An error occurred while retrieving target projects.

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Target

Show changes

Only incoming changes from source

Include changes to target since source was created

Commits on Source 40

[basics] adds LANG to terminal setup · 2ce13b82
ck85nori authored Feb 17, 2020
```
fixes #42
```
2ce13b82
reintroduces typo · a99a9de3
ck85nori authored Feb 17, 2020

a99a9de3
simplifies playground motivation · 97134fa2
ck85nori authored Feb 17, 2020

97134fa2
removes motivation everywhere · 69f23b08
ck85nori authored Feb 17, 2020
```
it's not really motivation
```
69f23b08
simplifies motivation structure to flowchart · f4072d20
ck85nori authored Feb 17, 2020
```
gitk was not a good vis
```
f4072d20
removes branch from motivation structure · 286e17c5
ck85nori authored Feb 17, 2020

286e17c5
removes fast speaker note · c758e91f
ck85nori authored Feb 17, 2020

c758e91f
removes boy scout rule for simplicity · 6b441459
ck85nori authored Feb 17, 2020

6b441459
fixes edit ribbon url · ae2de67a
ck85nori authored Feb 17, 2020
```
- edit basics.html directly
- in new window

fixes #25
```
ae2de67a
verify core editor config · d7e5ac31
Dirk Sarpe authored Feb 17, 2020
```
fixes 37
```
d7e5ac31
adds clarifications · 1ca9800e
ck85nori authored Feb 17, 2020

1ca9800e
cleans up collab in day 1 as prep for day 2 · 1cfe59fd
ck85nori authored Feb 17, 2020

1cfe59fd
adds or tomorrow to homework · 98b00ac0
ck85nori authored Feb 17, 2020

98b00ac0
hint at 2nd day in motivation automation · ab5940b6
ck85nori authored Feb 18, 2020

ab5940b6
adds 2nd day to agenda · a1cd6b14
ck85nori authored Feb 18, 2020

a1cd6b14
fixes git config --edit test · d7bb69c5
ck85nori authored Feb 18, 2020

d7bb69c5
adds tomorrow agenda to the end after homework · 7641b539
ck85nori authored Feb 21, 2020

7641b539
bumps reveal.js · 7ce45e41
ck85nori authored Sep 13, 2022

7ce45e41
bye bye dirk · 14218c96
ck85nori authored Sep 14, 2022

14218c96
fixes img rename from earlier · 4a9a0dfa
ck85nori authored Feb 7, 2022

4a9a0dfa
adds rdm use case dots · 2b901bb1
ck85nori authored Sep 14, 2022

2b901bb1
adds unlimited git power image · e956eabe
ck85nori authored Sep 14, 2022

e956eabe
s/tomorrow/advanced · 6461ef8d
ck85nori authored Sep 14, 2022

6461ef8d
s/master/main · 3f731b92
ck85nori authored Sep 14, 2022

3f731b92
diff config list and list global · cc78964b
ck85nori authored Sep 14, 2022

cc78964b
notes and highlighting · b7b2fbcb
ck85nori authored Sep 14, 2022

b7b2fbcb
janedoe@idiv · e74cbd4e
ck85nori authored Sep 14, 2022

e74cbd4e

replaces single quotes with double quotes · da984ec6

ck85nori authored Dec 7, 2022

single quotes don't work in cmd.exe, this is an issue when working from within
RStudio terminal on Windows because cmd.exe is default "shell" there

fixes #67

da984ec6

visualize git diff · 25c5cc21
ck85nori authored Jan 20, 2023

25c5cc21
shows link to cheat sheet · bd746e72
ck85nori authored Jan 20, 2023

bd746e72
puts homework in quotes · 28f4f492
ck85nori authored Jan 20, 2023

28f4f492
removes objectives section · 7528eab4
ck85nori authored Jan 20, 2023
```
was always a bit quirky, overlaps with goals and agenda, just drop it
```
7528eab4
revamps agenda · e189a7f3
ck85nori authored Jan 20, 2023

e189a7f3
[rdm] adds git for rdm and reproducibility presentation · 166ee749
ck85nori authored Sep 14, 2022

166ee749
wip · 0d1b4cac
ck85nori authored Jan 25, 2023

0d1b4cac
[basics/ribbon] switch to main instead of master · e67e0d3d
ck85nori authored Sep 18, 2023

e67e0d3d
[rdm/ribbon] switches to main and fixes wrong html link · f23fdbe2
ck85nori authored Sep 18, 2023

f23fdbe2
bumps reveal.js · 5420999d
ck85nori authored Oct 4, 2023

5420999d
adds git commands to the summary slides · a8222f26
ck85nori authored May 24, 2024
```
fixes #68
```
a8222f26
[advanced] adds regular faq from first advanced courses · 1a7f9522
ck85nori authored 5 months ago

1a7f9522

.gitignore

+9 −2

Original line number	Original line	Diff line number	Diff line
	paper.html
	paper.pdf
	img/git-remote-contributor.svg		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		*.pdf
			img/staging-area-diff.svg
			/img/rdm-use-case-merged.svg

.gitmodules

+3 −0

Original line number	Original line	Diff line number	Diff line
	[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

Makefile

+10 −0

Original line number	Original line	Diff line number	Diff line
	@@ -17,12 +17,22 @@ pandoc-papers.pdf: pandoc-papers.md
	-o pandoc-papers.pdf \		-o pandoc-papers.pdf \
	pandoc-papers.md		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

advanced.md

+7 −0

Original line number	Original line	Diff line number	Diff line
			# 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		# git advanced -- how to maintain a comprehensible history

	- when projects get bigger		- when projects get bigger

basics.html

+199 −201

File changed.

Preview size limit exceeded, changes collapsed.

img/git-remote-contributor.dot

+7 −7

Original line number	Original line	Diff line number	Diff line
	@@ -6,7 +6,7 @@ digraph {

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

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

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

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

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

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

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

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

	omaster -> master [label = "git pull"]		omain -> main [label = "git pull"]
	master -> omaster [label = "git push", constraint = false]		main -> omain [label = "git push", constraint = false]
	umaster -> master [label = "git pull upstream master", constraint = false]		umain -> main [label = "git pull upstream main", constraint = false]
	omaster -> umaster [label = "pull request (GitHub)\nmerge request (GitLab)", constraint = false]		omain -> umain [label = "pull request (GitHub)\nmerge request (GitLab)", constraint = false]
	}		}

img/git-remote-maintainer.dot

+8 −8

Original line number	Original line	Diff line number	Diff line
	@@ -6,7 +6,7 @@ digraph {

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

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

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

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

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

	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"]
	master -> omaster [label = "git push", constraint = false]		main -> omain [label = "git push", constraint = false]
	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]
	}		}

img/git-remote-solo.dot

+5 −5

Original line number	Original line	Diff line number	Diff line
	@@ -9,7 +9,7 @@ digraph {

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

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

	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"]
	}		}

img/draft_mess_half_size.png→img/motivation-draft-mess-half-size.png

(30.7 KiB)

File moved.

View file

img/draft_mess.png→img/motivation-draft-mess.png

(44.9 KiB)

File moved.

View file

img/motivation-structure.dot

0 → 100644

+10 −0

Original line number	Original line	Diff line number	Diff line
			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
			}

img/motivation-throwaway-playground.dot

+9 −9

Original line number	Original line	Diff line number	Diff line
	digraph {		digraph {
	node [shape = "box", style = "filled, rounded"]		node [shape = "box", style = "filled, rounded"]

	subgraph clustermaster {		subgraph clustermain {
	label = "master"		label = "main"

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

	master3[label = "ebe0262"]		main3[label = "..."]
	master2[label = "03f4f8d"]		main2[label = "..."]
	master1[label = "62a0ee9"]		main1[label = "..."]

	master3 -> master2 -> master1		main3 -> main2 -> main1
	}		}

	subgraph clusterplayground {		subgraph clusterplayground {
	@@ -18,11 +18,11 @@ digraph {

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

	playground2[label = "8b29f74"]		playground2[label = "visualization"]
	playground1[label = "7f295dd"]		playground1[label = "methods"]

	playground2 -> playground1		playground2 -> playground1
	}		}

	playground1 -> master2		playground1 -> main2
	}		}

img/rdm-use-case-data.dot

0 → 100644

+32 −0

Original line number	Original line	Diff line number	Diff line
			digraph {
			compound = true
			node [shape = "box", style = "filled, rounded"]

			subgraph cluster_script {
			label = "scripts"

			node [color = lightskyblue]

			script_version_b[label = "nature-v2"]
			}

			subgraph cluster_data {
			label = "data repository (not git!)"

			node [color = limegreen]

			data_version_a[label = "doi:blah/blah"]
			}

			subgraph cluster_paper {
			label = "paper"

			node [color = limegreen]

			paper_version_c[label = "nature-final"]
			}

			paper_version_c -> data_version_a [label = "\n\n", lhead = cluster_data]

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

img/rdm-use-case-merged.dot

0 → 100644

+63 −0

Original line number	Original line	Diff line number	Diff line
			digraph {
			compound = true
			node [shape = "box", style = "filled, rounded"]

			subgraph cluster_script {
			label = "scripts"

			node [color = lightskyblue]

			script_version_b[label = "nature-v2"]
			script_version_a[label = "nature-v1"]
			}

			subgraph cluster_data {
			label = "data repository (not git!)"

			node [color = limegreen]

			data_version_a[label = "doi:blah/blah"]
			}

			subgraph cluster_paper {
			label = "paper"

			node [color = limegreen]

			paper_version_a[label = "nature-review-1"]
			paper_version_b[label = "nature-review-2"]
			paper_version_c[label = "nature-final"]
			}

			subgraph cluster_software_a {
			label = "software A"

			node [color = orchid]

			software_a_version_a[label = "v2.1.6"]
			}

			subgraph cluster_software_b {
			label = "software B"

			node [color = orchid]

			software_b_version_b[label = "v0.3.4"]
			software_b_version_a[label = "v0.2.0"]
			}

			script_version_a -> software_a_version_a [label = "\n\n"]
			script_version_b -> software_a_version_a [label = "\n\n"]

			script_version_a -> software_b_version_a [label = "\n\n"]
			script_version_b -> software_b_version_b [label = "\n\n"]

			paper_version_a -> script_version_a [label = "\n\n"]
			paper_version_b -> script_version_b [label = "\n\n"]
			paper_version_c -> script_version_b [label = "\n\n"]

			paper_version_c -> data_version_a [label = "\n\n"]

			data_version_a -> script_version_b [label = "\n\n"]

			}

img/rdm-use-cases-a.dot

0 → 100644

+42 −0

Original line number	Original line	Diff line number	Diff line
			digraph {
			compound = true
			node [shape = "box", style = "filled, rounded"]

			subgraph cluster_software_a {
			label = "software A"

			node [color = orchid]

			software_a_version_a[label = "v2.1.6"]
			}

			subgraph cluster_software_b {
			label = "software B"

			node [color = orchid]

			software_b_version_a[label = "v0.2.0"]
			}

			subgraph cluster_script {
			label = "scripts"

			node [color = lightskyblue]

			script_version_a[label = "nature-v1"]
			}

			subgraph cluster_paper {
			label = "paper"

			node [color = limegreen]

			paper_version_a[label = "nature-review-1"]
			}

			script_version_a -> software_a_version_a [label = "\n\n"]

			script_version_a -> software_b_version_a [label = "\n\n"]

			paper_version_a -> script_version_a [label = "\n\n"]
			}

img/rdm-use-cases-b.dot

0 → 100644

+48 −0

Original line number	Original line	Diff line number	Diff line
			digraph {
			compound = true
			node [shape = "box", style = "filled, rounded"]

			subgraph cluster_software_a {
			label = "software A"

			node [color = orchid]

			software_a_version_a[label = "v2.1.6"]
			}

			subgraph cluster_software_b {
			label = "software B"

			node [color = orchid]

			software_b_version_b[label = "v0.3.4"]
			software_b_version_a[label = "v0.2.0"]
			}

			subgraph cluster_script {
			label = "scripts"

			node [color = lightskyblue]

			script_version_b[label = "nature-v2"]
			script_version_a[label = "nature-v1"]
			}

			subgraph cluster_paper {
			label = "paper"

			node [color = limegreen]

			paper_version_a[label = "nature-review-1"]
			paper_version_b[label = "nature-review-2"]
			}

			script_version_a -> software_a_version_a [label = "\n\n"]
			script_version_b -> software_a_version_a [label = "\n\n"]

			script_version_a -> software_b_version_a [label = "\n\n"]
			script_version_b -> software_b_version_b [label = "\n\n"]

			paper_version_a -> script_version_a [label = "\n\n"]
			paper_version_b -> script_version_b [label = "\n\n"]
			}

img/rdm-use-cases.dot

0 → 100644

+50 −0

Original line number	Original line	Diff line number	Diff line
			digraph {
			compound = true
			node [shape = "box", style = "filled, rounded"]

			subgraph cluster_software_a {
			label = "software A"

			node [color = orchid]

			software_a_version_a[label = "v2.1.6"]
			}

			subgraph cluster_software_b {
			label = "software B"

			node [color = orchid]

			software_b_version_b[label = "v0.3.4"]
			software_b_version_a[label = "v0.2.0"]
			}

			subgraph cluster_script {
			label = "scripts"

			node [color = lightskyblue]

			script_version_b[label = "nature-v2"]
			script_version_a[label = "nature-v1"]
			}

			subgraph cluster_paper {
			label = "paper"

			node [color = limegreen]

			paper_version_a[label = "nature-review-1"]
			paper_version_b[label = "nature-review-2"]
			paper_version_c[label = "nature-final"]
			}

			script_version_a -> software_a_version_a [label = "\n\n"]
			script_version_b -> software_a_version_a [label = "\n\n"]

			script_version_a -> software_b_version_a [label = "\n\n"]
			script_version_b -> software_b_version_b [label = "\n\n"]

			paper_version_a -> script_version_a [label = "\n\n"]
			paper_version_b -> script_version_b [label = "\n\n"]
			paper_version_c -> script_version_b [label = "\n\n"]
			}

img/staging-area-diff.dot

0 → 100644

+10 −0

Original line number	Original line	Diff line number	Diff line
			digraph {
			node [shape = "box", style = "filled,rounded"]

			workdir[label = "working directory\n(changes not staged for commit)", color = lightskyblue]
			stage[label = "staging area\n(changes to be committed)", color = orchid]
			repo[label = "repository\n(tracked content)", color = limegreen]

			workdir -> stage [label = "git diff"]
			stage -> repo [label = "git diff --staged"]
			}

img/unlimited-power.jpg

0 → 100644

+54.9 KiB

54.91 KiB

pandoc-cheat-sheet @ 2346a002

Original line number	Original line	Diff line number	Diff line
			Subproject commit 2346a002289757ee612bfd4b56b57db53e0c751b

pandoc-papers.md

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -10,7 +10,7 @@ intro

	## motivation #1		## motivation #1

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

	## motivation #2		## motivation #2

rdm.html

0 → 100644

+498 −0

Original line number	Original line	Diff line number	Diff line
			<!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

0 → 100644

+131 −0

Original line number	Original line	Diff line number	Diff line
			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

Original line number	Original line	Diff line number	Diff line
			---
			# 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
			...

reveal.js @ a4b7f9df

Original line number	Original line	Diff line number	Diff line
	Subproject commit 65bdccd5807b6dfecad6eb3ea38872436d291e81		Subproject commit a4b7f9dff7ef360afdb6d0cb53fd89063cbe0b66

Source

Target

Files