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Commits on Source 112

17445a20 splits setup in two parts
Oct 11, 2018
8dd6f2dc adds branch naming section
Oct 11, 2018
df96cad7 translates angler
Oct 11, 2018
5cc4c570 add additional speaker notes
Oct 11, 2018
431268ba uses simpler branch names in merge
Oct 12, 2018
7bf0d66f adds local viewing usage to readme
Oct 12, 2018
a57f5d54 adds motivation wars
Nov 26, 2018
7b245be9 adds bash basics section
Nov 26, 2018
6d1d4a75 updates install with experience from first session
Nov 26, 2018
6e22e0c7 gets rid of outdated drafts
Nov 26, 2018
8d896291 improves conflicts and rebase sections
Nov 28, 2018
2c34ba05 adds resources
Feb 4, 2019
69b52687 fixes typo
Feb 25, 2019
c97d7c07 reintroduces the typo
Mar 21, 2019
2345e6a1 fixes matrix image title
May 3, 2019
5290fc38 moves cheat sheet hand out location to setup
May 3, 2019
c0c6208c adds notes about terminal session preparation
May 3, 2019
cd6675e1 fixes section id
May 3, 2019
e366dad5 makes breaks dynamic
May 3, 2019
ea2f3618 removes open terminal note from setup
May 3, 2019
d214aaf3 re-seat based on cli exp
May 3, 2019
898c1670 motivation: improves automation section
May 3, 2019
54f535c4 makes motivation less about git specifically
May 3, 2019
fba0e636 improves notes about staging area
May 3, 2019
4a13192d fixes typo
May 3, 2019
c2fa1c83 reorganizes remotes chapter
May 3, 2019
b278b484 improves branch merge chapter
May 3, 2019
e95c096e splits install in two sections
May 3, 2019
23820c80 improves ui notes
May 3, 2019
885f57d2 improves platform specific setup section
May 3, 2019
c2435f16 consistent team decision notes
May 3, 2019
24a59e89 simplifies first summary
May 3, 2019
c54b3a88 splits review in two sections
May 3, 2019
51db1fd7 highlights goals in summary sections
May 3, 2019
a435dd24 adds criticism and commenting rulez
May 3, 2019
060c164c adds feedback homework
May 3, 2019
25d4a1c5 moves create repository task on its own slide
May 3, 2019
e1ab9047 adds more representative gitk history screenshot
May 3, 2019
4dd785b2 adds bash commands for editing files
May 3, 2019
1c09ba40 improves good commit message template
May 3, 2019
f7961ed0 removes git-pretty
May 3, 2019
f8d98c9a adds advanced notes
May 3, 2019
79d35c69 removes mostly outdated notes
May 3, 2019
46b0c48e removes outdated overview and course files
May 3, 2019
871f5703 adds rough content of pandoc papers
May 3, 2019
29a6709c builds paper to revealjs and pdf
May 3, 2019
58db4c97 updates paper
May 6, 2019
587dd51b updates pandoc papers
May 7, 2019
e6ed9eab fixes makefile dependency
May 7, 2019
52d2f1e8 fixes pandoc papers source
May 7, 2019
5be95050 updates pandoc papers
May 7, 2019
7cde4b24 adds notes from ydiv meeting
May 13, 2019
9f5ae7cc updates pandoc papers
May 29, 2019
a112ee05 updates pandoc papers
May 31, 2019
fcebbc36 updates pandoc papers
Jun 3, 2019
79de04f3 updates pandoc papers
Sep 5, 2019
cc6d1d2c improves first slide preparation notes
Sep 6, 2019
41135b17 removes contractions
Sep 9, 2019
038a49f6 adds funny collaboration image
Sep 9, 2019
f857f4ee Merge branch 'motivation/collab' into 'master'
Sep 9, 2019
9390e441 replaces checkout with switch and restore
Sep 9, 2019
c0d0a0d5 removes youtube motivation
Sep 9, 2019
1723cc92 adds more spacing to motivation wars
Sep 9, 2019
1904623b do collaboration in feature branches
Sep 13, 2019
d058eaee moves matrix to install
Sep 13, 2019
41f4a0dd fixes staging area dot
Nov 15, 2019
56d70506 clearify in notes what is interactive/demo
Nov 15, 2019
3f654e2c fixes typo
Nov 26, 2019
1c0c1f63 uses simple mac gui editor
Dec 12, 2019
cd323681 list global config
Dec 12, 2019
260ae922 drops autocrlf explanation
Dec 12, 2019
34146f25 adds note about why we prefer simple editors
Dec 12, 2019
2ce13b82 [basics] adds LANG to terminal setup
Feb 17, 2020
a99a9de3 reintroduces typo
Feb 17, 2020
97134fa2 simplifies playground motivation
Feb 17, 2020
69f23b08 removes motivation everywhere
Feb 17, 2020
f4072d20 simplifies motivation structure to flowchart
Feb 17, 2020
286e17c5 removes branch from motivation structure
Feb 17, 2020
c758e91f removes fast speaker note
Feb 17, 2020
6b441459 removes boy scout rule for simplicity
Feb 17, 2020
ae2de67a fixes edit ribbon url
Feb 17, 2020
d7e5ac31 verify core editor config
Feb 17, 2020
1ca9800e adds clarifications
Feb 17, 2020
1cfe59fd cleans up collab in day 1 as prep for day 2
Feb 17, 2020
98b00ac0 adds or tomorrow to homework
Feb 17, 2020
ab5940b6 hint at 2nd day in motivation automation
Feb 18, 2020
a1cd6b14 adds 2nd day to agenda
Feb 18, 2020
d7bb69c5 fixes git config --edit test
Feb 18, 2020
7641b539 adds tomorrow agenda to the end after homework
Feb 21, 2020
7ce45e41 bumps reveal.js
Sep 14, 2022
14218c96 bye bye dirk
Sep 14, 2022
4a9a0dfa fixes img rename from earlier
Sep 14, 2022
2b901bb1 adds rdm use case dots
Sep 14, 2022
e956eabe adds unlimited git power image
Sep 14, 2022
6461ef8d s/tomorrow/advanced
Sep 14, 2022
3f731b92 s/master/main
Sep 14, 2022
cc78964b diff config list and list global
Sep 14, 2022
b7b2fbcb notes and highlighting
Sep 14, 2022
e74cbd4e janedoe@idiv
Sep 14, 2022
da984ec6 replaces single quotes with double quotes
Dec 7, 2022

12 additional commits have been omitted to prevent performance issues.

.gitignore

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	@@ -2,5 +2,15 @@ img/git-remote-contributor.svg
	img/git-remote-maintainer.svg		img/git-remote-maintainer.svg
	img/git-remote-solo.svg		img/git-remote-solo.svg
	img/license-chooser.svg		img/license-chooser.svg
			img/motivation-structure.svg
	img/motivation-throwaway-playground.svg		img/motivation-throwaway-playground.svg
			img/rdm-use-case-data.svg
			img/rdm-use-cases-a.svg
			img/rdm-use-cases-b.svg
			img/rdm-use-cases.svg
	img/staging-area.svg		img/staging-area.svg
			paper.html
			paper.pdf
			*.pdf
			img/staging-area-diff.svg
			/img/rdm-use-case-merged.svg

.gitmodules

+3 −0

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	[submodule "reveal.js"]		[submodule "reveal.js"]
	path = reveal.js		path = reveal.js
	url = https://github.com/hakimel/reveal.js.git		url = https://github.com/hakimel/reveal.js.git
			[submodule "pandoc-cheat-sheet"]
			path = pandoc-cheat-sheet
			url = https://github.com/idiv-biodiversity/pandoc-cheat-sheet.git

0-Intro.md

deleted100644 → 0

+0 −118

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	# Introduction to git - a powerful version control system

	## block structure
	- Why git?
	- poll from registration
	- other points from our list
	- git installation hands on
	- git on the command line
	- navigate manipulate on cli
	- ls, pwd, cd, mv, rm, cp, mkdir, rmdir
	- short break (optional)
	- (like) try git on beamer (closed laptops)
	- try git would be 1.1 to 1.9
	- init
	- status
	- add
	- commit
	- log (metadata only)
	- short break (optional)
	- hands on - created project
	- multiple commits
	- multiple files
	- diff
	- log (with patch)
	- wrap up hands on
	- problems that occurred
	- conclusion

	## Why git?
	### Why would you want to use a VCS, e.g. git?
	- Summary of answers to question from registration.
	- git helps you to keep an overview of a project.

	### Thoughts from the net “Have you ever:”

	- Made a change to code, realised it was a mistake and wanted to revert back?
	- Lost code or had a backup that was too old?
	- Had to maintain multiple versions of a product?
	- Wanted to see the difference between two (or more) versions of your code?
	- Wanted to prove that a particular change broke or fixed a piece of code?
	- Wanted to review the history of some code?
	- Wanted to submit a change to someone else's code?
	- Wanted to share your code, or let other people work on your code?
	- Wanted to see how much work is being done, and where, when and by whom?
	- Wanted to experiment with a new feature without interfering with working code?

	In these cases, and no doubt others, a version control system should make your life easier.

	To misquote a friend: A civilised tool for a civilised age.

	by si618 at [https://stackoverflow.com/a/1408464](https://stackoverflow.com/a/1408464)


	## git installation hands on
	[instructions](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)

	### installation on ubuntu
	We will use the version from the git ppa:
	```bash
	sudo apt-get install ppa-purge
	sudo add-apt-repository ppa:git-core/ppa
	sudo apt-get update
	sudo apt-get dist-upgrade
	sudo apt-get install git
	```

	### installation on windows
	- [Download](https://git-scm.com/download/win)
	- choose 64 bit
	- portable if you do not have admin rights
	- default install options look OK
	- Git Bash
	- Windows Explorer context menue has Git Bash Here and Git GUI Here options
	- Windows credential window will pop up when accessing remotes with authentication

	### navigate and manipulate on cli
	- pwd
	- ls
	- cd
	- mv
	- rm
	- cp
	- mkdir
	- rmdir


	### configure git
	```bash
	git config --global user.name "Your Name"
	git config --global user.email "your.name@idiv.de"
	```
	- eventually additionally configuration for windows/linux/mac stuff
	- line break configuration done during install for windows
	- eventually mention difference global local

	## short break (optional)

	## show try git like tutorial on beamer (closed laptops)
	- try git would be 1.1 to 1.9
	- create project directory
	- init
	- status
	- add
	- commit
	- log (metadata only)

	## short break (optional)

	## hands on - created project
	- multiple commits
	- multiple files
	- diff
	- log (with patch)
	- test this with a windows and mac machine to see things like editor, linebreaks, etc.

	## wrap up hands on
	- problems that occurred
	- conclusion

Makefile

+23 −0

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	@@ -4,12 +4,35 @@ SUBDIRS = \
	$(SUBDIRS):		$(SUBDIRS):
	$(MAKE) -C $@		$(MAKE) -C $@

			pandoc-papers.pdf: pandoc-papers.md
			pandoc \
			-V aspectratio=169 \
			-V institute=iDiv \
			-V theme=Frankfurt \
			-V navigation=horizontal \
			-V logo=img/idiv-black-logo.png \
			--pdf-engine=xelatex \
			-s \
			-t beamer \
			-o pandoc-papers.pdf \
			pandoc-papers.md

			rdm.pdf: img rdm.md rdm.yml
			pandoc \
			--standalone \
			--from=markdown+yaml_metadata_block \
			--pdf-engine=xelatex \
			--template=pandoc-cheat-sheet/cheat-sheet.tex \
			-o rdm.pdf \
			rdm.yml rdm.md

	all: subdirs		all: subdirs

	clean:		clean:
	for dir in $(SUBDIRS); do \		for dir in $(SUBDIRS); do \
	$(MAKE) -C $$dir $@; \		$(MAKE) -C $$dir $@; \
	done		done
			rm -f rdm.pdf

	default: all		default: all

README.md

+25 −3

Original line number	Original line	Diff line number	Diff line
	# The Official iDiv git Seminar		# The Official iDiv git Seminars

	## Usage		## Usage

	- update reveal.js submodule		To view the presentations locally, you need to clone the repository
	- run make to create svg from dot sources		recursively, to also get a copy of [reveal.js][]:

			```bash
			git clone --recursive https://git.idiv.de/sc/edu/git-seminar.git
			```

			Then you also need to create the images from the [graphviz dot
			sources][graphviz]:

			```bash
			cd git-seminar
			make
			```

			Then you can view the presentations, e.g. the basics:

			```
			firefox basics.html
			```

	## Attribution		## Attribution

	- git logo by [Jason Long](https://twitter.com/jasonlong)		- git logo by [Jason Long](https://twitter.com/jasonlong)


			[graphviz]: http://www.graphviz.org/
			[reveal.js]: https://revealjs.com/#/

advanced.md

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+38 −0

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			# regular FAQ

			- 10-12 git integration RStudio / VS Code / others
			- 13-15 GitLab / GitHub project setup / importing existing projects / how to start and continue after that, project management, issue management
			- 15-16 GitLab / GitHub automation
			- 16-18 free for all

			# git advanced -- how to maintain a comprehensible history

			- when projects get bigger
			- show bad example with merge commits
			- show git-flow being harmful
			- show git-pretty

			Advanced git is not about edge use cases, it's all about keeping your history
			comprehensible, i.e. understandable.

			## trunk based development

			- project history, e.g. via `gitk` or `git lol`, should resemble a tree
			- for this section we're sticking to the tree metaphor
			- long-lived branches basically master (and releases)
			- long trunk of tree
			- dead branches on lower trunk (old, unmaintained releases), which may also be
			cut down in time if support is dropped
			- only clean merges (could have been ff)

			## final chapter

			- consider like backup slides
			- show goodies

			## resources

			- https://barro.github.io/2016/02/a-succesful-git-branching-model-considered-harmful/
			- https://stackoverflow.com/questions/14023648/why-does-my-git-history-look-like-a-christmas-tree
			- https://i.stack.imgur.com/ZsXT6.png
			- https://trunkbaseddevelopment.com

basics.html

+576 −284

File changed.

Preview size limit exceeded, changes collapsed.

css/crawl.css

0 → 100644

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			.star-wars {
			height: 800px;
			perspective: 400px;

			color: #feda4a;
			letter-spacing: 6px;
			}

			.crawl {
			position: relative;
			animation: crawl 120s linear;
			}

			.crawl > .title > h1 {
			color: #feda4a;
			}

			@keyframes crawl {
			0% {
			top: 0;
			transform: rotateX(20deg) translateZ(0);
			}

			100% {
			top: -6000px;
			transform: rotateX(25deg) translateZ(-2500px);
			}
			}

dia/rebase-vs-cherry-pick.dia

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	@@ -100,7 +100,7 @@
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	</dia:attribute>		</dia:attribute>
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	<dia:color val="#000000"/>		<dia:color val="#000000"/>
	@@ -194,7 +194,7 @@
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	@@ -208,7 +208,7 @@
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	</dia:attribute>		</dia:attribute>
	<dia:attribute name="pos">		<dia:attribute name="pos">
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	</dia:attribute>		</dia:attribute>
	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>
	@@ -227,7 +227,7 @@
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	<dia:attribute name="text">		<dia:attribute name="text">
	<dia:composite type="text">		<dia:composite type="text">
	@@ -241,7 +241,7 @@
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	</dia:attribute>		</dia:attribute>
	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>
	@@ -290,7 +290,7 @@
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	<dia:attribute name="text">		<dia:attribute name="text">
	<dia:composite type="text">		<dia:composite type="text">
	@@ -343,7 +343,7 @@ git rebase b c#</dia:string>
	<dia:point val="28,11"/>		<dia:point val="28,11"/>
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	<dia:attribute name="text">		<dia:attribute name="text">
	<dia:composite type="text">		<dia:composite type="text">
	@@ -357,7 +357,7 @@ git rebase b c#</dia:string>
	<dia:real val="0.80000000000000004"/>		<dia:real val="0.80000000000000004"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="pos">		<dia:attribute name="pos">
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	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>
	@@ -408,7 +408,7 @@ git rebase b c#</dia:string>
	<dia:real val="0.80000000000000004"/>		<dia:real val="0.80000000000000004"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="pos">		<dia:attribute name="pos">
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	</dia:attribute>		</dia:attribute>
	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>
	@@ -502,7 +502,7 @@ git rebase b c#</dia:string>
	<dia:point val="56,15"/>		<dia:point val="56,15"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="obj_bb">		<dia:attribute name="obj_bb">
	<dia:rectangle val="55.8075,14.2525;56.1925,15"/>		<dia:rectangle val="55.8075,14.255;56.1925,15"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="text">		<dia:attribute name="text">
	<dia:composite type="text">		<dia:composite type="text">
	@@ -516,7 +516,7 @@ git rebase b c#</dia:string>
	<dia:real val="0.80000000000000004"/>		<dia:real val="0.80000000000000004"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="pos">		<dia:attribute name="pos">
	<dia:point val="56,14.8475"/>		<dia:point val="56,14.8491"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>
	@@ -535,7 +535,7 @@ git rebase b c#</dia:string>
	<dia:point val="61,15"/>		<dia:point val="61,15"/>
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	<dia:attribute name="text">		<dia:attribute name="text">
	<dia:composite type="text">		<dia:composite type="text">
	@@ -549,7 +549,7 @@ git rebase b c#</dia:string>
	<dia:real val="0.80000000000000004"/>		<dia:real val="0.80000000000000004"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="pos">		<dia:attribute name="pos">
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	</dia:attribute>		</dia:attribute>
	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>
	@@ -598,14 +598,14 @@ git rebase b c#</dia:string>
	<dia:point val="56,5"/>		<dia:point val="56,5"/>
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	<dia:attribute name="obj_bb">		<dia:attribute name="obj_bb">
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	<dia:attribute name="text">		<dia:attribute name="text">
	<dia:composite type="text">		<dia:composite type="text">
	<dia:attribute name="string">		<dia:attribute name="string">
	<dia:string>#cherry-pick		<dia:string>#cherry-pick

	git checkout b		git switch b
	git cherry-pick a...c#</dia:string>		git cherry-pick a...c#</dia:string>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="font">		<dia:attribute name="font">
	@@ -652,7 +652,7 @@ git cherry-pick a...c#</dia:string>
	<dia:point val="51,11"/>		<dia:point val="51,11"/>
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	<dia:attribute name="obj_bb">		<dia:attribute name="obj_bb">
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	<dia:attribute name="text">		<dia:attribute name="text">
	<dia:composite type="text">		<dia:composite type="text">
	@@ -666,7 +666,7 @@ git cherry-pick a...c#</dia:string>
	<dia:real val="0.80000000000000004"/>		<dia:real val="0.80000000000000004"/>
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	<dia:attribute name="pos">		<dia:attribute name="pos">
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	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>

git-course.html

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	<!DOCTYPE html>
	<html>
	<head>
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	<meta name="author" content="Christian Krause" />
	<meta name="dcterms.date" content="2015-06-15" />
	<title>Git Workshop</title>
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	<section>
	<h1 class="title">Git Workshop</h1>
	<h3 class="author">Dirk Sarpe & Christian Krause</h3>

	<aside class="notes">
	<ul>
	<li>if you have questions ask them right away</li>
	</ul>
	</aside>
	</section>

	<section id="poll-why-are-you-here" class="titleslide slide level1" data-markdown>
	## Poll
	# Why are you here?

	Note:
	- Someone (like us) told you it ~~might be~~ is useful.
	- You never took the time to really learn it.
	- You already know and use it, want to show off / learn new tricks.

	- Somebody forced you to come here.
	- You wanted to get away from your desk for once and maybe take a nap.
	</section>

	<section id="outline" class="titleslide slide level1" data-markdown>
	# Outline

	1. Intro
	2. Git Commands
	3. GitLab / GitHub
	4. Workflows

	Note:
	- jeder Block ~ 1.5h
	- insgesamt 2h mit Pause
	- 8h - ein ganzer Tag git
	- ein-satz-beschreibungen zu den abschnitten
	- 0. why vcs, why git, getting started with git
	- 1. git basics
	- 2. web collaboration tools
	- 3. how to collaborate in organized manner
	</section>

	<section>
	<section class="titleslide slide level1" data-markdown>
	## Block 1
	# Introduction

	Note:
	- quickly talk about block outline
	- why vcs? why git?
	- installation git client
	- setup GitLab / GitHub accounts
	- getting started with git (try git)
	</section>

	<section class="slide level2" data-markdown>
	### Have you ever seen this?

	![foo](img/draft_mess.png)

	Note:
	- Dirk erklärt seine mess
	- wouldn't it be nicer to have
	</section>

	<section class="slide level2" data-markdown>
	### wouldn't it be nicer to have
	# version control

	```
	Dirk Sarpe 14 minutes ago fix reference
	Dirk Sarpe 5 days ago adapt figures to nature
	Christian Krause 6 days ago add figure captions
	Dirk Sarpe 7 weeks ago adds mean values to analysis
	Christian Krause 7 weeks ago adds abstract
	```

	Note:
	- git log --pretty=format'%an %ar %s'
	- and as you can see not only for source code
	</section>

	<section class="slide level2" data-markdown>
	## have you ever ...

	- review history (see diff)
	- wanted to go back in time
	- maintain multiple versions
	- hint: for different journals
	- try things out without breaking what works

	Note:
	-
	</section>

	<section class="slide level2" data-markdown>
	## have you ever ...

	- collaborate
	- who made that error
	- see project progress
	- lost code (no backup)

	Note:
	-
	</section>

	<section class="slide level2" data-markdown>
	# yes?

	Note:
	-
	</section>

	<section class="slide level2" data-markdown>
	# use vcs!

	Note:
	-
	</section>
	</section>

	<section>
	<section class="titleslide slide level1" data-markdown>
	## Block 1
	# git

	Note:
	-
	</section>

	<section class="titleslide slide level1" data-markdown>
	![git](img/what-is-git.jpg)

	Note:
	-
	</section>

	<section class="titleslide slide level1" data-markdown>
	![git](img/what-is-git-answer.jpg)

	Note:
	-
	</section>

	<section class="titleslide slide level1" data-markdown>
	![git](img/say-what.jpg)

	Note:
	-
	</section>

	<section class="titleslide slide level1" data-markdown>
	## what is git? (2nd try)
	### seriously

	# TODO image gitk all, visual representation of git parent child tree with remotes,
	tags, good commit messages, etc. mit local change der remote noch nicht da ist

	Note:
	- am bild dvcs erklären!
	</section>

	<section class="slide level2" data-markdown>
	![git](img/idontalwaysusevcs.jpg)

	Note:
	-
	</section>

	<section class="slide level2" data-markdown>
	## Why do we all use git?

	#### non-technical

	- any workflow
	- collaboration
	- experimentation
	- undo mistakes
	- state of the art (best tool for the job)
	- all the cool kids do it

	Note:
	-
	</section>

	<section class="slide level2" data-markdown>
	## Why do we all use git?

	#### technical

	- never lose data (not just remote but also file integrity)
	- easy conflict resolution
	- local (your own copy of everything)
	- implies speedy gonzales

	Note:
	-
	</section>
	</section>
	</section>

	<section>
	<section id="prereq" class="titleslide slide level1" data-markdown>
	### Block 1
	## Git Demo

	Note:
	- vorher fragen, wer alles client braucht und noch accounts braucht, damit wir wissen,
	wieviel zeit wir uns für try git nehmen können
	- config
	- init
	- git add foo bar
	- git commit -m 'foo bar'
	- prima
	</section>
	</section>

	<section>
	<section id="prereq" class="titleslide slide level1" data-markdown>
	### Block 1
	## Checking Prerequisites

	- GitHub / GitLab account
	- local git client installation
	- bonus: your own project without VCS

	Note:
	- wenn git client selbst nicht aufsetzen kann, dann bitte halbe stunde früher
	- registration to the course
	- git client includes your own notebook
	</section>
	</section>


	<section class="slide level2" data-markdown>
	##

	-

	Note:
	-
	</section>
	</section>

	<section>
	<section class="titleslide slide level1" data-markdown>
	# VCS for me

	-

	Note:
	-
	</section>

	<section class="slide level2" data-markdown>
	##

	-

	Note:
	-
	</section>
	</section>

	<section>
	<section class="titleslide slide level1" data-markdown>
	#

	-

	Note:
	-
	</section>

	<section class="slide level2" data-markdown>
	##

	-

	Note:
	-
	</section>
	</section>

	<section id="eof" data-background="img/trex.png"><h1>EOF</h1></section>
	</div>
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	@@ -6,7 +6,7 @@ digraph {

	node [color = orchid]		node [color = orchid]

	omaster[label = "master"]		omain[label = "main"]
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	subgraph clusterlocal {		subgraph clusterlocal {
	@@ -14,7 +14,7 @@ digraph {

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	@@ -22,11 +22,11 @@ digraph {

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	subgraph clusterlocal {		subgraph clusterlocal {
	@@ -14,7 +14,7 @@ digraph {

	node [color = orchid]		node [color = orchid]

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	}		}

	subgraph clusteralice {		subgraph clusteralice {
	@@ -22,7 +22,7 @@ digraph {

	node [color = limegreen]		node [color = limegreen]

	amaster[label = "master"]		amain[label = "main"]
	}		}

	subgraph clusterbob {		subgraph clusterbob {
	@@ -30,11 +30,11 @@ digraph {

	node [color = lightskyblue]		node [color = lightskyblue]

	bmaster[label = "master"]		bmain[label = "main"]
	}		}

	omaster -> master [label = "git pull"]		omain -> main [label = "git pull"]
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	amaster -> master [label = "git pull alice", constraint = false]		amain -> main [label = "git pull alice", constraint = false]
	bmaster -> master [label = "git pull bob", constraint = false]		bmain -> main [label = "git pull bob", constraint = false]
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	node [color = orchid]		node [color = orchid]

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	subgraph clusterlocal {		subgraph clusterlocal {
	@@ -17,10 +17,10 @@ digraph {

	node [color = orchid]		node [color = orchid]

	master[label = "master"]		main[label = "main"]
	}		}

	omaster -> master [label = "git fetch", style = dotted, ltail = clusterorigin, lhead = clusterlocal]		omain -> main [label = "git fetch", style = dotted, ltail = clusterorigin, lhead = clusterlocal]
	master -> omaster [label = "git push"]		main -> omain [label = "git push"]
	omaster -> master [label = "git pull"]		omain -> main [label = "git pull"]
	}		}

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			digraph {
			node [shape = "box", style = "filled, rounded"]

			master4[label = "Alice (today)\nfixes logic error", color = limegreen]
			master3[label = "Bob (yesterday)\nfixes typos", color = darkorchid1]
			master2[label = "Alice (three days ago)\nadds methods chapter", color = limegreen]
			master1[label = "...", color = grey]

			master4 -> master3 -> master2 -> master1
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	digraph {		digraph {
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	@@ -18,11 +18,11 @@ digraph {

	node [color = orchid]		node [color = orchid]

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	playground2 -> playground1		playground2 -> playground1
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			paper_version_c[label = "nature-final"]
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			paper_version_c -> data_version_a [label = "\n\n", lhead = cluster_data]

			data_version_a -> script_version_b [label = "\n\n", lhead = cluster_script]
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			data_version_a -> script_version_b [label = "\n\n"]

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			repo[label = "repository\n(tracked content)", color = limegreen]

			workdir -> stage [label = "git diff"]
			stage -> repo [label = "git diff --staged"]
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	@@ -10,10 +10,10 @@ digraph {
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	# stage -> untracked [label = "git unstage"]		# stage -> untracked [label = "git unstage"]

	workdir -> stage [label = "git stage file"]		workdir:sw -> stage:w [label = "git stage file"]
	stage -> workdir [label = "git unstage file"]		stage:e -> workdir:se [xlabel = "git unstage file"]

	# workdir -> discard [label = "git checkout"]		# workdir -> discard [label = "git restore"]
	# untracked -> discard [label = "rm"]		# untracked -> discard [label = "rm"]

	stage -> repo [label = "git commit"]		stage -> repo [label = "git commit"]

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index.html

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	<!DOCTYPE html>
	<html>
	<head>
	<meta charset="utf-8" />
	<meta name="author" content="Dirk Sarpe and Christian Krause" />
	<title>git basics</title>
	<meta name="apple-mobile-web-app-capable" content="yes" />
	<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
	<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no" />
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	<style type="text/css">code{white-space: pre;}</style>
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	<link rel="stylesheet" href="css/ribbon.css" />
	</head>

	<body>

	<!-- start of slides -->

	<div class="reveal">
	<div class="slides">
	<section id="title" data-markdown>
	# git seminar

	1. [for beginner-level git users](basics.html)
	</section>
	</div>
	</div>

	<!-- ribbon -->

	<div class="ribbon-wrapper right">
	<div class="ribbon">
	<a href="https://git.idiv.de/sc/edu/git-seminar">
	edit
	</a>
	</div>
	</div>

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notes.md

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	Basics
	======

	VCS für mich
	------------

	### config

	### init

	### add

	git add foo bar

	### commit

	git commit -m 'foo bar'

	prima -

	was hat sich nu verändert?
	--------------------------

	### log

	--stat

	-p

	### diff

	- was ändern
	- git diff
	- git commit -am

	### repo / stage / working

	- grafik raussuchen
	- wofür nutzen

	### add / reset / checkout

	diff und diff --staged und diff HEAD

	vcs mit backup
	--------------

	- github neues projekt --> projekteinbindung: clone / remote add origin foo
	- push
	- pull



	## merge

	mergetool linux = meld
	mac = ???
	windows = ???

	Workflows
	=========

	branching workflows
	-------------------

	was sind branches und wofür brauch ich sie? diese frage sollte eindeutig in diesem kapitel erklärt
	werden.

	### nvie successful git branching model

	### multi master

	paper with many journals

	same paper text - different theme file for page layout, graph layout, etc.

	## tips for papers

	git diff -w --ignore-blank-lines --word-diff

	Your Projects
	=============




	##### STuff

	- explain all collaboration workflows via github


	-

overview.md

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	Blöcke
	======

	each block is about 3 hours e.g. 9 - 12 including breaks

	0. Intro
	- Why git?
	- git installation hands on
	- show try git like tutorial on beamer (closed laptops)
	- hands on - created project
	- wrap up hands on

	1. Git Commands
	- working dir - index/stage - repo

	2. GitLab / GitHub
	- project maintanance
	- issues and PRs
	- "easier collaboration"

	3. VCS Workflows
	- how to collaborate in an organized manner

pandoc-cheat-sheet @ 2346a002

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			Subproject commit 2346a002289757ee612bfd4b56b57db53e0c751b

pandoc-papers.md

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			---
			title: pandoc papers
			subtitle: a future proof way to write
			author:
			- Christian Krause
			...

			intro
			=====

			## motivation #1

			![](img/motivation-draft-mess-half-size.png)

			## motivation #2

			- focus on content/writing
			- communication
			- avoid emails with attachments, right?
			- early and frequent reviews
			- get rid of MS Word, Google Docs, Dropbox, etc.

			## motivation #3

			- use version control with all its benefits
			- automated
			- spell checking
			- high quality typesetting
			- publishing
			- future proof way of doing things, meaning
			- tools are open source
			- tools are replaceable or optional
			- all content is plain text

			## agenda

			- short presentation including demo
			- learn tools and workflows
			- establish community


			tools
			=====

			## pandoc -- Swiss Army Knife of Text Conversion

			### source: markup

			- usually Markdown
			- less powerful than \LaTeX, but inline \LaTeX\ can be used

			### targets

			- high quality PDF via \LaTeX
			- others: HTML web page, EPUB, Office documents

			### templates

			- different journals
			- iDiv branding

			## Markdown

			### source

			```
			- easy to learn, read and write
			- ~~no~~ fewer distractions to procrastinate
			- inline \LaTeX\ if needed \rightarrow\ $a^2 + b^2 = c^2$
			```

			### rendered

			- easy to learn, read and write
			- ~~no~~ fewer distractions to procrastinate
			- inline \LaTeX\ if needed \rightarrow\ $a^2 + b^2 = c^2$

			## git & GitLab

			### git

			- version control
			- free backup

			### GitLab: [https://git.idiv.de](https://git.idiv.de)

			- self-hosted, full access control
			- communication: discussion and reviews
			- continuous integration i.e. spell checking
			- continuous deployment to e.g. cloud storage

			## visualization

			### Graphviz/dot

			- graph visualization language
			- define flowcharts with code
			- dot handles rendering to SVG

			### plotting

			- any programming language can be used
			- add results as CSV to repository
			- plot data to SVG e.g. using R with ggplot2 and svglite

			## build tool

			### make

			- glues everything together
			- automates build
			- render images from dot and CSV sources
			- build PDF
			- run spell check


			workflow
			========

			## workflow #1

			### [set up new project in GitLab](https://git.idiv.de/projects/new)

			- use project template
			- template is managed by our community
			- contains Makefile, README, CI/CD, ~~themes~~, visualization examples, etc.

			### writing

			- start writing the main document in Markdown
			- use text editor you're comfortable with

			## workflow #2

			### communication

			- invite contributors / collaborators to GitLab project
			- use GitLab project as main communication platform
			- discuss and review in
			- commit comments
			- issues
			- merge requests

			## workflow #3

			### continuous deployment

			- some parts are done automatically with the project template
			- deploy PDF to cloud storage:
			[https://portal.idiv.de/nextcloud/](https://portal.idiv.de/nextcloud/)
			- (uses DRAFT watermark ~~if commit not tagged~~)

			## demo

			(demo here only if all tools are already installed)


			your turn
			=========

			## discussion

			- Which tools do you currently use?
			- Anyone know pandoc-scholar?
			- Anyone know authorea?
			- What are your workflows?
			- How do you communicate, collaborate and review?
			- What annoys you the most? (i.e. how can we improve)

			## let's get started

			### create new project

			- https://git.idiv.de/projects/new
			- create from template \rightarrow\ instance \rightarrow\ pandoc
			- install tools from `README.md`
			- set up Nextcloud share and CD

			### editor: Atom

			- atom-latex for bib syntax highlighting
			- graphviz-preview-plus for dot syntax highlighting and preview
			- hard-wrap for wrapping paragraphs
			- language-pfm for pandoc flavored Markdown
			- language-r for R

			## issues

			### prose diff tool

			- hard wrap vs soft wrap
			- these issues might help:
			[gitlab-ce#25650](https://gitlab.com/gitlab-org/gitlab-ce/issues/25650),
			[gitlab-ce#26804](https://gitlab.com/gitlab-org/gitlab-ce/issues/26804)
			- [https://github.blog/2014-02-14-rendered-prose-diffs/](https://github.blog/2014-02-14-rendered-prose-diffs/)

			### spell checking

			- integrate editor spell checking with mdspell
			- per project editor integration
			- needs additional ignores, e.g. links, \LaTeX\ and citations


			community
			=========

			## contributing

			### [https://git.idiv.de/publishing](https://git.idiv.de/publishing)

			- contribute to project template about build / workflow related issues
			- e.g. if you need more packages for plotting
			- contribute to bibliography about new references
			- we may even import/sync an existing publication database
			- contribute to pandoc templates
			- had no need for them yet
			- we might add some iDiv corporate identity (talk with PR)
			- review-able template with link to join discussion at every paragraph

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			<!DOCTYPE html>
			<html>
			<head>
			<title>git@rdm</title>
			<link rel="stylesheet" href="reveal.js/dist/reveal.css">
			<link rel="stylesheet" href="reveal.js/dist/theme/black.css">
			<link rel="stylesheet" href="css/company-logo.css" />
			<link rel="stylesheet" href="css/ribbon.css" />
			<link rel="stylesheet" href="css/crawl.css" />
			</head>

			<body>
			<div class="reveal">
			<div class="slides">

			<!---------------------------------------------------------------------
			<!-- intro
			<!-------------------------------------------------------------------->

			<section>
			<section id="title" data-markdown>
			# git and rdm
			## (... and reproducibility)

			notes:
			- `make -B` to create images, then reload
			</section>

			<section id="intro-objectives" data-markdown>
			## objectives

			- show how git relates to RDM
			- ... and reproducibility
			</section>

			<section id="intro-agenda" data-markdown>
			## agenda

			1. motivation
			1. ~~teach *how* to use git/GitHub/GitLab~~
			1. use cases
			1. anti-patterns
			1. platforms
			1. Q & A

			notes:
			- feel free to interrupt with immediate questions
			- more involved detailed discussion as part of Q & A
			</section>

			<section id="intro-version-control" data-markdown>
			## about version control

			> records changes

			what who when (why)

			notes:
			- the why (aka context) is optional
			- you have to do this
			- you have to care about it
			</section>

			<section id="intro-about-git" data-markdown>
			## about git

			### best tool for the job

			- simple by design
			- powerful if needed
			- documentation / community
			- industry standard

			notes:
			- git name: "the stupid content tracker"
			- doc: finding answers with web searches
			</section>

			<section id="intro-about-me" data-markdown>
			## about me

			- scientific computing support @ iDiv since 2014
			- satisfied git user since 2010

			> There will never be a better version control system than git.
			>
			> -- Christian Krause, 2017
			</section>

			<section id="intro-about-you" data-markdown>
			## about you

			![people](img/people.jpg)

			notes:
			- who has never used any VCS before?
			- who actively maintains a VCS repository?
			</section>
			</section>

			<!---------------------------------------------------------------------
			<!-- motivation
			<!-------------------------------------------------------------------->

			<section>
			<section id="motivation" data-markdown>
			# motivation

			> Why should I use version control?

			notes:
			- motivation chapter is about the concept of version control
			- git is just a tool to do it
			</section>

			<section id="motivation-avoid-mess" data-markdown>
			## motivation #1
			### avoid mess

			![blah](img/motivation-draft-mess.png)

			notes:
			- who has seen such a mess?
			- who has contributed to such a mess?
			- who has created such a mess?
			</section>

			<section id="motivation-want-structure" data-markdown>
			## motivation #1
			### want structure

			![blah](img/motivation-structure.svg)

			notes:
			- structure: who, when
			- why is hidden (only shows message header, not body)
			- ability to inspect old versions and their diff
			- ability to revert/undo a change
			</section>

			<section id="motivation-playground" data-markdown>
			## motivation #2
			### throw-away playgrounds

			![playground](img/motivation-throwaway-playground.svg)

			notes:
			- test stuff without interfering
			- throw away if garbage
			- integrate if good
			- switch back and forth without pain
			</section>

			<section id="motivation-collaboration-1" data-markdown>
			## motivation #c
			### collaboration made easy

			<!-- do not fix this typo, it is here on purpose to show collab -->
			> This text cntains a typo.

			notes:
			- demo GitLab (change target branch to create merge request)
			- this is how you can do reviews of drafts
			- discuss this slide/chapter/section link
			</section>

			<section id="motivation-collaboration-2" data-markdown>
			## motivation #c

			![typo-pr](https://pbs.twimg.com/media/EDsklbLUEAMdusJ.png)

			notes:
			- might not seem like much
			- but you are still making the world a better place
			- and it is not too much effort
			</section>

			<section id="motivation-automation" data-markdown>
			## motivation #a
			### automation

			- *quality*
			- code analysis
			- spell check
			- software testing
			- enforce style guide
			- *deployment* (app store, web server)

			notes:
			- basically, everything you can script
			- refresh presentation before next slide
			</section>

			<section class="star-wars" id="motivation-wars">
			<div class="crawl">
			<div class="title">
			<h1>motivation #wars</h1>
			</div>

			<div data-markdown>
			1. view the *history* of changes

			1. know *why* someone changed it

			1. *revert* a bad change

			1. maintain *multiple versions*

			1. see the *diff* of two versions

			1. find commit *that broke* something

			1. have free *backup*

			1. have *non-interfering* playgrounds

			1. have *automated* testing

			1. have *automated* deployment

			1. *contribute* to a project

			1. *share* your code

			1. let other people do the work *for you*
			</div>

			<img src="http://i.giphy.com/90F8aUepslB84.gif" />
			</div>
			</section>
			</section>

			<!---------------------------------------------------------------------
			<!-- use cases
			<!-------------------------------------------------------------------->

			<section>
			<section id="use-cases" data-markdown>
			# use cases
			##### for
			### version control system (vcs)
			##### aka
			### source code management (scm)
			</section>

			<section id="use-case-software" data-markdown>
			## software

			- generic (as in parameterized)
			- (ideally) tested

			notes:
			- e.g. R package
			</section>

			<section id="use-case-scripting" data-markdown>
			## scripting
			##### aka
			### how to run `$software`

			- ... in `$environment`
			- digital lab notes
			- reproducibility !!1!
			- execution scalability

			notes:
			- separate software from scripting
			- `$enviroment`: multiple scripts/configurations for different
			environments:
			- EasyBuild, conda, singularity
			- RStudio server, HPC cluster
			- execution scalability: running software or script without having
			to change it
			- keep failed attempts in branches
			- e.g. highly parameterized software, make a record of bad
			parameter sets
			</section>

			<section id="use-case-publishing" data-markdown>
			# publishing
			### (markdown (with some tex))

			- paper / thesis / book
			- presentation
			- documentation
			- blog

			notes:
			- who is using markdown?
			- who is using tex?
			- who is using word? why?
			- markdown with tex
			- git.idiv.de/help
			- search for markdown
			- search for math
			- show example
			</section>

			<section id="use-case-integrated-1" data-markdown>
			## integration

			![run `make` to generate the image](img/rdm-use-cases-a.svg)

			notes:
			- software A: tried and tested, reference to compare to
			- software B: your experimental better version
			</section>

			<section id="use-case-integrated-2" data-markdown>
			## integration

			![run `make` to generate the image](img/rdm-use-cases-b.svg)
			</section>

			<section id="use-case-integrated-3" data-markdown>
			## integration

			![run `make` to generate the image](img/rdm-use-cases.svg)
			</section>

			<section id="use-case-integrated-data" data-markdown>
			## integration

			![run `make` to generate the image](img/rdm-use-case-data.svg)
			</section>
			</section>

			<!---------------------------------------------------------------------
			<!-- anti patterns
			<!-------------------------------------------------------------------->

			<section>
			<section id="anti-patterns" data-markdown>
			# anti-patterns

			![unlimited power](img/unlimited-power.jpg)

			notes:
			- does anyone know what an anti-pattern is?
			</section>

			<section id="anti-patterns-def" data-markdown>
			# anti-patterns

			> An anti-pattern is a common response to a recurring problem that
			is usually ineffective and risks being highly counterproductive.

			notes:
			- most anti-patterns about how to use git
			- focus here is on these relating to RDM and reproducibility
			</section>

			<section id="anti-pattern-binary" data-markdown>
			# binary files
			### (aka non-text)

			- no diff with binary
			- use textual representation
			- convert with automation

			notes:
			- can someone give me an example of text file?
			- markdown
			- source code, scripts (R, shell)
			- XSV
			- can someone give me an example of binary file?
			- compiled programs
			- MS word excel
			- PDF PS
			- don't just put everything in the repo, use *ignore
			</section>

			<section id="anti-pattern-big-data" data-markdown>
			# data in git
			## (scientific/big data)

			- version control for data is DIFFerent !!1!
			- git is VCS for text, not for data

			notes:
			- do you release data with every script change? no, too expensive
			- you don't ever put data files in a git repository
			- not even with LFS
			- big ball of mud, no metadata
			</section>
			</section>

			<!---------------------------------------------------------------------
			<!-- platforms
			<!-------------------------------------------------------------------->

			<section>
			<section id="platforms-list" data-markdown>
			# platforms

			- GitHub
			- https://github.com/idiv-biodiversity (cloud)
			- GitLab
			- https://gitlab.com (cloud)
			- https://git.idiv.de (self-hosted @ iDiv)
			</section>

			<section id="platforms-purpose" data-markdown>
			# platforms

			- enable collaboration
			- bug tracker / feature requests
			- documentation / wiki
			- project management tools
			- issue boards, milestones, gantt
			- trigger automation
			- publish/download releases
			</section>
			</section>

			<!---------------------------------------------------------------------
			<!-- q & a
			<!-------------------------------------------------------------------->

			<section>
			<section id="q-n-a" data-markdown>
			# Q & A

			notes:
			- walk through examples of software/script/publishing
			- walk through one of your use cases
			- demo consulting
			</section>

			<section id="consulting" data-markdown>
			# consulting

			[christian.krause@idiv.de](mailto:christian.krause@idiv.de)
			</section>
			</section>

			<!---------------------------------------------------------------------
			<!-- eof
			<!-------------------------------------------------------------------->

			<section id="eof" data-background="img/trex.png" data-markdown>
			### thanks for listening
			# EOF
			</section>

			<!---------------------------------------------------------------------
			<!-- backup
			<!-------------------------------------------------------------------->

			<section>
			<section id="backup" data-markdown>
			# backup slides
			</section>

			<section id="empty" data-markdown>
			</section>
			</section>
			</div>
			</div>

			<!-------------------------------------------------------------------------
			<!-- css/js
			<!------------------------------------------------------------------------>

			<!-- company logo -->

			<div class="logo-wrapper">
			<a href="https://www.idiv.de/">
			<img src="img/company-logo-small.png" />
			</a>
			</div>

			<!-- ribbon -->

			<div class="ribbon-wrapper right">
			<div class="ribbon">
			<a href="https://git.idiv.de/sc/edu/git-seminar/edit/main/rdm.html"
			target="_blank">
			edit
			</a>
			</div>
			</div>

			<!-- reveal.stuff -->

			<script src="reveal.js/dist/reveal.js"></script>
			<script src="reveal.js/plugin/highlight/highlight.js"></script>
			<script src="reveal.js/plugin/markdown/markdown.js"></script>
			<script src="reveal.js/plugin/notes/notes.js"></script>

			<script>
			Reveal.initialize({
			hash: true,
			plugins: [RevealHighlight, RevealMarkdown, RevealNotes]
			});
			</script>
			</body>
			</html>

rdm.md

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			git for RDM and reproducibility
			===============================

			checklist
			---------

			- software (a generic tool to do something)
			- [ ] use separate git repo for software
			- [ ] tag versions for reproducibility
			- [ ] keep software as generic as possible
			- scripts (how to use software)
			- [ ] use separate git repo for scripts
			- [ ] tag versions for reproducibility
			- [ ] software is configured here
			- [ ] reference used software tag
			- data management
			- [ ] publish dataset(s) to scientific data archive system
			- [ ] always attach proper metadata
			- [ ] get DOI for each version of the dataset(s) for reproducibility
			- [ ] reference used scripts tag
			- publishing
			- [ ] use separate git repo for paper/thesis/...
			- [ ] tag versions for draft/review/final
			- [ ] convert text/source to (binary) products
			- [ ] reference used scripts tag
			- [ ] reference used data DOI
			- platforms (GitLab, GitHub)
			- [ ] use platforms (GitLab, GitHub) for collaboration
			- [ ] review commits / merge requests
			- [ ] utilize project management tools
			- [ ] utilize automation for testing and publishing


			intro
			-----

			- version control system (VCS) records changes (what, who, when, why)
			- use platforms (GitLab, GitHub) for collaboration


			git use cases
			-------------

			### software

			- keep software as generic as possible
			- turn configuration/parameters into arguments, e.g. `myapp --seed=42`
			- this avoids having to rewrite software for parameter changes
			- use software testing to verify software does what it's supposed to do
			- tag versions to enable reproducibility

			### scripting

			- separate scripting from software
			- software: generic
			- scripting: software called with specific configuration/arguments
			- scripting means how to run the software
			- i.e. here is where the parameters/arguments go
			- think of it as digital lab notes
			- this enables reproducibility
			- specialized script variants for different environments, e.g.
			- laptop
			- RStudio / terminal server
			- HPC cluster
			- think about execution scalability, i.e. not having to change software and
			scripting when you want to change parameters
			- keep failed attempts in branches to keep history of what you tried and why it
			didn't work in commit message

			### publishing

			- for paper, thesis, book, presentation, documentation, blog posts
			- use programming languages code/scripts for plots, flowcharts, etc.
			- write text/paragraphs in markup language (e.g. markdown)
			- use automation workflows to
			- generate plot/flowchart code to image files
			- convert text with pandoc to PDF/PS/HTML/ebup
			- use platforms for review process

			## integration of use cases for reproducibility

			![](img/rdm-use-case-merged.svg)


			anti patterns
			-------------

			> An anti-pattern is a common response to a recurring problem that is usually
			> ineffective and risks being highly counterproductive.

			- most git anti-patterns are about how to use git
			- focus here is on these relating to RDM and reproducibility

			### binary files

			- git as VCS only good for text files
			- markdown
			- source code, scripts
			- (small) CSV
			- binary files can't be diff'ed, e.g.
			- compiled programs
			- MS word, excel
			- PDF, PS
			- JPEG, PNG
			- use textual representation, e.g.
			- graphviz dot for flowcharts
			- R ggplot and CSV for plots
			- use automation to convert textual representation to e.g. images
			- use gitignore to never add binary products to the repo

			### scientific data in git repos

			- data is often binary
			- git repo should be small, data blows it up, even if text
			- data has different release cycles than code
			- even git lfs (large file storage) is bad because still big ball of mud
			- scientific datasets need metadata!
			- use proper archive system for data


			platforms
			---------

			- enable collaboration
			- bug tracker / feature requests
			- documentation / wiki
			- project management tools
			- issue boards, milestones, gantt
			- trigger automation
			- publish/download releases
			- go to https://git.idiv.de log in and create new projects!

rdm.yml

0 → 100644

+37 −0

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			---
			# these are not shown in the document, they are just for metadata
			title: git RDM reproducibility check list cheat sheet
			author: Christian Krause
			lang: en
			keywords:
			- git
			- RDM
			- resource data management
			- reproducibility

			# highlighting increases readability
			linkcolor: blue

			# these LaTeX variables fit as much content on as few pages as possible
			documentclass: scrartcl
			pagestyle: empty
			papersize: a4paper
			geometry:
			- a4paper
			- left=1cm
			- right=1cm
			- top=1cm
			- bottom=1cm
			# you can also add "landscape" to geometry if you want more than 2 columns

			# fiddle with these to increase readability
			columns: 2
			fontsize: 9pt

			# this essentially disables justification, which can increase readability
			ragged: yes

			# color for header background
			sectionbg: BurntOrange
			subsectionbg: Apricot
			...

resources.md

+5 −3

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	- [r-and-version-control-for-the-solo-data-analyst](http://stackoverflow.com/questions/2712421/r-and-version-control-for-the-solo-data-analyst)		- [r-and-version-control-for-the-solo-data-analyst](http://stackoverflow.com/questions/2712421/r-and-version-control-for-the-solo-data-analyst)
	- [why-should-i-use-version-control](http://stackoverflow.com/questions/1408450/why-should-i-use-version-control)		- [why-should-i-use-version-control](http://stackoverflow.com/questions/1408450/why-should-i-use-version-control)
	- man 7 gitworkflows		- man 7 gitworkflows
	@@ -18,3 +17,6 @@
	- https://try.github.io/levels/1/challenges/1		- https://try.github.io/levels/1/challenges/1
	- https://betterexplained.com/articles/a-visual-guide-to-version-control/		- https://betterexplained.com/articles/a-visual-guide-to-version-control/
	- https://ellisp.github.io/blog/2016/09/16/version-control		- https://ellisp.github.io/blog/2016/09/16/version-control

			- https://www.linux.com/videos/terrible-ideas-git-corey-quinn-futureadvisor
			- https://media.ccc.de/v/froscon2017-1919-nicht_alltagliche_git-funktionen#video&t=1

reveal.js @ a4b7f9df

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	Subproject commit 65bdccd5807b6dfecad6eb3ea38872436d291e81		Subproject commit a4b7f9dff7ef360afdb6d0cb53fd89063cbe0b66

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