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  • sc/edu/git-seminar
  • mk21womu/git-seminar
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.gitignore
View file @ 1a7f9522
paper.html
paper.pdf
img/git-remote-contributor.svg
img/git-remote-maintainer.svg
img/git-remote-solo.svg
img/license-chooser.svg
img/motivation-structure.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
paper.html
paper.pdf
*.pdf
img/staging-area-diff.svg
/img/rdm-use-case-merged.svg
.gitmodules
View file @ 1a7f9522
[submodule "reveal.js"]
path = reveal.js
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
View file @ 1a7f9522
......@@ -17,12 +17,22 @@ pandoc-papers.pdf: pandoc-papers.md
-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
clean:
for dir in $(SUBDIRS); do \
$(MAKE) -C $$dir $@; \
done
rm -f rdm.pdf
default: all
......
advanced.md
View file @ 1a7f9522
# 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
......
basics.html
View file @ 1a7f9522
This diff is collapsed.
dia/rebase-vs-cherry-pick.dia
View file @ 1a7f9522
......@@ -100,7 +100,7 @@
<dia:real val="0.80000000000000004"/>
</dia:attribute>
<dia:attribute name="pos">
<dia:point val="30,18.6171"/>
<dia:point val="30,18.6161"/>
</dia:attribute>
<dia:attribute name="color">
<dia:color val="#000000"/>
......@@ -194,7 +194,7 @@
<dia:point val="33,15"/>
</dia:attribute>
<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 name="text">
<dia:composite type="text">
......@@ -208,7 +208,7 @@
<dia:real val="0.80000000000000004"/>
</dia:attribute>
<dia:attribute name="pos">
<dia:point val="33,14.8475"/>
<dia:point val="33,14.8491"/>
</dia:attribute>
<dia:attribute name="color">
<dia:color val="#000000"/>
......@@ -227,7 +227,7 @@
<dia:point val="38,15"/>
</dia:attribute>
<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 name="text">
<dia:composite type="text">
......@@ -241,7 +241,7 @@
<dia:real val="0.80000000000000004"/>
</dia:attribute>
<dia:attribute name="pos">
<dia:point val="38,14.8475"/>
<dia:point val="38,14.8491"/>
</dia:attribute>
<dia:attribute name="color">
<dia:color val="#000000"/>
......@@ -290,7 +290,7 @@
<dia:point val="33,5"/>
</dia:attribute>
<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 name="text">
<dia:composite type="text">
......@@ -343,7 +343,7 @@ git rebase b c#</dia:string>
<dia:point val="28,11"/>
</dia:attribute>
<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 name="text">
<dia:composite type="text">
......@@ -357,7 +357,7 @@ git rebase b c#</dia:string>
<dia:real val="0.80000000000000004"/>
</dia:attribute>
<dia:attribute name="pos">
<dia:point val="28,10.8475"/>
<dia:point val="28,10.8491"/>
</dia:attribute>
<dia:attribute name="color">
<dia:color val="#000000"/>
......@@ -408,7 +408,7 @@ git rebase b c#</dia:string>
<dia:real val="0.80000000000000004"/>
</dia:attribute>
<dia:attribute name="pos">
<dia:point val="51,12.195"/>
<dia:point val="51,12.1941"/>
</dia:attribute>
<dia:attribute name="color">
<dia:color val="#000000"/>
......@@ -502,7 +502,7 @@ git rebase b c#</dia:string>
<dia:point val="56,15"/>
</dia:attribute>
<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 name="text">
<dia:composite type="text">
......@@ -516,7 +516,7 @@ git rebase b c#</dia:string>
<dia:real val="0.80000000000000004"/>
</dia:attribute>
<dia:attribute name="pos">
<dia:point val="56,14.8475"/>
<dia:point val="56,14.8491"/>
</dia:attribute>
<dia:attribute name="color">
<dia:color val="#000000"/>
......@@ -535,7 +535,7 @@ git rebase b c#</dia:string>
<dia:point val="61,15"/>
</dia:attribute>
<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 name="text">
<dia:composite type="text">
......@@ -549,7 +549,7 @@ git rebase b c#</dia:string>
<dia:real val="0.80000000000000004"/>
</dia:attribute>
<dia:attribute name="pos">
<dia:point val="61,14.8475"/>
<dia:point val="61,14.8491"/>
</dia:attribute>
<dia:attribute name="color">
<dia:color val="#000000"/>
......@@ -598,14 +598,14 @@ git rebase b c#</dia:string>
<dia:point val="56,5"/>
</dia:attribute>
<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 name="text">
<dia:composite type="text">
<dia:attribute name="string">
<dia:string>#cherry-pick
git checkout b
git switch b
git cherry-pick a...c#</dia:string>
</dia:attribute>
<dia:attribute name="font">
......@@ -652,7 +652,7 @@ git cherry-pick a...c#</dia:string>
<dia:point val="51,11"/>
</dia:attribute>
<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 name="text">
<dia:composite type="text">
......@@ -666,7 +666,7 @@ git cherry-pick a...c#</dia:string>
<dia:real val="0.80000000000000004"/>
</dia:attribute>
<dia:attribute name="pos">
<dia:point val="51,10.8475"/>
<dia:point val="51,10.8491"/>
</dia:attribute>
<dia:attribute name="color">
<dia:color val="#000000"/>
......
img/git-remote-contributor.dot
View file @ 1a7f9522
......@@ -6,7 +6,7 @@ digraph {
node [color = orchid]
omaster[label = "master"]
omain[label = "main"]
}
subgraph clusterlocal {
......@@ -14,7 +14,7 @@ digraph {
node [color = orchid]
master[label = "master"]
main[label = "main"]
}
subgraph clusterupstream {
......@@ -22,11 +22,11 @@ digraph {
node [color = limegreen]
umaster[label = "master"]
umain[label = "main"]
}
omaster -> master [label = "git pull"]
master -> omaster [label = "git push", constraint = false]
umaster -> master [label = "git pull upstream master", constraint = false]
omaster -> umaster [label = "pull request (GitHub)\nmerge request (GitLab)", constraint = false]
omain -> main [label = "git pull"]
main -> omain [label = "git push", constraint = false]
umain -> main [label = "git pull upstream main", constraint = false]
omain -> umain [label = "pull request (GitHub)\nmerge request (GitLab)", constraint = false]
}
img/git-remote-maintainer.dot
View file @ 1a7f9522
......@@ -6,7 +6,7 @@ digraph {
node [color = orchid]
omaster[label = "master"]
omain[label = "main"]
}
subgraph clusterlocal {
......@@ -14,7 +14,7 @@ digraph {
node [color = orchid]
master[label = "master"]
main[label = "main"]
}
subgraph clusteralice {
......@@ -22,7 +22,7 @@ digraph {
node [color = limegreen]
amaster[label = "master"]
amain[label = "main"]
}
subgraph clusterbob {
......@@ -30,11 +30,11 @@ digraph {
node [color = lightskyblue]
bmaster[label = "master"]
bmain[label = "main"]
}
omaster -> master [label = "git pull"]
master -> omaster [label = "git push", constraint = false]
amaster -> master [label = "git pull alice", constraint = false]
bmaster -> master [label = "git pull bob", constraint = false]
omain -> main [label = "git pull"]
main -> omain [label = "git push", constraint = false]
amain -> main [label = "git pull alice", constraint = false]
bmain -> main [label = "git pull bob", constraint = false]
}
img/git-remote-solo.dot
View file @ 1a7f9522
......@@ -9,7 +9,7 @@ digraph {
node [color = orchid]
omaster[label = "master"]
omain[label = "main"]
}
subgraph clusterlocal {
......@@ -17,10 +17,10 @@ digraph {
node [color = orchid]
master[label = "master"]
main[label = "main"]
}
omaster -> master [label = "git fetch", style = dotted, ltail = clusterorigin, lhead = clusterlocal]
master -> omaster [label = "git push"]
omaster -> master [label = "git pull"]
omain -> main [label = "git fetch", style = dotted, ltail = clusterorigin, lhead = clusterlocal]
main -> omain [label = "git push"]
omain -> main [label = "git pull"]
}
img/draft_mess.png → img/motivation-draft-mess.png
View file @ 1a7f9522
File moved
img/motivation-structure.dot 0 → 100644
View file @ 1a7f9522
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
View file @ 1a7f9522
digraph {
node [shape = "box", style = "filled, rounded"]
subgraph clustermaster {
label = "master"
subgraph clustermain {
label = "main"
node [color = limegreen]
master3[label = "ebe0262"]
master2[label = "03f4f8d"]
master1[label = "62a0ee9"]
main3[label = "..."]
main2[label = "..."]
main1[label = "..."]
master3 -> master2 -> master1
main3 -> main2 -> main1
}
subgraph clusterplayground {
......@@ -18,11 +18,11 @@ digraph {
node [color = orchid]
playground2[label = "8b29f74"]
playground1[label = "7f295dd"]
playground2[label = "visualization"]
playground1[label = "methods"]
playground2 -> playground1
}
playground1 -> master2
playground1 -> main2
}
img/rdm-use-case-data.dot 0 → 100644
View file @ 1a7f9522
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
View file @ 1a7f9522
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
View file @ 1a7f9522
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
View file @ 1a7f9522
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
View file @ 1a7f9522
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
View file @ 1a7f9522
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
View file @ 1a7f9522
......@@ -10,10 +10,10 @@ digraph {
# untracked -> stage [label = "git add"]
# stage -> untracked [label = "git unstage"]
workdir -> stage [label = "git stage file"]
stage -> workdir [label = "git unstage file"]
workdir:sw -> stage:w [label = "git stage file"]
stage:e -> workdir:se [xlabel = "git unstage file"]
# workdir -> discard [label = "git checkout"]
# workdir -> discard [label = "git restore"]
# untracked -> discard [label = "rm"]
stage -> repo [label = "git commit"]
......