From 7ecef2db5fd2010b29f2ced5dd586bf70a29bc13 Mon Sep 17 00:00:00 2001
From: laurentheirendt <laurent.heirendt@uni.lu>
Date: Wed, 28 Aug 2019 19:02:15 +0200
Subject: [PATCH] adapt training slides to new theme
---
.../slides/best_practices.md | 2 +-
2019/2019-06-11_gitTraining/slides/branches.md | 8 ++++----
2019/2019-06-11_gitTraining/slides/cloneRepo.md | 2 +-
.../slides/configuration.md | 6 +++---
.../slides/essential_commands.md | 12 ++++++------
2019/2019-06-11_gitTraining/slides/forks.md | 15 +++++++--------
.../slides/github_gitlab.md | 2 +-
2019/2019-06-11_gitTraining/slides/index.md | 10 +++++-----
.../2019-06-11_gitTraining/slides/installation.md | 4 ++--
2019/2019-06-11_gitTraining/slides/merge.md | 2 +-
2019/2019-06-11_gitTraining/slides/overview.md | 2 +-
2019/2019-06-11_gitTraining/slides/qualityCode.md | 4 ++--
.../2019-06-11_gitTraining/slides/repro_crisis.md | 2 +-
2019/2019-06-11_gitTraining/slides/syncFork.md | 2 +-
2019/2019-06-11_gitTraining/slides/thanks.md | 6 +++---
2019/2019-06-11_gitTraining/slides/the_editor.md | 2 +-
.../2019-06-11_gitTraining/slides/the_terminal.md | 8 ++++----
2019/2019-06-11_gitTraining/slides/what_is_git.md | 6 +++---
2019/2019-06-11_gitTraining/slides/whatiscode.md | 2 +-
2019/2019-06-11_gitTraining/slides/wheel.md | 4 ++--
2019/2019-06-11_gitTraining/slides/whyCare.md | 4 ++--
21 files changed, 52 insertions(+), 53 deletions(-)
diff --git a/2019/2019-06-11_gitTraining/slides/best_practices.md b/2019/2019-06-11_gitTraining/slides/best_practices.md
index 8c7f524b..63c85174 100644
--- a/2019/2019-06-11_gitTraining/slides/best_practices.md
+++ b/2019/2019-06-11_gitTraining/slides/best_practices.md
@@ -1,4 +1,4 @@
-## Best practices
+# Best practices
* `pull` before `push`
diff --git a/2019/2019-06-11_gitTraining/slides/branches.md b/2019/2019-06-11_gitTraining/slides/branches.md
index d864042c..0c91358c 100644
--- a/2019/2019-06-11_gitTraining/slides/branches.md
+++ b/2019/2019-06-11_gitTraining/slides/branches.md
@@ -1,4 +1,4 @@
-## Development scheme
+# Development scheme
Generally, in a repository, there are guidelines for contributing.
@@ -26,7 +26,7 @@ A **version** of the code is referred to as a **branch**.
-## Branches
+# Branches
A **version** of the code (i.e., a **branch**) is made up of a sequence of code changes.
@@ -40,7 +40,7 @@ For instance, the `master` and `develop` branches can be represented as a timeli
-## Switch between branches
+# Switch between branches
List all branches of the repository with
```bash
@@ -70,7 +70,7 @@ If the local branch does not exist but the remote does, it is created automatica
-## Create your own version
+# Create your own version
Assume that you want to work on a file:
diff --git a/2019/2019-06-11_gitTraining/slides/cloneRepo.md b/2019/2019-06-11_gitTraining/slides/cloneRepo.md
index 788536d5..887a6e08 100644
--- a/2019/2019-06-11_gitTraining/slides/cloneRepo.md
+++ b/2019/2019-06-11_gitTraining/slides/cloneRepo.md
@@ -1,4 +1,4 @@
-## How do I start working on a repository?
+# How do I start working on a repository?
You have to `clone` it first:
diff --git a/2019/2019-06-11_gitTraining/slides/configuration.md b/2019/2019-06-11_gitTraining/slides/configuration.md
index b740a6a8..0b07cc41 100644
--- a/2019/2019-06-11_gitTraining/slides/configuration.md
+++ b/2019/2019-06-11_gitTraining/slides/configuration.md
@@ -1,4 +1,4 @@
-## How to configure `git`?
+# How to configure `git`?
```bash
$ git config --global user.name "Firstname Lastname"
@@ -17,7 +17,7 @@ Exit by typing `q`.
-## What is an SSH key?
+# What is an SSH key?
An SSH key is a secure access credential.
@@ -26,7 +26,7 @@ Communicate **securely** with Github/Gitlab **without** entering the username/pa
-## How do I get and set my SSH key?
+# How do I get and set my SSH key?
Check if you already have an SSH key:
diff --git a/2019/2019-06-11_gitTraining/slides/essential_commands.md b/2019/2019-06-11_gitTraining/slides/essential_commands.md
index f10dc08e..0fa56f47 100644
--- a/2019/2019-06-11_gitTraining/slides/essential_commands.md
+++ b/2019/2019-06-11_gitTraining/slides/essential_commands.md
@@ -1,4 +1,4 @@
-## The 5 essential commands
+# The 5 essential commands
**Yes**, you only need 5 commands!
@@ -16,7 +16,7 @@ $ git push <remote> <branch>
-## Pull the latest version of an existing branch
+# Pull the latest version of an existing branch
Pull the latest revision on branch `myBranch`:
```bash
@@ -33,7 +33,7 @@ $ git status
-## Modify a file
+# Modify a file
Copy the file `template.md` in the folder `_attendees` and rename it with your firstname:
@@ -46,7 +46,7 @@ Then, make your changes with your favorite editor!
-## Add your file to the stage
+# Add your file to the stage
First, check the repository status
```bash
@@ -74,7 +74,7 @@ exit with `q`
-## Add a commit message
+# Add a commit message
```bash
$ git commit -m "Add the profile of <myName>"
@@ -83,7 +83,7 @@ $ git status
-## Push your file to your fork
+# Push your file to your fork
```bash
$ git push origin myBranch
diff --git a/2019/2019-06-11_gitTraining/slides/forks.md b/2019/2019-06-11_gitTraining/slides/forks.md
index e3cec61f..3a4f61cd 100644
--- a/2019/2019-06-11_gitTraining/slides/forks.md
+++ b/2019/2019-06-11_gitTraining/slides/forks.md
@@ -1,18 +1,17 @@
-
-## What is a `fork`?
+# 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 ...
+# Not really ...
<img src="slides/img/fork-crossed.png" class="as-is" height="500em"/>
-## What is a `fork`?
+# What is a `fork`?
In general, when contributing to a repository, you only have **read** access.
@@ -26,7 +25,7 @@ In other words, you have to work on your own <font color="red">**fork**</font>.
-## How to get a fork?
+# How to get a fork?
Browse to the original repository and click on the button `Fork`:
@@ -36,7 +35,7 @@ Browse to the original repository and click on the button `Fork`:
-## Time to practice!
+# Time to practice!
Fork the practice repository: <br><br>
https://github.com/LCSB-BioCore/basic-git-practice
@@ -56,7 +55,7 @@ $ cd basic-git-practice
-## A note on shortcuts ...
+# A note on shortcuts ...
<font color="red">
Any other rudimentary method such as
@@ -70,7 +69,7 @@ shall **be avoided**!
-## How to update my fork?
+# How to update my fork?
As you have your own fork, it will not automatically update once the original repository is update.
diff --git a/2019/2019-06-11_gitTraining/slides/github_gitlab.md b/2019/2019-06-11_gitTraining/slides/github_gitlab.md
index 0b988f0f..84930c39 100644
--- a/2019/2019-06-11_gitTraining/slides/github_gitlab.md
+++ b/2019/2019-06-11_gitTraining/slides/github_gitlab.md
@@ -1,4 +1,4 @@
-## GitHub and GitLab
+# 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;"/>
diff --git a/2019/2019-06-11_gitTraining/slides/index.md b/2019/2019-06-11_gitTraining/slides/index.md
index 8985d5b2..a2726fc4 100644
--- a/2019/2019-06-11_gitTraining/slides/index.md
+++ b/2019/2019-06-11_gitTraining/slides/index.md
@@ -1,6 +1,6 @@
-## R3.school
-<br><br>
-#### June 11th, 2019
+# R3.school
+
+## June 11th, 2019
<div style="top: 6em; left: 0%; position: absolute;">
<img src="theme/img/lcsb_bg.png">
@@ -8,8 +8,8 @@
<div style="top: 5em; left: 60%; position: absolute;">
<img src="slides/img/r3-training-logo.png" height="200px">
- <br><br><br><br>
- <h3>git training for absolute beginners</h3>
+ <br><br><br>
+ <h1>git training for absolute beginners</h1>
<br><br><br><br>
<h4>
Laurent Heirendt, Ph.D.<br><br>
diff --git a/2019/2019-06-11_gitTraining/slides/installation.md b/2019/2019-06-11_gitTraining/slides/installation.md
index 8d9c0d24..506be614 100644
--- a/2019/2019-06-11_gitTraining/slides/installation.md
+++ b/2019/2019-06-11_gitTraining/slides/installation.md
@@ -1,4 +1,4 @@
-## Installation of `git`
+# Installation of `git`
<img src="slides/img/github_app.png" class="as-is" height="200" />
@@ -20,7 +20,7 @@ $ sudo apt-get install git-all
-## How to get started?
+# How to get started?
**macOS**
diff --git a/2019/2019-06-11_gitTraining/slides/merge.md b/2019/2019-06-11_gitTraining/slides/merge.md
index 6fc254c0..5b59e684 100644
--- a/2019/2019-06-11_gitTraining/slides/merge.md
+++ b/2019/2019-06-11_gitTraining/slides/merge.md
@@ -1,4 +1,4 @@
-## Pull and merge requests
+# 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.
diff --git a/2019/2019-06-11_gitTraining/slides/overview.md b/2019/2019-06-11_gitTraining/slides/overview.md
index 1cbf68c5..569ee378 100644
--- a/2019/2019-06-11_gitTraining/slides/overview.md
+++ b/2019/2019-06-11_gitTraining/slides/overview.md
@@ -1,4 +1,4 @@
-## Overview
+# Overview
1. **PART I**: Quality of computer code.
2. **PART II**: Basic git course
diff --git a/2019/2019-06-11_gitTraining/slides/qualityCode.md b/2019/2019-06-11_gitTraining/slides/qualityCode.md
index d81e2f0d..1cc539a1 100644
--- a/2019/2019-06-11_gitTraining/slides/qualityCode.md
+++ b/2019/2019-06-11_gitTraining/slides/qualityCode.md
@@ -1,4 +1,4 @@
-## Quality of computer code is relevant for everyone.
+# Quality of computer code is relevant for everyone.
`This does not concern me – I am only writing documentation or a script for generating a figure that I want to publish!`
[Anonymous researcher]
@@ -19,7 +19,7 @@
-## Attributes of high-quality computer code
+# Attributes of high-quality computer code
**Quality** of computer code can be seen as a **group of various attributes**.
diff --git a/2019/2019-06-11_gitTraining/slides/repro_crisis.md b/2019/2019-06-11_gitTraining/slides/repro_crisis.md
index 1fafdc6a..8e411c3b 100644
--- a/2019/2019-06-11_gitTraining/slides/repro_crisis.md
+++ b/2019/2019-06-11_gitTraining/slides/repro_crisis.md
@@ -1,4 +1,4 @@
-## Reproducibility crisis
+# Reproducibility crisis
<div align="center">
<img src="slides/img/reproCrisis.png">
diff --git a/2019/2019-06-11_gitTraining/slides/syncFork.md b/2019/2019-06-11_gitTraining/slides/syncFork.md
index 79b6f93e..a9088695 100644
--- a/2019/2019-06-11_gitTraining/slides/syncFork.md
+++ b/2019/2019-06-11_gitTraining/slides/syncFork.md
@@ -1,4 +1,4 @@
-## Synchronize your fork
+# Synchronize your fork
 Remember, we have to regularly update our own copy of the code.
diff --git a/2019/2019-06-11_gitTraining/slides/thanks.md b/2019/2019-06-11_gitTraining/slides/thanks.md
index 0f36cde7..9f1d826b 100644
--- a/2019/2019-06-11_gitTraining/slides/thanks.md
+++ b/2019/2019-06-11_gitTraining/slides/thanks.md
@@ -1,4 +1,4 @@
-## Let's refresh our memories
+# Let's refresh our memories
<div class="fragment">
@@ -22,7 +22,7 @@
-## References & Cheat sheet
+# References & Cheat sheet
[1]: Git Book: https://git-scm.com/book/en/v2
@@ -32,7 +32,7 @@
-## Thank you.
+# Thank you.
<img src="slides/img/r3-training-logo.png" height="200px">
diff --git a/2019/2019-06-11_gitTraining/slides/the_editor.md b/2019/2019-06-11_gitTraining/slides/the_editor.md
index 8bb979a8..bca1b494 100644
--- a/2019/2019-06-11_gitTraining/slides/the_editor.md
+++ b/2019/2019-06-11_gitTraining/slides/the_editor.md
@@ -1,4 +1,4 @@
-## The editor(s)
+# The editor(s)
Recommended editors:
diff --git a/2019/2019-06-11_gitTraining/slides/the_terminal.md b/2019/2019-06-11_gitTraining/slides/the_terminal.md
index cc5f5164..32e9979c 100644
--- a/2019/2019-06-11_gitTraining/slides/the_terminal.md
+++ b/2019/2019-06-11_gitTraining/slides/the_terminal.md
@@ -1,10 +1,10 @@
-## PART II
+# PART II
<br><br><h1>Basic git course</h1>
-## The terminal (shell)
+# The terminal (shell)
**macOS users:**
@@ -23,7 +23,7 @@ Launch default terminal.<br>
-## First steps in the terminal
+# First steps in the terminal
Starting the terminal presents itself with a line where you can enter a command
```bash
@@ -40,7 +40,7 @@ in your home directory (unless otherwise configured), denoted as `~/`.
-## Essential Linux commands
+# Essential Linux commands
List the contents of a directory
```bash
diff --git a/2019/2019-06-11_gitTraining/slides/what_is_git.md b/2019/2019-06-11_gitTraining/slides/what_is_git.md
index 0517919a..973cc059 100644
--- a/2019/2019-06-11_gitTraining/slides/what_is_git.md
+++ b/2019/2019-06-11_gitTraining/slides/what_is_git.md
@@ -1,4 +1,4 @@
-## What is `git`?
+# What is `git`?
<!--  -->
@@ -14,7 +14,7 @@ Designed and implemented in 2005 by **Linus Torvalds**
-## The inventor of `git`
+# The inventor of `git`
<div align="center">
<img src="slides/img/git_definition.png">
@@ -26,7 +26,7 @@ Linus Torvald (2007-06-14)
-## What is the use of `git`?
+# 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**)
diff --git a/2019/2019-06-11_gitTraining/slides/whatiscode.md b/2019/2019-06-11_gitTraining/slides/whatiscode.md
index c3756f14..8a7ec810 100644
--- a/2019/2019-06-11_gitTraining/slides/whatiscode.md
+++ b/2019/2019-06-11_gitTraining/slides/whatiscode.md
@@ -1,4 +1,4 @@
-## What is computer code?
+# What is computer code?
**Computer code**: Set of instructions executed by a computer
diff --git a/2019/2019-06-11_gitTraining/slides/wheel.md b/2019/2019-06-11_gitTraining/slides/wheel.md
index a961a327..789873bc 100644
--- a/2019/2019-06-11_gitTraining/slides/wheel.md
+++ b/2019/2019-06-11_gitTraining/slides/wheel.md
@@ -1,11 +1,11 @@
-## PART I
+# PART I
<br><br><h1>Quality of computer code.</h1><br>
<h1>Should you care? What if you didn't?</h1>
-## A true story ...
+# A true story ...
<div align="center">
<img src="slides/img/wheel.png">
diff --git a/2019/2019-06-11_gitTraining/slides/whyCare.md b/2019/2019-06-11_gitTraining/slides/whyCare.md
index f763e142..75d3c6b4 100644
--- a/2019/2019-06-11_gitTraining/slides/whyCare.md
+++ b/2019/2019-06-11_gitTraining/slides/whyCare.md
@@ -1,4 +1,4 @@
-## Why you should care (1)
+# Why you should care (1)
<div align="center">
<video width="40%" controls>
@@ -18,7 +18,7 @@ Ariane 5 launched with the same software as Ariane 4 - **the code had not been t
-## Why you should care (2)
+# Why you should care (2)
<div align="center">
<img src="slides/img/therac.png">
--
GitLab