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.gitignore
View file @ 1a7f9522
......@@ -2,5 +2,15 @@ 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
......@@ -4,12 +4,35 @@ SUBDIRS = \
$(SUBDIRS):
$(MAKE) -C $@
pandoc-papers.pdf: pandoc-papers.md
pandoc \
-V aspectratio=169 \
-V institute=iDiv \
-V theme=Frankfurt \
-V navigation=horizontal \
-V logo=img/idiv-black-logo.png \
--pdf-engine=xelatex \
-s \
-t beamer \
-o pandoc-papers.pdf \
pandoc-papers.md
rdm.pdf: img rdm.md rdm.yml
pandoc \
--standalone \
--from=markdown+yaml_metadata_block \
--pdf-engine=xelatex \
--template=pandoc-cheat-sheet/cheat-sheet.tex \
-o rdm.pdf \
rdm.yml rdm.md
all: subdirs
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
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dia/rebase-vs-cherry-pick.dia
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<dia:string>#cherry-pick
git checkout b
git switch b
git cherry-pick a...c#</dia:string>
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......@@ -652,7 +652,7 @@ git cherry-pick a...c#</dia:string>
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......
git-course.html deleted 100644 → 0
View file @ f8d98c9a
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="author" content="Christian Krause" />
<meta name="dcterms.date" content="2015-06-15" />
<title>Git Workshop</title>
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<link rel="stylesheet" href="reveal.js/css/reveal.css"/>
<style type="text/css">code{white-space: pre;}</style>
<link rel="stylesheet" href="reveal.js/css/theme/black.css" id="theme" />
<!-- If the query includes 'print-pdf', include the PDF print sheet -->
<script>
if( window.location.search.match( /print-pdf/gi ) ) {
var link = document.createElement( 'link' );
link.rel = 'stylesheet';
link.type = 'text/css';
link.href = 'reveal.js/css/print/pdf.css';
document.getElementsByTagName( 'head' )[0].appendChild( link );
}
</script>
<!--[if lt IE 9]>
<script src="reveal.js/lib/js/html5shiv.js"></script>
<![endif]-->
</head>
<body>
<div class="reveal">
<div class="slides">
<section>
<h1 class="title">Git Workshop</h1>
<h3 class="author">Dirk Sarpe & Christian Krause</h3>
<aside class="notes">
<ul>
<li>if you have questions ask them right away</li>
</ul>
</aside>
</section>
<section id="poll-why-are-you-here" class="titleslide slide level1" data-markdown>
## Poll
# Why are you here?
Note:
- Someone (like us) told you it ~~might be~~ **is** useful.
- You never took the time to really learn it.
- You already know and use it, want to show off / learn new tricks.
- Somebody forced you to come here.
- You wanted to get away from your desk for once and maybe take a nap.
</section>
<section id="outline" class="titleslide slide level1" data-markdown>
# Outline
1. Intro
2. Git Commands
3. GitLab / GitHub
4. Workflows
Note:
- jeder Block ~ 1.5h
- insgesamt 2h mit Pause
- 8h - ein ganzer Tag git
- ein-satz-beschreibungen zu den abschnitten
- 0. why vcs, why git, getting started with git
- 1. git basics
- 2. web collaboration tools
- 3. how to collaborate in organized manner
</section>
<section>
<section class="titleslide slide level1" data-markdown>
## Block 1
# Introduction
Note:
- quickly talk about block outline
- why vcs? why git?
- installation git client
- setup GitLab / GitHub accounts
- getting started with git (try git)
</section>
<section class="slide level2" data-markdown>
### Have you ever seen this?
![foo](img/draft_mess.png)
Note:
- Dirk erklärt seine mess
- wouldn't it be nicer to have
</section>
<section class="slide level2" data-markdown>
### wouldn't it be nicer to have
# version control
```
Dirk Sarpe 14 minutes ago fix reference
Dirk Sarpe 5 days ago adapt figures to nature
Christian Krause 6 days ago add figure captions
Dirk Sarpe 7 weeks ago adds mean values to analysis
Christian Krause 7 weeks ago adds abstract
```
Note:
- git log --pretty=format'%an %ar %s'
- and as you can see not only for source code
</section>
<section class="slide level2" data-markdown>
## have you ever ...
- review history (see diff)
- wanted to go back in time
- maintain multiple versions
- hint: for different journals
- try things out without breaking what works
Note:
-
</section>
<section class="slide level2" data-markdown>
## have you ever ...
- collaborate
- who made that error
- see project progress
- lost code (no backup)
Note:
-
</section>
<section class="slide level2" data-markdown>
# yes?
Note:
-
</section>
<section class="slide level2" data-markdown>
# use vcs!
Note:
-
</section>
</section>
<section>
<section class="titleslide slide level1" data-markdown>
## Block 1
# git
Note:
-
</section>
<section class="titleslide slide level1" data-markdown>
![git](img/what-is-git.jpg)
Note:
-
</section>
<section class="titleslide slide level1" data-markdown>
![git](img/what-is-git-answer.jpg)
Note:
-
</section>
<section class="titleslide slide level1" data-markdown>
![git](img/say-what.jpg)
Note:
-
</section>
<section class="titleslide slide level1" data-markdown>
## what is git? (2nd try)
### seriously
# TODO image gitk all, visual representation of git parent child tree with remotes,
tags, good commit messages, etc. mit local change der remote noch nicht da ist
Note:
- am bild dvcs erklären!
</section>
<section class="slide level2" data-markdown>
![git](img/idontalwaysusevcs.jpg)
Note:
-
</section>
<section class="slide level2" data-markdown>
## Why do we all use git?
#### non-technical
- any workflow
- collaboration
- experimentation
- undo mistakes
- state of the art (best tool for the job)
- all the cool kids do it
Note:
-
</section>
<section class="slide level2" data-markdown>
## Why do we all use git?
#### technical
- never lose data (not just remote but also file integrity)
- easy conflict resolution
- local (your own copy of everything)
- implies speedy gonzales
Note:
-
</section>
</section>
</section>
<section>
<section id="prereq" class="titleslide slide level1" data-markdown>
### Block 1
## Git Demo
Note:
- vorher fragen, wer alles client braucht und noch accounts braucht, damit wir wissen,
wieviel zeit wir uns für try git nehmen können
- config
- init
- git add foo bar
- git commit -m 'foo bar'
- prima
</section>
</section>
<section>
<section id="prereq" class="titleslide slide level1" data-markdown>
### Block 1
## Checking Prerequisites
- GitHub / GitLab account
- local git client installation
- bonus: your own project without VCS
Note:
- wenn git client selbst nicht aufsetzen kann, dann bitte halbe stunde früher
- registration to the course
- git client includes your own notebook
</section>
</section>
<section class="slide level2" data-markdown>
##
-
Note:
-
</section>
</section>
<section>
<section class="titleslide slide level1" data-markdown>
# VCS for me
-
Note:
-
</section>
<section class="slide level2" data-markdown>
##
-
Note:
-
</section>
</section>
<section>
<section class="titleslide slide level1" data-markdown>
#
-
Note:
-
</section>
<section class="slide level2" data-markdown>
##
-
Note:
-
</section>
</section>
<section id="eof" data-background="img/trex.png"><h1>EOF</h1></section>
</div>
</div>
<script src="reveal.js/lib/js/head.min.js"></script>
<script src="reveal.js/js/reveal.js"></script>
<script>
Reveal.initialize({
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progress: true,
history: true,
center: true,
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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/idiv-black-logo.png 0 → 100644
View file @ 1a7f9522
img/idiv-black-logo.png

10.1 KiB

img/idiv-black.png 0 → 100644
View file @ 1a7f9522
img/idiv-black.png

34.9 KiB

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"]
}