From b413be687d545ebb5210052375b91d67a7df6852 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Wed, 10 Oct 2012 16:33:17 +0200
Subject: [PATCH 1/5] imcomplete implementation of Repository, Paper classes

---
 papers/commands/add_cmd.py  |   7 +-
 papers/commands/init_cmd.py |   2 +-
 papers/commands/list_cmd.py |  21 +++---
 papers/commands/open_cmd.py |  29 +++-----
 papers/files.py             |   2 +-
 papers/paper.py             |  23 +++++++
 papers/pretty.py            |  30 ---------
 papers/repo.py              | 130 ++++++++++++++++++++++++++++++++++++
 8 files changed, 176 insertions(+), 68 deletions(-)
 create mode 100644 papers/paper.py
 create mode 100644 papers/repo.py

diff --git a/papers/commands/add_cmd.py b/papers/commands/add_cmd.py
index d870d3a..b73d599 100644
--- a/papers/commands/add_cmd.py
+++ b/papers/commands/add_cmd.py
@@ -7,6 +7,7 @@ except ImportError:
 from .. import color
 from .. import files
 from .. import pretty
+from .. import repo
 
 
 def parser(subparsers, config):
@@ -28,7 +29,7 @@ def command(config, pdffile, bibfile):
     files.check_file(fullbibpath)
 
     filename, ext = os.path.splitext(os.path.split(fullpdfpath)[1])
-    if ext != '.pdf' and ext != '.ps':
+    if ext != '.pdf' and ext !=   '.ps':
         print('{}warning{}: extention {}{}{} not recognized{}'.format(
                color.yellow, color.grey, color.cyan, ext, color.grey, color.end))
 
@@ -53,8 +54,8 @@ def command(config, pdffile, bibfile):
     papers.set('header', 'count', int(count) + 1)
     
     citekey = pretty.create_citekey(bib_data)
-    papers.set('papers', citekey, filename)
-    papers.set('citekeys', 'ck' + count, citekey)
+    papers.set('citekeys', citekey, filename)
+    papers.set('numbers', 'ck' + count, citekey)
 
     files.write_papers(papers)
     files.write_meta(meta, filename)
diff --git a/papers/commands/init_cmd.py b/papers/commands/init_cmd.py
index 136c7bb..f38bc5e 100644
--- a/papers/commands/init_cmd.py
+++ b/papers/commands/init_cmd.py
@@ -29,8 +29,8 @@ def command(config):
         papers = configparser.ConfigParser()
         papers.add_section('header')
         papers.set('header', 'count', 0)
-        papers.add_section('papers')
         papers.add_section('citekeys')
+        papers.add_section('numbers')
         files.write_papers(papers)
 
     else:
diff --git a/papers/commands/list_cmd.py b/papers/commands/list_cmd.py
index f3e0dfe..fe8da92 100644
--- a/papers/commands/list_cmd.py
+++ b/papers/commands/list_cmd.py
@@ -1,24 +1,21 @@
-from .. import files
-from .. import pretty
-from .. import color
-
 import subprocess
 import tempfile
 
+from .. import pretty
+from .. import color
+from .. import repo
+
 def parser(subparsers, config):
     parser = subparsers.add_parser('list', help="list all papers")
     return parser
 
 def command(config):
-    papers = files.load_papers()
-
+    rp = repo.Repository()
+    
     articles = []
-    for p in papers.options('citekeys'):
-        number = p[2:]
-        citekey = papers.get('citekeys', p)
-        filename = papers.get('papers', citekey)
-        bibdata = files.load_bibdata(filename + '.bibyaml')
-        bibdesc = pretty.bib_oneliner(bibdata)
+    for n in rp.numbers:
+        paper = paper_from_number(n, fatal = True)
+        bibdesc = pretty.bib_oneliner(paper.bibdata)
         articles.append('{:3d} {}{}{}{}   {}'.format(int(number), color.purple, citekey, color.end, (8-len(citekey))*' ', bibdesc))
 
     with tempfile.NamedTemporaryFile(suffix=".tmp", delete=True) as tmpf:
diff --git a/papers/commands/open_cmd.py b/papers/commands/open_cmd.py
index 983da8a..9780751 100644
--- a/papers/commands/open_cmd.py
+++ b/papers/commands/open_cmd.py
@@ -1,30 +1,17 @@
-try:
-    import ConfigParser as configparser
-except ImportError:
-    import configparser
 import subprocess
 
-from .. import files
 from .. import color
+from .. import repo
 
 def parser(subparsers, config):
-    parser = subparsers.add_parser('open', help="open the paper in a pdf viewer")
-    parser.add_argument("citekey", help="the paper associated citekey")
+    parser = subparsers.add_parser('open', help='{}open the paper in a pdf viewer{}'.format(color.normal, color.end))
+    parser.add_argument('citekey', help='{}the paper associated citekey{}'.format(color.normal, color.end))
     return parser
 
 def command(config, citekey):
-    papers = files.load_papers()
-    try:
-        filename = papers.get('papers', str(citekey))
-    except configparser.NoOptionError:
-        try:
-            ck = papers.get('citekeys', 'ck'+str(citekey))
-            filename = papers.get('papers', str(ck))
-        except configparser.NoOptionError:
-            print('{}error{}: paper with citekey or number {}{}{} not found{}'.format(
-                color.red, color.grey, color.cyan, citekey, color.grey, color.end))
-            exit(-1)
-    meta_data = files.load_meta(filename)
-    filepath = meta_data.get('metadata', 'path')
+    rp = repo.Repository()
+    paper = rp.paper_from_any(citekey, fatal = True)
+    filepath = paper.metadata.get('metadata', 'path')
+
     p = subprocess.Popen(['open', filepath])
-    print('{}{}{} opened.{}'.format(color.cyan, filepath, color.grey, color.end))
\ No newline at end of file
+    print('{}{}{} opened.{}'.format(color.filepath, filepath, color.normal, color.end))
\ No newline at end of file
diff --git a/papers/files.py b/papers/files.py
index bbe2ef4..8245c9a 100644
--- a/papers/files.py
+++ b/papers/files.py
@@ -110,7 +110,7 @@ def load_papers():
     return read_configfile(find_papersdir() + os.sep + 'papers')
 
 def load_bibdata(filename):
-    fullbibpath = find_papersdir() + os.sep + 'bibdata' + os.sep + filename
+    fullbibpath = find_papersdir() + os.sep + 'bibdata' + os.sep + filename + '.bibyaml'
     return load_externalbibfile(fullbibpath)
 
 def write_bibdata(bib_data, filename):
diff --git a/papers/paper.py b/papers/paper.py
new file mode 100644
index 0000000..305d0ed
--- /dev/null
+++ b/papers/paper.py
@@ -0,0 +1,23 @@
+import files
+import color
+
+class Paper(object):
+    """Paper class. The object is responsible for the integrity of its own data,
+    and for loading and writing it to disc.
+    """
+
+    @classmethod
+    def from_disc(cls, name):
+        p = Paper(name)
+        self.bib_data = files.load_bibdata(self.name)
+        self.metadata = files.load_meta(self.name)
+        self.citekey  = self.metadata.get('metadata', 'citekey')
+        self.number   = self.metadata.get('metadata', 'number')
+        return p
+
+    def __init__(self, name):
+        self.name = name
+        
+        
+        
+
diff --git a/papers/pretty.py b/papers/pretty.py
index 9b48790..bbad9aa 100644
--- a/papers/pretty.py
+++ b/papers/pretty.py
@@ -26,33 +26,3 @@ def bib_desc(bib_data):
     s += '\n'
     s += '\n'.join('{}: {}'.format(k, v) for k, v in article.fields.items())
     return s
-
-alphabet = 'abcdefghijklmopqrstuvwxyz'
-
-try:
-    import ConfigParser as configparser
-except ImportError:
-    import configparser
-import files
-
-def create_citekey(bib_data):
-    """Create a cite key unique to the paper"""
-    article = bib_data.entries[list(bib_data.entries.keys())[0]]
-    first_author = article.persons['author'][0]
-    year = article.fields['year']
-    prefix = '{}{}'.format(first_author.last()[0][:6], year[2:])
-
-    papers = files.load_papers()
-    letter = 0, False
-    citekey = None
-    
-    citekey = prefix
-    while not letter[1]:
-        try:
-            papers.get('papers', citekey)
-            citekey = prefix + alphabet[letter[0]]
-            letter = letter[0]+1, False
-        except configparser.NoOptionError:
-            letter = letter[0], True
-
-    return citekey
diff --git a/papers/repo.py b/papers/repo.py
new file mode 100644
index 0000000..cf436ae
--- /dev/null
+++ b/papers/repo.py
@@ -0,0 +1,130 @@
+try:
+    import ConfigParser as configparser
+except ImportError:
+    import configparser
+
+from paper import Paper
+
+alphabet = 'abcdefghijklmopqrstuvwxyz'
+
+
+class Repository(object):
+
+    def __init__(self):
+        self.paperdir = files.find_papersdir()
+        self.papers_config = files.load_papers()
+        self.citekeys = dict(ck, None for ck in self.paper_config.options('citekeys')
+        self.numbers = sorted(n[2:] for n in self.paper_config.options('numbers'))
+
+    # loading existing papers
+
+    def paper_from_number(self, number, fatal = True):
+        try:
+            citekey = self.papers_config.get('numbers', 'ck'+number)
+            return self.load_paper(citekey)
+        except configparser.NoOptionError:
+            if fatal:
+                print('{}error{}: no paper with number {}{}{}'.format(
+                    color.error, color.normal, color.citekey, citekey, color.end)
+                exit(-1)
+            raise IOError, 'file not found'
+            
+    def paper_from_citekey(self, citekey, fatal = True):
+        """Load a paper by its citekey from disk, if necessary."""
+        try:
+            paper = self.citekeys[citekey]
+            if paper is None:
+                name = self.papers_config.get('citekeys', citekey)
+                paper =  Paper.from_disc(name)
+                self.citekeys[citekey] = paper
+                return paper
+        except KeyError:
+            if fatal:
+                print('{}error{}: no paper with citekey {}{}{}'.format(
+                       color.error, color.normal, color.citekey, citekey, color.end)
+                exit(-1)
+            raise IOError, 'file not found'
+
+    def paper_from_any(self, key, fatal = True):
+        try:
+            return rp.paper_from_citekey(key, fatal = False)
+        except IOError:
+            try:
+                return rp.paper_from_number(key, fatal = False)
+            except IOError:
+                if fatal:
+                    print('{}error{}: paper with citekey or number {}{}{} not found{}'.format(
+                        color.error, color.normal, color.citekey, key, color.normal, color.end))
+                    exit(-1)
+                raise IOError, 'file not found'
+
+    # creating new papers
+    
+    def add_paper(self, pdffile, bibfile):
+        
+        fullpdfpath = os.path.abspath(pdffile)
+        fullbibpath = os.path.abspath(bibfile)
+        files.check_file(fullpdfpath)
+        files.check_file(fullbibpath)
+        
+        name, ext = os.path.splitext(os.path.split(fullpdfpath)[1])
+        if ext != '.pdf' and ext !=   '.ps':
+            print('{}warning{}: extension {}{}{} not recognized{}'.format(
+                   color.yellow, color.grey, color.cyan, ext, color.grey, color.end))
+        
+        # creating meta file
+        meta = create_meta(fullpdfpath, name, ext, bib_data)
+        
+        # creating bibyaml file
+        bib_data = files.load_externalbibfile(fullbibpath)
+        print('{}bibliographic data present in {}{}{}'.format(
+               color.grey, color.cyan, bibfile, color.end))
+        print(pretty.bib_desc(bib_data))
+        
+        # updating papersconfig    
+        citekey = pretty.create_citekey(bib_data)
+        papers.set('citekeys', citekey, name)
+        papers.set('numbers', 'ck' + count, citekey)
+        
+        # writing all to disk
+        files.write_bibdata(bib_data, name)
+        files.write_papers(papers)
+        files.write_meta(meta, name)
+
+    def create_meta(self, path, name, ext, bib_data):
+        citekey = create_citekey(bib_data, allowed = (,))
+        number = create_number()
+        
+        meta = configparser.ConfigParser()
+        meta.add_section('metadata')
+        
+        meta.set('metadata', 'name', name)
+        meta.set('metadata', 'extension', ext)
+        meta.set('metadata', 'path', os.path.normpath(fullpdfpath))
+        
+        meta.add_section('notes')
+        
+        return meta
+
+    def create_citekey(self, bib_data, allowed = (,)):
+        """Create a cite key unique to a given bib_data"""
+        article = bib_data.entries[list(bib_data.entries.keys())[0]]
+        first_author = article.persons['author'][0]
+        year = article.fields['year']
+        prefix = '{}{}'.format(first_author.last()[0][:6], year[2:])
+
+        letter = 0, False
+        citekey = None
+
+        citekey = prefix
+        while citekey in self.citekeys and citekey not in allowed:
+            citekey = prefix + alphabet[letter[0]]
+            letter += 1
+
+        return citekey
+        
+    def create_number(self, bib_data, allowed = []):
+        count = self.papers_config.get('header', 'count')
+        self.papers_config.set('header', 'count', count + 1)
+        return count
+        
\ No newline at end of file

From cdd27966389e82863b0aa6d3eb4dd406a1288027 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Thu, 11 Oct 2012 09:26:46 +0200
Subject: [PATCH 2/5] finished implementing the classes

a lowercase bug remain that force to move to another format than configparser. Which is just as well.
---
 .pit/pit-ac8c05c020d251c6   | 15 +++++++
 papers/commands/add_cmd.py  | 40 +----------------
 papers/commands/list_cmd.py |  4 +-
 papers/files.py             |  7 +++
 papers/paper.py             | 67 +++++++++++++++++++++++----
 papers/repo.py              | 90 ++++++++++++++-----------------------
 6 files changed, 118 insertions(+), 105 deletions(-)
 create mode 100644 .pit/pit-ac8c05c020d251c6

diff --git a/.pit/pit-ac8c05c020d251c6 b/.pit/pit-ac8c05c020d251c6
new file mode 100644
index 0000000..14a1e05
--- /dev/null
+++ b/.pit/pit-ac8c05c020d251c6
@@ -0,0 +1,15 @@
+[header]
+title = remove configparser for internal mapping
+id = ac8c05c020d251c6fa9ac5fc239038837b636b3b
+status = open
+type = bug
+author = Fabien Benureau
+mail = fabien.benureau+git@gmail.com
+date = 2012-10-11 at 07:25 UCT
+
+[eventlog]
+opened[0] = opened the 2012-10-11 at 07:25 UCT by Fabien Benureau
+
+[discussion]
+desc = # enter your description here
+
diff --git a/papers/commands/add_cmd.py b/papers/commands/add_cmd.py
index b73d599..0a0e55c 100644
--- a/papers/commands/add_cmd.py
+++ b/papers/commands/add_cmd.py
@@ -21,41 +21,5 @@ def command(config, pdffile, bibfile):
     :param pdffilepath  path (no url yet) to a pdf or ps file
     :param bibtex       bibtex file (in .bib, .bibml or .yaml format.
     """
-    papersdir = files.find_papersdir()
-
-    fullpdfpath = os.path.abspath(pdffile)
-    fullbibpath = os.path.abspath(bibfile)
-    files.check_file(fullpdfpath)
-    files.check_file(fullbibpath)
-
-    filename, ext = os.path.splitext(os.path.split(fullpdfpath)[1])
-    if ext != '.pdf' and ext !=   '.ps':
-        print('{}warning{}: extention {}{}{} not recognized{}'.format(
-               color.yellow, color.grey, color.cyan, ext, color.grey, color.end))
-
-    meta = configparser.ConfigParser()
-    meta.add_section('metadata')
-
-    meta.set('metadata', 'filename', filename)
-    meta.set('metadata', 'extension', ext)
-    meta.set('metadata', 'path', os.path.normpath(fullpdfpath))
-
-    meta.add_section('notes')
-
-    if bibfile is not None:
-        bib_data = files.load_externalbibfile(fullbibpath)
-        print('{}bibliographic data present in {}{}{}'.format(
-               color.grey, color.cyan, bibfile, color.end))
-        print(pretty.bib_desc(bib_data))
-        files.write_bibdata(bib_data, filename)
-
-    papers = files.load_papers()
-    count = papers.get('header', 'count')
-    papers.set('header', 'count', int(count) + 1)
-    
-    citekey = pretty.create_citekey(bib_data)
-    papers.set('citekeys', citekey, filename)
-    papers.set('numbers', 'ck' + count, citekey)
-
-    files.write_papers(papers)
-    files.write_meta(meta, filename)
+    rp = repo.Repository()
+    rp.add_paper(pdffile, bibfile)
\ No newline at end of file
diff --git a/papers/commands/list_cmd.py b/papers/commands/list_cmd.py
index fe8da92..fc19cc3 100644
--- a/papers/commands/list_cmd.py
+++ b/papers/commands/list_cmd.py
@@ -14,9 +14,9 @@ def command(config):
     
     articles = []
     for n in rp.numbers:
-        paper = paper_from_number(n, fatal = True)
+        paper = rp.paper_from_number(n, fatal = True)
         bibdesc = pretty.bib_oneliner(paper.bibdata)
-        articles.append('{:3d} {}{}{}{}   {}'.format(int(number), color.purple, citekey, color.end, (8-len(citekey))*' ', bibdesc))
+        articles.append('{:3d} {}{}{}{}   {}'.format(int(paper.number), color.purple, citekey, color.end, (8-len(paper.citekey))*' ', bibdesc))
 
     with tempfile.NamedTemporaryFile(suffix=".tmp", delete=True) as tmpf:
         tmpf.write('\n'.join(articles))
diff --git a/papers/files.py b/papers/files.py
index 8245c9a..7673e39 100644
--- a/papers/files.py
+++ b/papers/files.py
@@ -49,6 +49,13 @@ def find_papersdir():
 
     return _papersdir
 
+def name_from_path(fullpdfpath, verbose = False):
+    name, ext = os.path.splitext(os.path.split(fullpdfpath)[1])
+    if verbose:
+        if ext != '.pdf' and ext != '.ps':
+            print('{}warning{}: extension {}{}{} not recognized{}'.format(
+                   color.yellow, color.grey, color.cyan, ext, color.grey, color.end))
+    return name, ext    
 
 def check_file(filepath):
     if not os.path.exists(filepath):
diff --git a/papers/paper.py b/papers/paper.py
index 305d0ed..19ad81f 100644
--- a/papers/paper.py
+++ b/papers/paper.py
@@ -1,5 +1,12 @@
+import os
+try:
+    import ConfigParser as configparser
+except ImportError:
+    import configparser
+    
 import files
 import color
+import pretty
 
 class Paper(object):
     """Paper class. The object is responsible for the integrity of its own data,
@@ -7,17 +14,61 @@ class Paper(object):
     """
 
     @classmethod
-    def from_disc(cls, name):
-        p = Paper(name)
-        self.bib_data = files.load_bibdata(self.name)
-        self.metadata = files.load_meta(self.name)
-        self.citekey  = self.metadata.get('metadata', 'citekey')
-        self.number   = self.metadata.get('metadata', 'number')
+    def from_disc(cls, name, citekey = None, number = None):
+        bib_data = files.load_bibdata(self.name)
+        metadata = files.load_meta(self.name)
+        p = Paper(name, bib_data = bib_data, metadata = metadata, 
+                        citekey = citekey, number = number)
         return p
 
-    def __init__(self, name):
-        self.name = name
+    @classmethod
+    def from_bibpdffiles(cls, pdfpath, bibpath):
+        bib_data = cls.import_bibdata(bibpath)
+        name, meta = cls.import_meta(pdfpath, bib_data)
+        p = Paper(name, bib_data = bib_data, metadata = meta)
         
+        return p            
+
+    def __init__(self, name, bib_data = None, metadata = None, 
+                       citekey = None, number = None):
+        self.name = name
+        self.bib_data = bib_data
+        self.metadata = metadata
+        self.citekey  = citekey
+        self.number   = number
+                
+    def save_to_disc(self):
+        files.write_bibdata(self.bib_data, self.name)
+        files.write_meta(self.metadata, self.name)
+
+    @classmethod
+    def import_bibdata(cls, bibfile):        
+        """Import bibligraphic data from a .bibyaml, .bib or .bibtex file"""
+        fullbibpath = os.path.abspath(bibfile)
+        files.check_file(fullbibpath)
         
+        bib_data = files.load_externalbibfile(fullbibpath)
+        print('{}bibliographic data present in {}{}{}'.format(
+               color.grey, color.cyan, bibfile, color.end))
+        print(pretty.bib_desc(bib_data))
         
+        return bib_data
 
+    @classmethod
+    def import_meta(cls, pdfpath, bib_data):
+    
+        fullpdfpath = os.path.abspath(pdfpath)
+        files.check_file(fullpdfpath)
+    
+        name, ext = files.name_from_path(pdfpath)
+    
+        meta = configparser.ConfigParser()
+        meta.add_section('metadata')
+    
+        meta.set('metadata', 'name', name)
+        meta.set('metadata', 'extension', ext)
+        meta.set('metadata', 'path', os.path.normpath(fullpdfpath))
+    
+        meta.add_section('notes')
+        
+        return name, meta
diff --git a/papers/repo.py b/papers/repo.py
index cf436ae..405691b 100644
--- a/papers/repo.py
+++ b/papers/repo.py
@@ -3,6 +3,8 @@ try:
 except ImportError:
     import configparser
 
+import files
+import color
 from paper import Paper
 
 alphabet = 'abcdefghijklmopqrstuvwxyz'
@@ -13,19 +15,19 @@ class Repository(object):
     def __init__(self):
         self.paperdir = files.find_papersdir()
         self.papers_config = files.load_papers()
-        self.citekeys = dict(ck, None for ck in self.paper_config.options('citekeys')
-        self.numbers = sorted(n[2:] for n in self.paper_config.options('numbers'))
+        self.citekeys = dict((ck, name) for ck, name in self.papers_config.items('citekeys'))
+        self.numbers = sorted(n[2:] for n in self.papers_config.options('numbers'))
 
     # loading existing papers
 
     def paper_from_number(self, number, fatal = True):
         try:
             citekey = self.papers_config.get('numbers', 'ck'+number)
-            return self.load_paper(citekey)
+            return self.paper_from_citekey(citekey)
         except configparser.NoOptionError:
             if fatal:
                 print('{}error{}: no paper with number {}{}{}'.format(
-                    color.error, color.normal, color.citekey, citekey, color.end)
+                    color.error, color.normal, color.citekey, citekey, color.end))
                 exit(-1)
             raise IOError, 'file not found'
             
@@ -35,22 +37,22 @@ class Repository(object):
             paper = self.citekeys[citekey]
             if paper is None:
                 name = self.papers_config.get('citekeys', citekey)
-                paper =  Paper.from_disc(name)
-                self.citekeys[citekey] = paper
-                return paper
+            paper =  Paper.from_disc(name, citekey = citekey)
+            self.citekeys[citekey] = paper
+            return paper
         except KeyError:
             if fatal:
                 print('{}error{}: no paper with citekey {}{}{}'.format(
-                       color.error, color.normal, color.citekey, citekey, color.end)
+                       color.error, color.normal, color.citekey, citekey, color.end))
                 exit(-1)
             raise IOError, 'file not found'
 
     def paper_from_any(self, key, fatal = True):
         try:
-            return rp.paper_from_citekey(key, fatal = False)
+            return self.paper_from_citekey(key, fatal = False)
         except IOError:
             try:
-                return rp.paper_from_number(key, fatal = False)
+                return self.paper_from_number(key, fatal = False)
             except IOError:
                 if fatal:
                     print('{}error{}: paper with citekey or number {}{}{} not found{}'.format(
@@ -60,53 +62,28 @@ class Repository(object):
 
     # creating new papers
     
-    def add_paper(self, pdffile, bibfile):
-        
-        fullpdfpath = os.path.abspath(pdffile)
-        fullbibpath = os.path.abspath(bibfile)
-        files.check_file(fullpdfpath)
-        files.check_file(fullbibpath)
-        
-        name, ext = os.path.splitext(os.path.split(fullpdfpath)[1])
-        if ext != '.pdf' and ext !=   '.ps':
-            print('{}warning{}: extension {}{}{} not recognized{}'.format(
-                   color.yellow, color.grey, color.cyan, ext, color.grey, color.end))
-        
-        # creating meta file
-        meta = create_meta(fullpdfpath, name, ext, bib_data)
-        
-        # creating bibyaml file
-        bib_data = files.load_externalbibfile(fullbibpath)
-        print('{}bibliographic data present in {}{}{}'.format(
-               color.grey, color.cyan, bibfile, color.end))
-        print(pretty.bib_desc(bib_data))
-        
-        # updating papersconfig    
-        citekey = pretty.create_citekey(bib_data)
-        papers.set('citekeys', citekey, name)
-        papers.set('numbers', 'ck' + count, citekey)
+    def add_paper(self, pdfpath, bibpath):
         
+        p = Paper.from_bibpdffiles(pdfpath, bibpath)        
+
+        # updating papersconfig
+        p.citekey = self.create_citekey(p.bib_data)
+        p.number  = self.create_number()
+
+        self.papers_config.set('citekeys', p.citekey, p.name)
+        self.papers_config.set('numbers', 'ck' + str(p.number), p.citekey)
+
+        self.citekeys[p.citekey] = p.name
+        self.numbers.append(str(p.number))
+        self.numbers.sort()
+               
         # writing all to disk
-        files.write_bibdata(bib_data, name)
-        files.write_papers(papers)
-        files.write_meta(meta, name)
+        files.write_papers(self.papers_config)
+        p.save_to_disc()
 
-    def create_meta(self, path, name, ext, bib_data):
-        citekey = create_citekey(bib_data, allowed = (,))
-        number = create_number()
-        
-        meta = configparser.ConfigParser()
-        meta.add_section('metadata')
-        
-        meta.set('metadata', 'name', name)
-        meta.set('metadata', 'extension', ext)
-        meta.set('metadata', 'path', os.path.normpath(fullpdfpath))
-        
-        meta.add_section('notes')
-        
-        return meta
+        return p
 
-    def create_citekey(self, bib_data, allowed = (,)):
+    def create_citekey(self, bib_data, allowed = tuple()):
         """Create a cite key unique to a given bib_data"""
         article = bib_data.entries[list(bib_data.entries.keys())[0]]
         first_author = article.persons['author'][0]
@@ -123,8 +100,7 @@ class Repository(object):
 
         return citekey
         
-    def create_number(self, bib_data, allowed = []):
-        count = self.papers_config.get('header', 'count')
+    def create_number(self):
+        count = self.papers_config.getint('header', 'count')
         self.papers_config.set('header', 'count', count + 1)
-        return count
-        
\ No newline at end of file
+        return count
\ No newline at end of file

From 09b737b2103fe2f19abad21201272589157588b8 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Thu, 11 Oct 2012 19:57:56 +0200
Subject: [PATCH 3/5] removed configparser in favor of yaml

---
 .pit/pit-956ed1a521100b3b   |  3 +-
 .pit/pit-ac8c05c020d251c6   |  3 +-
 papers/commands/init_cmd.py | 11 ++++---
 papers/commands/list_cmd.py |  6 ++--
 papers/commands/open_cmd.py |  2 +-
 papers/files.py             | 57 ++++++++++++++++++++-----------------
 papers/paper.py             | 28 +++++++-----------
 papers/repo.py              | 38 +++++++++++--------------
 8 files changed, 71 insertions(+), 77 deletions(-)

diff --git a/.pit/pit-956ed1a521100b3b b/.pit/pit-956ed1a521100b3b
index b4faf58..4dac007 100644
--- a/.pit/pit-956ed1a521100b3b
+++ b/.pit/pit-956ed1a521100b3b
@@ -1,7 +1,7 @@
 [header]
 title = citekey support
 id = 956ed1a521100b3b0bb0638f61b3b5a03204ffa6
-status = open
+status = closed
 type = feature
 author = Fabien Benureau
 mail = fabien.benureau+git@gmail.com
@@ -9,6 +9,7 @@ date = 2012-10-05 at 15:00 UCT
 
 [eventlog]
 opened[0] = opened the 2012-10-05 at 15:00 UCT by Fabien Benureau
+closed[1] = closed the 2012-10-11 at 17:57(UCT) by Fabien Benureau
 
 [discussion]
 desc = # enter your description here
diff --git a/.pit/pit-ac8c05c020d251c6 b/.pit/pit-ac8c05c020d251c6
index 14a1e05..e753aba 100644
--- a/.pit/pit-ac8c05c020d251c6
+++ b/.pit/pit-ac8c05c020d251c6
@@ -1,7 +1,7 @@
 [header]
 title = remove configparser for internal mapping
 id = ac8c05c020d251c6fa9ac5fc239038837b636b3b
-status = open
+status = closed
 type = bug
 author = Fabien Benureau
 mail = fabien.benureau+git@gmail.com
@@ -9,6 +9,7 @@ date = 2012-10-11 at 07:25 UCT
 
 [eventlog]
 opened[0] = opened the 2012-10-11 at 07:25 UCT by Fabien Benureau
+closed[1] = closed the 2012-10-11 at 17:57(UCT) by Fabien Benureau
 
 [discussion]
 desc = # enter your description here
diff --git a/papers/commands/init_cmd.py b/papers/commands/init_cmd.py
index f38bc5e..66fd3f9 100644
--- a/papers/commands/init_cmd.py
+++ b/papers/commands/init_cmd.py
@@ -26,12 +26,11 @@ def command(config):
         os.makedirs(papersdir+os.sep+'bibdata')
         os.makedirs(papersdir+os.sep+'meta')
         
-        papers = configparser.ConfigParser()
-        papers.add_section('header')
-        papers.set('header', 'count', 0)
-        papers.add_section('citekeys')
-        papers.add_section('numbers')
-        files.write_papers(papers)
+        papers = {}
+        papers['count'] = 0
+        papers['citekeys'] = {}
+        papers['numbers'] = {}
+        files.save_papers(papers)
 
     else:
         print('{}error {} : papers already present in {}{}{}'.format(
diff --git a/papers/commands/list_cmd.py b/papers/commands/list_cmd.py
index fc19cc3..9e49bd5 100644
--- a/papers/commands/list_cmd.py
+++ b/papers/commands/list_cmd.py
@@ -13,10 +13,10 @@ def command(config):
     rp = repo.Repository()
     
     articles = []
-    for n in rp.numbers:
+    for n in sorted(rp.numbers.keys()):
         paper = rp.paper_from_number(n, fatal = True)
-        bibdesc = pretty.bib_oneliner(paper.bibdata)
-        articles.append('{:3d} {}{}{}{}   {}'.format(int(paper.number), color.purple, citekey, color.end, (8-len(paper.citekey))*' ', bibdesc))
+        bibdesc = pretty.bib_oneliner(paper.bib_data)
+        articles.append('{:3d} {}{}{}{}   {}'.format(int(paper.number), color.purple, paper.citekey, color.end, (8-len(paper.citekey))*' ', bibdesc))
 
     with tempfile.NamedTemporaryFile(suffix=".tmp", delete=True) as tmpf:
         tmpf.write('\n'.join(articles))
diff --git a/papers/commands/open_cmd.py b/papers/commands/open_cmd.py
index 9780751..8788a25 100644
--- a/papers/commands/open_cmd.py
+++ b/papers/commands/open_cmd.py
@@ -11,7 +11,7 @@ def parser(subparsers, config):
 def command(config, citekey):
     rp = repo.Repository()
     paper = rp.paper_from_any(citekey, fatal = True)
-    filepath = paper.metadata.get('metadata', 'path')
+    filepath = paper.metadata['path']
 
     p = subprocess.Popen(['open', filepath])
     print('{}{}{} opened.{}'.format(color.filepath, filepath, color.normal, color.end))
\ No newline at end of file
diff --git a/papers/files.py b/papers/files.py
index 7673e39..ee98ca7 100644
--- a/papers/files.py
+++ b/papers/files.py
@@ -8,6 +8,8 @@ try:
 except ImportError:
     import configparser
     
+import yaml
+    
 import color
 
 try:
@@ -66,29 +68,46 @@ def check_file(filepath):
         print '{}error{}: {}{}{} is not a file{}'.format(
                color.red, color.grey, color.cyan, filepath, color.grey, color.end)
         exit(-1)
+        
+# yaml I/O
 
-def write_configfile(config, filepath):
+def write_yamlfile(filepath, datamap):
     try:
         with open(filepath, 'w') as f:
-            config.write(f)
+            yaml.dump(datamap, f)
     except IOError as e:
-        print '{}error{} : impossible to write on file {}{:s}{}'.format(
+        print '{}error{} : impossible to read file {}{:s}{}'.format(
                color.red, color.grey, color.cyan, filepath, color.end)
-        print 'Verify permissions'
         exit(-1)
 
-def read_configfile(filepath):
+def read_yamlfile(filepath):
+    check_file(filepath)
     try:
         with open(filepath, 'r') as f:
-            config = configparser.ConfigParser()
-            config.readfp(f)
-            return config
+            return yaml.load(f)
     except IOError as e:
         print '{}error{} : impossible to read file {}{:s}{}'.format(
-               color.red, color.grey, color.cyan, filepath, color.end)
-        print 'Verify permissions'
+               color.red, color.grey, color.cyan, paperdir, color.end)
         exit(-1)
 
+def save_papers(datamap):
+    paperyaml = find_papersdir() + os.sep + 'papers.yaml'
+    write_yamlfile(paperyaml, datamap)
+
+def load_papers():
+    paperyaml = find_papersdir() + os.sep + 'papers.yaml'
+    return read_yamlfile(paperyaml)
+
+def save_meta(meta_data, filename):
+    filepath = find_papersdir() + os.sep + 'meta' + os.sep + filename + '.meta'
+    write_yamlfile(filepath, meta_data)
+
+def load_meta(filename):
+    filepath = find_papersdir() + os.sep + 'meta' + os.sep + filename + '.meta'
+    return read_yamlfile(filepath)
+
+# specific to bibliography data
+
 def load_externalbibfile(fullbibpath):
     check_file(fullbibpath)
 
@@ -109,31 +128,17 @@ def load_externalbibfile(fullbibpath):
 
     return bib_data
 
-
-def write_papers(config):
-    write_configfile(config, find_papersdir() + os.sep + 'papers')
-
-def load_papers():
-    return read_configfile(find_papersdir() + os.sep + 'papers')
-
 def load_bibdata(filename):
     fullbibpath = find_papersdir() + os.sep + 'bibdata' + os.sep + filename + '.bibyaml'
     return load_externalbibfile(fullbibpath)
 
-def write_bibdata(bib_data, filename):
+def save_bibdata(bib_data, filename):
     filepath = find_papersdir() + os.sep + 'bibdata' + os.sep + filename + '.bibyaml'
     with open(filepath, 'w') as f:
         parser = pybtex.database.output.bibyaml.Writer()
         parser.write_stream(bib_data, f)
 
-def write_meta(meta_data, filename):
-    filepath = find_papersdir() + os.sep + 'meta' + os.sep + filename + '.meta'
-    write_configfile(meta_data, filepath)
-
-def load_meta(filename):
-    filepath = find_papersdir() + os.sep + 'meta' + os.sep + filename + '.meta'
-    return read_configfile(filepath)
-
+# vim input
 
 try:
     EDITOR = os.environ['EDITOR']
diff --git a/papers/paper.py b/papers/paper.py
index 19ad81f..2ad9073 100644
--- a/papers/paper.py
+++ b/papers/paper.py
@@ -1,8 +1,4 @@
 import os
-try:
-    import ConfigParser as configparser
-except ImportError:
-    import configparser
     
 import files
 import color
@@ -15,8 +11,8 @@ class Paper(object):
 
     @classmethod
     def from_disc(cls, name, citekey = None, number = None):
-        bib_data = files.load_bibdata(self.name)
-        metadata = files.load_meta(self.name)
+        bib_data = files.load_bibdata(name)
+        metadata = files.load_meta(name)
         p = Paper(name, bib_data = bib_data, metadata = metadata, 
                         citekey = citekey, number = number)
         return p
@@ -24,7 +20,7 @@ class Paper(object):
     @classmethod
     def from_bibpdffiles(cls, pdfpath, bibpath):
         bib_data = cls.import_bibdata(bibpath)
-        name, meta = cls.import_meta(pdfpath, bib_data)
+        name, meta = cls.create_meta(pdfpath, bib_data)
         p = Paper(name, bib_data = bib_data, metadata = meta)
         
         return p            
@@ -38,14 +34,13 @@ class Paper(object):
         self.number   = number
                 
     def save_to_disc(self):
-        files.write_bibdata(self.bib_data, self.name)
-        files.write_meta(self.metadata, self.name)
+        files.save_bibdata(self.bib_data, self.name)
+        files.save_meta(self.metadata, self.name)
 
     @classmethod
     def import_bibdata(cls, bibfile):        
         """Import bibligraphic data from a .bibyaml, .bib or .bibtex file"""
         fullbibpath = os.path.abspath(bibfile)
-        files.check_file(fullbibpath)
         
         bib_data = files.load_externalbibfile(fullbibpath)
         print('{}bibliographic data present in {}{}{}'.format(
@@ -55,20 +50,19 @@ class Paper(object):
         return bib_data
 
     @classmethod
-    def import_meta(cls, pdfpath, bib_data):
+    def create_meta(cls, pdfpath, bib_data):
     
         fullpdfpath = os.path.abspath(pdfpath)
         files.check_file(fullpdfpath)
     
         name, ext = files.name_from_path(pdfpath)
     
-        meta = configparser.ConfigParser()
-        meta.add_section('metadata')
+        meta = {}
     
-        meta.set('metadata', 'name', name)
-        meta.set('metadata', 'extension', ext)
-        meta.set('metadata', 'path', os.path.normpath(fullpdfpath))
+        meta['name'] = name
+        meta['extension'] = ext
+        meta['path'] = fullpdfpath
     
-        meta.add_section('notes')
+        meta['notes'] = []
         
         return name, meta
diff --git a/papers/repo.py b/papers/repo.py
index 405691b..9fdb980 100644
--- a/papers/repo.py
+++ b/papers/repo.py
@@ -1,8 +1,3 @@
-try:
-    import ConfigParser as configparser
-except ImportError:
-    import configparser
-
 import files
 import color
 from paper import Paper
@@ -15,16 +10,18 @@ class Repository(object):
     def __init__(self):
         self.paperdir = files.find_papersdir()
         self.papers_config = files.load_papers()
-        self.citekeys = dict((ck, name) for ck, name in self.papers_config.items('citekeys'))
-        self.numbers = sorted(n[2:] for n in self.papers_config.options('numbers'))
+        self.citekeys = self.papers_config['citekeys']
+        self.numbers  = self.papers_config['numbers']
 
     # loading existing papers
 
     def paper_from_number(self, number, fatal = True):
         try:
-            citekey = self.papers_config.get('numbers', 'ck'+number)
-            return self.paper_from_citekey(citekey)
-        except configparser.NoOptionError:
+            citekey = self.numbers[int(number)]
+            paper = self.paper_from_citekey(citekey)
+            paper.number = int(number)
+            return paper
+        except KeyError:
             if fatal:
                 print('{}error{}: no paper with number {}{}{}'.format(
                     color.error, color.normal, color.citekey, citekey, color.end))
@@ -34,11 +31,9 @@ class Repository(object):
     def paper_from_citekey(self, citekey, fatal = True):
         """Load a paper by its citekey from disk, if necessary."""
         try:
-            paper = self.citekeys[citekey]
-            if paper is None:
-                name = self.papers_config.get('citekeys', citekey)
-            paper =  Paper.from_disc(name, citekey = citekey)
-            self.citekeys[citekey] = paper
+            name = self.citekeys[citekey]
+            paper = Paper.from_disc(name, citekey = citekey)
+            paper.citekey = citekey
             return paper
         except KeyError:
             if fatal:
@@ -70,15 +65,14 @@ class Repository(object):
         p.citekey = self.create_citekey(p.bib_data)
         p.number  = self.create_number()
 
-        self.papers_config.set('citekeys', p.citekey, p.name)
-        self.papers_config.set('numbers', 'ck' + str(p.number), p.citekey)
+        self.papers_config['citekeys'][p.citekey] = p.name
+        self.papers_config['numbers'][p.number] = p.citekey
 
         self.citekeys[p.citekey] = p.name
-        self.numbers.append(str(p.number))
-        self.numbers.sort()
+        self.numbers[p.number] = p.citekey
                
         # writing all to disk
-        files.write_papers(self.papers_config)
+        files.save_papers(self.papers_config)
         p.save_to_disc()
 
         return p
@@ -101,6 +95,6 @@ class Repository(object):
         return citekey
         
     def create_number(self):
-        count = self.papers_config.getint('header', 'count')
-        self.papers_config.set('header', 'count', count + 1)
+        count = int(self.papers_config['count'])
+        self.papers_config['count'] = count + 1
         return count
\ No newline at end of file

From 443329d7cf8006c3d52b0de75825ce33e39c5ed5 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier.mangin@inria.fr>
Date: Mon, 22 Oct 2012 04:09:12 +0200
Subject: [PATCH 4/5] Fix bug in citekey generation.

---
 papers/repo.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/papers/repo.py b/papers/repo.py
index 9fdb980..99f85d3 100644
--- a/papers/repo.py
+++ b/papers/repo.py
@@ -84,12 +84,12 @@ class Repository(object):
         year = article.fields['year']
         prefix = '{}{}'.format(first_author.last()[0][:6], year[2:])
 
-        letter = 0, False
+        letter = 0
         citekey = None
 
         citekey = prefix
         while citekey in self.citekeys and citekey not in allowed:
-            citekey = prefix + alphabet[letter[0]]
+            citekey = prefix + alphabet[letter]
             letter += 1
 
         return citekey
@@ -97,4 +97,4 @@ class Repository(object):
     def create_number(self):
         count = int(self.papers_config['count'])
         self.papers_config['count'] = count + 1
-        return count
\ No newline at end of file
+        return count

From 2d57a2080c1a912b8575f67dc9f0e852dfdca43f Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier.mangin@inria.fr>
Date: Mon, 22 Oct 2012 05:00:04 +0200
Subject: [PATCH 5/5] Adds handling of the case where no document file is
 defined.

---
 papers/commands/open_cmd.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/papers/commands/open_cmd.py b/papers/commands/open_cmd.py
index 8788a25..b1dd0bf 100644
--- a/papers/commands/open_cmd.py
+++ b/papers/commands/open_cmd.py
@@ -2,6 +2,7 @@ import subprocess
 
 from .. import color
 from .. import repo
+from ..paper import NoDocumentFile
 
 def parser(subparsers, config):
     parser = subparsers.add_parser('open', help='{}open the paper in a pdf viewer{}'.format(color.normal, color.end))
@@ -11,7 +12,15 @@ def parser(subparsers, config):
 def command(config, citekey):
     rp = repo.Repository()
     paper = rp.paper_from_any(citekey, fatal = True)
-    filepath = paper.metadata['path']
+    try:
+        if paper.check_file():
+            filepath = paper.get_file_path()
+
+            p = subprocess.Popen(['open', filepath])
+            print('{}{}{} opened.{}'.format(
+                color.filepath, filepath, color.normal, color.end))
+    except NoDocumentFile:
+        print('{}error{}: No document associated to this entry {}{}{}'.format(
+            color.error, color.normal, color.citekey, citekey, color.end))
+        exit(-1)
 
-    p = subprocess.Popen(['open', filepath])
-    print('{}{}{} opened.{}'.format(color.filepath, filepath, color.normal, color.end))
\ No newline at end of file