From e458ec56e35e30bac67093c11234b574633faee9 Mon Sep 17 00:00:00 2001
From: laurentheirendt <laurent.heirendt@uni.lu>
Date: Thu, 19 May 2022 15:32:45 +0200
Subject: [PATCH] draft slides
---
.../slides/advanced.md | 0
.../slides/branches.md | 42 ---------
.../slides/cloneRepo.md | 4 +-
.../slides/configuration.md | 36 --------
.../slides/forks.md | 90 -------------------
.../slides/github_gitlab.md | 18 ----
.../slides/index copy.md | 21 -----
.../slides/list.json | 10 +--
.../slides/merge.md | 13 ---
.../slides/overview copy.md | 15 ----
.../slides/overview.md | 10 ++-
.../slides/the_editor.md | 12 ---
.../slides/the_terminal copy.md | 70 ---------------
.../slides/what_is_git.md | 40 ---------
14 files changed, 12 insertions(+), 369 deletions(-)
create mode 100644 2022/2022-06-14_git-trilogy-part-3/slides/advanced.md
delete mode 100644 2022/2022-06-14_git-trilogy-part-3/slides/forks.md
delete mode 100644 2022/2022-06-14_git-trilogy-part-3/slides/github_gitlab.md
delete mode 100644 2022/2022-06-14_git-trilogy-part-3/slides/index copy.md
delete mode 100644 2022/2022-06-14_git-trilogy-part-3/slides/merge.md
delete mode 100644 2022/2022-06-14_git-trilogy-part-3/slides/overview copy.md
delete mode 100644 2022/2022-06-14_git-trilogy-part-3/slides/the_editor.md
delete mode 100644 2022/2022-06-14_git-trilogy-part-3/slides/the_terminal copy.md
delete mode 100644 2022/2022-06-14_git-trilogy-part-3/slides/what_is_git.md
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/advanced.md b/2022/2022-06-14_git-trilogy-part-3/slides/advanced.md
new file mode 100644
index 00000000..e69de29b
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/branches.md b/2022/2022-06-14_git-trilogy-part-3/slides/branches.md
index 0c91358c..48af7a38 100644
--- a/2022/2022-06-14_git-trilogy-part-3/slides/branches.md
+++ b/2022/2022-06-14_git-trilogy-part-3/slides/branches.md
@@ -1,45 +1,3 @@
-# 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">
-
- 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
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/cloneRepo.md b/2022/2022-06-14_git-trilogy-part-3/slides/cloneRepo.md
index dac03e4c..c587f16b 100644
--- a/2022/2022-06-14_git-trilogy-part-3/slides/cloneRepo.md
+++ b/2022/2022-06-14_git-trilogy-part-3/slides/cloneRepo.md
@@ -3,12 +3,12 @@
You have to `clone` it first:
```bash
-$ git clone git@github.com:LCSB-BioCore/basic-git-practice.git
+$ git clone ssh://git@gitlab.lcsb.uni.lu:8022/R3/school/git/basic-practice-pages.git
```
If you did not configure your SSH key, clone using HTTPS:
```bash
-$ git clone https://github.com/LCSB-BioCore/basic-git-practice.git
+$ git clone https://gitlab.lcsb.uni.lu/R3/school/git/basic-practice-pages
```
You will be prompted to enter your credentials.
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/configuration.md b/2022/2022-06-14_git-trilogy-part-3/slides/configuration.md
index 39ca62da..c1cc0e00 100644
--- a/2022/2022-06-14_git-trilogy-part-3/slides/configuration.md
+++ b/2022/2022-06-14_git-trilogy-part-3/slides/configuration.md
@@ -14,39 +14,3 @@ $ 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
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/forks.md b/2022/2022-06-14_git-trilogy-part-3/slides/forks.md
deleted file mode 100644
index fa7389a8..00000000
--- a/2022/2022-06-14_git-trilogy-part-3/slides/forks.md
+++ /dev/null
@@ -1,90 +0,0 @@
-# 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`:
-
-
-
-<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<br><br>
-
-
-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
-```
-
-<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>
-
-<br>
-
-**Why?**
-
-
-
-# How to update my fork?
-
-As you have your own fork, it will not automatically be updated once the original repository is updated.
-
- You have to update it yourself!
-
-<br>
-
-**More on that later!**
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/github_gitlab.md b/2022/2022-06-14_git-trilogy-part-3/slides/github_gitlab.md
deleted file mode 100644
index fa8e34ed..00000000
--- a/2022/2022-06-14_git-trilogy-part-3/slides/github_gitlab.md
+++ /dev/null
@@ -1,18 +0,0 @@
-# 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://gitlab.lcsb.uni.lu](https://gitlab.lcsb.uni.lu)
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/index copy.md b/2022/2022-06-14_git-trilogy-part-3/slides/index copy.md
deleted file mode 100644
index eebd26f5..00000000
--- a/2022/2022-06-14_git-trilogy-part-3/slides/index copy.md
+++ /dev/null
@@ -1,21 +0,0 @@
-# Elixir-LU training (R3.school)
-
-## October 20th, 2021
-
-<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/elixir.png" height="200px">
- <img src="slides/img/r3-training-logo.png" height="200px">
- <br><br><br><br>
- <h1>Basic git training</h1>
- <br><br><br><br>
- <h4>
- Laurent Heirendt, Ph.D.<br>
- laurent.heirendt@uni.lu<br>
- <i>ELIXIR/LU, Luxembourg Centre for Systems Biomedicine</i>
- </h4>
-</div>
-
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/list.json b/2022/2022-06-14_git-trilogy-part-3/slides/list.json
index 5794aa13..8ba3861f 100644
--- a/2022/2022-06-14_git-trilogy-part-3/slides/list.json
+++ b/2022/2022-06-14_git-trilogy-part-3/slides/list.json
@@ -1,18 +1,12 @@
[
{ "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": "advanced.md" },
{ "filename": "thanks.md" }
-]
+]
\ No newline at end of file
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/merge.md b/2022/2022-06-14_git-trilogy-part-3/slides/merge.md
deleted file mode 100644
index 42d288de..00000000
--- a/2022/2022-06-14_git-trilogy-part-3/slides/merge.md
+++ /dev/null
@@ -1,13 +0,0 @@
-# Pull (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
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/overview copy.md b/2022/2022-06-14_git-trilogy-part-3/slides/overview copy.md
deleted file mode 100644
index 1cb37bc5..00000000
--- a/2022/2022-06-14_git-trilogy-part-3/slides/overview copy.md
+++ /dev/null
@@ -1,15 +0,0 @@
-# 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
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/overview.md b/2022/2022-06-14_git-trilogy-part-3/slides/overview.md
index 2f6a1ec4..7bedee3f 100644
--- a/2022/2022-06-14_git-trilogy-part-3/slides/overview.md
+++ b/2022/2022-06-14_git-trilogy-part-3/slides/overview.md
@@ -1,4 +1,10 @@
# Overview
-0. Subject 1
-1. Subject 2
+1. The terminal
+2. Installation of `git`
+3. How do I configure `git`?
+4. Where and how to start?
+5. The 5 essential commands (`pull` / `status` / `add` / `commit` / `push`)
+6. How do I synchronize my fork?
+7. What if things go wrong?
+8. Best practices
\ No newline at end of file
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/the_editor.md b/2022/2022-06-14_git-trilogy-part-3/slides/the_editor.md
deleted file mode 100644
index 46c04292..00000000
--- a/2022/2022-06-14_git-trilogy-part-3/slides/the_editor.md
+++ /dev/null
@@ -1,12 +0,0 @@
-# The editor(s)
-
-Recommended editors:
-
-- **Visual Studio Code** [https://code.visualstudio.com](https://code.visualstudio.com)
-- **Atom** [https://atom.io](https://atom.io)
-
-*Note*: Other editors can, of course, also be used. Examples:
-- IntelliJ IDEA [https://www.jetbrains.com/idea](https://www.jetbrains.com/idea)
-- Sublime Text [https://www.sublimetext.com](https://www.sublimetext.com)
-
-<img src="slides/img/icon-live-demo.png" height="100px">
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/the_terminal copy.md b/2022/2022-06-14_git-trilogy-part-3/slides/the_terminal copy.md
deleted file mode 100644
index 43c527f2..00000000
--- a/2022/2022-06-14_git-trilogy-part-3/slides/the_terminal copy.md
+++ /dev/null
@@ -1,70 +0,0 @@
-# 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 `~/`.
-
-<br>
-
-**Is `git` properly installed?**
-
-```bash
-$ git --version
-# git version 2.33.1
-```
-
-
-
-# Essential Linux commands
-
-List the contents of a directory
-```bash
-$ ls
-```
-
-You can list more details with:
-```bash
-$ ls -lah
-```
-
-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
-```
-
-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
diff --git a/2022/2022-06-14_git-trilogy-part-3/slides/what_is_git.md b/2022/2022-06-14_git-trilogy-part-3/slides/what_is_git.md
deleted file mode 100644
index 973cc059..00000000
--- a/2022/2022-06-14_git-trilogy-part-3/slides/what_is_git.md
+++ /dev/null
@@ -1,40 +0,0 @@
-# What is `git`?
-
-<!--  -->
-
-`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*
-
-
-
-# The inventor of `git`
-
-<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.`
-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
-
-note:
-
-Other points to mention:
-* 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.
--
GitLab