Merge branch 'develop' into 'master'

Regular merge of develop

See merge request R3/school/courses!50

2019/2019-10-03_basicGitTraining-SIU/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 PR**
+* Get your code **reviewed** by your peers (submit a PR!)
+* Submit a PR **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!**

2019/2019-10-03_basicGitTraining-SIU/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 (i)
+
+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"/>
+
+
+
+
+# Create your own version (ii)
+
+Push your version to your fork:
+```bash
+$ git push origin myBranch
+```
+
+<img src="slides/img/icon-live-demo.png" height="100px">

2019/2019-10-03_basicGitTraining-SIU/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 `firstNameLastname.md` in the folder `_attendees` and rename it with your first and last names:
+
+```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

2019/2019-10-03_basicGitTraining-SIU/slides/forks.md

+# What is a `fork`?
+
+<br><br>
+<center><img src="slides/img/fork.jpg" class="as-is" height="500em"/></center>
+<!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
+
+
+
+# Not really ...
+
+<br><br>
+<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>.
+
+<br>
+<h2>How to get a fork?</h1>
+
+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)
+
+
+
+
+# Time to practice!
+
+Fork the practice repository: <br><br>
+https://github.com/LCSB-BioCore/basic-git-practice
+
+Then, clone your fork to your home directory!
+
+```bash
+$ git clone git@github.com:<yourName>/basic-git-practice.git
+```
+
+Change to the practice directory with:
+```bash
+$ cd basic-git-practice
+```
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+If you did not configure your SSH key, clone using HTTPS:
+```bash
+$ git clone https://github.com/<yourName>/basic-git-practice.git
+```
+
+
+
+# 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 update once the original repository is update.
+
+![bulb](slides/img/bulb.png) You have to update it yourself!
+
+**More on that later!**
+

2019/2019-10-03_basicGitTraining-SIU/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)
+- **GitLab**: [https://gitlab.com](https://gitlab.com)
\ No newline at end of file

2019/2019-10-03_basicGitTraining-SIU/slides/img

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

2019/2019-10-03_basicGitTraining-SIU/slides/index.md

+# R3.school
+
+## October 3rd, 2019
+
+<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>Basic git training</h1>
+    <br><br><br><br>
+    <h4>
+        Laurent Heirendt, Ph.D.<br>
+        laurent.heirendt@uni.lu<br>
+        <i>Luxembourg Centre for Systems Biomedicine</i>
+    </h4>
+</div>

2019/2019-10-03_basicGitTraining-SIU/slides/list.json

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

2019/2019-10-03_basicGitTraining-SIU/slides/merge.md

+# Pull and merge requests
+
+If you want your changes to be reflected on the `develop` or `master` branches,
+**submit a PR** via the Github 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

2019/2019-10-03_basicGitTraining-SIU/slides/overview.md

+# Overview
+
+1. What is `git`? What is the use of `git`?
+2. GitHub and GitLab
+3. The terminal
+4. What is a fork?
+5. What are branches?
+6. The 5 essential commands (`pull` / `status` / `add` / `commit` / `push`)
+7. What are merge/pull requests?
+8. How do I synchronize my fork?
+9. Best practices

2019/2019-10-03_basicGitTraining-SIU/slides/syncFork.md

+# Synchronize your fork (i)
+
+![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
+$ git remote add upstream git@github.com:LCSB-BioCore/basic-git-practice.git
+```
+
+![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 (download) the changes from upstream (fetch = pull & merge)
+```bash
+$ git fetch upstream
+```
+
+
+
+# Synchronize your fork (ii)
+
+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.
+
+<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file

2019/2019-10-03_basicGitTraining-SIU/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]: GitHub training services: https://services.github.com/training/
+
+[3]: Cheat sheet: http://rogerdudler.github.io/git-guide
+
+
+
+# Thank you.
+
+<img src="slides/img/r3-training-logo.png" height="200px">
+
+Contact us if you need help:
+
+r3lab.core@uni.lu
+

2019/2019-10-03_basicGitTraining-SIU/slides/the_terminal.md

+# Note on Microsoft Azure Devops
+
+This course aims at the basics of using `git`.
+
+In order to understand the concepts of `git`, the terminal will be used instead of any GUI.
+The same terminology applies.
+
+More info on Azure Devops & Git: https://docs.microsoft.com/en-us/azure/devops/repos/git/
+
+
+
+# First steps in the terminal
+
+Starting the terminal presents itself with a line where you can enter a command
+```bash
+cesar@myComputer>
+```
+
+Often written, for covenience, as
+```bash
+$
+```
+
+When you open your terminal (shell), you are located
+in your home directory (unless otherwise configured), denoted as `~/`.
+
+
+
+# Essential Linux commands (i)
+
+List the contents of a directory
+```bash
+$ ls #-lash
+```
+
+Create a directory
+```bash
+$ mkdir myNewDirectory
+```
+
+Change the directory to a specific folder
+```bash
+$ cd myNewDirectory
+```
+
+Change the directory 1 level and 2 levels up
+```bash
+$ cd ..
+# 1 level up
+
+$ cd ../..
+# 2 levels up
+```
+
+
+
+# Essential Linux commands (ii)
+
+Move a file or a directory
+```bash
+$ mv myFile.m myNewDirectory/.
+```
+
+
+Rename a file or a directory
+```bash
+$ mv myFile.m myNewFile.m
+$ mv myNewDirectory myDirectory
+```
\ No newline at end of file

2019/2019-10-03_basicGitTraining-SIU/slides/what_is_git.md

+# What is `git`? (i)
+
+<!-- ![](slides/img/git_definition.png) -->
+
+`git` is a **version control system** (VCS) for tracking changes in computer files and coordinating work on those files among multiple people [1].
+
+Designed and implemented in 2005 by **Linus Torvalds**
+
+<div align="center">
+<img src="slides/img/linus.jpg">
+</div>
+
+[1] *https://en.wikipedia.org/wiki/Git*
+
+
+
+# What is `git`? (ii)
+
+<div align="center">
+<img src="slides/img/git_definition.png">
+</div>
+
+`I'm an egotistical bastard, and I name all my projects after myself.
+First Linux, now git.`
+<br>
+Linus Torvald (2007-06-14)
+
+
+
+# What is the use of `git`?
+
+* No need to fully rewrite code; **reuse code** and **save time**
+
+* Keep the changes you made over time (**history**)
+
+* Allows you to **backtrack** (if necessary) and undo unwanted changes
+
+* Easily **add contributions** of your collaborators to the main code base
+
+<br>
+Other points:
+
+- git shall not be considered as a nuisance, but as a tool that should help to track and trace the code.
+
+- git is not to track performance. Not using it shows exactly the opposite.