pages.git
+```
+
+Change to the practice directory with:
+```bash
+$ cd basic-practice-pages
+```
+
+
+
+# A note on shortcuts ...
+
+<font color="red">
+Any other rudimentary method such as
+
+*'I simply download the `.zip` and unzip it - works like a charm!'*
+
+shall **be avoided**!
+</font>
+
+**Why?**
+
+
+
+# How to update my fork?
+
+As you have your own fork, it will not automatically be updated once the original repository is updated.
+
+![bulb](slides/img/bulb.png) You have to update it yourself!
+
+<br>
+
+**More on that later!**
+

2020/2020-03-30_basicGitTraining/slides/github_gitlab.md

+# GitHub and GitLab
+
+<img src="https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png" alt="GitHub" style="width: 200px;"/>
+<img src="https://gitlab.com/gitlab-com/gitlab-artwork/raw/master/logo/logo-extra-whitespace.png" alt="GitLab" style="width: 200px;"/>
+
+GitHub and GitLab are VCS systems.
+
+GitHub/Gitlab are both **publicly available**, but GitLab can be **on-premise**.
+
+Positive point: GitHub and GitLab are (almost) the same.
+
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+
+- **GitHub**: [https://github.com](https://github.com)
+- Public GitLab: [https://gitlab.com](https://gitlab.com)
+- LCSB specific: [https://git-r3lab.uni.lu](https://git-r3lab.uni.lu)
\ No newline at end of file

2020/2020-03-30_basicGitTraining/slides/img

+../../../2019/2019-06-11_basicGitTraining/slides/img
\ No newline at end of file

2020/2020-03-30_basicGitTraining/slides/index.md

+# R3.school
+
+## March 30th, 2020
+
+<div style="top: 6em; left: 0%; position: absolute;">
+    <img src="theme/img/lcsb_bg.png">
+</div>
+
+<div style="top: 5em; left: 60%; position: absolute;">
+    <img src="slides/img/r3-training-logo.png" height="200px">
+    <br><br><br>
+    <h1>git training for beginners</h1>
+    <br><br><br><br>
+    <h4>
+        Laurent Heirendt, Ph.D.<br><br>
+        laurent.heirendt@uni.lu<br><br>
+        <i>Luxembourg Centre for Systems Biomedicine</i>
+    </h4>
+</div>

2020/2020-03-30_basicGitTraining/slides/installation.md

+# The terminal (shell)
+
+**macOS users:**
+
+> Start the Terminal from your `/Applications` directoy.
+
+![bulb](slides/img/bulb.png) Install iTerm2: [https://www.iterm2.com](https://www.iterm2.com)
+
+<br>
+
+**Windows users:**
+
+> Install Git Bash: [https://git-scm.com/download/win](https://git-scm.com/download/win)
+
+<br>
+
+**Linux users:**
+
+> Launch default terminal.<br>
+![bulb](slides/img/bulb.png) Install Terminator: [https://launchpad.net/terminator](https://launchpad.net/terminator)
+
+
+
+# Installation of `git`
+
+<img src="slides/img/github_app.png" class="as-is" height="200" />
+
+**macOS**
+
+> Install *Xcode Command Line Tools*
+
+<br>
+
+**Windows**
+
+> Install Git Bash: <br>`https://git-scm.com/download/win`
+
+<br>
+
+**Linux (Ubuntu)**
+
+```bash
+$ sudo apt-get install git-all
+```
+
+
+
+# How to get started?
+
+**macOS**
+
+> Start the `Terminal` or `iTerm`.
+
+<br>
+
+**Windows**
+
+> Start `GUI Bash`.
+
+<br>
+
+**Linux (Ubuntu)**
+
+> Start the `Terminal` or `Terminator`.

2020/2020-03-30_basicGitTraining/slides/list.json

+[
+    { "filename": "index.md" },
+    { "filename": "overview.md" },
+    { "filename": "what_is_git.md" },
+    { "filename": "github_gitlab.md" },
+    { "filename": "installation.md" },
+    { "filename": "the_terminal.md" },
+    { "filename": "the_editor.md" },
+    { "filename": "configuration.md" },
+    { "filename": "cloneRepo.md" },
+    { "filename": "forks.md" },
+    { "filename": "branches.md" },
+    { "filename": "essential_commands.md" },
+    { "filename": "merge.md" },
+    { "filename": "syncFork.md" },
+    { "filename": "best_practices.md" },
+    { "filename": "thanks.md" }
+]

2020/2020-03-30_basicGitTraining/slides/merge.md

+# Merge (pull) requests
+
+If you want your changes to be reflected on the `develop` or `master` branches,
+**submit a merge request (MR)** via the git-r3lab interface.
+
+Use the **interface** to make use of your peers to review your code!
+<img src="slides/img/branch-merge.png" class="branch-merge" height="500em"/>
+
+Once merged, you can delete the branch via the interface.
+
+<div class="fragment">
+
+<img src="slides/img/icon-live-demo.png" height="100px" >
\ No newline at end of file

2020/2020-03-30_basicGitTraining/slides/overview.md

+# Overview
+
+1. What is `git`? What is the use of `git`?
+2. GitHub and GitLab
+3. The terminal
+4. Installation of `git`
+5. The editor
+6. How do I configure `git`?
+7. Where and how to start?
+8. What is a fork?
+9. What are branches?
+10. The 5 essential commands (`pull` / `status` / `add` / `commit` / `push`)
+11. What are merge/pull requests?
+12. How do I synchronize my fork?
+13. Best practices
\ No newline at end of file

2020/2020-03-30_basicGitTraining/slides/syncFork.md

+# Synchronize your fork
+
+![bulb](slides/img/bulb.png) Remember, we have to regularly update our own copy of the code.
+
+
+Add the `upstream` address (original/protected repository)
+```bash
+$ URL=ssh://git@git-r3lab-server.uni.lu:8022/R3/school/git/basic-practice-pages.git
+$ git remote add upstream $URL
+```
+
+![bulb](slides/img/bulb.png) Note the change in the URL.
+
+
+You can then check whether the remote address is set correctly
+```bash
+$ git remote -v
+```
+
+<div class="fragment">
+
+Fetch the changes from upstream (similar to pull)
+```bash
+$ git fetch upstream
+```
+
+
+
+
+Merge the retrieved changes on the `master` branch:
+```bash
+$ git checkout master
+$ git merge upstream/master
+$ git push origin master
+```
+
+<div class="fragment">
+
+Do the same for the `develop` branch:
+
+```bash
+$ git checkout develop
+$ git merge upstream/develop
+$ git push origin develop
+```
+
+<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file

2020/2020-03-30_basicGitTraining/slides/thanks.md

+# Let's refresh our memories
+
+<div class="fragment">
+
+- What is a **fork**?
+
+<div class="fragment">
+
+- What are **branches**?
+
+<div class="fragment">
+
+- Can I have **multiple branches** in my fork?
+
+<div class="fragment">
+
+- What is a good **development scheme**?
+
+<div class="fragment">
+
+- What are the **5 essential commands**?
+
+
+
+# References & Cheat sheet
+
+1. Git Book: https://git-scm.com/book/en/v2
+
+2. Cheat sheet: http://rogerdudler.github.io/git-guide
+
+