.gitignore

@@ -1,5 +1,2 @@
 CONFIG
 *.pyc
-build
-dist
-*.egg-info

bbbib.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+WHERE=$( cd $(dirname $0) ; pwd -P )
+
+# default configs
+if [[ -e "$WHERE/CONFIG" ]]; then
+	source $WHERE/CONFIG
+fi
+
+OPTIND=1 #reset getopts
+
+while getopts :b: opts; do
+	case $opts in
+		b)
+			BIB=$OPTARG
+			;;
+		?)
+			echo "invalid option -$OPTARG";
+			exit;
+			;;
+		:)
+			echo "option -$OPTARG requires an argument";
+			exit;
+			;;
+	esac
+done
+
+shift $((OPTIND-1))
+
+# bibliography exists?
+if [[ -z "$BIB" ]]; then
+	echo "No bibliography"
+	exit;
+fi 
+
+./parse/refactorbib.py -i $BIB 
+#node $BIBLIOGRAPHE_PATH/refactorbib.js --data $BIB --index --print

bin/iiindex

@@ -1,27 +0,0 @@
-#!/usr/bin/env python
-
-import os, sys, glob
-
-from nnnotes import parse
-
-if __name__ == '__main__':
-
-	indexfile = '.indx'
-
-	notes = glob.glob('*.mmd')
-	if len(notes) > 1:
-		sys.exit('More or less *.mmd files than expected.')
-	elif len(notes) < 1:
-		sys.exit('No *.mmd in current directory.')
-
-	try:
-		note = open(notes[0], 'r+')
-	except:
-		sys.exit('Cannot open ' + notes[0])
-
-	with open(indexfile, 'w') as indx:
-		parse.run(note, indx)
-
-
-
-

bin/iiinject

@@ -1,40 +0,0 @@
-#!/usr/bin/env python
-
-import os, sys, glob, json
-
-from nnnotes import compare, inject
-
-if __name__ == '__main__':
-
-	indexfile = '.indx'
-
-	pdfs = glob.glob('*.pdf')
-	if len(pdfs) > 1:
-		sys.exit('More than one pdf in current directory. No obvious choice. Aborting.')
-
-	if len(pdfs) == 1:
-		pdf = pdfs[0]
-		if os.path.isfile(indexfile):
-			tmp = '.tmp'
-			os.system('plfr -json ' + pdf + ' > ' + tmp)     	### relying on plfr
-			diff = compare.run(indexfile, tmp)				### new highlights in pdf?
-			
-			with open(tmp, 'w') as fptmp:
-				json.dump(diff, fptmp)
-			indexfile = tmp
-
-		else:
-			os.system('plfr -json ' + pdf + ' > ' + indexfile)
-
-
-	notes = glob.glob('*.mmd')
-	if len(notes) > 1:
-		sys.exit('More or less *.mmd files than expected.')
-	elif len(notes) < 1:
-		sys.exit('No *.mmd in current directory.')
-
-	note = notes[0]
-	inject.run(note, indexfile)
-
-	if os.path.isfile('.tmp'):
-		os.remove('.tmp')

bin/nnnote

@@ -1,83 +0,0 @@
-#!/usr/bin/env python
-
-import os, sys, argparse, shutil, subprocess
-import getpass, time
-
-from nnnotes import TEMPLATE_PATH
-
-def yes_no(question):
-
-	sys.stdout.write(question)
-
-	yes = set(['yes','y', 'ye', ''])
-	no = set(['no','n'])
-
-	choice = raw_input().lower()
-	if choice in yes:
-	   return True
-	elif choice in no:
-	   return False
-	else:
-	   sys.stdout.write("Please respond with 'yes' or 'no'")
-
-def check_note_exists(title):
-
-	if os.path.isdir(title):
-		q = yes_no('The note already exists in the current directory.\nDo you want to proceed and erase the current note? [y/n] ')
-		if not q:
-			sys.exit('Notes already exists. Aborting.')
-		return True
-	return False
-
-
-if __name__ == '__main__':
-
-	p = argparse.ArgumentParser()
-	p.add_argument('-t', '--title', action="store", help="title of the note", required=True)
-	p.add_argument('-f', '--file', action="store", help="(pdf) file to extract notes from")
-	p.add_argument('-b', '--bibtex', action="store", help="bibtex file containing bibliographical information")
-	p.add_argument('-i', '--bibtexitem', action="store", help="name of the item in the bibtex file")
-	p.add_argument('-s', '--style', action="store", help="bibliographic style")
-
-	args = p.parse_args()
-
-	if not check_note_exists(args.title):
-		# make directory for the note
-		os.makedirs(args.title)
-
-	# copy template files -- this needs to change....
-	#home = os.path.dirname(os.path.realpath(__file__))
-	os.system('cp -aR ' + TEMPLATE_PATH + '/* ' + args.title)
-
-	os.chdir(args.title)
-
-	# copy note file if it exists
-	if args.file is not None and os.path.isfile(args.file):
-		shutil.copy2(args.file, os.path.basename(args.file))
-
-	# style
-	style_arg = ''
-	if args.style is not None:
-		os.system('sed -i.bak "s#CSL\ :=#CSL\ := ' + args.style + '#g" Makefile')
-		style_arg = '-s ' + args.style
-
-	# bibtex item
-	bibtexitem_arg = ''
-	if args.bibtexitem is not None:
-		bibtexitem_arg = '-i ' + args.bibtexitem
-
-	# generate bibliographic element
-	if args.bibtex is not None and os.path.isfile(args.bibtex):
-		os.system('sed -i.bak "s#BIB\ :=#BIB\ := ' + args.bibtex + '#g" Makefile')
-		ref = '> ' + subprocess.check_output('csl_unsorted ' + args.bibtex + ' ' + bibtexitem_arg + ' ' + style_arg + ' -f md', shell=True).rstrip()
-		os.system('sed -i.bak "s~*MACHINE-REF*~' + ref + '~g ; s~%\ title~%\ ' + ref + '~g" notes.mmd')
-
-	author = getpass.getuser()
-	date = time.strftime("%d/%m/%Y")
-
-	os.system('sed -i.bak "s~%\ author~%\ ' + author + '~g ; s~%\ date~%\ ' + date + '~g" notes.mmd')
-
-	# cleanup
-	os.system('rm *.bak')
-	os.chdir('..')
-

nnnew.sh

@@ -0,0 +1,110 @@
+#!/bin/bash
+
+#Black        0;30     Dark Gray     1;30
+#Blue         0;34     Light Blue    1;34
+#Green        0;32     Light Green   1;32
+#Cyan         0;36     Light Cyan    1;36
+#Red          0;31     Light Red     1;31
+#Purple       0;35     Light Purple  1;35
+#Brown/Orange 0;33     Yellow        1;33
+#Light Gray   0;37     White         1;37
+
+BLUE='\033[0;34m'
+NC='\033[0m'
+
+WHERE=$( cd $(dirname $0) ; pwd -P )
+
+# default configs
+if [[ -e "$WHERE/CONFIG" ]]; then
+	source $WHERE/CONFIG
+fi
+
+print_usage() {
+	printf "usage: ${BLUE}nnnew.sh -t [title] -f [pdf file] -b [json biblio] -s [style] -r [reference]${NC}"
+}
+
+OPTIND=1 #reset getopts
+
+while getopts t:f:b:s:r: opts; do
+	case $opts in
+		t)
+			TITLE=$OPTARG
+			;;
+		f)
+			FILE=$OPTARG
+			;;
+		b)
+			BIB=$OPTARG
+			;;
+		s)
+			STYLE=$OPTARG
+			;;
+		r)
+			REF=$OPTARG
+			;;			
+		?)
+			#echo "invalid option -$OPTARG";
+			print_usage
+			exit;
+			;;
+		:)
+			echo "option -$OPTARG requires an argument";
+			print_usage
+			exit;
+			;;
+	esac
+done
+
+shift $((OPTIND-1))
+
+if [[ -z "$TITLE" ]]; then
+	echo "No title provided. Aborting."
+	print_usage
+	exit;
+fi
+
+if [[ -d "$TITLE" ]]; then
+	read -p "Specified note already exists... Do you wish to continue? " yn
+	case $yn in
+        [Yy]* ) rm -r $TITLE; break;;
+        [Nn]* ) exit;;
+        * ) echo "Please answer yes or no.";;		
+	esac
+fi
+
+printf "\n-----\ntitle: $TITLE\nfile: $FILE\nbib: $BIB\ncsl: $STYLE\nref: $REF\nbibliographe: $BIBLIOGRAPHE_PATH\n-----\n"
+
+# output
+mkdir -p $TITLE
+
+# copy templates
+cp -aR $WHERE/template/* $TITLE
+
+cd $TITLE
+
+touch notes.mmd
+
+# file exists? copy to output
+[ -z "$FILE" ] && echo "No file to copy. Make sure to reference in text in the note!" || curl -O $FILE 
+
+# bibliography exists? fix makefile accordingly
+[ -z "$BIB" ] && echo "No bibliography" || sed -i.bak "s#BIB\ :=#BIB\ := $BIB#g" Makefile
+
+# csl style exists? fix makefile accordingly
+[ -z "$STYLE" ] && echo "No csl style" || sed -i.bak "s#CSL\ :=#CSL\ := $STYLE#g" Makefile
+
+if [ -z "$BIBLIOGRAPHE_PATH" ]; then
+	echo "No bibliographe"	
+else
+	./parse/refactorbib.py $BIB > tmpbib.json
+	REFERENCE=$(node $BIBLIOGRAPHE_PATH/generatebib.js --data tmpbib.json --items [\"$REF\"] --output md)
+	AUTHOR=$(whoami)
+	DATE=$(date +%Y\-%m\-%d)
+	echo $REFERENCE
+	rm tmpbib.json
+	sed -i.bak "s~*MACHINE-REF*~$REFERENCE~g ; s~%\ title~%\ $REFERENCE~g ; s~%\ author~%\ $AUTHOR~g ; s~%\ date~%\ $DATE~g" notes.mmd
+fi
+
+# cleanup
+rm *.bak
+cd ..

nnnotes/__init__.py

@@ -1,3 +0,0 @@
-import os
-
-TEMPLATE_PATH = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'template')

parse/compare.py

@@ -1,8 +1,4 @@
 #!/usr/bin/env python
-
-# compares two json formatted indexes
-# and return the difference 
-
 import sys, os, string, json
 from operator import attrgetter
 
@@ -12,8 +8,8 @@ fp2 = ''
 def difference(data1, data2):
 	output = {'QUOTES' : [], 'NOTES' : []}
 
-	d1 = {i['quote'].rstrip(): i for i in data1['QUOTES']}
-	d2 = {i['quote'].rstrip(): i for i in data2['QUOTES']}
+	d1 = {i['quote']: i for i in data1['QUOTES']}
+	d2 = {i['quote']: i for i in data2['QUOTES']}
 
 	#create sets
 	s1 = set(d1.keys())
@@ -51,32 +47,28 @@ def open_file(p):
 		sys.exit('File %s does not exists... Aborting.' % p)
 	return open(p, 'rb')
 
-def run(filename1, filename2):
-
-	#open files
+if __name__ == '__main__':
+	if len(sys.argv) < 2:
+		sys.exit('No input file... Aborting.')
 	try:
-		fp1 = open_file(filename1)
+		fp1 = open_file(sys.argv[1])
 	except:
-		sys.exit("Can't open file " + filename1 + ". Aborting.")
-
+		sys.exit("Can't open file " + sys.argv[1] + ". Aborting.")
+	if len(sys.argv) < 3:
+		fp2 = sys.stdin
+	else:
 		try:
-		fp2 = open_file(filename2)
+			fp2 = open_file(sys.argv[2])
 		except:
-		# it may be std.in
-		try:
-			fp2 = filename2
-			fp2.tell()
-		except:
-			sys.exit("Can't open file " + filename2 + ". Aborting.")
+			sys.exit("Can't open file " + sys.argv[2] + ". Aborting.")
 
-	#read data
 	try:
 		sdata = fp1.read()
 		data1 = json.loads(sdata)
 	except:
-		e = "<compare> Error loading data from" + filename1 + ". Aborting.\n"
+		e = "<compare> Error loading data from" + sys.argv[1] + ". Aborting.\n"
 		if sdata:
-			e += "Traceback: " + sdata
+			e += "Traceback: " + sdata1
 		fp2.close()
 		sys.exit(e)		
 	finally:
@@ -94,21 +86,11 @@ def run(filename1, filename2):
 	finally:
 		fp2.close()
 
-	#process
 	data = difference(data1, data2)
 
 	data['QUOTES'] = sorted(data['QUOTES'], key=lambda entry: int(entry['pp']))
 	data['NOTES'] = sorted(data['NOTES'], key=lambda entry: int(entry['pp']))
 
-	#dump
-	return data
-
-#main allows unix piping
-if __name__ == '__main__':
-	if len(sys.argv) < 2:
-		sys.exit('No input file... Aborting.')
-
-	json.dump(run(sys.argv[1], sys.stdin), sys.stdout)
-
+	json.dump(data, sys.stdout)
 
 

parse/compare.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+INDXFILE='.indx'
+
+for i in *.mmd; do
+    f=$i
+done
+
+if [[ ! -f $INDXFILE ]]; then
+	make --quiet index
+elif [[ $f -nt $INDXFILE ]]; then
+	rm $INDXFILE
+	make --quiet index
+fi	
+
+#parse-skim.sh | compare.py .indx
+
+parse-plfr.sh | compare.py .indx

parse/inject.py

@@ -1,9 +1,4 @@
 #!/usr/bin/env python
-
-# reads (1) a formatted md file, (2) json formatted index
-# and injects (sorts and appends) in the md file the information 
-# contained in the index
-
 from statemachine import StateMachine
 import sys, os, string, json, shutil, codecs, traceback
 
@@ -19,6 +14,7 @@ def error(c):
 	sys.stderr.write('Unidentifiable line:\n'+ l)
 
 def eof(c):
+	print "eof"
 	return
 
 def parse(c):
@@ -124,13 +120,10 @@ def emit_quotes(list):
 
 def emit_quote(data):
 	emit_line("<!--page " + data['pp'] + "-->\n\n")
-	emit_line(">\"" + data['quote'] + "\" p." + data['pp'] + "\n")
+	emit_line(">\"" + data['quote'] + "\" pp." + data['pp'] + "\n")
 	emit_line('\n')
 
 def emit_remaining_notes():
-
-	print "emit_remaining_notes"
-
 	rest = []
 	for i in notes:
 		rest.extend(notes[i])	
@@ -175,27 +168,25 @@ def backupfile(p):
 	shutil.copy2(p, bak)
 	return codecs.open(bak, 'r', 'utf-8')
 
-def run(filename1, filename2):
-
-	global fileout, fileref, notes, quotes, notes_cnt
 
+if __name__ == '__main__':
+	if len(sys.argv) < 2:
+		sys.exit('No input file... Aborting.')
 	# fp1 should be the incoming .mmd file
 	try:
-		fileref = backupfile(filename1)
-		fileout = open_fileoutput(filename1)
+		fileref = backupfile(sys.argv[1])
+		fileout = open_fileoutput(sys.argv[1])
 		fileout.seek(0)
 	except:
-		sys.exit("Can't open file " + filename1 + ". Aborting.")
+		sys.exit("Can't open file " + sys.argv[1] + ". Aborting.")
 
+	if len(sys.argv) < 3:
+		fp2 = sys.stdin
+	else:
 		try:
-		fp2 = open_file(filename2)
+			fp2 = open_file(sys.argv[2])
 		except:
-		# it may be stdin
-		try:
-			fp2 = filename2
-			fp2.tell()
-		except:
-			sys.exit("Can't open file " + filename2 + ". Aborting.")
+			sys.exit("Can't open file " + sys.argv[2] + ". Aborting.")
 
 	# fp2 should be the incoming (json) data to inject in fp1
 
@@ -220,6 +211,8 @@ def run(filename1, filename2):
 	quotes = reoder(data['QUOTES'])
 	notes = reoder(data['NOTES'])
 
+	print quotes
+
 	notes_cnt = 0
 
 	try:
@@ -241,23 +234,8 @@ def run(filename1, filename2):
 	finally:
 		fileout.close()
 		fileref.close()
-		return trace
-			
-#main allows unix piping
-if __name__ == '__main__':
-	if len(sys.argv) < 2:
-		sys.exit('No input file... Aborting.')
-
-	if len(sys.argv) < 3:
-		fp2 = sys.stdin
-	else:
-		fp2 = sys.argv[2]
-
-	trace = run(sys.argv[1], fp2)
 		sys.exit(trace)
 
 
 
 
-
-

parse/inject.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+for i in *.mmd; do
+    f=$i
+done
+
+if [[ -z '$f' ]]; then
+	echo "No mmd file (markdown source file) in directory... Aborting.";
+	exit;
+fi
+
+# inject new nnnotes in source file
+compare.sh | inject.py $f
+
+# update index
+make --quiet index

parse/parse-plfr.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+for i in *.pdf; do
+    f=$i
+done
+
+if [[ -d '$f' ]]; then
+	echo "$f No pdf file in directory... Aborting.";
+	exit;
+fi
+
+plfr -json $f
+

parse/parse-skim.py

@@ -0,0 +1,77 @@
+#!/usr/bin/python
+
+from statemachine import StateMachine
+import sys, string, json
+
+output = {'QUOTES' : [], 'NOTES' : []}
+
+def error(c):
+	fp, l = c
+	sys.stderr.write('Unidentifiable line:\n'+ l)
+
+def eof(c):
+	print json.dumps(output, sys.stdout)
+
+def parse(c):
+	fp, l = c
+	while 1:
+		line = fp.readline()
+		if not line: return eof, (fp, line)
+		if line[:1] == '*': return section(line), (fp, line)
+		else: continue	
+
+def highlight(c):
+	fp, l = c
+	p = page(l)
+	text = fp.readline()
+	output['QUOTES'].append({'pp' : p, 'quote' : text.strip()})
+	return parse(c)
+
+def anchored_note(c):
+	fp, l = c
+	p = page(l)
+	text = fp.readline()
+	fp.readline()
+	note = fp.readline()	
+	output['QUOTES'].append({'pp' : p, 'quote' : text.strip()})
+	output['NOTES'].append({'pp' : p, 'note' : note.strip()})
+	return parse(c)
+
+def box(c):
+	fp, l = c
+	p = page(l)
+	text = fp.readline()	
+	output['QUOTES'].append({'pp' : p, 'quote' : text.strip()})
+	return parse(c)
+
+def text_note(c):
+	fp, l = c
+	p = page(l)
+	text = fp.readline()
+	output['NOTES'].append({'pp' : p, 'note' : text.strip()})
+	return parse(c)
+
+## helper fncts
+def section(line):
+	line = string.upper(line)
+	if string.find(line, 'HIGHLIGHT') >= 0: return highlight
+	elif string.find(line, 'ANCHORED NOTE') >= 0: return anchored_note
+	elif string.find(line, 'BOX') >= 0: return box
+	elif string.find(line, 'TEXT NOTE') >= 0: return text_note
+	else: return parse
+
+def page(line):	
+	return line.rstrip('\n').split(',')[-1].split(' ')[-1]
+
+if __name__ == '__main__':
+	m = StateMachine();
+	m.add_state(parse)
+	m.add_state(highlight)
+	m.add_state(anchored_note)
+	m.add_state(box)
+	m.add_state(text_note)
+	m.add_state(error, end_state=1)
+	m.add_state(eof, end_state=1)
+	m.set_start(parse)
+	m.run((sys.stdin, ''))
+

parse/parse-skim.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+for i in *.pdf; do
+    f=$i
+done
+
+if [[ -d '$f' ]]; then
+	echo "$f No pdf file in directory... Aborting.";
+	exit;
+fi
+
+filename="${f%.*}".txt
+
+skimnotes get -format txt $f
+
+if [[ ! -f $filename ]]; then
+	echo "No skim notes in pdf $f. Aborting.";
+	exit;
+fi
+
+parse-skim.py < $filename
+
+rm $filename

parse/parse.py

@@ -1,8 +1,5 @@
 #!/usr/bin/env python
 
-# parses the information containned in a formatted md file
-# and constructs a json formatted index
-
 from statemachine import StateMachine
 import sys, string, re, json
 
@@ -20,14 +17,14 @@ def is_tag_identifier(line):
 
 markups = {'QUOTES' : (is_quote_identifier, 'pp', 'tags', 'quote', 'fpc'), 'NOTES' : (is_note_identifier, '#', 'tags', 'note', 'fpc')}
 output = {'QUOTES' : [], 'NOTES' : []}
-fpindex = None
 
 def error(c):
 	fp, l = c
 	sys.stderr.write('Unidentifiable line:\n'+ l)
 
 def eof(c):
-	json.dump(output, fpindex)
+	fpindx = open('.indx','wb')
+	json.dump(output, fpindx)
 
 def parse(c):
 	fp, l = c
@@ -126,16 +123,12 @@ def escape_quote(line):
 	if(not line.strip().startswith('>')):
 		return line
 	l = re.sub('\"*\"', '', line.strip()[1:])
-	return re.sub('p.[0-9]+', '', l)
+	return re.sub('pp.[0-9]+', '', l)
 
 def escape_note(line):
 	return re.sub('^[0-9]+.', '', line).strip()
 
-def run(fpin, fpout):
-
-	global fpindex
-
-	fpindex = fpout
+if __name__ == '__main__':
 	m = StateMachine();
 	m.add_state(parse)
 	m.add_state(NOTES)
@@ -144,9 +137,4 @@ def run(fpin, fpout):
 	m.add_state(error, end_state=1)
 	m.add_state(eof, end_state=1)
 	m.set_start(parse)
-	m.run((fpin, ''))	
-
-#main allows unix piping
-if __name__ == '__main__':
-	fpindx = open('.indx','wb')
-	run(sys.stdin, fpindx)
+	m.run((sys.stdin, ''))

parse/refactorbib.py

@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+import sys, os, json
+from optparse import OptionParser
+
+def open_file(p):
+	if not os.path.exists(p):
+		sys.exit('File %s does not exists... Aborting.' % p)
+	return open(p, 'rb')
+
+def refactor(data):
+
+	data_out = {}
+	for d in data:
+		nid = ''
+		if(d['author']):
+			nid = d['author'][0]['family'] + d['issued']['date-parts'][0][0]
+		elif(d['editor']):
+			nid = d['editor'][0]['family'] + d['issued']['date-parts'][0][0]
+
+		if nid in data_out:
+			for c in range(97, 122):
+				nid = nid + chr(c)
+				if not nid in data:
+					break
+		data_out[nid] = d
+
+	return data_out
+
+
+if __name__ == '__main__':
+
+	p = OptionParser();
+	p.add_option('-i', '--index', action="store_true", help="prints out index")
+
+	options, args = p.parse_args()
+
+	if len(args) < 1:
+		sys.exit('No input file... Aborting.')
+	try:
+		fp = open_file(args[0])
+	except:
+		sys.exit("Can't open file " + args[0] + ". Aborting.")
+
+	try:
+		data = json.loads(fp.read())
+	except:
+		e = "<refactorbib> Error loading data from" + sys.argv[1] + ". Aborting.\n"
+		if sdata:
+			e += "Traceback: " + sdata1
+		sys.exit(e)		
+	finally:
+		fp.close()
+
+	out = refactor(data)
+
+	if options.index:
+		for e in out.keys():
+			print '> ' + e + ' - ' + out[e]['title'] + '  '
+	else:
+		print json.dumps(out, sort_keys=True, indent=2, separators=(',', ': '))
+
+
+

rrref.sh

@@ -0,0 +1,59 @@
+#!/bin/bash
+
+WHERE=$( cd $(dirname $0) ; pwd -P )
+
+# default configs
+if [[ -e "$WHERE/CONFIG" ]]; then
+	source $WHERE/CONFIG
+fi
+
+OUT=txt # defaults to txt output
+OPTIND=1 #reset getopts
+
+while getopts :b:r:o: opts; do
+	case $opts in
+		b)
+			BIB=$OPTARG
+			;;
+		r)
+			REF=$OPTARG
+			;;			
+		o)
+			OUT=$OPTARG
+			;;			
+		?)
+			echo "invalid option -$OPTARG";
+			exit;
+			;;
+		:)
+			echo "option -$OPTARG requires an argument";
+			exit;
+			;;
+	esac
+done
+
+shift $((OPTIND-1))
+
+# bibliographe's path set?
+if [[ -z "$BIBLIOGRAPHE_PATH" ]]; then 
+	echo "No bibliographe"; 
+	exit;
+fi
+
+# bibliography exists?
+if [[ -z "$BIB" ]]; then
+	echo "No bibliography"
+	exit;
+fi 
+
+# referebce exists?
+if [[ -z "$REF" ]]; then
+	echo "No reference"
+	exit;
+fi 
+
+./parse/refactorbib.py $BIB > tmpbib.json
+REFERENCE=$(node $BIBLIOGRAPHE_PATH/generatebib.js --data tmpbib.json --items [\"$REF\"] --output $OUT)
+echo $REFERENCE
+rm tmpbib.json
+

setup.py

@@ -1,26 +0,0 @@
-#!/usr/bin/env python
-
-import os, sys
-from setuptools import setup, find_packages
-
-PACKAGE = 'nnnotes'
-
-with open('README') as file:
-    README = file.read()
-
-setup(
-	name = 'nnnotes',
-	version = 'v0',
-	packages = find_packages(),
-	package_data = {PACKAGE: ['template/Makefile', 'template/*.mmd', 'template/p/*']},
-	scripts = ['bin/nnnote', 'bin/iiindex', 'bin/iiinject'],
-	provides=[PACKAGE],
-	author = 'gauthiier',
-	author_email = 'd@gauthiier.info',
-	url = 'https://github.com/gauthiier/nnnotes',
-	long_description=README,
-	classifiers=[
-        "Topic :: Utilities",
-        "License :: MIT License",
-    ]
-)

template/Makefile

@@ -16,25 +16,22 @@ $(OUT)%.pdf : %.mmd
 #html
 HTML := $(patsubst %.mmd,$(OUT)%.html,$(wildcard *.mmd))
 
-$(OUT)%.html: %.mmd
+$(OUT)%.html : %.mmd
 	pandoc $< -s -t html5 --template=p/nnnote-template.html5 --filter pandoc-citeproc --csl $(CSL) --bibliography $(BIB) -o $@
 
-all: dir $(HTML) index
+all : dir $(HTML) index
 
-index:
-	iiindex
+index :
+	parse.py < $(wildcard *.mmd)
                         
-inject:
-	iiinject
-                        
-clean:
+clean :
 	rm -f $(HTML)
 	rm -f $(PDF)
 
 neat:
 	rm *.bak
 
-rebuild: clean all
+rebuild : clean all
 
-dir: 
+dir : 
 	mkdir -p $(OUT)