Merge branch 'git-training-june-2019' into 'develop'

Slides for git training

See merge request R3/outreach/presentations!7

2019/2019-06-11_gitTraining/Gruntfile.coffee

+# Generated on 2013-11-27 using generator-reveal 0.3.2
+module.exports = (grunt) ->
+
+    grunt.loadNpmTasks 'grunt-gh-pages'
+
+    grunt.initConfig
+
+        "gh-pages":
+            "gh-pages":
+                options:
+                    base: "dist"
+                src: [ '**' ]
+
+        watch:
+
+            livereload:
+                options:
+                    livereload: true
+                files: [
+                    'index.html'
+                    'slides/*.md'
+                    'slides/*.html'
+                    'theme/js/*.js'
+                ]
+
+            index:
+                files: [
+                    'theme/templates/_index.html'
+                    'theme/templates/_section.html'
+                    'slides/list.json'
+                ]
+                tasks: ['buildIndex']
+
+            coffeelint:
+                files: ['Gruntfile.coffee']
+                tasks: ['coffeelint']
+
+            jshint:
+                files: ['theme/js/*.js']
+                tasks: ['jshint']
+
+        connect:
+
+            livereload:
+                options:
+                    port: 9000
+                    # Change hostname to '0.0.0.0' to access
+                    # the server from outside.
+                    hostname: 'localhost'
+                    base: '.'
+                    open: true
+                    livereload: true
+
+        coffeelint:
+
+            options:
+                indentation:
+                    value: 4
+
+            all: ['Gruntfile.coffee']
+
+        jshint:
+
+            all: ['theme/js/*.js']
+
+        copy:
+
+            dist:
+                files: [{
+                    expand: true
+                    src: [
+                        'slides/**'
+                        'theme/**'
+                        'theme/css/**'
+                        'theme/js/**'
+                        'slides/img/**'
+                    ]
+                    dest: 'public/'
+                },{
+                    expand: true
+                    src: ['index.html']
+                    dest: 'public/'
+                    filter: 'isFile'
+                }]
+
+
+    # Load all grunt tasks.
+    require('load-grunt-tasks')(grunt)
+
+    grunt.registerTask 'buildIndex',
+        'Build theme/templates/_index.html and slides/list.json.',
+        ->
+            indexTemplate = grunt.file.read 'theme/templates/_index.html'
+            sectionTemplate = grunt.file.read 'theme/templates/_section.html'
+            slides = grunt.file.readJSON 'slides/list.json'
+
+            html = grunt.template.process indexTemplate, data:
+                slides:
+                    slides
+                section: (slide) ->
+                    grunt.template.process sectionTemplate, data:
+                        slide:
+                            slide
+            grunt.file.write 'index.html', html
+
+    grunt.registerTask 'test',
+        '*Lint* javascript and coffee files.', [
+            'coffeelint'
+            'jshint'
+        ]
+
+    grunt.registerTask 'server',
+        'Run presentation locally and start watch process (living document).', [
+            'buildIndex'
+            'connect:livereload'
+            'watch'
+        ]
+
+    grunt.registerTask 'dist',
+        'Save presentation files to *public* directory.', [
+            'test'
+            'buildIndex'
+            'copy'
+        ]
+
+    # Define default task.
+    grunt.registerTask 'default', [
+        'test'
+        'server'
+    ]

2019/2019-06-11_gitTraining/package.json

+{
+  "name": "template",
+  "version": "0.0.1",
+  "private": true,
+  "devDependencies": {
+    "grunt": "~0.4.1",
+    "grunt-coffeelint": "0.0.7",
+    "grunt-contrib-connect": "~0.5.0",
+    "grunt-contrib-copy": "~0.4.1",
+    "grunt-contrib-jshint": "~0.7.0",
+    "grunt-contrib-sass": "^1.0.0",
+    "grunt-contrib-watch": "~0.5.3",
+    "grunt-gh-pages": "~0.9.0",
+    "load-grunt-tasks": "~0.2.0"
+  },
+  "engines": {
+    "node": ">=0.8.0"
+  },
+  "scripts": {
+    "test": "grunt test"
+  }
+}

2019/2019-06-11_gitTraining/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
+
+<br><br>
+Remember: **A `push` a day keeps conflicts away!**

2019/2019-06-11_gitTraining/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
+```
+
+<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 function for adding 2 numbers.
+
+<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">

2019/2019-06-11_gitTraining/slides/cloneRepo.md

+## How do I start working on a repository?
+
+You have to `clone` it first:
+
+```bash
+$ git clone git@github.com:userName/myRepo.git myRepo
+```
+
+If you did not configure your SSH key, clone using HTTPS:
+```bash
+$ git clone https://github.com/userName/myRepo.git myRepo
+```
+
+You will be prompted to enter your credentials.

2019/2019-06-11_gitTraining/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
+```
+
+Then, add the SSH key to Github/Gitlab.
+
+<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file

2019/2019-06-11_gitTraining/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 template.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">
+
+**ADVANCED**: see your changes in the terminal
+```bash
+$ git diff
+```
+exit with `q`
+
+<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)
+```
+
+
+
+## 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

2019/2019-06-11_gitTraining/slides/forks.md

+
+## What is a `fork`?
+
+<img src="slides/img/fork.jpg" class="as-is" height="500em"/>
+<!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
+
+
+
+## Not really ...
+
+<img src="slides/img/fork-crossed.png" class="as-is" height="500em"/>
+
+
+
+## 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://github.com/LCSB-BioCore/basic-git-practice
+
+Then, clone your fork to your home directory!
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+```bash
+$ git clone git@github.com:<yourName>/basic-git-practice.git
+```
+
+Change to the practice directory with:
+```bash
+$ cd basic-git-practice
+```
+
+
+
+## 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!**
+

2019/2019-06-11_gitTraining/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