diff --git a/img/rdm-use-cases-a.dot b/img/rdm-use-cases-a.dot
index 0182f9f24a60b5e76a4cac823ff2144bdd806812..137593ac0cc4f751ce0a0ff855b5f89c096719e2 100644
--- a/img/rdm-use-cases-a.dot
+++ b/img/rdm-use-cases-a.dot
@@ -34,9 +34,9 @@ digraph {
paper_version_a[label = "nature-review-1"]
}
- script_version_a -> software_a_version_a [label = "\n\n", lhead = cluster_software_a]
+ script_version_a -> software_a_version_a [label = "\n\n"]
- script_version_a -> software_b_version_a [label = "\n\n", lhead = cluster_software_b]
+ script_version_a -> software_b_version_a [label = "\n\n"]
- paper_version_a -> script_version_a [label = "\n\n", lhead = cluster_script]
+ paper_version_a -> script_version_a [label = "\n\n"]
}
diff --git a/img/rdm-use-cases-b.dot b/img/rdm-use-cases-b.dot
index 91e10b18ca0da08f664f1d05516d057bb849e2e0..84543afc2b10d9b7c3bdccddc277347cabf718a1 100644
--- a/img/rdm-use-cases-b.dot
+++ b/img/rdm-use-cases-b.dot
@@ -37,12 +37,12 @@ digraph {
paper_version_b[label = "nature-review-2"]
}
- script_version_a -> software_a_version_a [label = "\n\n", lhead = cluster_software_a]
- script_version_b -> software_a_version_a [label = "\n\n", lhead = cluster_software_a]
+ 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", lhead = cluster_software_b]
- script_version_b -> software_b_version_b [label = "\n\n", lhead = cluster_software_b]
+ 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", lhead = cluster_script]
- paper_version_b -> script_version_b [label = "\n\n", lhead = cluster_script]
+ paper_version_a -> script_version_a [label = "\n\n"]
+ paper_version_b -> script_version_b [label = "\n\n"]
}
diff --git a/img/rdm-use-cases.dot b/img/rdm-use-cases.dot
index 45fdd1095b36a657a040877165a59d4630248979..eefbc1c2ced646bc7d18026dab623a8f840e5af4 100644
--- a/img/rdm-use-cases.dot
+++ b/img/rdm-use-cases.dot
@@ -38,13 +38,13 @@ digraph {
paper_version_c[label = "nature-final"]
}
- script_version_a -> software_a_version_a [label = "\n\n", lhead = cluster_software_a]
- script_version_b -> software_a_version_a [label = "\n\n", lhead = cluster_software_a]
+ 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", lhead = cluster_software_b]
- script_version_b -> software_b_version_b [label = "\n\n", lhead = cluster_software_b]
+ 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", lhead = cluster_script]
- paper_version_b -> script_version_b [label = "\n\n", lhead = cluster_script]
- paper_version_c -> script_version_b [label = "\n\n", lhead = cluster_script]
+ 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"]
}
diff --git a/rdm.html b/rdm.html
new file mode 100644
index 0000000000000000000000000000000000000000..545da9cd0de53afe089d2a6d9aa067a76e2c78e5
--- /dev/null
+++ b/rdm.html
@@ -0,0 +1,498 @@
+<!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
+
+ 
+
+ 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
+
+ 
+
+ 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
+
+ 
+
+ 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
+
+ 
+
+ 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
+
+ 
+
+ 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
+
+ 
+
+ 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
+
+ 
+ </section>
+
+ <section id="use-case-integrated-3" data-markdown>
+ ## integration
+
+ 
+ </section>
+
+ <section id="use-case-integrated-data" data-markdown>
+ ## integration
+
+ 
+ </section>
+ </section>
+
+ <!---------------------------------------------------------------------
+ <!-- anti patterns
+ <!-------------------------------------------------------------------->
+
+ <section>
+ <section id="anti-patterns" data-markdown>
+ # anti-patterns
+
+ 
+
+ 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 **DIFF**erent !!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/master/basics.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>