Commit 7ecef2db authored by Laurent Heirendt's avatar Laurent Heirendt
Browse files

adapt training slides to new theme

parent a305ac94
## Best practices
# Best practices
* `pull` before `push`
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## 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:
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## How do I start working on a repository?
# How do I start working on a repository?
You have to `clone` it first:
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## 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:
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## 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
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## 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.
......
## 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;"/>
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## 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>
......
## 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**
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## 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.
......
## Overview
# Overview
1. **PART I**: Quality of computer code.
2. **PART II**: Basic git course
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## 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**.
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## Reproducibility crisis
# Reproducibility crisis
<div align="center">
<img src="slides/img/reproCrisis.png">
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## Synchronize your fork
# Synchronize your fork
![bulb](slides/img/bulb.png) Remember, we have to regularly update our own copy of the code.
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## 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">
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## The editor(s)
# The editor(s)
Recommended editors:
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## 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
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## What is `git`?
# What is `git`?
<!-- ![](slides/img/git_definition.png) -->
......@@ -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**)
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## What is computer code?
# What is computer code?
**Computer code**: Set of instructions executed by a computer
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## 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">
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