e6ed9eab8229f2e477dd12cf7adf90066d10f709 to main · Scientific Computing / education / git-seminar

.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

+16 −1

Original line number	Original line	Diff line number	Diff line
	@@ -10,7 +10,21 @@ pandoc-papers.pdf: pandoc-papers.md
	-V institute=iDiv \		-V institute=iDiv \
	-V theme=Frankfurt \		-V theme=Frankfurt \
	-V navigation=horizontal \		-V navigation=horizontal \
	-s paper.md -t beamer -o pandoc-papers.pdf		-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

	@@ -18,6 +32,7 @@ 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

+290 −261

File changed.

Preview size limit exceeded, changes collapsed.

dia/rebase-vs-cherry-pick.dia

+17 −17

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	@@ -100,7 +100,7 @@
	<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="30,18.6171"/>		<dia:point val="30,18.6161"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>
	@@ -194,7 +194,7 @@
	<dia:point val="33,15"/>		<dia:point val="33,15"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="obj_bb">		<dia:attribute name="obj_bb">
	<dia:rectangle val="32.8075,14.2525;33.1925,15"/>		<dia:rectangle val="32.8075,14.255;33.1925,15"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="text">		<dia:attribute name="text">
	<dia:composite type="text">		<dia:composite type="text">
	@@ -208,7 +208,7 @@
	<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="33,14.8475"/>		<dia:point val="33,14.8491"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>
	@@ -227,7 +227,7 @@
	<dia:point val="38,15"/>		<dia:point val="38,15"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="obj_bb">		<dia:attribute name="obj_bb">
	<dia:rectangle val="37.8075,14.2525;38.1925,15"/>		<dia:rectangle val="37.8075,14.255;38.1925,15"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="text">		<dia:attribute name="text">
	<dia:composite type="text">		<dia:composite type="text">
	@@ -241,7 +241,7 @@
	<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="38,14.8475"/>		<dia:point val="38,14.8491"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>
	@@ -290,7 +290,7 @@
	<dia:point val="33,5"/>		<dia:point val="33,5"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="obj_bb">		<dia:attribute name="obj_bb">
	<dia:rectangle val="30.8137,4.38631;35.2049,6.78988"/>		<dia:rectangle val="30.8137,4.40594;35.1863,6.75094"/>
	</dia:attribute>		</dia:attribute>
	<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"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="obj_bb">		<dia:attribute name="obj_bb">
	<dia:rectangle val="27.8075,10.2525;28.1925,11"/>		<dia:rectangle val="27.8075,10.255;28.1925,11"/>
	</dia:attribute>		</dia:attribute>
	<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">
	<dia:point val="28,10.8475"/>		<dia:point val="28,10.8491"/>
	</dia:attribute>		</dia:attribute>
	<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">
	<dia:point val="51,12.195"/>		<dia:point val="51,12.1941"/>
	</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"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="obj_bb">		<dia:attribute name="obj_bb">
	<dia:rectangle val="60.8075,14.2525;61.1925,15"/>		<dia:rectangle val="60.8075,14.255;61.1925,15"/>
	</dia:attribute>		</dia:attribute>
	<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">
	<dia:point val="61,14.8475"/>		<dia:point val="61,14.8491"/>
	</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"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="obj_bb">		<dia:attribute name="obj_bb">
	<dia:rectangle val="52.9162,4.38631;59.1024,7.58988"/>		<dia:rectangle val="52.9175,4.38731;59.1011,7.58819"/>
	</dia:attribute>		</dia:attribute>
	<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"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="obj_bb">		<dia:attribute name="obj_bb">
	<dia:rectangle val="50.8075,10.2525;51.1925,11"/>		<dia:rectangle val="50.8075,10.255;51.1925,11"/>
	</dia:attribute>		</dia:attribute>
	<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"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="pos">		<dia:attribute name="pos">
	<dia:point val="51,10.8475"/>		<dia:point val="51,10.8491"/>
	</dia:attribute>		</dia:attribute>
	<dia:attribute name="color">		<dia:attribute name="color">
	<dia:color val="#000000"/>		<dia:color val="#000000"/>

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/idiv-black-logo.png

0 → 100644

+10.1 KiB

10.05 KiB

img/idiv-black.png

0 → 100644

+34.9 KiB

34.89 KiB

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)

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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

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			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

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			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/staging-area.dot

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	@@ -10,10 +10,10 @@ digraph {
	# untracked -> stage [label = "git add"]		# untracked -> stage [label = "git add"]
	# 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"]

img/unlimited-power.jpg

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pandoc-cheat-sheet @ 2346a002

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			Subproject commit 2346a002289757ee612bfd4b56b57db53e0c751b

pandoc-papers.md

+113 −86

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

	# intro		intro
			=====

	## goals		## motivation #1

	- focus on content/writing		![](img/motivation-draft-mess-half-size.png)
	- version control
	- next generation communication		## motivation #2

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

			## motivation #3

			- use version control with all its benefits
			- automated
			- spell checking
	- high quality typesetting		- 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

	# tools		## agenda

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


			tools
			=====

			## pandoc -- Swiss Army Knife of Text Conversion

	### source: markup		### source: markup

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

	### targets		### targets

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

	### templates		### templates

	- different journals		- different journals
	- iDiv branding		- iDiv branding
	- draft branding

	## Markdown		## Markdown

	### rendered

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

	### source		### source

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

	### git		### git
	@@ -60,6 +86,7 @@

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

	## visualization		## visualization
	@@ -68,124 +95,124 @@

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

	### R scripts		### plotting

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

	## make		## build tool

	### simple build tool		### make

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


	# workflow		workflow
			========

	## workflow #1		## workflow #1

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

	- set up project in GitLab		- use project template
	- use pandoc papers project template		- template is managed by our community
	- project template is managed by our community		- contains Makefile, README, CI/CD, ~~themes~~, visualization examples, etc.
	- contains Makefile, README, themes, CD, etc.
	- add contributors / collaborators

	### writing		### writing

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

	## workflow #2		## workflow #2

	### communication		### communication

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

	## workflow #3		## workflow #3

	### continuous deployment		### continuous deployment

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

	### templates		## demo

	- manage templates in our community		(demo here only if all tools are already installed)
	- keep in separate git repository
	- use git sub-module to include
	- share with all@idiv / world

	# misc

	## helpful commands		your turn
			=========

	```bash		## discussion
	# better diff command for text
	git diff -w --ignore-blank-lines --word-diff

	# watch source and build if changes		- Which tools do you currently use?
	watchexec -w paper.md -- make paper.pdf		- 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

	## community #1		- https://git.idiv.de/projects/new
			- create from template \rightarrow\ instance \rightarrow\ pandoc
			- install tools from `README.md`
			- set up Nextcloud share and CD

	### pandoc paper project template		### editor: Atom

	- `README.md` with instructions how to build		- atom-latex for bib syntax highlighting
	- `Makefile` with general build instructions		- graphviz-preview-plus for dot syntax highlighting and preview
	- include pandoc LaTeX themes via sub-module		- hard-wrap for wrapping paragraphs
	- CD pipeline instructions		- language-pfm for pandoc flavored Markdown
	- `main.md` with hello world document using includes for chapters		- language-r for R
	- example dot file for flowchart
	- example CSV and R script to generate charts
	- `.gitignore` with default products

	## community #2		## issues

	### prose diff tool		### prose diff tool

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

	### continuous deployment		### spell checking

	- we don't have solid CD yet
	- can CD deploy to Nextcloud share?

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

	- repository with LaTeX templates for pandoc
	- review-able PDF template with link to join discussion at every paragraph

	# your turn		community
			=========
	## discussion

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

	## let's use it		### [https://git.idiv.de/publishing](https://git.idiv.de/publishing)

	- install tools		- contribute to project template about build / workflow related issues
	- install editor		- e.g. if you need more packages for plotting
	- set up git project		- contribute to bibliography about new references
	- convert existing documents to Markdown		- we may even import/sync an existing publication database
	- build with pandoc		- 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

rdm.html

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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!

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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
			...

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basics.html

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pandoc-papers.md

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rdm.md

rdm.yml

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