View this manual online at https://rcdata.nau.edu/genomic-ml/animint2-manual/Ch00-preface.html

Compile this manual by typing jekyll build on the command line. Jekyll/ruby versions tested include

thocking@silene:~/projects/animint-book(master)$ jekyll --version
jekyll 3.1.2
thocking@silene:~/projects/animint-book(master*)$ ruby --version
ruby 2.1.1p76 (2014-02-24 revision 45161) [x86_64-linux]

(base) tdhock@maude-MacBookPro:~/R/animint2(geom-oop)$ jekyll --version
jekyll 3.1.6
(base) tdhock@maude-MacBookPro:~/R/animint2(geom-oop)$ ruby --version
ruby 2.5.1p57 (2018-03-29 revision 63029) [x86_64-linux-gnu]

Versions of R and packages are documented in _plugins/knit.R

pandoc known to work is version=1.19.2.4, does not work with 2.14.2

wget https://github.com/jgm/pandoc/releases/download/1.19.2/pandoc-1.19.2-1-amd64.deb
mkdir pandoc
ar p pandoc-1.19.2-1-amd64.deb data.tar.gz | tar xvz --strip-components 2 -C pandoc

(base) tdhock@maude-MacBookPro:~/projects/animint2-manual(master*)$ /usr/bin/pandoc --version
pandoc 1.19.2.4
Compiled with pandoc-types 1.17.0.5, texmath 0.9.4.4, skylighting 0.3.3.1
Default user data directory: /home/tdhock/.pandoc
Copyright (C) 2006-2016 John MacFarlane
Web:  http://pandoc.org
This is free software; see the source for copying conditions.
There is no warranty, not even for merchantability or fitness
for a particular purpose.

(base) tdhock@maude-MacBookPro:~/projects/animint2-manual(master*)$ pandoc --version
pandoc 2.14.2
Compiled with pandoc-types 1.22, texmath 0.12.3.1, skylighting 0.11,
citeproc 0.5, ipynb 0.1.0.1
User data directory: /home/tdhock/.local/share/pandoc
Copyright (C) 2006-2021 John MacFarlane. Web:  https://pandoc.org
This is free software; see the source for copying conditions. There is no
warranty, not even for merchantability or fitness for a particular purpose.

~/bin/pandoc is too new, created ./bin/pandoc symlink to old /usr/bin/pandoc and then compile via bash build.sh which contains:

PATH=bin:$PATH jekyll b

Also make sure that animint2-manual/_plugins/library (used for interactive testing) is symlinked to animint2-manual/library (used for rendering, could be confusing if they are different).

To edit Rmd in emacs try https://github.com/vspinu/polymode via https://github.com/tdhock/dotfiles/blob/master/.emacs

TODOs

• chapter with geom_abline + coord_equal for comparing baseline + proposed algos.
• setup travis?
• what to do about slow loading? split Rmd files so that there is only one animint in each? or recode the renderer so that it only loads when you scroll down and the animint div becomes visible?
• use http://rstudio.github.io/tufte/ or https://bookdown.org/ ?
• https://bitpay.com for accepting donations? or just create a bitcoin wallet?

How to add a chapter

• Create ChXX-foo.Rmd
• Add a link in _layouts/default.html
• Add a paragraph/link in Ch00-preface.Rmd
• Add a paragraph/link in the preceding chapter.
• Rename following chapters and update links if necessary.