sbib improve and rg bool

check-battery.sh

@@ -11,9 +11,15 @@ REM=`grep -i "charge_now" $BATTERY/uevent | awk -F= '{ print $2 }'`
 FULL=`grep -i "charge_full_design" $BATTERY/uevent | awk -F= '{ print $2 }'`
 PERCENT=`echo $(( $REM * 100 / $FULL ))`
 
-if [ $PERCENT -le "11" ]; then
+echo 'battery % is '$PERCENT
+
+if [ $PERCENT -le "23" ]; then
   #/usr/bin/i3-nagbar -m "Low battery"
-  #echo 'low battery '$PERCENT
   notify-send --urgency=critical "Low battery $PERCENT%"
 fi
 
+if [ $PERCENT -le "7" ]; then
+  echo "powering down..."
+  systemctl suspend
+fi
+

cp2figs.sh

@@ -1,5 +1,4 @@
 #!/bin/bash
-#!/bin/bash
 if [ "$1" == "-h" ] ; then
     echo "
           cp2figs.sh - copy and convert image to figure assets folder and put html figure string containing relative link to the asset on system clipboard

dark

@@ -0,0 +1,29 @@
+#!/bin/bash
+#dark: control display color contrast from terminal
+#usage: dark, dark 1, dark on, dark 0, dark off 
+#James B. Ackman 2022-05-02T22:53:41-07:00  
+
+set -e #exit if an error
+mode=${1:-"dark"}
+
+if [[ $1 == "0" || $1 == "off"  ]]; then
+  mode=light
+  scheme=base16-atelier-dune-light.sh
+  # scheme=base16-classic-light.sh
+  # scheme=base16-gruvbox-light-hard.sh
+  TaskTheme="light-256"
+else
+  mode=dark
+  # scheme=base16-atelier-dune.sh
+  # scheme=base16-classic-dark.sh
+  scheme=base16-gruvbox-dark-hard.sh
+  TaskTheme="dark-gray-256"
+fi
+ 
+#if exist base16 shell color scheme, switch to scheme
+ln -sf ~/.config/base16-shell/scripts/$scheme ~/.base16_theme
+sh ~/.base16_theme
+
+#if exist taskwarrior taskrc file, switch the color scheme 
+sed -i -E "s|include /usr/share/doc/task/rc/[a-z1256-]+.theme|include /usr/share/doc/task/rc/$TaskTheme.theme|" ~/.config/task/taskrc
+

dim

@@ -7,7 +7,7 @@
 
 #check kernel backlight driver names on your machine: `ls -l /sys/class/backlight/*`
 #then set following var, e.g. acpi_video0 nv_backlight or intel_backlight
-backlightDriver="intel_backlight"
+backlightDriver="acpi_video0"
 set -e #exit if an error
 percentValue=$1
 

dimr

@@ -1,3 +1,2 @@
 #!/bin/bash
 redshift -l 38:-122 -t 5500:3500 -g 0.8 -v 
-

f

@@ -4,7 +4,8 @@ if [ "$1" == "-h" ] ; then
     f - fuzzy preview and open text files or pdfs
          usage:
           f 
-          f p
+          f p #then type <enter> to preview
+          f p #then type <ctrl-s> to save pdf with spdf.sh 
 
          depends: 
           fzf
@@ -18,6 +19,8 @@ fi
 
 set -e #exit if an error
 
+#todo: simplify.
+
 if [ "$1" == "p" ]; then
 
     ls *.pdf | fzf --preview 'pdftotext -l 2 -nopgbrk -q {1} -' \
@@ -28,14 +31,21 @@ fi
 
 if [ -z "$1" ]; then
     #FZF_DEFAULT_COMMAND=rg -i --files --glob "!.git/*"
-    # fzf --delimiter : --preview 'less {1}' \
+    fzf --delimiter : --preview 'bat --color always --style=numbers --line-range=:500 {1}' \
-    fzf --delimiter : --preview 'bat --color=always --style=numbers --line-range=:500 {}' \
+        --preview-window=up:70% --bind "enter:execute(xdg-open {1})" 
-        --preview-window=up:70% --bind "enter:execute-silent(gvim {1} &)" 
+#        --preview-window=up:70% --bind "enter:execute($VISUAL {1})" 
+
+     # fzf --delimiter : --preview 'bat --color=always --style=numbers --line-range=:500 {}' \
+
+        # --preview-window=up:70% --bind "enter:execute-silent(gvim {1} &)" 
 
 else
     # rg $1 | fzf --delimiter : --preview 'less {1}' \
     # todo: replace this with a series elif blocks mapping selective previews and downstream application bindings to a set of desired filetypes
-    ls *.$1 | fzf --delimiter : --preview 'bat --color=always --style=numbers --line-range=:500 {}' \
+    #use xdg-mime, filetype info for opening
-        --preview-window=up:70% --bind "enter:execute-silent(gvim {1} &)" 
+    ls *$1 | fzf --delimiter : --preview 'bat --color always --style=numbers --line-range=:500 {1}' \
+        --preview-window=up:70% --bind "enter:execute(xdg-open {1})" 
+
+        # --preview-window=up:70% --bind "enter:execute-silent(gvim {1} &)" 
 fi
 

fetch_citation

@@ -0,0 +1,49 @@
+#!/bin/bash
+if [ "$1" == "-h" ] ; then
+    echo "
+    fetch_citation - extract citation for citekey in a bibtex.bib or bibjson.json file
+
+         usage:
+          fetch_citation citeKey
+
+         depends: 
+          grep, sed, echo
+          pandoc
+          pandoc-citeproc
+          wl-copy
+
+         defaults:
+          Set the required default file locations (csl file, bib file)
+ 
+    "
+    exit 0
+fi
+
+#Setup defaults
+cslFile=${2:-$HOME/projects/learn/bibd/bibd-md.csl}
+bibdFile=${3:-$HOME/projects/learn/bibd/OMEGA.bib}
+# bibdFile=${2:-$HOME/projects/learn/bibd/OMEGA.json}
+cd $(dirname $bibdFile)
+set -e #exit if an error
+
+#requires one citeKey string as input
+citeKey=$1
+
+#method1
+#todo: use json with jq
+# outCitation=$(pandoc -f latex <(echo "\cite{$citeKey}") -t plain -o - --bibliography $bibdFile --citeproc --csl $cslFile | tail -n +3)
+
+#method2
+#need to use a temporary bib file as input to pandoc because parsing a large bib file is too slow, but json input would be faster
+#and because pandoc expects a file input for bibliography
+tmpName=$(mktemp --suffix=.bib)
+str3=$(grep -A 30 $citeKey, $bibdFile)
+echo $str3 | sed -E "s|(.+\} ?\}).+|\1|" > $tmpName
+outCitation=$(pandoc -f latex <(echo "\cite{$citeKey}") -t plain -o - --bibliography $tmpName --citeproc --csl $cslFile | tail -n +3)
+rm $tmpName
+
+#tail -n +61 $fn | sed -E "s#(.+\}\})#\1#"
+# fzf --preview="head {}" --preview-window=up:30%
+# fzf --preview="file {}" --preview-window=down:1
+echo $outCitation
+echo $outCitation | wl-copy

reveal.sh

@@ -15,6 +15,9 @@ set -e
 
 appPath="$HOME/projects/dev/reveal.js"
 portNumber=${2:-8000}
+fn=$1 #markdown document to render e.g. neuroanatomy1.md
+basefn=$(basename $fn)
+fullfn=$(realpath $fn)
 
 if [[ ! -d $appPath ]]; then
     echo "reveal.js not found"
@@ -23,13 +26,10 @@ else
     cd $appPath
 fi
 
-fn=$1 #markdown document to render e.g. neuroanatomy1.md
-basefn=$(basename $fn)
 if [[ ! -e $basefn ]]; then
-    ln -s $fn $basefn
+  ln -s $fullfn $basefn 
 fi
 
-
 #add markdown filename into html title tag
 fn2=$(echo $basefn | sed -E 's/[0-9]{2,4}-//g' | sed 's/\.md//') #prep filename
 sed -i -E "s|(<title>).+(<\/title>)|\1$fn2\2|" index.html #swap in document title

s

@@ -0,0 +1,24 @@
+#! /usr/bin/python
+# adapted from https://stackoverflow.com/questions/59052703/grep-or-ripgrep-how-to-find-only-files-that-match-multiple-patterns-not-only-o
+
+import sys
+import subprocess
+from itertools import permutations
+
+usage = """
+Search with multiple keywords across files within current and subdirs using ripgrep. Provides boolean AND type search.
+
+Usage: s keyword1 keyword2
+e.g. s cerebral cetacean sand | f 
+"""
+ 
+# Check that the user puts in an argument, else print the usage variable, then quit.
+if len(sys.argv)< 2:
+    print (usage)
+    sys.exit(0)
+
+rgarg = '|'.join(('.*'.join(x) for x in permutations(sys.argv[1:])))
+cmd = ['rg', '-lUi', '--multiline-dotall', rgarg, '.']
+#  print(' '.join(cmd))
+proc = subprocess.run(cmd, capture_output=True)
+sys.stdout.write(proc.stdout.decode('utf-8'))

sbib

@@ -12,13 +12,20 @@ if [ "$1" == "-h" ] ; then
           # pass a custom citation style and database
           sbib a citeprocStyle.csl bibdFile.json
 
+          Then press <enter> to open pdf
+          and press <ctrl-c> to copy citation to clipboard
+
+          note: 
+           # to convert a bib to json, run
+           # pandoc bibdFile.bib -t csljson -o bibdFile.json
+
+
          depends: 
           fzf
           git grep
           sed tail
           bat or less
-          pandoc
+          fetch_citation, pandoc, pandoc-citeproc
-          pandoc-citeproc
           zathura (or other fast pdf viewer)
           echo
           wl-copy
@@ -32,9 +39,9 @@ if [ "$1" == "-h" ] ; then
 fi
 
 #Setup defaults
-cslFile=${2:-$HOME/projects/bibd/bibd-md.csl}
+cslFile=${2:-$HOME/projects/learn/bibd/bibd-md.csl}
-bibdFile=${3:-$HOME/projects/bibd/OMEGA.bib}
+bibdFile=${3:-$HOME/projects/learn/bibd/OMEGA.bib}
-# bibdFile=${2:-$HOME/projects/bibd/OMEGA.json}
+# bibdFile=${2:-$HOME/projects/learn/bibd/OMEGA.json}
 cd $(dirname $bibdFile)
 set -e #exit if an error
 
@@ -49,28 +56,9 @@ view_bib() {
     # str=$(git grep -E --line-number $sPattern $bibdFile | fzf --delimiter : --preview 'less {1}' --preview-window=:up:70%:+{2}-5)
     str=$(git grep -E --line-number $sPattern $bibdFile | fzf --delimiter : --preview 'bat --color=always --style=numbers --line-range=:500 {1}' --preview-window=:up:70%:+{2}-5)
 
-
     # extract citation key from the fzf string
     citeKey=$(echo $str | sed -E "s|$(basename $bibdFile):[0-9]+:@[a-zA-Z]+\{(.+),|\1|")
-
+    fetch_citation citeKey
-    #method1
-    #todo: use json with jq
-    # outCitation=$(pandoc -f latex <(echo "\cite{$citeKey}") -t plain -o - --bibliography $bibdFile --citeproc --csl $cslFile | tail -n +3)
-
-    #method2
-    #need to use a temporary bib file as input to pandoc because parsing a large bib file is too slow, but json input would be faster
-    #and because pandoc expects a file input for bibliography
-    tmpName=$(mktemp --suffix=.bib)
-    str3=$(grep -A 30 $citeKey $bibdFile)
-    echo $str3 | sed -E "s|(.+\} ?\}).+|\1|" > $tmpName
-    outCitation=$(pandoc -f latex <(echo "\cite{$citeKey}") -t plain -o - --bibliography $tmpName --citeproc --csl $cslFile | tail -n +3)
-    rm $tmpName
-
-    #tail -n +61 $fn | sed -E "s#(.+\}\})#\1#"
-    # fzf --preview="head {}" --preview-window=up:30%
-    # fzf --preview="file {}" --preview-window=down:1
-    echo $outCitation
-    echo $outCitation | wl-copy
 }
 
 
@@ -80,9 +68,12 @@ view_json() {
     # urlStr=$(jq -r '.[] | select(.id==env.citeKey).URL' $bibdFile)
 
     #actually this is the good one, opens pdfs quickly
-    jq -r '.[] | [.id, .title, .abstract, .keyword, .DOI, .PMID, .author[]?.family, .issued[]?[0]?[0], .["container-title"], .URL] | join("  ")' $bibdFile | fzf --preview 'echo {}' --preview-window=:up:70%:wrap --bind "enter:execute-silent(zathura {-1} &)"
+    jq -r '.[] | [.id, .title, .abstract, .keyword, .DOI, .PMID, .author[]?.family, .issued[]?[0]?[0], .["container-title"], .URL] | join("  ")' $bibdFile | fzf --preview 'echo {}' --preview-window=:up:70%:wrap \
-}
+    --bind "enter:execute-silent(zathura {-1} &)" \
+    --bind "ctrl-c:execute-silent(fetch_citation {1})"
 
+#    --bind "ctrl-c:execute(notify-send {1})"
+}
 
 
 #set pattern to the null character '\0' for search all, else search only cite keys
@@ -93,7 +84,7 @@ else
 fi
 
 if [ "$1" == "j" ]; then
-    bibdFile=${3:-$HOME/projects/bibd/OMEGA.json}
+    bibdFile=${3:-$HOME/projects/learn/bibd/OMEGA.json}
     view_json
 else
     view_bib

sdoi.sh

@@ -24,8 +24,8 @@ set -e #exit if an error
 doi=$1
 fn=$2
 styleSheet=${pubmedStyleSheet:-$HOME/bin/pubmed2bibtex.xsl}
-bibdFileOut=${bibdFileOut:-$HOME/projects/bibd/OMEGA.bib}
+bibdFileOut=${bibdFileOut:-$HOME/projects/learn/bibd/OMEGA.bib}
-pdfPathOut=${pdfPathOut:-$HOME/projects/bibd/papers}
+pdfPathOut=${pdfPathOut:-$HOME/projects/learn/bibd/papers}
 relPath=$(basename $pdfPathOut)
 
 #define functions
@@ -45,7 +45,7 @@ import_bib() {
 fetchBib_pubmed() {
   #request pubmed xml and transform into bibtex
   curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$uid&retmode=xml" > $tmpBib.xml
-  xsltproc --novalid $styleSheet $tmpBib.xml > $tmpBib
+  xsltproc --novalid $styleSheet $tmpBib.xml >> $tmpBib
 }
 
 fetchBib_doiDotOrg() {
@@ -69,7 +69,9 @@ extract_name() {
 
 append_bibfile() {
   #import bibtex
-  #first grep for a uid (doi) in case its already in db
+  #replace pubmed field with pmid
+  sed -i -E "s|(\W*)pubmed = |\1pmid = |" $tmpBib
+  #grep for a uid (doi) in case its already in db
   if [[ -z $(rg $doi $bibdFileOut) ]]; then
     echo "importing $tmpBib"
     cat $tmpBib >> $bibdFileOut
@@ -91,7 +93,7 @@ append_pdf() {
 
 clean_up() {
   #clean up
-  rm -f $tmpBib.bib $tmpBib.bib.xml
+  rm -f $tmpBib $tmpBib.xml
   exit 1
 }
 
@@ -118,5 +120,6 @@ if [ -s "$tmpBib" ]; then
   import_bib
 else
   echo "sorry, doi not found.."
+  exit 1
 fi
 

spdf.sh

@@ -1,18 +1,16 @@
 #!/bin/bash
 if [ "$1" == "-h" ] ; then
     echo "
-        spdf - search for a doi within a pdf. If found, use sdoi.sh to query pubmed, and append bibtex entry with the pdf to your local bib database file
+        spdf - search for a doi within a pdf. If found, print the doi and then use sdoi.sh to query pubmed and append a bibtex entry with the pdf to your local bib database file
 
          usage:
           spdf.sh file.pdf
 
          depends:
           pdftotext - from ghostscript or poppler or texlive ?
-          xsltproc, xmllint - xml programs from libxml
-          pubmed2bibtex.xsl - xml processor stylesheet
 
          defaults:
-          Set the three required default file locations (xsl file, bib file, pdf directory)
+          See sdoi.sh
           "
     exit 0
 fi
@@ -37,6 +35,8 @@ fi
 if [ -z "$doi" ]; then
   echo "doi not found"
   exit 1
+else
+  echo $doi
 fi
 
 sdoi.sh $doi $fn

wm_spawn

@@ -0,0 +1,9 @@
+#!/bin/bash
+if [ -n "$TMUX" ] ; then
+    # tmux session running
+    # tmux split-window -h "nvim \"$*\""
+    tmux split-window -h $EDITOR $1
+else
+    # alacritty -e "nvim \"$*\""
+    alacritty -e bash -ic "$EDITOR $1" &
+fi