.gitignore

-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

 [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

@@ -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

+# 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

dia/rebase-vs-cherry-pick.dia

@@ -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

@@ -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

@@ -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

@@ -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/motivation-structure.dot

+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

 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

+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

+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

+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

+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

+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

+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

@@ -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"]