Merge branch 'master' into feat/new_config

Add StringIO and BytesIO to FakeIO.
Fixes bytes/string problem in update()

pubs/commands/tag_cmd.py

@@ -19,33 +19,29 @@ The different use cases are :
 
 import re
 
-from ..repo import Repository, InvalidReference
+from ..repo import Repository
-
 from ..uis import get_ui
 from .. import pretty
 from .. import color
 
+
 def parser(subparsers):
     parser = subparsers.add_parser('tag', help="add, remove and show tags")
-    parser.add_argument('citekeyOrTag', nargs='?', default = None,
+    parser.add_argument('citekeyOrTag', nargs='?', default=None,
                         help='citekey or tag.')
-    parser.add_argument('tags', nargs='*', default = None,
+    parser.add_argument('tags', nargs='?', default=None,
                         help='If the previous argument was a citekey, then '
-                             'then a list of tags separated by a +.')
+                             'a list of tags separated by a +.')
     # TODO find a way to display clear help for multiple command semantics,
     #      indistinguisable for argparse. (fabien, 201306)
     return parser
 
-def _parse_tags(list_tags):
-    """Transform 'math-ai network -search' in ['+math', '-ai', '+network', '-search']"""
-    tags = []
-    for s in list_tags:
-        tags += _parse_tag_seq(s)
-    return tags
 
 def _parse_tag_seq(s):
     """Transform 'math-ai' in ['+math', '-ai']"""
     tags = []
+    if s[0] == ':':
+        s = '-' + s[1:]
     if s[0] not in ['+', '-']:
         s = '+' + s
     last = 0
@@ -62,6 +58,7 @@ def _parse_tag_seq(s):
         tags.append(s[last:])
     return tags
 
+
 def _tag_groups(tags):
     plus_tags, minus_tags = [], []
     for tag in tags:
@@ -79,7 +76,6 @@ def command(conf, args):
     citekeyOrTag = args.citekeyOrTag
     tags = args.tags
 
-
     rp = Repository(conf)
 
     if citekeyOrTag is None:
@@ -87,20 +83,21 @@ def command(conf, args):
     else:
         if rp.databroker.exists(citekeyOrTag):
             p = rp.pull_paper(citekeyOrTag)
-            if tags == []:
+            if tags is None:
                 ui.message(color.dye_out(' '.join(sorted(p.tags)), 'tag'))
             else:
-                add_tags, remove_tags = _tag_groups(_parse_tags(tags))
+                add_tags, remove_tags = _tag_groups(_parse_tag_seq(tags))
                 for tag in add_tags:
                     p.add_tag(tag)
                 for tag in remove_tags:
                     p.remove_tag(tag)
                 rp.push_paper(p, overwrite=True)
+        elif tags is not None:
+            ui.error(ui.error('no entry found for citekey {}.'.format(citekeyOrTag)))
+            ui.exit()
         else:
             # case where we want to find papers with specific tags
-            all_tags = [citekeyOrTag]
+            included, excluded = _tag_groups(_parse_tag_seq(citekeyOrTag))
-            all_tags += tags
-            included, excluded = _tag_groups(_parse_tags(all_tags))
             papers_list = []
             for p in rp.all_papers():
                 if (p.tags.issuperset(included) and
@@ -108,4 +105,4 @@ def command(conf, args):
                     papers_list.append(p)
 
             ui.message('\n'.join(pretty.paper_oneliner(p)
-                                   for p in papers_list))
+                                 for p in papers_list))

pubs/uis.py

@@ -27,11 +27,13 @@ def _get_encoding(conf):
         return enc or 'utf-8'
     return conf.get('terminal-encoding', enc or 'utf-8')
 
+
 def get_ui():
     if _ui is None:
         return PrintUI() # no editor support. (#FIXME?)
     return _ui
 
+
 def init_ui(conf):
     global _ui
     _ui = InputUI(conf)

pubs/update.py

@@ -1,6 +1,6 @@
 import shutil
-import StringIO
 
+import io
 from . import config
 from . import uis
 from . import color
@@ -81,7 +81,7 @@ def update(conf, code_version, repo_version, path=None):
         # comparing potential changes
         with open(path, 'r') as f:
             old_conf_text = f.read()
-        new_conf_text = StringIO.StringIO()
+        new_conf_text = io.BytesIO()
         default_conf.write(outfile=new_conf_text)
 
         if new_conf_text.getvalue() != old_conf_text:

readme.md

@@ -52,6 +52,17 @@ This ensure that your reference file is always up-to-date; you can cite a paper
 
 and then add `\cite{Loeb_2012}` in your manuscript. After running the bash script, the citation will correctly appear in your compiled pdf.
 
+Customization
+-------------
+Pubs is designed to interact well with your command line tool chain. You can add custom commands to pubs by defining aliases in your config file. Here are a few examples.
+
+    [alias]
+    print = open -w lp
+    count = !pubs list -k | wc -l
+
+For more advanced functionalities, pubs also support plugins. Actually *alias* is itself a plugin!
+
+
 Requirements
 ------------
 - python >= 2.7 or >= 3.3

tests/fake_env.py

@@ -103,6 +103,8 @@ class FakeIO(object):
         fakefs_stringio = self.fake_open.Call(*args, **kwargs)
         return UnicodeStringIOWrapper(fakefs_stringio)
 
+    BytesIO = real_io.BytesIO
+    StringIO = real_io.StringIO
 
 def create_fake_fs(module_list):
 

tests/test_tag.py

@@ -2,20 +2,25 @@
 import unittest
 
 import dotdot
-from pubs.commands.tag_cmd import _parse_tags, _tag_groups
+from pubs.commands.tag_cmd import _parse_tag_seq, _tag_groups
 
 class TestTag(unittest.TestCase):
 
-    def test_tag_parsing(self):
+    def test_parse_tags(self):
+        self.assertEqual(['+abc', '+def9'], _parse_tag_seq('abc+def9'))
+        self.assertEqual(['+abc', '-def9'], _parse_tag_seq('abc-def9'))
+        self.assertEqual(['-abc', '-def9'], _parse_tag_seq('-abc-def9'))
+        self.assertEqual(['+abc', '-def9'], _parse_tag_seq('+abc-def9'))
 
-        self.assertEqual(['+abc', '+def9'], _parse_tags([ 'abc+def9']))
+    def test_tag_groups(self):
-        self.assertEqual(['+abc', '-def9'], _parse_tags([ 'abc-def9']))
+        self.assertEqual(({'math', 'romance'}, {'war'}),
-        self.assertEqual(['-abc', '-def9'], _parse_tags(['-abc-def9']))
+                         _tag_groups(_parse_tag_seq('-war+math+romance')))
-        self.assertEqual(['+abc', '-def9'], _parse_tags(['+abc-def9']))
+        self.assertEqual(({'math', 'romance'}, {'war'}),
-
+                         _tag_groups(_parse_tag_seq(':war+math+romance')))
-        self.assertEqual(({'math', 'romance'}, {'war'}), _tag_groups(_parse_tags(['-war+math+romance'])))
+        self.assertEqual(({'math', 'romance'}, {'war'}),
-        self.assertEqual(({'math', 'romance'}, {'war'}), _tag_groups(_parse_tags(['+math+romance-war'])))
+                         _tag_groups(_parse_tag_seq('+math+romance-war')))
-        self.assertEqual(({'math', 'romance'}, {'war'}), _tag_groups(_parse_tags(['math+romance-war'])))
+        self.assertEqual(({'math', 'romance'}, {'war'}),
+                         _tag_groups(_parse_tag_seq('math+romance-war')))
 
 
 if __name__ == '__main__':

tests/test_usecase.py

@@ -7,8 +7,7 @@ import os
 import dotdot
 import fake_env
 
-from pubs import pubs_cmd
+from pubs import pubs_cmd, update, color, content, filebroker, uis, p3, endecoder
-from pubs import color, content, filebroker, uis, p3, endecoder
 from pubs.config import conf
 import configobj
 
@@ -58,7 +57,7 @@ class CommandTestCase(unittest.TestCase):
     maxDiff = 1000000
 
     def setUp(self):
-        self.fs = fake_env.create_fake_fs([content, filebroker, conf, init_cmd, import_cmd, configobj])
+        self.fs = fake_env.create_fake_fs([content, filebroker, conf, init_cmd, import_cmd, configobj, update])
         self.default_pubs_dir = self.fs['os'].path.expanduser('~/.pubs')
 
     def execute_cmds(self, cmds, capture_output=CAPTURE_OUTPUT):
@@ -118,7 +117,7 @@ class DataCommandTestCase(CommandTestCase):
     """
 
     def setUp(self):
-        CommandTestCase.setUp(self)
+        super(DataCommandTestCase, self).setUp()
         fake_env.copy_dir(self.fs, os.path.join(os.path.dirname(__file__), 'data'), 'data')
 
 
@@ -251,6 +250,76 @@ class TestList(DataCommandTestCase):
         self.assertEqual(0 + 1, len(outs[-1].split('\n')))
 
 
+class TestTag(DataCommandTestCase):
+
+    def setUp(self):
+        super(TestTag, self).setUp()
+        init = ['pubs init',
+                'pubs add data/pagerank.bib',
+                'pubs add -k Turing1950 data/turing1950.bib',
+               ]
+        self.execute_cmds(init)
+
+    def test_add_tag(self):
+        cmds = ['pubs tag Page99 search',
+                'pubs tag Turing1950 ai',
+                'pubs list',
+                ]
+        correct = ['',
+                   '',
+                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) | search\n' +
+                   '[Turing1950] Turing, Alan M "Computing machinery and intelligence" Mind (1950) | ai\n',
+                   ]
+        out = self.execute_cmds(cmds)
+        self.assertEqual(out, correct)
+
+    def test_add_tags(self):
+        """Adds several tags at once.
+        Also checks that tags printed in alphabetic order.
+        """
+        cmds = ['pubs tag Page99 search+network',
+                'pubs list',
+                ]
+        correct = ['',
+                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) | network,search\n' +
+                   '[Turing1950] Turing, Alan M "Computing machinery and intelligence" Mind (1950) \n',
+                   ]
+        out = self.execute_cmds(cmds)
+        self.assertEqual(out, correct)
+
+    def test_remove_tag(self):
+        cmds = ['pubs tag Page99 search+network',
+                'pubs tag Page99 :network',
+                'pubs list',
+                ]
+        correct = ['',
+                   '',
+                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) | search\n' +
+                   '[Turing1950] Turing, Alan M "Computing machinery and intelligence" Mind (1950) \n',
+                   ]
+        out = self.execute_cmds(cmds)
+        self.assertEqual(out, correct)
+
+    def test_add_remove_tag(self):
+        cmds = ['pubs tag Page99 a',
+                'pubs tag Page99 b-a',
+                'pubs list',
+                ]
+        correct = ['',
+                   '',
+                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) | b\n' +
+                   '[Turing1950] Turing, Alan M "Computing machinery and intelligence" Mind (1950) \n',
+                   ]
+        out = self.execute_cmds(cmds)
+        self.assertEqual(out, correct)
+
+    def test_wrong_citekey(self):
+        cmds = ['pubs tag Page999 a',
+                ]
+        with self.assertRaises(SystemExit):
+            self.execute_cmds(cmds)
+
+
 class TestUsecase(DataCommandTestCase):
 
     def test_first(self):