diff --git a/2019/2019-06-11_gitTraining/slides/best_practices.md b/2019/2019-06-11_gitTraining/slides/best_practices.md index 8c7f524bec573b3c9b983d8b67e047c5c2017567..63c851741e6196ca01e129708adb3ed494c38807 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 d864042c7edf7bcec8f01bfc1920eb71e9ac7f6c..0c91358cb047d118836dd31d9e93cf8655f06601 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 788536d5cc1798eaea98db8293fded8c483512d3..887a6e087e73a14ef7ad3790f9e7d0d67ce04b14 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 b740a6a8703e37977aea0e84e625546542e3e4f7..0b07cc4185a35481545f81af5e0f4d8fbc3de063 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 f10dc08e62278f60153ad82c4d3272c8a787070f..0fa56f47884b92c3b64762cf696fed6f7a014b7b 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 e3cec61f6c1fb2447439bf8080dddad92e82aa5a..3a4f61cd17127ecdde35fe52154da3d65b0a94bf 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 0b988f0fa4306cf9fd2e86e006a5a85e22254d34..84930c3922e96a6f2bb75d3ed85881aa19c2e2de 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 8985d5b2c0226a203d151ea1805c86f0e80781ff..a2726fc450ceafef47b4ad4f7b56bdc0319902d3 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 8d9c0d24b597a680332201d0b3a8e589455b542d..506be614073e67dd22fc042230ccb1eb236a9792 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 6fc254c04b9cbc8e89f65e842eddb4d2db1ff195..5b59e684ec66bb668ce48a929608f4de6f238807 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 1cbf68c55a033e8045ef57984300d8e4b2d84d58..569ee3789fd8f0a16e39ac938b9f7c5764adce04 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 d81e2f0d7388f491c11e0612a91f773ee6af0b17..1cc539a1162524f2c56a6b38cc648deca2dd08c7 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 1fafdc6a689692e290c9f8dcd4f070ce4402c1f7..8e411c3b8a50de544cdc79ab423a97f97d0407af 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 79b6f93eccdd241adcd5fc65d4f4491effcac66c..a908869569972adac700f623ec73566b8af5d90c 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 0f36cde75b96379ad2672c83fc36b088c221be82..9f1d826bb46c503b32d1f228512970e726c00618 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 8bb979a8efb5e184854941794b9dbabf00ea7f43..bca1b494ce0faed1f5806db841240fd513467d0d 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 cc5f516412582a14f9cfece3ae1860d342b7afe2..32e9979c1fc4d3eeb5286280c4b132bcb4fba8d5 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 0517919a7fa679d19b9ad7d8ec13ad38ea03f8b0..973cc0593ed0b3b993e870f74c9e0794301e278e 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 c3756f148d43e8e29b06c23d80bf03482d599dc8..8a7ec810845093821daaaba558c5c1fe777500c1 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 a961a32778000d900832a0333e28037e8683a9f8..789873bca8091e220bf2f81085af88a9ccd66953 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 f763e142c16007d30f31a96be2b0dbc8d7d3706f..75d3c6b492993927a4d793c470fe5a2996a2f721 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">