Initial commit

7 files changed, 346 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..e5f7a48
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+bak
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..8f9447e
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,3 @@
+.PHONY: install
+install:
+	./install
diff --git a/bashrc b/bashrc
new file mode 100644
index 0000000..9dcdd4b
--- /dev/null
+++ b/bashrc
@@ -0,0 +1,135 @@
+# vim: foldmethod=marker ts=4 sw=4
+# editor {{{
+# Prefer neovim over vim over vi
+if [ -e /usr/bin/nvim ]
+then
+    EDITOR=/usr/bin/nvim
+else 
+    if [ -e /usr/bin/vim ]
+    then
+		EDITOR=/usr/bin/nvim
+    else
+		EDITOR=/usr/bin/vi
+    fi
+fi
+# }}}
+# private bin {{{
+if [ -d ~/bin ] ; then
+    PATH=~/bin:"${PATH}"
+fi
+# }}}
+# R {{{
+# littler scripts distributed with the littler package
+PATH=/usr/local/lib/R/site-library/littler/examples:"${PATH}"
+
+# RPython
+export RPYTHON_PYTHON_VERSION=3
+
+# Vim-R-plugin
+# From r-plugin-bash-setup help page in Vim-R-plugin (Debian package 1.2-1)
+# Change the TERM environment variable (to get 256 colors) and make Vim 
+# connect to th X Server even if running in a terminal emulator (many of 
+# the plugin features depend on this). Now only needed for "old" vim
+# like vim 7.4 from Debian stable
+if [ "x$DISPLAY" != "x" ]
+then
+		if [ "screen" = "$TERM" ]
+		then
+				export TERM=screen-256color
+		else
+				export TERM=xterm-256color
+		fi
+		alias vim='vim --servername VIM'
+fi
+
+alias tarxz='tar --use-compress-program=pxz -c -v -f'
+
+# Path where the R sources are
+export RTOP=~/svn/R
+# }}}
+# debian {{{
+export DEBEMAIL=jranke@uni-bremen.de
+export DEBFULLNAME="Johannes Ranke"
+# }}}
+# rdkit {{{
+# RDKIT (commented out on 2015-10-02 as I am using the Debian package python-rdkit
+#export RDBASE="$HOME/git/rdkit"
+#export LD_LIBRARY_PATH="$RDBASE/lib"
+#export PYTHONPATH="${PYTHONPATH}:$RDBASE:$HOME/ariance/aeras/libreoffice:$HOME/py"
+# }}}
+# prompt {{{
+force_color_prompt=yes
+
+# identify the current chroot 
+if [ -z "$debian_chroot" ] && [ -r /etc/debian_chroot ]; then
+		debian_chroot=$(cat /etc/debian_chroot)
+fi
+
+if [ -n "$force_color_prompt" ]; then
+		if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
+				# We have color support; assume it's compliant with Ecma-48
+				# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
+				# a case would tend to support setf rather than setaf.)
+				color_prompt=yes
+		else
+				color_prompt=
+		fi
+fi
+
+source ~/.git-prompt.sh
+
+if [ "$color_prompt" = yes ]; then
+		PS1="${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$(__git_ps1)\$ "
+else
+		PS1="${debian_chroot:+($debian_chroot)}\u@\h:\w\$(__git_ps1)\$ "
+fi
+unset color_prompt force_color_prompt
+# }}}
+# history {{{
+# See bash(1) for more options
+HISTCONTROL=ignoredups:ignorespace
+shopt -s histappend
+HISTSIZE=1000
+HISTFILESIZE=2000
+# }}}
+# ls, dir and grep {{{
+# enable color support of ls and also add handy aliases
+if [ -x /usr/bin/dircolors ]; then
+    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
+    alias ls='ls --color=auto'
+    alias dir='dir --color=auto'
+    alias vdir='vdir --color=auto'
+
+    alias grep='grep --color=auto'
+    alias fgrep='fgrep --color=auto'
+    alias egrep='egrep --color=auto'
+fi
+
+# some more ls aliases
+alias ll='ls -alF'
+alias la='ls -A'
+alias l='ls -CF'
+alias lh='ls -lh'
+# }}}
+# alert {{{
+# Add an "alert" alias for long running commands.  Use like so:
+#   sleep 10; alert
+alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'
+# }}}
+# bash completion {{{
+# enable programmable completion features (you don't need to enable
+# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
+# sources /etc/bash.bashrc).
+if [ -f /etc/bash_completion ] && ! shopt -oq posix; then
+    . /etc/bash_completion
+fi
+# }}}
+# {{{varia
+# check the window size after each command and, if necessary,
+# update the values of LINES and COLUMNS.
+shopt -s checkwinsize
+
+# make less more friendly for non-text input files, see lesspipe(1)
+[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"
+# }}}
+export EDITOR PATH
diff --git a/bin/a4copy b/bin/a4copy
new file mode 100755
index 0000000..de45664
--- /dev/null
+++ b/bin/a4copy
@@ -0,0 +1,26 @@
+#!/bin/sh
+ 
+usage()
+{
+echo "Usage: a4copy [Lineart|Gray|Color]"
+}
+
+#test to see if the mode and a filename have been entered
+if [ $# -lt 1 ] ; then usage ; exit 1 ; fi
+mode=$1
+
+echo Now scanning your A4 document to pdf
+
+#scan the A4 binary(b&w) file uncompressed at 300dpi to temporary file
+scanimage \
+    --mode $mode \
+    -x 210 -y 296 \
+    --resolution 300 \
+    --format=tiff > temp-copy.tif
+
+#convert to pdf with G4 compression
+tiff2pdf temp-copy.tif -p A4 -q G4 -o temp-copy.pdf
+rm temp-copy.tif
+
+#print pdf
+lpr temp-copy.pdf
diff --git a/bin/pdfscan b/bin/pdfscan
new file mode 100755
index 0000000..5b71b30
--- /dev/null
+++ b/bin/pdfscan
@@ -0,0 +1,33 @@
+#!/bin/sh
+ 
+usage()
+{
+echo "Usage: pdfscan [Lineart|Gray|Color] [resolution] <nameofimage>"
+}
+
+#test to see if the mode and a filename have been entered
+if [ $# -lt 3 ] ; then usage ; exit 1 ; fi
+mode=$1
+resolution=$2
+name=$3
+
+#read output of help command to get scanner device name
+#scanner=`scanimage --help | tail --lines=1 `
+
+echo Now scanning your A4 document to pdf
+#echo Now scanning your A4 document on $scanner
+
+#scan the A4 binary(b&w) file uncompressed at 300dpi to temporary file
+#scanimage -d $scanner \
+scanimage \
+    --mode $mode \
+    -x 210 -y 296 \
+    --resolution $resolution \
+    --format=tiff > temp-$name.tif
+
+#convert to pdf with G4 compression
+tiff2pdf temp-$name.tif -p A4 -q G4 -o $name.pdf
+rm temp-$name.tif
+
+#display pdf
+okular $name.pdf
diff --git a/install b/install
new file mode 100755
index 0000000..86167d2
--- /dev/null
+++ b/install
@@ -0,0 +1,24 @@
+#!/bin/bash
+# run this script as ./install as we set its working dir from $BASH_SOURCE
+cd $(dirname $BASH_SOURCE)
+
+# the path of the working dir
+BASE=$(pwd)
+
+# dotfiles to install
+for dotfile in bashrc vimrc; do
+  mkdir -pv bak  
+  [ -e ~/.$dotfile ] && mv -v ~/.$dotfile bak/.$dotfile
+  ln -sfv $BASE/$dotfile ~/.$dotfile
+done
+
+# git-prompt
+if [ ! -e ~/.git-prompt.sh ]; then
+  curl https://raw.githubusercontent.com/git/git/master/contrib/completion/git-prompt.sh -o ~/.git-prompt.sh
+fi
+
+# scripts
+mkdir -pv ~/bin
+for bin in $BASE/bin/*; do
+  ln -svf $bin ~/bin
+done
diff --git a/vimrc b/vimrc
new file mode 100644
index 0000000..f3ad315
--- /dev/null
+++ b/vimrc
@@ -0,0 +1,124 @@
+" vim: foldmethod=marker foldlevel=0 ts=2 sw=2
+
+" default settings (much is handled by tpope/sensible) {{{1
+set ts=2
+set sw=2
+set expandtab
+filetype plugin on
+filetype indent on
+
+" to ease the use of plugin mappings
+let maplocalleader = ","
+let mapleader = ";"
+
+" Plugins managed by vim-plug {{{1
+call plug#begin('~/.vim/plugged')
+
+Plug 'tpope/vim-fugitive'
+Plug 'tpope/vim-sensible'
+Plug 'tpope/vim-scriptease' " gives me K for looking up docs in vim scripts
+Plug 'hrp/EnhancedCommentify'
+Plug 'jalvesaq/R-Vim-runtime'
+Plug 'jranke/vim-pandoc', { 'branch': 'rmd' }
+Plug 'vim-pandoc/vim-pandoc-syntax'
+
+if !has('nvim')
+	Plug 'jranke/Vim-R-plugin' " for my vim version 7.4, legacy plugin not maintained by Jakson any more
+else
+	Plug 'jalvesaq/Nvim-R'
+endif
+
+call plug#end()
+
+" legacy Vim-R-plugin plugin {{{1
+if !has('nvim')
+	"let vimrplugin_vsplit = 0
+	"let vimrplugin_rconsole_width = 100
+
+	"let vimrplugin_pdfviewer = "/usr/bin/okular"
+	"let vimrplugin_openpdf = 0
+	let vimrplugin_assign = 0
+	"let vimrplugin_objbr_place = "script,left"
+	let r_syntax_folding = 1
+	let rmd_syn_hl_chunk = 1
+
+  let vimrplugin_map_r = 1 " is silent per default, therefore tried
+	"vnoremap  r  *@<Esc>:call SendSelectionToR("echo", "down")<CR>
+  " but this does not work as expected
+else
+	vmap r <Esc>:call SendSelectionToR("echo", "down")<CR>
+	"let R_source_args = "print.eval = TRUE"
+	let R_vsplit = 1
+	let R_assign = 0
+endif
+
+" R syntax {{{1
+let r_syntax_folding = 0
+let rmd_syn_hl_chunk = 1
+
+" Search {{{1
+set infercase
+"set hlsearch
+set incsearch
+
+" Showmarks {{{1
+let marksCloseWhenSelected = 0
+let showmarks_include="abcdefghijklmnopqrstuvwxyz"
+
+" Syntax folding for tex and markdown {{{1
+" for syntax/tex.vim
+let g:tex_fold_enabled=1
+" for syntax/markdown.vim
+let g:rmd_syn_fold=1
+
+" Beamer/tex environments - should go to some after/tex.vim script {{{1
+noremap \bf i\begin{frame}{}<Space>%{{{3<CR><CR>\end{frame}<CR><ESC>3k14li
+noremap \bi i\begin{itemize}[<+->]<CR>\item <CR>\end{itemize}<ESC>k8li
+noremap \bc i\begin{center}<CR><CR>\end{center}<CR><ESC>2ki
+noremap \bt i\begin{table}\begin{tabular}{}<CR><CR>\end{tabular}\end{table}<CR><ESC>3ki
+noremap \bo i\begin{columns}<CR>\begin{column}{}<CR>\end{column}<CR>\end{columns}<CR><ESC>3k17li
+noremap \bs i\source{}<ESC>li
+noremap \eq i\question[2]<CR>\begin{solution}[2cm]<CR>\end{solution}<CR><ESC>3kA
+
+" EnhancedCommentify {{{1
+vmap +  <Plug>Comment
+vmap -  <Plug>DeComment
+
+" pandoc {{{1
+let pandoc#folding#fold_yaml=1
+let pandoc#folding#level=2
+let pandoc#folding#fdc=0
+let pandoc#syntax#conceal#use=0
+
+" Show syntax highlighting under the cursor {{{1
+" http://vim.wikia.com/wiki/Identify_the_syntax_highlighting_group_used_at_the_cursor
+map <F10> :echo "hi<" . synIDattr(synID(line("."),col("."),1),"name") . '> trans<'
+      \ . synIDattr(synID(line("."),col("."),0),"name") . "> lo<"
+      \ . synIDattr(synIDtrans(synID(line("."),col("."),1)),"name") . ">"<CR>
+
+" Show syntax highlighting group in status line 
+" http://vim.wikia.com/wiki/Showing_syntax_highlight_group_in_statusline
+function! SyntaxItem()
+  return synIDattr(synID(line("."),col("."),1),"name")
+endfunction
+
+" Status line {{{1
+if has('statusline')
+  set statusline=%#Question#                   " set highlighting
+  set statusline+=%-2.2n\                      " buffer number
+  set statusline+=%#WarningMsg#                " set highlighting
+  set statusline+=%f\                          " file name
+  set statusline+=%#Question#                  " set highlighting
+  set statusline+=%h%m%r%w\                    " flags
+  set statusline+=%{strlen(&ft)?&ft:'none'},   " file type
+  set statusline+=%{(&fenc==\"\"?&enc:&fenc)}, " encoding
+  set statusline+=%{((exists(\"+bomb\")\ &&\ &bomb)?\"B,\":\"\")} " BOM
+  set statusline+=%{&fileformat},              " file format
+  set statusline+=%{&spelllang},               " language of spelling checker
+  set statusline+=%{SyntaxItem()}              " syntax highlight group under cursor
+  set statusline+=%=                           " ident to the right
+  set statusline+=0x%-8B\                      " character code under cursor
+  set statusline+=%-7.(%l,%c%V%)\ %<%P         " cursor position/offset
+endif
+
+set laststatus=2