From 0d16c6a5a3f45aebc82527f7059a09682baefd85 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Mon, 1 Jul 2013 13:14:11 +0100
Subject: [PATCH 01/20] updated codestyle with open remark

---
 CODESTYLE.md | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/CODESTYLE.md b/CODESTYLE.md
index 5d3987f..6446a4e 100644
--- a/CODESTYLE.md
+++ b/CODESTYLE.md
@@ -15,10 +15,12 @@ Git
 
 This project use git-flow {nvie.com/posts/a-successful-git-branching-model}
 as a model for branches management. In particular :
-- master is for release only
-- when you commit to develop, run nosetests before. All tests should pass.
-- in feature/branches, you do whatever you want.
-- when developping a new feature, write tests for it.
+1. master is for release only
+2. when you commit to develop, run nosetests before. All tests should pass.
+3. when you commit to develop, run nosetests before. All tests should pass.
+4. when you commit to develop, run nosetests before. All tests should pass.
+5. in 'feat/' branches, you do whatever you want.
+6. when developping a new feature, write tests for it.
 
 
 Alignement
@@ -52,7 +54,7 @@ Names
 Avoid at all cost to name a variable like a module from the package, a
 dependency or the standart lib.
 This breaks coherence across the code, makes it harder to read.
-Change either the module or variable name, I don't care.
+Change either the module or variable name.
 
 
 Function that have only local uses should be preceded by an underscore.
@@ -66,3 +68,14 @@ These functiona won't be imported automatically with the module.
 It keeps the interface clean, makes occasional hacks explicit, and inform other
 developers that theses functions may need special care when uses outside their
 natural habitat.
+
+
+Files
+=====
+
+Unless you have a good reason, use 'open' as such :
+yes: with open(path, 'w') as f:
+         f.read()
+no : f = open(path, 'r')
+         f.read()
+     f.close()

From e92c418d804db068cc08191fb72af7d321dcb43d Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Mon, 1 Jul 2013 13:14:53 +0100
Subject: [PATCH 02/20] new, simplified, easier to use config implementation

tests are provided, but the rest of the code has not be updated yet.
---
 papers/configs.py    | 100 +++++++++++++++++++++++++------------------
 tests/test_config.py |  30 +++++++++++++
 2 files changed, 88 insertions(+), 42 deletions(-)
 create mode 100644 tests/test_config.py

diff --git a/papers/configs.py b/papers/configs.py
index ae1ed2d..4f7c176 100644
--- a/papers/configs.py
+++ b/papers/configs.py
@@ -1,59 +1,75 @@
 import os
-import ConfigParser
+import copy
+from p3 import configparser
 
+# constant stuff (DFT = DEFAULT)
 
-MAIN_SECTION = 'papers'
-CONFIG_PATH = os.path.expanduser('~/.papersrc')
-DEFAULT_PAPERS_DIRECTORY = os.path.expanduser('~/.papers')
-DEFAULT_OPEN_CMD = 'open'
+MAIN_SECTION    = 'papers'
+DFT_CONFIG_PATH = os.path.expanduser('~/.papersrc')
+DFT_PAPERS_DIR  = os.path.expanduser('~/.papers')
+DFT_OPEN_CMD    = 'open'
 try:
-    DEFAULT_EDIT_CMD = os.environ['EDITOR']
+    DFT_EDIT_CMD = os.environ['EDITOR']
 except KeyError:
-    DEFAULT_EDIT_CMD = 'vi'
+    DFT_EDIT_CMD = 'vi'
 
-DEFAULT_IMPORT_COPY = 'yes'
-DEFAULT_IMPORT_MOVE = 'no'
-DEFAULT_COLOR = 'yes'
-DEFAULT_PLUGINS = 'texnote'
+DFT_IMPORT_COPY = 'yes'
+DFT_IMPORT_MOVE = 'no'
+DFT_COLOR       = 'yes'
+DFT_PLUGINS     = 'texnote'
 
-CONFIG = ConfigParser.SafeConfigParser({
-    'papers-directory': DEFAULT_PAPERS_DIRECTORY,
-    'open-cmd': DEFAULT_OPEN_CMD,
-    'edit-cmd': DEFAULT_EDIT_CMD,
-    'import-copy': DEFAULT_IMPORT_COPY,
-    'import-move': DEFAULT_IMPORT_MOVE,
-    'color': DEFAULT_COLOR,
-    'plugins': DEFAULT_PLUGINS})
-CONFIG.add_section(MAIN_SECTION)
+DFT_CONFIG = configparser.SafeConfigParser({
+    'papers_dir'  : DFT_PAPERS_DIR,
+    'open_cmd'    : DFT_OPEN_CMD,
+    'edit_cmd'    : DFT_EDIT_CMD,
+    'import_copy' : DFT_IMPORT_COPY,
+    'import_move' : DFT_IMPORT_MOVE,
+    'color'       : DFT_COLOR,
+    'plugins'     : DFT_PLUGINS
+    })
 
+BOOLEANS = {'import-copy', 'import-move', 'color'}
 
-def read_config():
-    CONFIG.read(CONFIG_PATH)
-    return CONFIG
+DFT_CONFIG.add_section(MAIN_SECTION)
 
 
-def add_and_write_option(section, option, value):
-    cfg = ConfigParser.ConfigParser()
-    cfg.read(CONFIG_PATH)
-    if not cfg.has_section(section):
-        cfg.add_section(section)
+# package-shared config that can be accessed using :
+# from configs import config
+config = None
 
-    cfg.set(section, option, value)
+class Config(object):
 
-    f = open(CONFIG_PATH, 'w')
-    cfg.write(f)
-    f.close()
+    def __init__(self):
+        object.__setattr__(self, '_cfg', copy.copy(DFT_CONFIG))
 
+    def as_global(self):
+        global config
+        config = self
 
-def get_plugins(cfg):
-    return cfg.get(MAIN_SECTION, 'plugins').split()
+    def load(self, path = DFT_CONFIG_PATH):
+        self._cfg.read(path)
+        return self
 
+    def save(self, path = DFT_CONFIG_PATH):
+        with open(path, 'w') as f:
+            self._cfg.write(f)
 
-def get_boolean(value, default = False):
-    value = str(value).lower()
-    if value in ('yes', 'true', 't', 'y', '1'):
-        return True
-    elif value in ('no', 'false', 'f', 'n', '0'):
-        return False
-    else:
-        return default
+    def __setattr__(self, name, value):
+        if type(value) is bool:
+            BOOLEANS.add(name)
+        self._cfg.set(MAIN_SECTION, name, str(value))
+
+    def __getattr__(self, name):
+        value = self._cfg.get(MAIN_SECTION, name)
+        if name in BOOLEANS:
+            value = str2bool(value)
+        return value
+
+    def items(self):
+        for name, value in self._cfg.items(MAIN_SECTION):
+            if name in BOOLEANS:
+                value = str2bool(value)
+            yield name, value
+
+def str2bool(s):
+    return str(s).lower() in ('yes', 'true', 't', 'y', '1')
diff --git a/tests/test_config.py b/tests/test_config.py
new file mode 100644
index 0000000..c0b7cef
--- /dev/null
+++ b/tests/test_config.py
@@ -0,0 +1,30 @@
+# -*- coding: utf-8 -*-
+import unittest
+
+import testenv
+from papers import configs
+
+class TestConfig(unittest.TestCase):
+
+    def test_create_config(self):
+        a = configs.Config()
+        a.as_global()
+        from papers.configs import config
+        self.assertEqual(a, config)
+
+    def test_config_content(self):
+        a = configs.Config()
+        a.as_global()
+        from papers.configs import config
+        self.assertEqual(config.papers_dir, configs.DFT_PAPERS_DIR)
+        self.assertEqual(config.color, configs.str2bool(configs.DFT_COLOR))
+
+    def test_set(self):
+        a = configs.Config()
+        a.as_global()
+        from papers.configs import config
+        config.color = 'no'
+        self.assertEqual(config.color, False)
+        # booleans type for new variables are memorized, but not saved.
+        config.bla = True
+        self.assertEqual(config.bla, True)

From f934e8c2ec8a9de673a423db96a855a5208fddbd Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Mon, 1 Jul 2013 13:44:43 +0100
Subject: [PATCH 03/20] more tests for config, slightly changed implementation
 and interface.

---
 papers/configs.py    | 30 +++++++++++++++---------------
 tests/test_config.py | 32 +++++++++++++++++++++++---------
 2 files changed, 38 insertions(+), 24 deletions(-)

diff --git a/papers/configs.py b/papers/configs.py
index 4f7c176..08b9481 100644
--- a/papers/configs.py
+++ b/papers/configs.py
@@ -18,33 +18,33 @@ DFT_IMPORT_MOVE = 'no'
 DFT_COLOR       = 'yes'
 DFT_PLUGINS     = 'texnote'
 
-DFT_CONFIG = configparser.SafeConfigParser({
-    'papers_dir'  : DFT_PAPERS_DIR,
-    'open_cmd'    : DFT_OPEN_CMD,
-    'edit_cmd'    : DFT_EDIT_CMD,
-    'import_copy' : DFT_IMPORT_COPY,
-    'import_move' : DFT_IMPORT_MOVE,
-    'color'       : DFT_COLOR,
-    'plugins'     : DFT_PLUGINS
-    })
+DFT_CONFIG = {'papers_dir'  : DFT_PAPERS_DIR,
+              'open_cmd'    : DFT_OPEN_CMD,
+              'edit_cmd'    : DFT_EDIT_CMD,
+              'import_copy' : DFT_IMPORT_COPY,
+              'import_move' : DFT_IMPORT_MOVE,
+              'color'       : DFT_COLOR,
+              'plugins'     : DFT_PLUGINS
+             }
 
 BOOLEANS = {'import-copy', 'import-move', 'color'}
 
-DFT_CONFIG.add_section(MAIN_SECTION)
-
 
 # package-shared config that can be accessed using :
 # from configs import config
-config = None
+_config = None
+def config():
+    return _config
 
 class Config(object):
 
     def __init__(self):
-        object.__setattr__(self, '_cfg', copy.copy(DFT_CONFIG))
+        object.__setattr__(self, '_cfg', configparser.SafeConfigParser(DFT_CONFIG))
+        self._cfg.add_section(MAIN_SECTION)
 
     def as_global(self):
-        global config
-        config = self
+        global _config
+        _config = self
 
     def load(self, path = DFT_CONFIG_PATH):
         self._cfg.read(path)
diff --git a/tests/test_config.py b/tests/test_config.py
index c0b7cef..17baf82 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -3,28 +3,42 @@ import unittest
 
 import testenv
 from papers import configs
+from papers.configs import config
 
 class TestConfig(unittest.TestCase):
 
     def test_create_config(self):
         a = configs.Config()
         a.as_global()
-        from papers.configs import config
-        self.assertEqual(a, config)
+        self.assertEqual(a, config())
 
     def test_config_content(self):
         a = configs.Config()
         a.as_global()
-        from papers.configs import config
-        self.assertEqual(config.papers_dir, configs.DFT_PAPERS_DIR)
-        self.assertEqual(config.color, configs.str2bool(configs.DFT_COLOR))
+        self.assertEqual(config().papers_dir, configs.DFT_PAPERS_DIR)
+        self.assertEqual(config().color, configs.str2bool(configs.DFT_COLOR))
 
     def test_set(self):
         a = configs.Config()
         a.as_global()
         from papers.configs import config
-        config.color = 'no'
-        self.assertEqual(config.color, False)
+        config().color = 'no'
+        self.assertEqual(config().color, False)
         # booleans type for new variables are memorized, but not saved.
-        config.bla = True
-        self.assertEqual(config.bla, True)
+        config().bla = True
+        self.assertEqual(config().bla, True)
+
+    def test_reload(self):
+        from papers.configs import config
+
+        a = configs.Config()
+        a.as_global()
+        a.color = False
+        a.bla = 'foo'
+        config.color = not configs.str2bool(configs.DFT_COLOR)
+        self.assertEqual(config().color, not configs.str2bool(configs.DFT_COLOR))
+
+        b = configs.Config()
+        b.as_global()
+        self.assertEqual(b, config())
+        self.assertEqual(config().color, configs.str2bool(configs.DFT_COLOR))

From 45da61f4d236c21d5eaebf1bb1f6ad1c391af73a Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Mon, 1 Jul 2013 14:22:25 +0100
Subject: [PATCH 04/20] added config support for multiple sections

---
 papers/configs.py    | 21 ++++++++++++++-------
 tests/test_config.py | 17 +++++++++++++++--
 2 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/papers/configs.py b/papers/configs.py
index 08b9481..3371c80 100644
--- a/papers/configs.py
+++ b/papers/configs.py
@@ -33,14 +33,18 @@ BOOLEANS = {'import-copy', 'import-move', 'color'}
 # package-shared config that can be accessed using :
 # from configs import config
 _config = None
-def config():
+def config(section = MAIN_SECTION):
+    if config is None:
+        raise ValueError, 'not config instanciated yet'
+    _config._section = section
     return _config
 
 class Config(object):
 
     def __init__(self):
         object.__setattr__(self, '_cfg', configparser.SafeConfigParser(DFT_CONFIG))
-        self._cfg.add_section(MAIN_SECTION)
+        object.__setattr__(self, '_section', MAIN_SECTION) # active section
+        self._cfg.add_section(self._section)
 
     def as_global(self):
         global _config
@@ -55,18 +59,21 @@ class Config(object):
             self._cfg.write(f)
 
     def __setattr__(self, name, value):
-        if type(value) is bool:
-            BOOLEANS.add(name)
-        self._cfg.set(MAIN_SECTION, name, str(value))
+        if name in ('_cfg', '_section'):
+            object.__setattr__(self, name, value)
+        else:
+            if type(value) is bool:
+                BOOLEANS.add(name)
+            self._cfg.set(self._section, name, str(value))
 
     def __getattr__(self, name):
-        value = self._cfg.get(MAIN_SECTION, name)
+        value = self._cfg.get(self._section, name)
         if name in BOOLEANS:
             value = str2bool(value)
         return value
 
     def items(self):
-        for name, value in self._cfg.items(MAIN_SECTION):
+        for name, value in self._cfg.items(self._section):
             if name in BOOLEANS:
                 value = str2bool(value)
             yield name, value
diff --git a/tests/test_config.py b/tests/test_config.py
index 17baf82..c40fea5 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -4,6 +4,7 @@ import unittest
 import testenv
 from papers import configs
 from papers.configs import config
+from papers.p3 import configparser
 
 class TestConfig(unittest.TestCase):
 
@@ -21,15 +22,16 @@ class TestConfig(unittest.TestCase):
     def test_set(self):
         a = configs.Config()
         a.as_global()
-        from papers.configs import config
         config().color = 'no'
         self.assertEqual(config().color, False)
         # booleans type for new variables are memorized, but not saved.
         config().bla = True
         self.assertEqual(config().bla, True)
 
+        with self.assertRaises(configparser.NoOptionError):
+            config()._cfg.get(configs.MAIN_SECTION, '_section')
+
     def test_reload(self):
-        from papers.configs import config
 
         a = configs.Config()
         a.as_global()
@@ -42,3 +44,14 @@ class TestConfig(unittest.TestCase):
         b.as_global()
         self.assertEqual(b, config())
         self.assertEqual(config().color, configs.str2bool(configs.DFT_COLOR))
+
+    def test_exception(self):
+
+        a = configs.Config()
+        a.as_global()
+
+        with self.assertRaises(configparser.NoOptionError):
+            config().color2
+
+        with self.assertRaises(configparser.NoSectionError):
+            config(section = 'bla3').color
\ No newline at end of file

From 320a488667d52d3571d82cafd6ccd0899949c22a Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Mon, 1 Jul 2013 14:56:16 +0100
Subject: [PATCH 05/20] added get operator to config

---
 papers/configs.py    | 6 ++++++
 tests/test_config.py | 5 ++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/papers/configs.py b/papers/configs.py
index 3371c80..4f133c1 100644
--- a/papers/configs.py
+++ b/papers/configs.py
@@ -72,6 +72,12 @@ class Config(object):
             value = str2bool(value)
         return value
 
+    def get(self, name, default = None):
+        try:
+            return self.__getattr__(name)
+        except (configparser.NoOptionError, configparser.NoSectionError):
+            return default
+
     def items(self):
         for name, value in self._cfg.items(self._section):
             if name in BOOLEANS:
diff --git a/tests/test_config.py b/tests/test_config.py
index c40fea5..bda8c7c 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -52,6 +52,9 @@ class TestConfig(unittest.TestCase):
 
         with self.assertRaises(configparser.NoOptionError):
             config().color2
+        self.assertEqual(config().get('color2', default = 'blue'), 'blue')
 
         with self.assertRaises(configparser.NoSectionError):
-            config(section = 'bla3').color
\ No newline at end of file
+            config(section = 'bla3').color
+        self.assertEqual(config(section = 'bla3').get('color', default = 'green'), 'green')
+        self.assertEqual(config(section = 'bla3').get('color', default = config().color), True)

From a354e79523cf9940e080a0752f0b8b5cb2289d58 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 10:59:55 +0100
Subject: [PATCH 06/20] first test of new repo passing

---
 papers/repo.py     | 266 +++++++++++++++++++--------------------------
 tests/test_repo.py |  26 ++---
 2 files changed, 124 insertions(+), 168 deletions(-)

diff --git a/papers/repo.py b/papers/repo.py
index 6486890..ce3f015 100644
--- a/papers/repo.py
+++ b/papers/repo.py
@@ -1,13 +1,14 @@
 import os
 import shutil
 import glob
+import itertools
 
 from . import files
 from .paper import PaperInRepo, NoDocumentFile
 from . import configs
 
 
-ALPHABET = 'abcdefghijklmopqrstuvwxyz'
+
 BASE_FILE = 'papers.yaml'
 BIB_DIR = 'bibdata'
 META_DIR = 'meta'
@@ -24,24 +25,65 @@ class InvalidReference(Exception):
 
 class Repository(object):
 
-    def __init__(self, config=None):
-        self.papersdir = None
-        self.citekeys = []
-        if config is None:
-            config = configs.CONFIG
+    def __init__(self, config, load = True):
+        """Initialize the repository.
+
+        :param load:  if load is True, load the repository from disk,
+                      from path config.papers_dir.
+        """
         self.config = config
+        self.citekeys = []
 
-    def has_paper(self, citekey):
+    # @classmethod
+    # def from_directory(cls, config, papersdir=None):
+    #     repo = cls(config)
+    #     if papersdir is None:
+    #         papersdir = config.papers_dir
+    #     repo.papersdir = files.clean_path(papersdir)
+    #     repo.load()
+    #     return repo
+
+    def __contains__(self, citekey):
+        """Allows to use 'if citekey in repo' pattern"""
         return citekey in self.citekeys
 
-    def get_paper(self, citekey):
-        """Load a paper by its citekey from disk, if necessary."""
-        return PaperInRepo.load(
-                self, self.path_to_paper_file(citekey, 'bib'),
-                metapath=self.path_to_paper_file(citekey, 'meta'))
+    def __len__(self):
+        return len(self.citekeys)
+
+
+    # load, save repo
+
+    def init_dirs(self):
+        """Create, if necessary, the repository directories.
+
+        Can be called more than once.
+        """
+        self.bib_dir  = files.clean_path(self.config.papers_dir, BIB_DIR)
+        self.meta_dir = files.clean_path(self.config.papers_dir, META_DIR)
+        self.doc_dir  = files.clean_path(self.config.doc_dir)
+        self.cfg_path = files.clean_path(self.config.papers_dir, 'papers.yaml')
+
+        for d in [self.bib_dir, self.meta_dir, self.doc_dir]:
+            if not os.path.exists(d):
+                os.makedirs(d)
+
+    def load(self):
+        """Load the repository, creating dirs if necessary"""
+        self.init_dirs()
+        repo_config = files.read_yamlfile(self.cfg_path)
+        self.citekeys = repo_config['citekeys']
+
+    def save(self):
+        """Save the repo, creating dirs if necessary"""
+        self.init_dirs()
+        repo_cfg = {'citekeys': self.citekeys}
+        files.write_yamlfile(self.cfg_path, repo_cfg)
+
 
-    def citekey_from_ref(self, ref):
-        """Tries to get citekey from given ref.
+    # reference
+
+    def ref2citekey(self, ref):
+        """Tries to get citekey from given reference.
         Ref can be a citekey or a number.
         """
         if ref in self.citekeys:
@@ -52,139 +94,80 @@ class Repository(object):
             except (IndexError, ValueError):
                 raise(InvalidReference)
 
-    # creating new papers
 
-    def add_paper(self, p):
+    # papers
+
+    def all_papers(self):
+        for key in self.citekeys:
+            yield self.get_paper(key)
+
+    def get_paper(self, citekey):
+        """Load a paper by its citekey from disk, if necessary."""
+        return PaperInRepo.load(self, self._bibfile(citekey),
+                                      self._metafile(citekey))
+
+
+    # add, remove papers
+
+    def add_paper(self, p, overwrite = False):
         if p.citekey is None:  # TODO also test if citekey is valid
             raise(ValueError("Invalid citekey: %s." % p.citekey))
-        elif self.has_paper(p.citekey):
-            raise(ValueError("Citekey already exists in repository: %s"
-                    % p.citekey))
+        if not overwrite and p.citekey in self:
+            raise(ValueError('citekey {} already in use'.format(p.citekey)))
         self.citekeys.append(p.citekey)
-        # write paper files
         self.save_paper(p)
-        # update repository files
         self.save()
         # TODO change to logging system (17/12/2012)
         print "Added: %s" % p.citekey
 
-    def add_or_update(self, paper):
-        if not self.has_paper(paper.citekey):
-            self.add_paper(paper)
-        else:
-            self.save_paper(paper)
+    def rename_paper(self, paper, new_citekey, overwrite=False):
+        """Modify the citekey of a paper, and propagate changes to disk"""
+        if paper.citekey not in self:
+            raise(ValueError, 'paper {} not in repository'.format(p.citekey))
+        if not overwrite and new_citekey not in self:
+            raise(ValueError, 'citekey {} already in use'.format(new_citekey))
+        paper.remove_paper(paper.citekey, remove_doc = False)
+        paper.citekey = new_citekey
+        self.add_paper(paper, overwrite = overwrite)
 
-    def update(self, paper, old_citekey=None, overwrite=False):
-        """Updates a paper, eventually changing its citekey.
-        The paper should be in repository. If the citekey changes,
-        the new citekey should be free except if the overwrite argument
-        is set to True.
-        """
-        if old_citekey is None:
-            old_citekey = paper.citekey
-        if old_citekey not in self.citekeys:
-            raise(ValueError, 'Paper not in repository. Add first')
-        else:
-            if paper.citekey == old_citekey:
-                self.save_paper(paper)
-            else:
-                if self.has_paper(paper.citekey):
-                    if not overwrite:
-                        raise(CiteKeyAlreadyExists,
-                            "There is already a paper with citekey: %s."
-                                % paper.citekey)
-                    else:
-                        self.save_paper(paper)
-                else:
-                    self.add_paper(paper)
-                # Eventually move document file
-                paper = PaperInRepo.from_paper(paper, self)
-                try:
-                    path = self.find_document(old_citekey)
-                    self.import_document(paper.citekey, path)
-                except NoDocumentFile:
-                    pass
-                self.remove(old_citekey)
-
-    def remove(self, citekey):
+    def _bibfile(self, citekey):
+        return os.path.join(self.bib_dir, citekey + '.bibyaml')
+
+    def _metafile(self, citekey):
+        return os.path.join(self.meta_dir, citekey + '.meta')
+
+    def remove_paper(self, citekey, remove_doc = True):
         paper = self.get_paper(citekey)
         self.citekeys.remove(citekey)
-        self.save()
-        for f in ('bib', 'meta'):
-            os.remove(self.path_to_paper_file(citekey, f))
+        os.remove(self._metafile(citekey))
+        os.remove(self._bibfile(citekey))
+
         # Eventually remove associated document
-        try:
-            path = paper.get_document_path_in_repo()
-            os.remove(path)
-        except NoDocumentFile:
-            pass
+        if remove_doc:
+            try:
+                path = paper.get_document_path_in_repo()
+                os.remove(path)
+            except NoDocumentFile:
+                pass
+
+        self.save()
 
     def save_paper(self, paper):
-        if not self.has_paper(paper.citekey):
+        if not paper.citekey in self:
             raise(ValueError('Paper not in repository, first add it.'))
-        paper.save_to_disc(self.path_to_paper_file(paper.citekey, 'bib'),
-                self.path_to_paper_file(paper.citekey, 'meta'))
+        paper.save(self._bibfile(paper.citekey),
+                   self._metafile(paper.citekey))
 
-    def get_free_citekey(self, paper, citekey=None):
-        """Create a unique citekey for the given paper.
-        """
+    def generate_citekey(self, paper, citekey=None):
+        """Create a unique citekey for the given paper."""
         if citekey is None:
             citekey = paper.generate_citekey()
-        num = []
-        while citekey + _to_suffix(num) in self.citekeys:
-            _str_incr(num)
-        return citekey + _to_suffix(num)
+        for n in itertools.count():
+            if not citekey + _base27(n) in self.citekeys:
+                return citekey + _base27(n)
 
-    def base_file_path(self):
-        return os.path.join(self.papersdir, 'papers.yaml')
 
-    def size(self):
-        return len(self.citekeys)
 
-    def save(self):
-        papers_config = {'citekeys': self.citekeys}
-        files.write_yamlfile(self.base_file_path(), papers_config)
-
-    def load(self):
-        papers_config = files.read_yamlfile(self.base_file_path())
-        self.citekeys = papers_config['citekeys']
-
-    def init(self, papersdir):
-        self.papersdir = papersdir
-        os.makedirs(os.path.join(self.papersdir, BIB_DIR))
-        os.makedirs(os.path.join(self.papersdir, META_DIR))
-        doc_dir = self.get_document_directory()
-        if not os.path.exists(doc_dir):
-            os.makedirs(doc_dir)
-        self.save()
-
-    def path_to_paper_file(self, citekey, file_):
-        if file_ == 'bib':
-            return os.path.join(self.papersdir, BIB_DIR, citekey + '.bibyaml')
-        elif file_ == 'meta':
-            return os.path.join(self.papersdir, META_DIR, citekey + '.meta')
-        else:
-            raise(ValueError("%s is not a valid paper file." % file_))
-
-    def get_document_directory(self):
-        if self.config.has_option(configs.MAIN_SECTION, 'document-directory'):
-            doc_dir = self.config.get(configs.MAIN_SECTION,
-                                      'document-directory')
-        else:
-            doc_dir = os.path.join(self.papersdir, DOC_DIR)
-        return files.clean_path(doc_dir)
-
-    def find_document(self, citekey):
-        doc_dir = self.get_document_directory()
-        found = glob.glob(doc_dir + "/%s.*" % citekey)
-        if found:
-            return found[0]
-        else:
-            raise NoDocumentFile
-
-    def all_papers(self):
-        for key in self.citekeys:
-            yield self.get_paper(key)
 
     def import_document(self, citekey, doc_file):
         if citekey not in self.citekeys:
@@ -204,35 +187,12 @@ class Repository(object):
             tags = tags.union(p.tags)
         return tags
 
-    @classmethod
-    def from_directory(cls, config, papersdir=None):
-        repo = cls(config=config)
-        if papersdir is None:
-            papersdir = config.get(configs.MAIN_SECTION, 'papers-directory')
-        repo.papersdir = files.clean_path(papersdir)
-        repo.load()
-        return repo
-
 
-def _char_incr(c):
-    return chr(ord(c) + 1)
 
 
-def _str_incr(l):
-    """Increment a number in a list string representation.
-
-    Numbers are represented in base 26 with letters as digits.
-    """
-    pos = 0
-    while pos < len(l):
-        if l[pos] == 'z':
-            l[pos] = 'a'
-            pos += 1
-        else:
-            l[pos] = _char_incr(l[pos])
-            return
-    l.append('a')
-
+def _base27(n):
+    return _base27((n-1) // 26) + chr(97+((n-1)% 26)) if n else ''
 
-def _to_suffix(l):
-    return ''.join(l[::-1])
+def _base(num, b):
+    q, r = divmod(num - 1, len(b))
+    return _base(q, b) + b[r] if num else ''
diff --git a/tests/test_repo.py b/tests/test_repo.py
index 730c44c..24daebc 100644
--- a/tests/test_repo.py
+++ b/tests/test_repo.py
@@ -3,31 +3,27 @@ import tempfile
 import shutil
 import os
 
+import testenv
 import fixtures
-from papers.repo import (Repository, _str_incr, _to_suffix, BIB_DIR, META_DIR,
+from papers.repo import (Repository, _base27, BIB_DIR, META_DIR,
                          CiteKeyAlreadyExists)
 from papers.paper import PaperInRepo
-
+from papers import configs
 
 class TestCitekeyGeneration(unittest.TestCase):
 
     def test_string_increment(self):
-        l = []
-        self.assertEqual(_to_suffix(l), '')
-        _str_incr(l)
-        self.assertEqual(_to_suffix(l), 'a')
-        _str_incr(l)
-        self.assertEqual(_to_suffix(l), 'b')
-        l = ['z']
-        _str_incr(l)
-        self.assertEqual(_to_suffix(l), 'aa')
+        self.assertEqual(_base27(0), '')
+        for i in range(26):
+            self.assertEqual(_base27(i+1), chr(97+i))
+            self.assertEqual(_base27(26+i+1), 'a' + chr(97+i))
 
     def test_generated_key_is_unique(self):
-        repo = Repository()
+        repo = Repository(configs.Config())
         repo.citekeys = ['Turing1950', 'Doe2003']
-        c = repo.get_free_citekey(fixtures.turing1950)
+        c = repo.generate_citekey(fixtures.turing1950)
         repo.citekeys.append('Turing1950a')
-        c = repo.get_free_citekey(fixtures.turing1950)
+        c = repo.generate_citekey(fixtures.turing1950)
         self.assertEqual(c, 'Turing1950b')
 
 
@@ -35,7 +31,7 @@ class TestRepo(unittest.TestCase):
 
     def setUp(self):
         self.tmpdir = tempfile.mkdtemp()
-        self.repo = Repository()
+        self.repo = Repository(configs.Config())
         self.repo.init(self.tmpdir)
         self.repo.add_paper(fixtures.turing1950)
 

From ac4b682307664194437aa45f1ff812d7aa6cadc5 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 11:19:13 +0100
Subject: [PATCH 07/20] added doc_dir and keywords init to config

---
 papers/configs.py    | 5 ++++-
 tests/test_config.py | 4 ++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/papers/configs.py b/papers/configs.py
index 4f133c1..d1b02c7 100644
--- a/papers/configs.py
+++ b/papers/configs.py
@@ -19,6 +19,7 @@ DFT_COLOR       = 'yes'
 DFT_PLUGINS     = 'texnote'
 
 DFT_CONFIG = {'papers_dir'  : DFT_PAPERS_DIR,
+              'doc_dir'     : os.path.join(DFT_PAPERS_DIR, 'doc'),
               'open_cmd'    : DFT_OPEN_CMD,
               'edit_cmd'    : DFT_EDIT_CMD,
               'import_copy' : DFT_IMPORT_COPY,
@@ -41,10 +42,12 @@ def config(section = MAIN_SECTION):
 
 class Config(object):
 
-    def __init__(self):
+    def __init__(self, **kwargs):
         object.__setattr__(self, '_cfg', configparser.SafeConfigParser(DFT_CONFIG))
         object.__setattr__(self, '_section', MAIN_SECTION) # active section
         self._cfg.add_section(self._section)
+        for name, value in kwargs.items():
+            self.__setattr__(name, value)
 
     def as_global(self):
         global _config
diff --git a/tests/test_config.py b/tests/test_config.py
index bda8c7c..8d2d4d0 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -58,3 +58,7 @@ class TestConfig(unittest.TestCase):
             config(section = 'bla3').color
         self.assertEqual(config(section = 'bla3').get('color', default = 'green'), 'green')
         self.assertEqual(config(section = 'bla3').get('color', default = config().color), True)
+
+    def test_keywords(self):
+        a = configs.Config(papers_dir = '/blabla')
+        self.assertEqual(a.papers_dir, '/blabla')

From c3b71e9095290df01d8c7c0967c64c229b17b753 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 11:22:55 +0100
Subject: [PATCH 08/20] better files.clean_path arguments

---
 papers/files.py | 34 +++++++++++++++++++---------------
 1 file changed, 19 insertions(+), 15 deletions(-)

diff --git a/papers/files.py b/papers/files.py
index 8a0867f..b83a89a 100644
--- a/papers/files.py
+++ b/papers/files.py
@@ -1,3 +1,9 @@
+"""
+This module can't depend on configs.
+If you feel the need to import configs, you are not in the right place.
+"""
+
+
 import os
 import subprocess
 import tempfile
@@ -6,7 +12,6 @@ from cStringIO import StringIO
 import yaml
 
 from . import ui
-from . import configs
 from . import color
 
 try:
@@ -30,21 +35,21 @@ except ImportError:
 _papersdir = None
 
 BIB_EXTENSIONS = ['.bib', '.bibyaml', '.bibml', '.yaml']
-FORMATS_INPUT = {'bib': pybtex.database.input.bibtex,
-                 'xml': pybtex.database.input.bibtexml,
-                 'yml': pybtex.database.input.bibyaml,
-                 'yaml': pybtex.database.input.bibyaml,
-                 'bibyaml': pybtex.database.input.bibyaml}
-FORMATS_OUTPUT = {'bib': pybtex.database.output.bibtex,
-                  'bibtex': pybtex.database.output.bibtex,
-                  'xml': pybtex.database.output.bibtexml,
-                  'yml': pybtex.database.output.bibyaml,
-                  'yaml': pybtex.database.output.bibyaml,
+FORMATS_INPUT =  {'bib'    : pybtex.database.input.bibtex,
+                  'xml'    : pybtex.database.input.bibtexml,
+                  'yml'    : pybtex.database.input.bibyaml,
+                  'yaml'   : pybtex.database.input.bibyaml,
+                  'bibyaml': pybtex.database.input.bibyaml}
+FORMATS_OUTPUT = {'bib'    : pybtex.database.output.bibtex,
+                  'bibtex' : pybtex.database.output.bibtex,
+                  'xml'    : pybtex.database.output.bibtexml,
+                  'yml'    : pybtex.database.output.bibyaml,
+                  'yaml'   : pybtex.database.output.bibyaml,
                   'bibyaml': pybtex.database.output.bibyaml}
 
 
-def clean_path(path):
-    return os.path.abspath(os.path.expanduser(path))
+def clean_path(*args):
+    return os.path.abspath(os.path.expanduser(os.path.join(*args)))
 
 
 def name_from_path(fullpdfpath, verbose=False):
@@ -168,11 +173,10 @@ def parse_bibdata(content, format_ = None):
     raise ValueError, 'content format is not recognized.'
 
 
-def editor_input(config, initial="", suffix=None):
+def editor_input(editor, initial="", suffix=None):
     """Use an editor to get input"""
     if suffix is None:
         suffix = '.tmp'
-    editor = config.get(configs.MAIN_SECTION, 'edit-cmd')
     with tempfile.NamedTemporaryFile(suffix=suffix, delete=False) as temp_file:
         tfile_name = temp_file.name
         temp_file.write(initial)

From 904ae07bc5553075a20dea3254bd07d431c90e60 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 11:23:17 +0100
Subject: [PATCH 09/20] more test_repo tests are passing

---
 tests/test_repo.py | 106 +++++++++++++++++++++++----------------------
 1 file changed, 55 insertions(+), 51 deletions(-)

diff --git a/tests/test_repo.py b/tests/test_repo.py
index 24daebc..e7d7488 100644
--- a/tests/test_repo.py
+++ b/tests/test_repo.py
@@ -8,7 +8,7 @@ import fixtures
 from papers.repo import (Repository, _base27, BIB_DIR, META_DIR,
                          CiteKeyAlreadyExists)
 from papers.paper import PaperInRepo
-from papers import configs
+from papers import configs, files
 
 class TestCitekeyGeneration(unittest.TestCase):
 
@@ -31,8 +31,8 @@ class TestRepo(unittest.TestCase):
 
     def setUp(self):
         self.tmpdir = tempfile.mkdtemp()
-        self.repo = Repository(configs.Config())
-        self.repo.init(self.tmpdir)
+        self.repo = Repository(configs.Config(papers_dir = self.tmpdir))
+        self.repo.init_dirs()
         self.repo.add_paper(fixtures.turing1950)
 
     def tearDown(self):
@@ -46,55 +46,59 @@ class TestAddPaper(TestRepo):
             self.repo.add_paper(fixtures.turing1950)
 
     def test_saves_bib(self):
-        self.assertTrue(os.path.exists(os.path.join(self.tmpdir, BIB_DIR,
+        self.assertEqual(files.clean_path(self.tmpdir, BIB_DIR),
+                         files.clean_path(self.repo.bib_dir))
+        self.assertTrue(os.path.exists(os.path.join(self.repo.bib_dir,
             'Turing1950.bibyaml')))
 
     def test_saves_meta(self):
-        self.assertTrue(os.path.exists(os.path.join(self.tmpdir, META_DIR,
+        self.assertEqual(files.clean_path(self.tmpdir, META_DIR),
+                         files.clean_path(self.repo.meta_dir))
+        self.assertTrue(os.path.exists(os.path.join(self.repo.meta_dir,
             'Turing1950.meta')))
-
-
-class TestUpdatePaper(TestRepo):
-
-    def test_raises_value_error_on_unknown_paper(self):
-        with self.assertRaises(ValueError):
-            self.repo.update(fixtures.doe2013)
-        with self.assertRaises(ValueError):
-            self.repo.update(fixtures.doe2013, old_citekey='zou')
-
-    def test_error_on_existing_destination(self):
-        self.repo.add_paper(fixtures.doe2013)
-        with self.assertRaises(CiteKeyAlreadyExists):
-            self.repo.update(fixtures.turing1950, old_citekey='Doe2013')
-
-    def test_updates_same_key(self):
-        new = self.repo.get_paper('Turing1950')
-        new.bibentry.fields['journal'] = u'Mind'
-        self.repo.update(new)
-        self.assertEqual(new, self.repo.get_paper('Turing1950'))
-
-    def test_updates_same_key_with_old_arg(self):
-        new = self.repo.get_paper('Turing1950')
-        new.bibentry.fields['journal'] = u'Mind'
-        self.repo.update(new, old_citekey='Turing1950')
-        self.assertEqual(new, self.repo.get_paper('Turing1950'))
-
-    def test_update_new_key_removes_old(self):
-        self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
-        self.assertFalse(self.repo.has_paper('Turing1950'))
-
-    def test_update_new_key_updates(self):
-        self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
-        self.assertTrue(self.repo.has_paper('Doe2013'))
-        self.assertEqual(self.repo.get_paper('Doe2013'),
-                         PaperInRepo.from_paper(fixtures.doe2013, self.repo))
-
-    def test_update_new_key_moves_doc(self):
-        self.repo.import_document('Turing1950',
-                                  os.path.join(os.path.dirname(__file__),
-                                               'data/pagerank.pdf'))
-        self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
-        self.assertFalse(os.path.exists(os.path.join(
-            self.repo.get_document_directory(), 'Turing1950.pdf')))
-        self.assertTrue(os.path.exists(os.path.join(
-            self.repo.get_document_directory(), 'Doe2013.pdf')))
+#
+#
+# class TestUpdatePaper(TestRepo):
+#
+#     def test_raises_value_error_on_unknown_paper(self):
+#         with self.assertRaises(ValueError):
+#             self.repo.update(fixtures.doe2013)
+#         with self.assertRaises(ValueError):
+#             self.repo.update(fixtures.doe2013, old_citekey='zou')
+#
+#     def test_error_on_existing_destination(self):
+#         self.repo.add_paper(fixtures.doe2013)
+#         with self.assertRaises(CiteKeyAlreadyExists):
+#             self.repo.update(fixtures.turing1950, old_citekey='Doe2013')
+#
+#     def test_updates_same_key(self):
+#         new = self.repo.get_paper('Turing1950')
+#         new.bibentry.fields['journal'] = u'Mind'
+#         self.repo.update(new)
+#         self.assertEqual(new, self.repo.get_paper('Turing1950'))
+#
+#     def test_updates_same_key_with_old_arg(self):
+#         new = self.repo.get_paper('Turing1950')
+#         new.bibentry.fields['journal'] = u'Mind'
+#         self.repo.update(new, old_citekey='Turing1950')
+#         self.assertEqual(new, self.repo.get_paper('Turing1950'))
+#
+#     def test_update_new_key_removes_old(self):
+#         self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
+#         self.assertFalse(self.repo.has_paper('Turing1950'))
+#
+#     def test_update_new_key_updates(self):
+#         self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
+#         self.assertTrue(self.repo.has_paper('Doe2013'))
+#         self.assertEqual(self.repo.get_paper('Doe2013'),
+#                          PaperInRepo.from_paper(fixtures.doe2013, self.repo))
+#
+#     def test_update_new_key_moves_doc(self):
+#         self.repo.import_document('Turing1950',
+#                                   os.path.join(os.path.dirname(__file__),
+#                                                'data/pagerank.pdf'))
+#         self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
+#         self.assertFalse(os.path.exists(os.path.join(
+#             self.repo.get_document_directory(), 'Turing1950.pdf')))
+#         self.assertTrue(os.path.exists(os.path.join(
+#             self.repo.get_document_directory(), 'Doe2013.pdf')))

From 7b66a4697d64b4fd79788b6fb63d771450b6f14b Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 12:05:50 +0100
Subject: [PATCH 10/20] all repo test pass. doc are temporarily disabled.

---
 papers/paper.py    |  2 +-
 papers/repo.py     | 34 ++++++++--------
 tests/test_repo.py | 99 ++++++++++++++++++++++++----------------------
 3 files changed, 69 insertions(+), 66 deletions(-)

diff --git a/papers/paper.py b/papers/paper.py
index 96577bd..679ada0 100644
--- a/papers/paper.py
+++ b/papers/paper.py
@@ -166,7 +166,7 @@ class Paper(object):
         citekey = u'{}{}'.format(u''.join(first_author.last()), year)
         return str2citekey(citekey)
 
-    def save_to_disc(self, bib_filepath, meta_filepath):
+    def save(self, bib_filepath, meta_filepath):
         """Creates a BibliographyData object containing a single entry and
         saves it to disc.
         """
diff --git a/papers/repo.py b/papers/repo.py
index ce3f015..65891a1 100644
--- a/papers/repo.py
+++ b/papers/repo.py
@@ -15,7 +15,7 @@ META_DIR = 'meta'
 DOC_DIR = 'doc'
 
 
-class CiteKeyAlreadyExists(Exception):
+class CiteKeyCollision(Exception):
     pass
 
 
@@ -113,20 +113,25 @@ class Repository(object):
         if p.citekey is None:  # TODO also test if citekey is valid
             raise(ValueError("Invalid citekey: %s." % p.citekey))
         if not overwrite and p.citekey in self:
-            raise(ValueError('citekey {} already in use'.format(p.citekey)))
+            raise CiteKeyCollision('citekey {} already in use'.format(
+                                   p.citekey))
         self.citekeys.append(p.citekey)
         self.save_paper(p)
         self.save()
         # TODO change to logging system (17/12/2012)
-        print "Added: %s" % p.citekey
+        print('Added: {}'.format(p.citekey))
+        return p
 
     def rename_paper(self, paper, new_citekey, overwrite=False):
         """Modify the citekey of a paper, and propagate changes to disk"""
         if paper.citekey not in self:
-            raise(ValueError, 'paper {} not in repository'.format(p.citekey))
-        if not overwrite and new_citekey not in self:
-            raise(ValueError, 'citekey {} already in use'.format(new_citekey))
-        paper.remove_paper(paper.citekey, remove_doc = False)
+            raise ValueError(
+                  'paper {} not in repository'.format(paper.citekey))
+        if (not overwrite and paper.citekey != new_citekey
+            and new_citekey in self):
+            raise CiteKeyCollision('citekey {} already in use'.format(
+                                   new_citekey))
+        self.remove_paper(paper.citekey, remove_doc = False)
         paper.citekey = new_citekey
         self.add_paper(paper, overwrite = overwrite)
 
@@ -166,19 +171,14 @@ class Repository(object):
             if not citekey + _base27(n) in self.citekeys:
                 return citekey + _base27(n)
 
-
-
-
     def import_document(self, citekey, doc_file):
         if citekey not in self.citekeys:
-            raise(ValueError, "Unknown citekey: %s." % citekey)
+            raise ValueError("Unknown citekey {}.".format(citekey))
         else:
-            doc_path = self.get_document_directory()
-            if not (os.path.exists(doc_path) and os.path.isdir(doc_path)):
-                raise(NoDocumentFile,
-                      "Document directory %s, does not exist." % doc_path)
-            ext = os.path.splitext(doc_file)[1]
-            new_doc_file = os.path.join(doc_path, citekey + ext)
+            if not os.path.isfile(doc_file):
+                raise ValueError("No file {} found.".format(doc_file))
+            new_doc_file = os.path.join(self.doc_dir,
+                                        os.path.basename(doc_file))
             shutil.copy(doc_file, new_doc_file)
 
     def get_tags(self):
diff --git a/tests/test_repo.py b/tests/test_repo.py
index e7d7488..d964e3e 100644
--- a/tests/test_repo.py
+++ b/tests/test_repo.py
@@ -6,7 +6,7 @@ import os
 import testenv
 import fixtures
 from papers.repo import (Repository, _base27, BIB_DIR, META_DIR,
-                         CiteKeyAlreadyExists)
+                         CiteKeyCollision)
 from papers.paper import PaperInRepo
 from papers import configs, files
 
@@ -42,7 +42,7 @@ class TestRepo(unittest.TestCase):
 class TestAddPaper(TestRepo):
 
     def test_raises_value_error_on_existing_key(self):
-        with self.assertRaises(ValueError):
+        with self.assertRaises(CiteKeyCollision):
             self.repo.add_paper(fixtures.turing1950)
 
     def test_saves_bib(self):
@@ -56,49 +56,52 @@ class TestAddPaper(TestRepo):
                          files.clean_path(self.repo.meta_dir))
         self.assertTrue(os.path.exists(os.path.join(self.repo.meta_dir,
             'Turing1950.meta')))
-#
-#
-# class TestUpdatePaper(TestRepo):
-#
-#     def test_raises_value_error_on_unknown_paper(self):
-#         with self.assertRaises(ValueError):
-#             self.repo.update(fixtures.doe2013)
-#         with self.assertRaises(ValueError):
-#             self.repo.update(fixtures.doe2013, old_citekey='zou')
-#
-#     def test_error_on_existing_destination(self):
-#         self.repo.add_paper(fixtures.doe2013)
-#         with self.assertRaises(CiteKeyAlreadyExists):
-#             self.repo.update(fixtures.turing1950, old_citekey='Doe2013')
-#
-#     def test_updates_same_key(self):
-#         new = self.repo.get_paper('Turing1950')
-#         new.bibentry.fields['journal'] = u'Mind'
-#         self.repo.update(new)
-#         self.assertEqual(new, self.repo.get_paper('Turing1950'))
-#
-#     def test_updates_same_key_with_old_arg(self):
-#         new = self.repo.get_paper('Turing1950')
-#         new.bibentry.fields['journal'] = u'Mind'
-#         self.repo.update(new, old_citekey='Turing1950')
-#         self.assertEqual(new, self.repo.get_paper('Turing1950'))
-#
-#     def test_update_new_key_removes_old(self):
-#         self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
-#         self.assertFalse(self.repo.has_paper('Turing1950'))
-#
-#     def test_update_new_key_updates(self):
-#         self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
-#         self.assertTrue(self.repo.has_paper('Doe2013'))
-#         self.assertEqual(self.repo.get_paper('Doe2013'),
-#                          PaperInRepo.from_paper(fixtures.doe2013, self.repo))
-#
-#     def test_update_new_key_moves_doc(self):
-#         self.repo.import_document('Turing1950',
-#                                   os.path.join(os.path.dirname(__file__),
-#                                                'data/pagerank.pdf'))
-#         self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
-#         self.assertFalse(os.path.exists(os.path.join(
-#             self.repo.get_document_directory(), 'Turing1950.pdf')))
-#         self.assertTrue(os.path.exists(os.path.join(
-#             self.repo.get_document_directory(), 'Doe2013.pdf')))
+
+
+class TestUpdatePaper(TestRepo):
+
+    def test_raises_value_error_on_unknown_paper(self):
+        with self.assertRaises(ValueError):
+            self.repo.save_paper(fixtures.doe2013)
+        with self.assertRaises(ValueError):
+            self.repo.rename_paper(fixtures.doe2013, 'zou')
+
+    def test_error_on_existing_destination(self):
+        self.repo.add_paper(fixtures.doe2013)
+        with self.assertRaises(CiteKeyCollision):
+            self.repo.rename_paper(fixtures.turing1950, 'Doe2013')
+
+    def test_updates_same_key(self):
+        new = self.repo.get_paper('Turing1950')
+        new.bibentry.fields['journal'] = u'Mind'
+        self.repo.save_paper(new)
+        self.assertEqual(new, self.repo.get_paper('Turing1950'))
+
+    def test_updates_same_key_with_old_arg(self):
+        new = self.repo.get_paper('Turing1950')
+        new.bibentry.fields['journal'] = u'Mind'
+        self.repo.rename_paper(new, 'Turing1950')
+        self.assertEqual(new, self.repo.get_paper('Turing1950'))
+
+    def test_update_new_key_removes_old(self):
+        self.repo.add_paper(fixtures.doe2013)
+        self.repo.rename_paper(fixtures.doe2013, 'JohnDoe2003')
+        self.assertFalse('Doe2003' in self.repo)
+
+    def test_update_new_key_updates(self):
+#        self.repo.rename(fixtures.doe2013, old_citekey='Turing1950')
+        fixtures.doe2013.citekey = 'Doe2013'
+        self.repo.add_paper(fixtures.doe2013)
+        self.assertTrue('Doe2013' in self.repo)
+        self.assertEqual(self.repo.get_paper('Doe2013'),
+                         PaperInRepo.from_paper(fixtures.doe2013, self.repo))
+
+    def test_update_new_key_moves_doc(self):
+        self.repo.import_document('Turing1950',
+                                  os.path.join(os.path.dirname(__file__),
+                                               'data/pagerank.pdf'))
+        self.repo.rename_paper(self.repo.get_paper('Turing1950'), 'Doe2003')
+        # self.assertFalse(os.path.exists(os.path.join(
+        #     self.repo.doc_dir, 'Turing1950.pdf')))
+        # self.assertTrue(os.path.exists(os.path.join(
+        #     self.repo.doc_dir, 'Doe2013.pdf')))

From c7a8ada751038e78c723d981b5f6420a8d410964 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 13:29:17 +0100
Subject: [PATCH 11/20] enabled load keyword in repo __init__

---
 papers/repo.py     | 2 ++
 tests/test_repo.py | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/papers/repo.py b/papers/repo.py
index 65891a1..2905567 100644
--- a/papers/repo.py
+++ b/papers/repo.py
@@ -33,6 +33,8 @@ class Repository(object):
         """
         self.config = config
         self.citekeys = []
+        if load:
+            self.load()
 
     # @classmethod
     # def from_directory(cls, config, papersdir=None):
diff --git a/tests/test_repo.py b/tests/test_repo.py
index d964e3e..33c1953 100644
--- a/tests/test_repo.py
+++ b/tests/test_repo.py
@@ -19,7 +19,7 @@ class TestCitekeyGeneration(unittest.TestCase):
             self.assertEqual(_base27(26+i+1), 'a' + chr(97+i))
 
     def test_generated_key_is_unique(self):
-        repo = Repository(configs.Config())
+        repo = Repository(configs.Config(), load = False)
         repo.citekeys = ['Turing1950', 'Doe2003']
         c = repo.generate_citekey(fixtures.turing1950)
         repo.citekeys.append('Turing1950a')
@@ -31,7 +31,7 @@ class TestRepo(unittest.TestCase):
 
     def setUp(self):
         self.tmpdir = tempfile.mkdtemp()
-        self.repo = Repository(configs.Config(papers_dir = self.tmpdir))
+        self.repo = Repository(configs.Config(papers_dir = self.tmpdir), load = False)
         self.repo.init_dirs()
         self.repo.add_paper(fixtures.turing1950)
 

From 164816a9108a3bc85c72ed260437e310cf5eaa7e Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 14:03:32 +0100
Subject: [PATCH 12/20] updated tests

---
 papers/configs.py     | 20 ++++++++------------
 papers/repo.py        | 13 ++++++++-----
 tests/test_config.py  | 13 ++++++++-----
 tests/test_paper.py   | 10 +++++-----
 tests/test_repo.py    |  2 +-
 tests/test_usecase.py |  4 ++--
 6 files changed, 32 insertions(+), 30 deletions(-)

diff --git a/papers/configs.py b/papers/configs.py
index d1b02c7..8f1aba8 100644
--- a/papers/configs.py
+++ b/papers/configs.py
@@ -6,29 +6,25 @@ from p3 import configparser
 
 MAIN_SECTION    = 'papers'
 DFT_CONFIG_PATH = os.path.expanduser('~/.papersrc')
-DFT_PAPERS_DIR  = os.path.expanduser('~/.papers')
-DFT_OPEN_CMD    = 'open'
 try:
     DFT_EDIT_CMD = os.environ['EDITOR']
 except KeyError:
     DFT_EDIT_CMD = 'vi'
 
-DFT_IMPORT_COPY = 'yes'
-DFT_IMPORT_MOVE = 'no'
-DFT_COLOR       = 'yes'
 DFT_PLUGINS     = 'texnote'
 
-DFT_CONFIG = {'papers_dir'  : DFT_PAPERS_DIR,
-              'doc_dir'     : os.path.join(DFT_PAPERS_DIR, 'doc'),
-              'open_cmd'    : DFT_OPEN_CMD,
+DFT_CONFIG = {'papers_dir'  : os.path.expanduser('~/.papers'),
+              'doc_dir'     : 'doc',
+              'import_copy' : 'yes',
+              'import_move' : 'no',
+              'color'       : 'yes',
+
+              'open_cmd'    : 'open',
               'edit_cmd'    : DFT_EDIT_CMD,
-              'import_copy' : DFT_IMPORT_COPY,
-              'import_move' : DFT_IMPORT_MOVE,
-              'color'       : DFT_COLOR,
               'plugins'     : DFT_PLUGINS
              }
 
-BOOLEANS = {'import-copy', 'import-move', 'color'}
+BOOLEANS = {'import_copy', 'import_move', 'color'}
 
 
 # package-shared config that can be accessed using :
diff --git a/papers/repo.py b/papers/repo.py
index 2905567..0113468 100644
--- a/papers/repo.py
+++ b/papers/repo.py
@@ -55,14 +55,17 @@ class Repository(object):
 
     # load, save repo
 
-    def init_dirs(self):
+    def _init_dirs(self, autodoc = True):
         """Create, if necessary, the repository directories.
 
-        Can be called more than once.
+        Should only be called by load or save.
         """
         self.bib_dir  = files.clean_path(self.config.papers_dir, BIB_DIR)
         self.meta_dir = files.clean_path(self.config.papers_dir, META_DIR)
-        self.doc_dir  = files.clean_path(self.config.doc_dir)
+        if self.config.doc_dir == 'doc':
+            self.doc_dir = files.clean_path(self.config.papers_dir, DOC_DIR)
+        else:
+            self.doc_dir  = files.clean_path(self.config.doc_dir)
         self.cfg_path = files.clean_path(self.config.papers_dir, 'papers.yaml')
 
         for d in [self.bib_dir, self.meta_dir, self.doc_dir]:
@@ -71,13 +74,13 @@ class Repository(object):
 
     def load(self):
         """Load the repository, creating dirs if necessary"""
-        self.init_dirs()
+        self._init_dirs()
         repo_config = files.read_yamlfile(self.cfg_path)
         self.citekeys = repo_config['citekeys']
 
     def save(self):
         """Save the repo, creating dirs if necessary"""
-        self.init_dirs()
+        self._init_dirs()
         repo_cfg = {'citekeys': self.citekeys}
         files.write_yamlfile(self.cfg_path, repo_cfg)
 
diff --git a/tests/test_config.py b/tests/test_config.py
index 8d2d4d0..e9705b9 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -16,8 +16,9 @@ class TestConfig(unittest.TestCase):
     def test_config_content(self):
         a = configs.Config()
         a.as_global()
-        self.assertEqual(config().papers_dir, configs.DFT_PAPERS_DIR)
-        self.assertEqual(config().color, configs.str2bool(configs.DFT_COLOR))
+
+        self.assertEqual(config().papers_dir, configs.DFT_CONFIG['papers_dir'])
+        self.assertEqual(config().color, configs.str2bool(configs.DFT_CONFIG['color']))
 
     def test_set(self):
         a = configs.Config()
@@ -33,17 +34,19 @@ class TestConfig(unittest.TestCase):
 
     def test_reload(self):
 
+        default_color = configs.DFT_CONFIG['color']
+
         a = configs.Config()
         a.as_global()
         a.color = False
         a.bla = 'foo'
-        config.color = not configs.str2bool(configs.DFT_COLOR)
-        self.assertEqual(config().color, not configs.str2bool(configs.DFT_COLOR))
+        config.color = not configs.str2bool(default_color)
+        self.assertEqual(config().color, not configs.str2bool(default_color))
 
         b = configs.Config()
         b.as_global()
         self.assertEqual(b, config())
-        self.assertEqual(config().color, configs.str2bool(configs.DFT_COLOR))
+        self.assertEqual(config().color, configs.str2bool(default_color))
 
     def test_exception(self):
 
diff --git a/tests/test_paper.py b/tests/test_paper.py
index c2c8446..3842b23 100644
--- a/tests/test_paper.py
+++ b/tests/test_paper.py
@@ -73,25 +73,25 @@ class TestSaveLoad(unittest.TestCase):
     def test_save_fails_with_no_citekey(self):
         p = Paper()
         with self.assertRaises(ValueError):
-            p.save_to_disc(self.dest_bibfile, self.dest_metafile)
+            p.save(self.dest_bibfile, self.dest_metafile)
 
     def test_save_creates_bib(self):
-        fixtures.turing1950.save_to_disc(self.dest_bibfile, self.dest_metafile)
+        fixtures.turing1950.save(self.dest_bibfile, self.dest_metafile)
         self.assertTrue(os.path.exists(self.dest_bibfile))
 
     def test_save_creates_meta(self):
-        fixtures.turing1950.save_to_disc(self.dest_bibfile, self.dest_metafile)
+        fixtures.turing1950.save(self.dest_bibfile, self.dest_metafile)
         self.assertTrue(os.path.exists(self.dest_metafile))
 
     def test_save_right_bib(self):
-        fixtures.turing1950.save_to_disc(self.dest_bibfile, self.dest_metafile)
+        fixtures.turing1950.save(self.dest_bibfile, self.dest_metafile)
         with open(self.dest_bibfile, 'r') as f:
             written = yaml.load(f)
             ok = yaml.load(BIB)
             self.assertEqual(written, ok)
 
     def test_save_right_meta(self):
-        fixtures.turing1950.save_to_disc(self.dest_bibfile, self.dest_metafile)
+        fixtures.turing1950.save(self.dest_bibfile, self.dest_metafile)
         with open(self.dest_metafile, 'r') as f:
             written = yaml.load(f)
             ok = yaml.load(META)
diff --git a/tests/test_repo.py b/tests/test_repo.py
index 33c1953..0b8098a 100644
--- a/tests/test_repo.py
+++ b/tests/test_repo.py
@@ -32,7 +32,7 @@ class TestRepo(unittest.TestCase):
     def setUp(self):
         self.tmpdir = tempfile.mkdtemp()
         self.repo = Repository(configs.Config(papers_dir = self.tmpdir), load = False)
-        self.repo.init_dirs()
+        self.repo.save()
         self.repo.add_paper(fixtures.turing1950)
 
     def tearDown(self):
diff --git a/tests/test_usecase.py b/tests/test_usecase.py
index 0c091df..79590a1 100644
--- a/tests/test_usecase.py
+++ b/tests/test_usecase.py
@@ -102,7 +102,7 @@ class TestAdd(unittest.TestCase):
 
         papers_cmd.execute('papers init -p /not_default'.split())
         papers_cmd.execute('papers add -b /data/pagerank.bib -d /data/pagerank.pdf'.split())
-        self.assertEqual(set(fake_os.listdir('/not_default/doc')), {'Page99.pdf'})
+        self.assertEqual(set(fake_os.listdir('/not_default/doc')), {'pagerank.pdf'})
 
 
 class TestList(unittest.TestCase):
@@ -122,7 +122,7 @@ class TestUsecase(unittest.TestCase):
 
     def test_first(self):
 
-        correct = ['Initializing papers in /paper_first/.\n',
+        correct = ['Initializing papers in /paper_first.\n',
                    'Added: Page99\n',
                    '0: [Page99] L. Page et al. "The PageRank Citation Ranking Bringing Order to the Web"  (1999) \n',
                    '',

From e4f7017fdbe1df26285f6d87cf5380f49841dca0 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 14:04:05 +0100
Subject: [PATCH 13/20] commands updated to new config, new repo

---
 papers/commands/add_cmd.py         | 10 +++++-----
 papers/commands/add_library_cmd.py |  8 ++++----
 papers/commands/attach_cmd.py      | 10 +++++-----
 papers/commands/edit_cmd.py        |  9 +++++----
 papers/commands/export_cmd.py      |  8 ++++----
 papers/commands/helpers.py         |  2 +-
 papers/commands/import_cmd.py      | 11 +++++------
 papers/commands/init_cmd.py        | 29 ++++++++++++++---------------
 papers/commands/list_cmd.py        |  7 ++++---
 papers/commands/open_cmd.py        |  8 ++++----
 papers/commands/remove_cmd.py      | 12 ++++++------
 papers/commands/tag_cmd.py         | 13 +++++++------
 papers/commands/update_cmd.py      |  4 ++--
 papers/commands/websearch_cmd.py   |  4 ++--
 14 files changed, 68 insertions(+), 67 deletions(-)

diff --git a/papers/commands/add_cmd.py b/papers/commands/add_cmd.py
index 8a97537..838e090 100644
--- a/papers/commands/add_cmd.py
+++ b/papers/commands/add_cmd.py
@@ -1,11 +1,11 @@
 from .. import repo
 from .. import files
 from ..paper import Paper, NoDocumentFile, get_bibentry_from_string
-from .. import configs
+from ..configs import config
 from .helpers import add_paper_with_docfile, extract_doc_path_from_bibdata
 
 
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('add', help='add a paper to the repository')
     parser.add_argument('-b', '--bibfile',
                         help='bibtex, bibtexml or bibyaml file', default=None)
@@ -19,14 +19,14 @@ def parser(subparsers, config):
     return parser
 
 
-def command(config, ui, bibfile, docfile, tags, copy):
+def command(ui, bibfile, docfile, tags, copy):
     """
     :param bibfile: bibtex file (in .bib, .bibml or .yaml format.
     :param docfile: path (no url yet) to a pdf or ps file
     """
     if copy is None:
-        copy = config.get(configs.MAIN_SECTION, 'import-copy')
-    rp = repo.Repository.from_directory(config)
+        copy = config().import_copy
+    rp = repo.Repository(config())
     if bibfile is None:
         cont = True
         bibstr = ''
diff --git a/papers/commands/add_library_cmd.py b/papers/commands/add_library_cmd.py
index 3161d50..7fbdd9e 100644
--- a/papers/commands/add_library_cmd.py
+++ b/papers/commands/add_library_cmd.py
@@ -1,18 +1,18 @@
 from .. import repo
 from ..paper import Paper
+from ..configs import config
 
-
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('add_library',
             help='add a set of papers to the repository')
     parser.add_argument('bibfile', help='bibtex, bibtexml or bibyaml file')
     return parser
 
 
-def command(config, ui, bibfile):
+def command(ui, bibfile):
     """
     :param bibtex       bibtex file (in .bib, .bibml or .yaml format.
     """
-    rp = repo.Repository.from_directory(config)
+    rp = repo.Repository.from_directory(config())
     for p in Paper.many_from_bib(bibfile):
         rp.add_paper(p)
diff --git a/papers/commands/attach_cmd.py b/papers/commands/attach_cmd.py
index b0d8eb3..3b51945 100644
--- a/papers/commands/attach_cmd.py
+++ b/papers/commands/attach_cmd.py
@@ -1,10 +1,10 @@
 from .. import repo
-from .. import configs
+from ..configs import config
 from .helpers import (add_references_argument, parse_reference,
                       add_docfile_to_paper)
 
 
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('attach',
             help='attach a document to an existing paper')
     parser.add_argument('-c', '--copy', action='store_true', default=None,
@@ -16,14 +16,14 @@ def parser(subparsers, config):
     return parser
 
 
-def command(config, ui, copy, reference, document):
+def command(ui, copy, reference, document):
     """
     :param bibfile: bibtex file (in .bib, .bibml or .yaml format.
     :param docfile: path (no url yet) to a pdf or ps file
     """
     if copy is None:
-        copy = config.get(configs.MAIN_SECTION, 'import-copy')
-    rp = repo.Repository.from_directory(config)
+        copy = config().import_copy
+    rp = repo.Repository(config())
     key = parse_reference(ui, rp, reference)
     paper = rp.get_paper(key)
     try:
diff --git a/papers/commands/edit_cmd.py b/papers/commands/edit_cmd.py
index dd630ef..2d379ca 100644
--- a/papers/commands/edit_cmd.py
+++ b/papers/commands/edit_cmd.py
@@ -2,9 +2,10 @@ from ..files import editor_input
 from .. import repo
 from ..paper import get_bibentry_from_string, get_safe_metadata_from_content
 from .helpers import add_references_argument, parse_reference
+from ..configs import config
 
 
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('edit',
             help='open the paper bibliographic file in an editor')
     parser.add_argument('-m', '--meta', action='store_true', default=False,
@@ -13,8 +14,8 @@ def parser(subparsers, config):
     return parser
 
 
-def command(config, ui, meta, reference):
-    rp = repo.Repository.from_directory(config)
+def command(ui, meta, reference):
+    rp = repo.Repository.from_directory(config())
     key = parse_reference(ui, rp, reference)
     paper = rp.get_paper(key)
     to_edit = 'bib'
@@ -25,7 +26,7 @@ def command(config, ui, meta, reference):
         content = f.read()
     while True:
         # Get new content from user
-        content = editor_input(config, content)
+        content = editor_input(config().edit_cmd, content)
         new_key = key
         bib = None
         metadata = None
diff --git a/papers/commands/export_cmd.py b/papers/commands/export_cmd.py
index 338026a..82e1f04 100644
--- a/papers/commands/export_cmd.py
+++ b/papers/commands/export_cmd.py
@@ -5,9 +5,9 @@ from pybtex.database import BibliographyData
 from .. import repo
 from .. import files
 from .helpers import parse_references, add_references_argument
+from ..configs import config
 
-
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('export',
             help='export bibliography')
     parser.add_argument('-f', '--bib-format', default='bibtex',
@@ -16,11 +16,11 @@ def parser(subparsers, config):
     return parser
 
 
-def command(config, ui, bib_format, references):
+def command(ui, bib_format, references):
     """
     :param bib_format       (in 'bibtex', 'yaml')
     """
-    rp = repo.Repository.from_directory(config)
+    rp = repo.Repository.from_directory(config())
     papers = [rp.get_paper(c)
               for c in parse_references(ui, rp, references)]
     if len(papers) == 0:
diff --git a/papers/commands/helpers.py b/papers/commands/helpers.py
index 33988b4..c9df8a7 100644
--- a/papers/commands/helpers.py
+++ b/papers/commands/helpers.py
@@ -42,7 +42,7 @@ def extract_doc_path_from_bibdata(paper, ui):
 
 def parse_reference(ui, rp, ref):
     try:
-        return rp.citekey_from_ref(ref)
+        return rp.ref2citekey(ref)
     except InvalidReference:
         ui.error("no paper with reference: %s."
                     % color.dye(ref, color.citekey))
diff --git a/papers/commands/import_cmd.py b/papers/commands/import_cmd.py
index bb2a3cd..b883310 100644
--- a/papers/commands/import_cmd.py
+++ b/papers/commands/import_cmd.py
@@ -1,10 +1,9 @@
 from .. import repo
 from ..paper import Paper
 from .helpers import add_paper_with_docfile, extract_doc_path_from_bibdata
-from .. import configs
+from ..configs import config
 
-
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('import',
             help='import paper(s) to the repository')
     parser.add_argument('bibpath',
@@ -16,13 +15,13 @@ def parser(subparsers, config):
     return parser
 
 
-def command(config, ui, bibpath, copy):
+def command(ui, bibpath, copy):
     """
     :param bibpath: path (no url yet) to a bibliography file
     """
     if copy is None:
-        copy = config.get(configs.MAIN_SECTION, 'import-copy')
-    rp = repo.Repository.from_directory(config)
+        copy = config().import_copy
+    rp = repo.Repository.from_directory(config())
     # Extract papers from bib
     papers = Paper.many_from_path(bibpath, fatal=False)
     for p in papers:
diff --git a/papers/commands/init_cmd.py b/papers/commands/init_cmd.py
index 948a66b..d80f649 100644
--- a/papers/commands/init_cmd.py
+++ b/papers/commands/init_cmd.py
@@ -3,10 +3,11 @@
 import os
 
 from ..repo import Repository
-from .. import configs
+from ..configs import config
 from .. import color
+from .. import files
 
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('init',
                                    help="initialize the papers directory")
     parser.add_argument('-p', '--path', default=None,
@@ -17,21 +18,19 @@ def parser(subparsers, config):
     return parser
 
 
-def command(config, ui, path, doc_dir):
+def command(ui, path, doc_dir):
     """Create a .papers directory"""
-    if path is None:
-        papersdir = config.get('papers', 'papers-directory')
-    else:
-        papersdir = os.path.join(os.getcwd(), path)
-        configs.add_and_write_option('papers', 'papers-directory', papersdir)
-    if os.path.exists(papersdir):
-        if len(os.listdir(papersdir)) > 0:
+    if path is not None:
+        config().papers_dir = files.clean_path(os.getcwd(), path)
+    ppd = config().papers_dir
+    if os.path.exists(ppd) and len(os.listdir(ppd)) > 0:
             ui.error('directory {} is not empty.'.format(
-                                 color.dye(papersdir, color.filepath)))
+                                 color.dye(ppd, color.filepath)))
             ui.exit()
 
     ui.print_('Initializing papers in {}.'.format(
-              color.dye(papersdir, color.filepath)))
-    repo = Repository()
-    repo.init(papersdir)  # Creates directories
-    repo.save()  # Saves empty repository description
\ No newline at end of file
+              color.dye(ppd, color.filepath)))
+
+    repo = Repository(config(), load = False)
+    repo.save()
+    config().save()
diff --git a/papers/commands/list_cmd.py b/papers/commands/list_cmd.py
index bfa8edd..88f4f4b 100644
--- a/papers/commands/list_cmd.py
+++ b/papers/commands/list_cmd.py
@@ -2,9 +2,10 @@ from .. import pretty
 from .. import repo
 from .. import color
 from . import helpers
+from ..configs import config
 
 
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('list', help="list papers")
     parser.add_argument('-k', '--citekeys-only', action='store_true',
             default=False, dest='citekeys',
@@ -14,8 +15,8 @@ def parser(subparsers, config):
     return parser
 
 
-def command(config, ui, citekeys, query):
-    rp = repo.Repository.from_directory(config)
+def command(ui, citekeys, query):
+    rp = repo.Repository(config())
     papers = [(n, p) for n, p in enumerate(rp.all_papers())
               if test_paper(query, p)]
     ui.print_('\n'.join(helpers.paper_oneliner(p, n = n, citekey_only = citekeys) for n, p in papers))
diff --git a/papers/commands/open_cmd.py b/papers/commands/open_cmd.py
index ad1c832..26623d2 100644
--- a/papers/commands/open_cmd.py
+++ b/papers/commands/open_cmd.py
@@ -2,12 +2,12 @@ import subprocess
 
 from .. import repo
 from ..paper import NoDocumentFile
-from .. import configs
+from ..configs import config
 from .. import color
 from .helpers import add_references_argument, parse_reference
 
 
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('open',
             help='open the paper in a pdf viewer')
     parser.add_argument('-w', '--with', dest='with_command', default=None,
@@ -16,12 +16,12 @@ def parser(subparsers, config):
     return parser
 
 
-def command(config, ui, with_command, reference):
+def command(ui, with_command, reference):
     rp = repo.Repository.from_directory(config)
     key = parse_reference(ui, rp, reference)
     paper = rp.get_paper(key)
     if with_command is None:
-        with_command = config.get(configs.MAIN_SECTION, 'open-cmd')
+        with_command = config().open_cmd
     try:
         filepath = paper.get_document_path()
         subprocess.Popen([with_command, filepath])
diff --git a/papers/commands/remove_cmd.py b/papers/commands/remove_cmd.py
index 00147f6..8c38483 100644
--- a/papers/commands/remove_cmd.py
+++ b/papers/commands/remove_cmd.py
@@ -1,12 +1,12 @@
 from .. import repo
 from .. import color
-from .. import configs
+from ..configs import config
 from .helpers import add_references_argument, parse_references
 
 from ..events import RemoveEvent
 
 
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('remove', help='removes a paper')
     parser.add_argument('-f', '--force', action='store_true', default=None,
     help="does not prompt for confirmation.")
@@ -14,8 +14,8 @@ def parser(subparsers, config):
     return parser
 
 
-def command(config, ui, force, references):
-    rp = repo.Repository.from_directory(config)
+def command(ui, force, references):
+    rp = repo.Repository(config())
     citekeys = parse_references(ui, rp, references)
     if force is None:
         are_you_sure = ("Are you sure you want to delete paper(s) [%s]"
@@ -24,7 +24,7 @@ def command(config, ui, force, references):
         sure = ui.input_yn(question=are_you_sure, default='n')
     if force or sure:
         for c in citekeys:
-            rmevent = RemoveEvent(config, ui, c)
+            rmevent = RemoveEvent(ui, c)
             rmevent.send()
 
-            rp.remove(c)
+            rp.remove_paper(c)
diff --git a/papers/commands/tag_cmd.py b/papers/commands/tag_cmd.py
index d76deb4..0228ee3 100644
--- a/papers/commands/tag_cmd.py
+++ b/papers/commands/tag_cmd.py
@@ -19,8 +19,9 @@ The different use cases are :
 
 from ..repo import Repository, InvalidReference
 from . import helpers
+from ..configs import config
 
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('tag', help="add, remove and show tags")
     parser.add_argument('referenceOrTag', nargs='?', default = None,
                         help='reference to the paper (citekey or number), or '
@@ -43,12 +44,12 @@ def _parse_tags(s):
     for m in re.finditer(r'[+-]', s):
         if m.start() == last:
             if last != 0:
-                raise ValueError, 'could not match tag expression'
+                raise ValueError('could not match tag expression')
         else:
             tags.append(s[last:(m.start())])
         last = m.start()
     if last == len(s):
-        raise ValueError, 'could not match tag expression'
+        raise ValueError('could not match tag expression')
     else:
         tags.append(s[last:])
     return tags
@@ -63,16 +64,16 @@ def _tag_groups(tags):
             minus_tags.append(tag[1:])
     return set(plus_tags), set(minus_tags)
 
-def command(config, ui, referenceOrTag, tags):
+def command(ui, referenceOrTag, tags):
     """Add, remove and show tags"""
-    rp = Repository.from_directory(config)
+    rp = Repository(config())
 
     if referenceOrTag is None:
         for tag in rp.get_tags():
             ui.print_(tag)
     else:
         try:
-            citekey = rp.citekey_from_ref(referenceOrTag)
+            citekey = rp.ref2citekey(referenceOrTag)
             p = rp.get_paper(citekey)
             if tags is None:
                 ui.print_(' '.join(p.tags))
diff --git a/papers/commands/update_cmd.py b/papers/commands/update_cmd.py
index 6c521b9..041d955 100644
--- a/papers/commands/update_cmd.py
+++ b/papers/commands/update_cmd.py
@@ -1,12 +1,12 @@
 from .. import repo
 from .. import color
 
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('update', help='update the repository to the lastest format')
     return parser
 
 
-def command(config, ui):
+def command(ui):
     rp = repo.Repository.from_directory(config)
     msg = ("You should backup the paper directory {} before continuing."
            "Continue ?").format(color.dye(rp.papersdir, color.filepath))
diff --git a/papers/commands/websearch_cmd.py b/papers/commands/websearch_cmd.py
index be05e4e..1f61670 100644
--- a/papers/commands/websearch_cmd.py
+++ b/papers/commands/websearch_cmd.py
@@ -2,7 +2,7 @@ import webbrowser
 import urllib
 
 
-def parser(subparsers, config):
+def parser(subparsers):
     parser = subparsers.add_parser('websearch',
                                    help="launch a search on Google Scholar")
     parser.add_argument("search_string", nargs = '*',
@@ -10,7 +10,7 @@ def parser(subparsers, config):
     return parser
 
 
-def command(config, ui, search_string):
+def command(ui, search_string):
     print search_string
     url = ("https://scholar.google.fr/scholar?q=%s&lr="
            % (urllib.quote_plus(' '.join(search_string))))

From f528aa8a67062a80dbc6fe5445a9652df90dbb81 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 14:05:32 +0100
Subject: [PATCH 14/20] updated core. almost all tests are passing

---
 papers/events.py                |  3 +--
 papers/papers_cmd.py            | 11 +++++++----
 papers/plugin.py                | 16 ++++++++--------
 papers/plugs/texnote/texnote.py | 24 +++++++++++-------------
 papers/ui.py                    |  5 +----
 5 files changed, 28 insertions(+), 31 deletions(-)

diff --git a/papers/events.py b/papers/events.py
index efd94d6..29771a6 100644
--- a/papers/events.py
+++ b/papers/events.py
@@ -28,7 +28,6 @@ class Event(object):
 
 
 class RemoveEvent(Event):
-    def __init__(self, config, ui, citekey):
-        self.config = config
+    def __init__(self, ui, citekey):
         self.ui = ui
         self.citekey = citekey
diff --git a/papers/papers_cmd.py b/papers/papers_cmd.py
index eb59bff..dfa93fa 100644
--- a/papers/papers_cmd.py
+++ b/papers/papers_cmd.py
@@ -28,11 +28,15 @@ cmds = collections.OrderedDict([
 
 
 def execute(raw_args = sys.argv):
-    config = configs.read_config()
+    # loading config
+    config = configs.Config()
+    config.load()
+    config.as_global()
+
     ui = UI(config)
 
     # Extend with plugin commands
-    plugin.load_plugins(config, ui, configs.get_plugins(config))
+    plugin.load_plugins(ui, config.plugins.split())
     for p in plugin.get_plugins().values():
         cmds.update(collections.OrderedDict([(p.name, p)]))
 
@@ -40,10 +44,9 @@ def execute(raw_args = sys.argv):
     subparsers = parser.add_subparsers(title="valid commands", dest="command")
 
     for cmd_mod in cmds.values():
-        subparser = cmd_mod.parser(subparsers, config)  # why do we return the subparser ?
+        subparser = cmd_mod.parser(subparsers)  # why do we return the subparser ?
 
     args = parser.parse_args(raw_args[1:])
-    args.config = config
 
     args.ui = ui
     cmd = args.command
diff --git a/papers/plugin.py b/papers/plugin.py
index 7794e3f..f5479a6 100644
--- a/papers/plugin.py
+++ b/papers/plugin.py
@@ -1,4 +1,5 @@
 import importlib
+from .configs import config
 
 PLUGIN_NAMESPACE = 'plugs'
 
@@ -11,20 +12,19 @@ class PapersPlugin(object):
     functionality by defining a subclass of PapersPlugin and overriding
     the abstract methods defined here.
     """
-    def __init__(self, config, ui):
+    def __init__(self, ui):
         """Perform one-time plugin setup.
         """
         self.name = self.__module__.split('.')[-1]
-        self.config = config
         self.ui = ui
 
-    #config and ui and given again to stay consistent with the core papers cmd.
+    #ui and given again to stay consistent with the core papers cmd.
     #two options:
     #- create specific cases in script papers/papers
-    #- do not store self.config and self.ui and use them if needed when command is called
+    #- do not store self.ui and use them if needed when command is called
     #this may end up with a lot of function with config/ui in argument
     #or just keep it that way...
-    def parser(self, subparsers, config):
+    def parser(self, subparsers):
         """ Should retrun the parser with plugins specific command.
         This is a basic example
         """
@@ -32,7 +32,7 @@ class PapersPlugin(object):
         parser.add_argument('strings', nargs='*', help='the strings')
         return parser
 
-    def command(self, config, ui, strings):
+    def command(self, ui, strings):
         """This function will be called with argument defined in the parser above
         This is a basic example
         """
@@ -47,7 +47,7 @@ class PapersPlugin(object):
             raise RuntimeError("{} instance not created".format(cls.__name__))
 
 
-def load_plugins(config, ui, names):
+def load_plugins(ui, names):
     """Imports the modules for a sequence of plugin names. Each name
     must be the name of a Python module under the "PLUGIN_NAMESPACE" namespace
     package in sys.path; the module indicated should contain the
@@ -69,7 +69,7 @@ def load_plugins(config, ui, names):
                     if isinstance(obj, type) and issubclass(obj, PapersPlugin) \
                             and obj != PapersPlugin:
                         _classes.append(obj)
-                        _instances[obj] = obj(config, ui)
+                        _instances[obj] = obj(ui)
 
         except:
             ui.warning('error loading plugin {}'.format(name))
diff --git a/papers/plugs/texnote/texnote.py b/papers/plugs/texnote/texnote.py
index d550156..bd33326 100644
--- a/papers/plugs/texnote/texnote.py
+++ b/papers/plugs/texnote/texnote.py
@@ -3,7 +3,7 @@ import shutil
 import subprocess
 
 from ... import repo
-from ... import configs
+from ...configs import config
 from ... import files
 from ...plugin import PapersPlugin
 from ...commands.helpers import add_references_argument, parse_reference
@@ -18,7 +18,7 @@ TEXNOTE_DIR = 'texnote'
 
 class TexnotePlugin(PapersPlugin):
 
-    def parser(self, subparsers, config):
+    def parser(self, subparsers):
         parser = subparsers.add_parser(self.name, help="edit advance note in latex")
         sub = parser.add_subparsers(title="valid texnote commands", dest="texcmd")
         p = sub.add_parser("remove", help="remove a reference")
@@ -29,11 +29,11 @@ class TexnotePlugin(PapersPlugin):
         parser.add_argument('-v', '--view', action='store_true', help='open the paper in a pdf viewer', default=None)
         return parser
 
-    def command(self, config, ui, texcmd, reference, view):
+    def command(self, ui, texcmd, reference, view):
         if view is not None:
             subprocess.Popen(['papers', 'open', reference])
         if texcmd == 'edit':
-            open_texnote(config, ui, reference)
+            open_texnote(ui, reference)
 
     def toto(self):
         print "toto"
@@ -47,7 +47,8 @@ class TexnotePlugin(PapersPlugin):
 def remove(rmevent):
     texplug = TexnotePlugin.get_instance()
     texplug.toto()
-    rp = repo.Repository.from_directory(rmevent.config)
+    # HACK : transfer repo via RemoveEvent, do not recreate one
+    rp = repo.Repository(config())
     paper = rp.get_paper(parse_reference(rmevent.ui, rp, rmevent.citekey))
     if 'texnote' in paper.metadata:
         try:
@@ -59,8 +60,9 @@ def remove(rmevent):
         files.save_meta(paper.metadata, metapath)
 
 
-def open_texnote(config, ui, ref):
-    rp = repo.Repository.from_directory(config)
+def open_texnote(ui, ref):
+    # HACK : transfer repo via arguments, do not recreate one
+    rp = repo.Repository(config())
     paper = rp.get_paper(parse_reference(ui, rp, ref))
 
     #ugly to recode like for the doc field
@@ -83,12 +85,8 @@ def open_texnote(config, ui, ref):
     autofill_texnote(texnote_path, paper.bibentry)
 
     #open the file using the config editor
-    if config.has_option(TEXNOTE_SECTION, 'edit-cmd'):
-        #os.system(config.get(TEXNOTE_SECTION, 'edit-cmd') + ' ' + texnote_path + " &")
-        subprocess.Popen([config.get(TEXNOTE_SECTION, 'edit-cmd'), texnote_path])
-    else:
-        #os.system(config.get(configs.MAIN_SECTION, 'edit-cmd') + ' ' + texnote_path + " &")
-        subprocess.Popen([config.get(configs.MAIN_SECTION, 'edit-cmd'), texnote_path])
+    edit_cmd = config(TEXTNOTE_SECTION).get('edit_cmd', config().edit_cmd)
+    subprocess.Popen([edit_cmd, texnote_path])
 
 
 ##### ugly replace by proper #####
diff --git a/papers/ui.py b/papers/ui.py
index 50cd382..fa6c1a4 100644
--- a/papers/ui.py
+++ b/papers/ui.py
@@ -3,8 +3,6 @@ import sys
 from .beets_ui import _encoding, input_
 
 from . import color
-from . import configs
-
 
 class UI:
     """UI class. Stores configuration parameters and system information.
@@ -12,8 +10,7 @@ class UI:
 
     def __init__(self, config):
         self.encoding = _encoding(config)
-        color_enable = configs.get_boolean(config.get('papers', 'color'))
-        color.setup(color_enable)
+        color.setup(config.color)
 
     def print_(self, *strings):
         """Like print, but rather than raising an error when a character

From 9614593192452be3e6413573ecd5de782d5930ac Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 15:57:28 +0100
Subject: [PATCH 15/20] version system

---
 papers/__init__.py | 1 +
 papers/configs.py  | 1 +
 setup.py           | 2 +-
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/papers/__init__.py b/papers/__init__.py
index e69de29..fe95ae2 100644
--- a/papers/__init__.py
+++ b/papers/__init__.py
@@ -0,0 +1 @@
+__version__ = 3
\ No newline at end of file
diff --git a/papers/configs.py b/papers/configs.py
index 8f1aba8..776e5f5 100644
--- a/papers/configs.py
+++ b/papers/configs.py
@@ -18,6 +18,7 @@ DFT_CONFIG = {'papers_dir'  : os.path.expanduser('~/.papers'),
               'import_copy' : 'yes',
               'import_move' : 'no',
               'color'       : 'yes',
+              'version'     : 3,
 
               'open_cmd'    : 'open',
               'edit_cmd'    : DFT_EDIT_CMD,
diff --git a/setup.py b/setup.py
index e0c3119..2512683 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
 from setuptools import setup, find_packages
 
 setup(name='papers',
-      version='1',
+      version='3',
       author='Fabien Benureau, Olivier Mangin, Jonathan Grizou',
       author_email='fabien.benureau+inria@gmail.com',
       url='',

From 3c0f575b92aa3ea1b78ef7e5785f3f78abc65cfa Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 15:58:12 +0100
Subject: [PATCH 16/20] backtracked on changes. repo is passing all tests

---
 papers/repo.py        | 27 ++++++++++++++++++++++++---
 tests/test_repo.py    |  8 ++++----
 tests/test_usecase.py | 15 ++++++++++-----
 3 files changed, 38 insertions(+), 12 deletions(-)

diff --git a/papers/repo.py b/papers/repo.py
index 0113468..8f67424 100644
--- a/papers/repo.py
+++ b/papers/repo.py
@@ -136,9 +136,23 @@ class Repository(object):
             and new_citekey in self):
             raise CiteKeyCollision('citekey {} already in use'.format(
                                    new_citekey))
+
         self.remove_paper(paper.citekey, remove_doc = False)
+        old_citekey = paper.citekey
         paper.citekey = new_citekey
         self.add_paper(paper, overwrite = overwrite)
+        self._move_doc(old_citekey, paper)
+
+    def _move_doc(self, old_citekey, paper):
+        """Fragile. Make more robust"""
+        try:
+            old_docfile = self.find_document(old_citekey)
+            ext = os.path.splitext(old_docfile)[1]
+            new_docfile = os.path.join(self.doc_dir, paper.citekey + ext)
+            shutil.move(old_docfile, new_docfile)
+            paper.set_external_document(new_docfile)
+        except NoDocumentFile:
+            pass
 
     def _bibfile(self, citekey):
         return os.path.join(self.bib_dir, citekey + '.bibyaml')
@@ -176,14 +190,21 @@ class Repository(object):
             if not citekey + _base27(n) in self.citekeys:
                 return citekey + _base27(n)
 
+    def find_document(self, citekey):
+        found = glob.glob('{}/{}.*'.format(self.doc_dir, citekey))
+        if found:
+            return found[0]
+        else:
+            raise NoDocumentFile
+
     def import_document(self, citekey, doc_file):
         if citekey not in self.citekeys:
-            raise ValueError("Unknown citekey {}.".format(citekey))
+            raise(ValueError, "Unknown citekey: %s." % citekey)
         else:
             if not os.path.isfile(doc_file):
                 raise ValueError("No file {} found.".format(doc_file))
-            new_doc_file = os.path.join(self.doc_dir,
-                                        os.path.basename(doc_file))
+            ext = os.path.splitext(doc_file)[1]
+            new_doc_file = os.path.join(self.doc_dir, citekey + ext)
             shutil.copy(doc_file, new_doc_file)
 
     def get_tags(self):
diff --git a/tests/test_repo.py b/tests/test_repo.py
index 0b8098a..58ef258 100644
--- a/tests/test_repo.py
+++ b/tests/test_repo.py
@@ -101,7 +101,7 @@ class TestUpdatePaper(TestRepo):
                                   os.path.join(os.path.dirname(__file__),
                                                'data/pagerank.pdf'))
         self.repo.rename_paper(self.repo.get_paper('Turing1950'), 'Doe2003')
-        # self.assertFalse(os.path.exists(os.path.join(
-        #     self.repo.doc_dir, 'Turing1950.pdf')))
-        # self.assertTrue(os.path.exists(os.path.join(
-        #     self.repo.doc_dir, 'Doe2013.pdf')))
+        self.assertFalse(os.path.exists(os.path.join(
+            self.repo.doc_dir, 'Turing1950.pdf')))
+        self.assertTrue(os.path.exists(os.path.join(
+            self.repo.doc_dir, 'Doe2003.pdf')))
diff --git a/tests/test_usecase.py b/tests/test_usecase.py
index 79590a1..16d008d 100644
--- a/tests/test_usecase.py
+++ b/tests/test_usecase.py
@@ -1,10 +1,11 @@
-import sys, os
+import sys, os, shutil, glob
 import unittest
 import pkgutil
 
 import testenv
 import fake_filesystem
 import fake_filesystem_shutil
+import fake_filesystem_glob
 
 from papers import papers_cmd
 from papers import color
@@ -12,23 +13,27 @@ from papers.p3 import io
 
 real_os = os
 real_open = open
+real_shutil = shutil
+real_glob = glob
 
-fake_os, fake_open, fake_shutil = None, None, None
+fake_os, fake_open, fake_shutil, fake_glob = None, None, None, None
 
 def _create_fake_fs():
-    global fake_os, fake_open, fake_shutil
+    global fake_os, fake_open, fake_shutil, fake_glob
 
     fake_fs = fake_filesystem.FakeFilesystem()
     fake_os = fake_filesystem.FakeOsModule(fake_fs)
     fake_open = fake_filesystem.FakeFileOpen(fake_fs)
     fake_shutil = fake_filesystem_shutil.FakeShutilModule(fake_fs)
+    fake_glob = fake_filesystem_glob.FakeGlobModule(fake_fs)
 
     fake_fs.CreateDirectory(fake_os.path.expanduser('~'))
     __builtins__['open'] = fake_open
     __builtins__['file'] = fake_open
 
-    sys.modules['os'] = fake_os
+    sys.modules['os']     = fake_os
     sys.modules['shutil'] = fake_shutil
+    sys.modules['glob']   = fake_glob
 
     import papers
     for importer, modname, ispkg in pkgutil.walk_packages(
@@ -102,7 +107,7 @@ class TestAdd(unittest.TestCase):
 
         papers_cmd.execute('papers init -p /not_default'.split())
         papers_cmd.execute('papers add -b /data/pagerank.bib -d /data/pagerank.pdf'.split())
-        self.assertEqual(set(fake_os.listdir('/not_default/doc')), {'pagerank.pdf'})
+        self.assertEqual(set(fake_os.listdir('/not_default/doc')), {'Page99.pdf'})
 
 
 class TestList(unittest.TestCase):

From 4e9ce17c71c78b4b1bda6581d9704dadf72b3424 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 15:58:35 +0100
Subject: [PATCH 17/20] adapted update to version 3

---
 papers/commands/update_cmd.py | 58 +++++++++++++++++++++++++++++------
 1 file changed, 48 insertions(+), 10 deletions(-)

diff --git a/papers/commands/update_cmd.py b/papers/commands/update_cmd.py
index 041d955..bcf65ee 100644
--- a/papers/commands/update_cmd.py
+++ b/papers/commands/update_cmd.py
@@ -1,5 +1,8 @@
+import sys
+
 from .. import repo
 from .. import color
+from ..configs import config
 
 def parser(subparsers):
     parser = subparsers.add_parser('update', help='update the repository to the lastest format')
@@ -7,13 +10,48 @@ def parser(subparsers):
 
 
 def command(ui):
-    rp = repo.Repository.from_directory(config)
-    msg = ("You should backup the paper directory {} before continuing."
-           "Continue ?").format(color.dye(rp.papersdir, color.filepath))
-    sure = ui.input_yn(question=msg, default='n')
-    if sure:
-        for p in rp.all_papers():
-            tags = set(p.metadata['tags'])
-            tags = tags.union(p.metadata['labels'])
-            p.metadata.pop('labels', [])
-            rp.save_paper(p)
+    rp = repo.Repository(config())
+    code_version = papers.__version__
+    repo_version = config().version
+
+    if repo_version == code_version:
+        ui._print('You papers repository is up-to-date.')
+        sys.exit(0)
+    elif repo_version <= code_version:
+        ui._print('Your repository was generated with an newer version of papers.\n'
+                  'You should not use papers until you install the newest version.')
+        sys.exit(0)
+    else:
+        msg = ("You should backup the paper directory {} before continuing."
+               "Continue ?").format(color.dye(rp.papersdir, color.filepath))
+        sure = ui.input_yn(question=msg, default='n')
+        if not sure:
+            sys.exit(0)
+
+        if repo_version == 1:
+            for p in rp.all_papers():
+                tags = set(p.metadata['tags'])
+                tags = tags.union(p.metadata['labels'])
+                p.metadata.pop('labels', [])
+                rp.save_paper(p)
+            repo_version = 2
+        if repo_version == 2:
+            # update config
+            cfg_update = [('papers-directory', 'papers_dir'),
+                          ('open-cmd', 'open_cmd'),
+                          ('edit-cmd', 'edit_cmd'),
+                          ('import-copy', 'import_copy'),
+                          ('import-move', 'import_move'),
+                         ]
+            for old, new in cfg_update:
+                try:
+                    config().__setattr__('papers', new, config()._cfg.get('papers', old))
+                    config()._cfg.remove_option('papers', old)
+                except Exception:
+                    pass
+            config().save()
+            repo_version = 3
+
+
+        config().version = repo_version
+        config().save()
\ No newline at end of file

From dc73c987c8960bf4c7b846c7cebdefbcb5cdd67a Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 16:42:37 +0100
Subject: [PATCH 18/20] update command for config v2 to v3

---
 papers/commands/update_cmd.py | 23 +++++++++++++----------
 papers/configs.py             |  6 +++++-
 tests/test_config.py          |  2 ++
 3 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/papers/commands/update_cmd.py b/papers/commands/update_cmd.py
index bcf65ee..6c6eb91 100644
--- a/papers/commands/update_cmd.py
+++ b/papers/commands/update_cmd.py
@@ -3,6 +3,7 @@ import sys
 from .. import repo
 from .. import color
 from ..configs import config
+from ..__init__ import __version__
 
 def parser(subparsers):
     parser = subparsers.add_parser('update', help='update the repository to the lastest format')
@@ -10,33 +11,36 @@ def parser(subparsers):
 
 
 def command(ui):
-    rp = repo.Repository(config())
-    code_version = papers.__version__
-    repo_version = config().version
+    code_version = __version__
+    repo_version = int(config().version)
 
     if repo_version == code_version:
-        ui._print('You papers repository is up-to-date.')
+        ui.print_('You papers repository is up-to-date.')
         sys.exit(0)
-    elif repo_version <= code_version:
-        ui._print('Your repository was generated with an newer version of papers.\n'
+    elif repo_version > code_version:
+        ui.print_('Your repository was generated with an newer version of papers.\n'
                   'You should not use papers until you install the newest version.')
         sys.exit(0)
     else:
         msg = ("You should backup the paper directory {} before continuing."
-               "Continue ?").format(color.dye(rp.papersdir, color.filepath))
+               "Continue ?").format(color.dye(config().papers_dir, color.filepath))
         sure = ui.input_yn(question=msg, default='n')
         if not sure:
             sys.exit(0)
 
         if repo_version == 1:
+            rp = repo.Repository(config())
             for p in rp.all_papers():
                 tags = set(p.metadata['tags'])
                 tags = tags.union(p.metadata['labels'])
                 p.metadata.pop('labels', [])
                 rp.save_paper(p)
             repo_version = 2
+
+
         if repo_version == 2:
             # update config
+            print 'bla'
             cfg_update = [('papers-directory', 'papers_dir'),
                           ('open-cmd', 'open_cmd'),
                           ('edit-cmd', 'edit_cmd'),
@@ -45,13 +49,12 @@ def command(ui):
                          ]
             for old, new in cfg_update:
                 try:
-                    config().__setattr__('papers', new, config()._cfg.get('papers', old))
+                    config()._cfg.set('papers', new, config()._cfg.get('papers', old))
                     config()._cfg.remove_option('papers', old)
                 except Exception:
                     pass
             config().save()
             repo_version = 3
 
-
         config().version = repo_version
-        config().save()
\ No newline at end of file
+        config().save()
diff --git a/papers/configs.py b/papers/configs.py
index 776e5f5..5d66e19 100644
--- a/papers/configs.py
+++ b/papers/configs.py
@@ -40,9 +40,13 @@ def config(section = MAIN_SECTION):
 class Config(object):
 
     def __init__(self, **kwargs):
-        object.__setattr__(self, '_cfg', configparser.SafeConfigParser(DFT_CONFIG))
         object.__setattr__(self, '_section', MAIN_SECTION) # active section
+        object.__setattr__(self, '_cfg', configparser.SafeConfigParser())
+
         self._cfg.add_section(self._section)
+        for name, value in DFT_CONFIG.items():
+            self._cfg.set(self._section, name, str(value))
+
         for name, value in kwargs.items():
             self.__setattr__(name, value)
 
diff --git a/tests/test_config.py b/tests/test_config.py
index e9705b9..1f7faa6 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -25,9 +25,11 @@ class TestConfig(unittest.TestCase):
         a.as_global()
         config().color = 'no'
         self.assertEqual(config().color, False)
+        self.assertEqual(config('papers').color, False)
         # booleans type for new variables are memorized, but not saved.
         config().bla = True
         self.assertEqual(config().bla, True)
+        self.assertEqual(config('papers').bla, True)
 
         with self.assertRaises(configparser.NoOptionError):
             config()._cfg.get(configs.MAIN_SECTION, '_section')

From fc47328cbfa0aca13f7288ec3ff55f6e66b85f38 Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 16:45:34 +0100
Subject: [PATCH 19/20] FIX in config spotted by Jonathan

---
 papers/configs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/papers/configs.py b/papers/configs.py
index 5d66e19..5a9fbdf 100644
--- a/papers/configs.py
+++ b/papers/configs.py
@@ -32,7 +32,7 @@ BOOLEANS = {'import_copy', 'import_move', 'color'}
 # from configs import config
 _config = None
 def config(section = MAIN_SECTION):
-    if config is None:
+    if _config is None:
         raise ValueError, 'not config instanciated yet'
     _config._section = section
     return _config

From 1be61baf21d7516cc246e283b865057f63468c9f Mon Sep 17 00:00:00 2001
From: Fabien Benureau <fabien.benureau+git@gmail.com>
Date: Tue, 2 Jul 2013 17:21:59 +0100
Subject: [PATCH 20/20] added testenv import to test current code

---
 tests/test_events.py | 1 +
 tests/test_paper.py  | 1 +
 2 files changed, 2 insertions(+)

diff --git a/tests/test_events.py b/tests/test_events.py
index 0b509a3..705925f 100644
--- a/tests/test_events.py
+++ b/tests/test_events.py
@@ -1,5 +1,6 @@
 from unittest import TestCase
 
+import testenv
 from papers.events import Event
 
 
diff --git a/tests/test_paper.py b/tests/test_paper.py
index 3842b23..03fa010 100644
--- a/tests/test_paper.py
+++ b/tests/test_paper.py
@@ -7,6 +7,7 @@ import shutil
 import yaml
 from pybtex.database import Person
 
+import testenv
 import fixtures
 from papers.paper import Paper