From d06c8da29b11a660697f72affb9dbc4de6565462 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Wed, 8 Apr 2020 09:23:57 +0900
Subject: [PATCH 01/45] fix #219: doc add -L

---
 pubs/commands/add_cmd.py | 2 +-
 pubs/commands/doc_cmd.py | 2 +-
 readme.md                | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pubs/commands/add_cmd.py b/pubs/commands/add_cmd.py
index 1aa2ec7..a2af9cd 100644
--- a/pubs/commands/add_cmd.py
+++ b/pubs/commands/add_cmd.py
@@ -156,6 +156,6 @@ def command(conf, args):
         if doc_add == 'move':
             ui.message('{} was moved to the pubs repository.'.format(docfile))
         elif doc_add == 'copy':
-                ui.message('{} was copied to the pubs repository.'.format(docfile))
+            ui.message('{} was copied to the pubs repository.'.format(docfile))
 
     rp.close()
diff --git a/pubs/commands/doc_cmd.py b/pubs/commands/doc_cmd.py
index 277c006..d1a44df 100644
--- a/pubs/commands/doc_cmd.py
+++ b/pubs/commands/doc_cmd.py
@@ -34,7 +34,7 @@ def parser(subparsers, conf):
                             ).completer = CiteKeyCompletion(conf)
     add_exclusives = add_parser.add_mutually_exclusive_group()
     add_exclusives.add_argument(
-        '-L', '--link', action='store_false', dest='link', default=False,
+        '-L', '--link', action='store_true', dest='link', default=False,
         help='do not copy document files, just create a link')
     add_exclusives.add_argument(
         '-M', '--move', action='store_true', dest='move', default=False,
diff --git a/readme.md b/readme.md
index d596f18..33fdadd 100644
--- a/readme.md
+++ b/readme.md
@@ -111,7 +111,7 @@ Pubs comes with a git plugin that automatically commits your changes. You only n
 You can then also conveniently interact with the git repository by using `pubs git <regular git commands>`.
 
 
-## Multiple pubs Repository
+## Multiple pubs Repositories
 
 You may want to have different pubs repositories, for different projects. To create an alternate repository:
   ```

From 246a00671e78b9d4353cea9b2eb0c0d07e3682c5 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Wed, 8 Apr 2020 11:06:22 +0900
Subject: [PATCH 02/45] fix #220: errno error.

---
 pubs/uis.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pubs/uis.py b/pubs/uis.py
index 46258ce..fc96aed 100644
--- a/pubs/uis.py
+++ b/pubs/uis.py
@@ -3,6 +3,7 @@ from __future__ import print_function, unicode_literals
 import os
 import sys
 import shlex
+import errno
 import locale
 import codecs
 import tempfile
@@ -237,7 +238,7 @@ class InputUI(PrintUI):
         try:
             subprocess.call(cmd)
         except OSError as e:
-            if e.errno == os.errno.ENOENT:
+            if e.errno == errno.ENOENT:
                 self.error(("Error while calling editor '{}'. The editor may "
                             "not be present. You can change the text editor "
                             "that pubs uses by setting the $EDITOR environment "

From 2f6e0d4e85b81077fb7e484baec43f63982bed27 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Sun, 3 May 2020 16:03:21 -0700
Subject: [PATCH 03/45] Fix #223: update python versions in travis.

- remove python version unsupported by pyfakefs from testing in Travis,
- add python 3.8.
---
 .travis.yml | 34 ++++++++--------------------------
 readme.md   |  2 +-
 2 files changed, 9 insertions(+), 27 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index cbd0ad2..9f84fc9 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,11 +3,6 @@ matrix:
   include:
 
     # Full tests (with online API)
-    - os: linux
-      language: python
-      python: 2.7
-      env:
-        - TO_TEST=TEST_FULL
     - os: linux
       language: python
       python: 3.7
@@ -15,16 +10,6 @@ matrix:
       sudo: true
       env:
         - TO_TEST=TEST_FULL
-    - os: osx
-      language: generic
-      python: 2.7
-      env:
-        - TO_TEST=TEST_FULL
-      # before_install:
-      #   - python2 --version
-      #   - pip2 install -U virtualenv
-      #   - virtualenv env -p python2
-      #   - source env/bin/activate
     - os: osx
       language: generic
       python: ">=3.6"
@@ -38,28 +23,25 @@ matrix:
     # Mock tests (with mock API)
     - os: linux
       language: python
-      python: 3.3
-      env:
-        - TO_TEST=TEST_MOCK
-    - os: linux
-      language: python
-      python: 3.4
+      python: 3.5
       env:
         - TO_TEST=TEST_MOCK
     - os: linux
       language: python
-      python: 3.5
+      python: 3.6
       env:
         - TO_TEST=TEST_MOCK
     - os: linux
       language: python
-      python: 3.6
+      dist: xenial
+      python: 3.7
+      sudo: true
       env:
         - TO_TEST=TEST_MOCK
     - os: linux
       language: python
       dist: xenial
-      python: 3.7
+      python: 3.8
       sudo: true
       env:
         - TO_TEST=TEST_MOCK
@@ -76,7 +58,7 @@ matrix:
       language: python
       dist: xenial
       sudo: true
-      python: 3.7
+      python: 3.8
       env:
         - TO_TEST=INSTALL
       if: type = cron
@@ -94,7 +76,7 @@ matrix:
       if: type = cron
 
   allow_failures:
-    - python: 3.3
+    - python: 2.7
 
 # command to run tests
 script:
diff --git a/readme.md b/readme.md
index 33fdadd..aa4c691 100644
--- a/readme.md
+++ b/readme.md
@@ -15,7 +15,7 @@ correct bugs, but have no short-term plans to add major features to it. Pubs doe
 is supposed to do: help us do science, so now we are mostly doing that.
 
 **Notice:** pubs is relatively stable but comes with no warranty; do keep backups of your data.
-**Notice:** pubs currently works with Python 2.7, but support will be dropped as soon as maintaining it becomes tedious.
+**Notice:** pubs currently works with Python 2.7, but support is being dropped (tests are not run anymore).
 
 ## Installation
 

From 44b0c5b4c9533dafa30db72752d424cf4681ffb6 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Wed, 8 Apr 2020 11:12:02 +0900
Subject: [PATCH 04/45] colors in edit command dialogs

---
 pubs/commands/edit_cmd.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/pubs/commands/edit_cmd.py b/pubs/commands/edit_cmd.py
index 431d19c..d4ad366 100644
--- a/pubs/commands/edit_cmd.py
+++ b/pubs/commands/edit_cmd.py
@@ -2,6 +2,7 @@ from __future__ import unicode_literals
 
 from ..paper import Paper
 from .. import repo
+from .. import color
 
 from ..uis import get_ui
 from ..endecoder import EnDecoder
@@ -55,17 +56,18 @@ def command(conf, args):
                 new_paper = Paper(paper.citekey, paper.bibdata,
                                   metadata=content)
                 rp.push_paper(new_paper, overwrite=True, event=False)
-                ui.info(('The metadata of paper `{}`  was successfully '
-                         'edited.'.format(citekey)))
+                ui.info(("The metadata of paper '{}' was successfully "
+                         "edited.".format(color.dye_out(citekey, 'citekey'))))
             else:
                 new_paper = Paper.from_bibentry(content,
                                                 metadata=paper.metadata)
                 if rp.rename_paper(new_paper, old_citekey=paper.citekey):
-                    ui.info(('Paper `{}` was successfully edited and renamed '
-                             'as `{}`.'.format(citekey, new_paper.citekey)))
+                    ui.info(("Paper '{}' was successfully edited and renamed "
+                             "as '{}'.".format(color.dye_out(citekey, 'citekey'),
+                                               color.dye_out(new_paper.citekey, 'citekey'))))
                 else:
-                    ui.info(('Paper `{}` was successfully edited.'.format(
-                        citekey)))
+                    ui.info(("Paper '{}' was successfully edited.".format(
+                             color.dye_out(citekey, 'citekey'))))
             break
 
         except coder.BibDecodingError:
@@ -84,7 +86,7 @@ def command(conf, args):
                 break
             elif choice == 'overwrite':
                 paper = rp.push_paper(paper, overwrite=True)
-                ui.info(('Paper `{}` was overwritten.'.format(citekey)))
+                ui.info(('Paper `{}` was overwritten.'.format(color.dye_out(citekey, 'citekey'))))
                 break
             # else edit again
         # Also handle malformed bibtex and metadata

From 7776b65de21ab339a7717dbdbd12c11864837bfe Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Mon, 4 May 2020 22:05:11 +0900
Subject: [PATCH 05/45] number of displayed authors configurable

fix #212
---
 pubs/commands/list_cmd.py |  2 +-
 pubs/config/spec.py       |  3 +++
 pubs/pretty.py            | 27 +++++++++++++++++++--------
 tests/test_pretty.py      | 10 ++++++++++
 tests/test_usecase.py     |  3 ++-
 5 files changed, 35 insertions(+), 10 deletions(-)

diff --git a/pubs/commands/list_cmd.py b/pubs/commands/list_cmd.py
index b615e54..a382544 100644
--- a/pubs/commands/list_cmd.py
+++ b/pubs/commands/list_cmd.py
@@ -54,7 +54,7 @@ def command(conf, args):
         papers = sorted(papers, key=date_added)
     if len(papers) > 0:
         ui.message('\n'.join(
-            pretty.paper_oneliner(p, citekey_only=args.citekeys)
+            pretty.paper_oneliner(p, citekey_only=args.citekeys, n_authors=conf['main']['n_authors'])
             for p in papers))
 
     rp.close()
diff --git a/pubs/config/spec.py b/pubs/config/spec.py
index 4c50f4c..a31d1b4 100644
--- a/pubs/config/spec.py
+++ b/pubs/config/spec.py
@@ -27,6 +27,9 @@ edit_cmd = string(default='')
 # Which default extension to use when creating a note file.
 note_extension = string(default='txt')
 
+# How many authors to display in
+n_authors = integer(default=3)
+
 # If true debug mode is on which means exceptions are not catched and
 # the full python stack is printed.
 debug = boolean(default=False)
diff --git a/pubs/pretty.py b/pubs/pretty.py
index 0c951e6..369c3e4 100644
--- a/pubs/pretty.py
+++ b/pubs/pretty.py
@@ -23,19 +23,30 @@ def person_repr(p):
         ' '.join(p.lineage(abbr=True))] if s)
 
 
-def short_authors(bibdata):
+def short_authors(bibdata, n_authors=3):
+    """
+    :param n_authors:  number of authors to display completely. Additional authors will be
+                       represented by 'et al.'.
+    """
     try:
         authors = [p for p in bibdata['author']]
-        if len(authors) < 3:
-            return ' and '.join(authors)
+        if 0 < n_authors < len(authors):
+            authors_str = '{} et al.'.format(authors[0])
         else:
-            return authors[0] + (' et al.' if len(authors) > 1 else '')
+            authors_str = ' and '.join(authors)
+
+        # if n_authors > 0:
+        #     authors = authors[:n_authors]
+        # authors_str = ' and '.join(authors)
+        # if 0 < n_authors < len(bibdata['author']):
+        #     authors_str += ' et al.'
+        return authors_str
     except KeyError:  # When no author is defined
         return ''
 
 
-def bib_oneliner(bibdata):
-    authors = short_authors(bibdata)
+def bib_oneliner(bibdata, n_authors=3):
+    authors = short_authors(bibdata, n_authors=n_authors)
     journal = ''
     if 'journal' in bibdata:
         journal = ' ' + bibdata['journal']
@@ -60,11 +71,11 @@ def bib_desc(bib_data):
     return s
 
 
-def paper_oneliner(p, citekey_only=False):
+def paper_oneliner(p, citekey_only=False, n_authors=3):
     if citekey_only:
         return p.citekey
     else:
-        bibdesc = bib_oneliner(p.get_unicode_bibdata())
+        bibdesc = bib_oneliner(p.get_unicode_bibdata(), n_authors=n_authors)
         doc_str = ''
         if p.docpath is not None:
             doc_extension = os.path.splitext(p.docpath)[1]
diff --git a/tests/test_pretty.py b/tests/test_pretty.py
index 0c09211..cc9f4f4 100644
--- a/tests/test_pretty.py
+++ b/tests/test_pretty.py
@@ -28,5 +28,15 @@ class TestPretty(unittest.TestCase):
         line = 'Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web."'
         self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'])), line)
 
+    def test_oneliner_n_authors(self):
+        decoder = endecoder.EnDecoder()
+        bibdata = decoder.decode_bibdata(bibtex_raw0)
+        for n_authors in [1, 2, 3]:
+            line = 'Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999)'
+            self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'], n_authors=n_authors)), line)
+        for n_authors in [-1, 0, 4, 5, 10]:
+            line = 'Page, Lawrence and Brin, Sergey and Motwani, Rajeev and Winograd, Terry "The PageRank Citation Ranking: Bringing Order to the Web." (1999)'
+            self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'], n_authors=n_authors)), line)
+
 if __name__ == '__main__':
     unittest.main()
diff --git a/tests/test_usecase.py b/tests/test_usecase.py
index 348366e..5004919 100644
--- a/tests/test_usecase.py
+++ b/tests/test_usecase.py
@@ -1079,7 +1079,8 @@ class TestUsecase(DataCommandTestCase):
                 'pubs add -d data/no-ext data/pagerank.bib',
                 'pubs list',
                ]
-        self.assertEqual(correct, self.execute_cmds(cmds, capture_output=True))
+        actual = self.execute_cmds(cmds, capture_output=True)
+        self.assertEqual(correct, actual)
 
     @mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
     def test_readme(self, reqget):

From ad85fe9df87a512465bcd500896ff972433c3356 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Tue, 5 May 2020 00:50:37 +0900
Subject: [PATCH 06/45] add usecase test for n_authors

---
 tests/test_usecase.py | 41 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 34 insertions(+), 7 deletions(-)

diff --git a/tests/test_usecase.py b/tests/test_usecase.py
index 5004919..faa4bbe 100644
--- a/tests/test_usecase.py
+++ b/tests/test_usecase.py
@@ -25,8 +25,8 @@ import fixtures
 
 
 # makes the tests very noisy
-PRINT_OUTPUT   = False
-CAPTURE_OUTPUT = True
+PRINT_OUTPUT   = True
+CAPTURE_OUTPUT = False
 
 
 class FakeSystemExit(Exception):
@@ -161,11 +161,19 @@ class CommandTestCase(fake_env.TestFakeFs):
     def tearDown(self):
         pass
 
+    def update_config(self, config_update, path=None):
+        """Allow to set the config parameters. Must have done a `pubs init` beforehand."""
+        if path is None:
+            path = self.default_conf_path
+        cfg = conf.load_conf(path=path)
+        for section, section_update in config_update.items():
+            cfg[section].update(section_update)
+        conf.save_conf(cfg, path=path)
+
+
 
 class DataCommandTestCase(CommandTestCase):
-    """Abstract TestCase intializing the fake filesystem and
-    copying fake data.
-    """
+    """Abstract TestCase intializing the fake filesystem and copying fake data."""
 
     def setUp(self, nsec_stat=True):
         super(DataCommandTestCase, self).setUp(nsec_stat=nsec_stat)
@@ -182,8 +190,7 @@ class DataCommandTestCase(CommandTestCase):
 
 
 class URLContentTestCase(DataCommandTestCase):
-    """Mocks access to online files by using files in data directory.
-    """
+    """Mocks access to online files by using files in data directory."""
 
     def setUp(self):
         super(URLContentTestCase, self).setUp()
@@ -209,6 +216,8 @@ class URLContentTestCase(DataCommandTestCase):
         content.url_exists = self._original_url_exist
 
 
+
+
 # Actual tests
 
 class TestAlone(CommandTestCase):
@@ -1146,5 +1155,23 @@ class TestCache(DataCommandTestCase):
         self.assertEqual(line1, out[4])
 
 
+class TestConfigChange(DataCommandTestCase):
+
+    def test_n_authors_default(self):
+        line_al   = '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
+        line_full = '[Page99] Page, Lawrence and Brin, Sergey and Motwani, Rajeev and Winograd, Terry "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
+
+        self.execute_cmds(['pubs init', 'pubs add data/pagerank.bib'])
+
+        for n_authors in [1, 2, 3]:
+            self.update_config({'main': {'n_authors': n_authors}})
+            self.execute_cmds([('pubs list', None, line_al, None)])
+
+        for n_authors in [-1, 0, 4, 5, 10]:
+            self.update_config({'main': {'n_authors': n_authors}})
+            self.execute_cmds([('pubs list', None, line_full, None)])
+
+
+
 if __name__ == '__main__':
     unittest.main(verbosity=2)

From 1b8728f4f6197a59ed0277031a62dc10332a744f Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Tue, 5 May 2020 01:00:26 +0900
Subject: [PATCH 07/45] minor: fix output flags in usecase

---
 tests/test_usecase.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_usecase.py b/tests/test_usecase.py
index faa4bbe..b0044fa 100644
--- a/tests/test_usecase.py
+++ b/tests/test_usecase.py
@@ -25,8 +25,8 @@ import fixtures
 
 
 # makes the tests very noisy
-PRINT_OUTPUT   = True
-CAPTURE_OUTPUT = False
+PRINT_OUTPUT   = False
+CAPTURE_OUTPUT = True
 
 
 class FakeSystemExit(Exception):

From a30e75a5e6c0ab45fe580ae576e6f9bb56101ca8 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Tue, 5 May 2020 01:11:07 +0900
Subject: [PATCH 08/45] support all one_liner + fix deprecation warnings in
 utils

---
 pubs/commands/add_cmd.py |  2 +-
 pubs/commands/tag_cmd.py |  2 +-
 pubs/config/spec.py      |  3 ++-
 pubs/utils.py            | 12 ++++++------
 4 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/pubs/commands/add_cmd.py b/pubs/commands/add_cmd.py
index a2af9cd..74e5a46 100644
--- a/pubs/commands/add_cmd.py
+++ b/pubs/commands/add_cmd.py
@@ -147,7 +147,7 @@ def command(conf, args):
         doc_add = conf['main']['doc_add']
 
     rp.push_paper(p)
-    ui.message('added to pubs:\n{}'.format(pretty.paper_oneliner(p)))
+    ui.message('added to pubs:\n{}'.format(pretty.paper_oneliner(p, n_authors=conf['main']['n_authors'])))
     if docfile is not None:
         rp.push_doc(p.citekey, docfile, copy=(doc_add in ('copy', 'move')))
         if doc_add == 'move' and content.content_type(docfile) != 'url':
diff --git a/pubs/commands/tag_cmd.py b/pubs/commands/tag_cmd.py
index da656b4..90d6d9c 100644
--- a/pubs/commands/tag_cmd.py
+++ b/pubs/commands/tag_cmd.py
@@ -117,7 +117,7 @@ def command(conf, args):
                     len(p.tags.intersection(excluded)) == 0):
                     papers_list.append(p)
 
-            ui.message('\n'.join(pretty.paper_oneliner(p)
+            ui.message('\n'.join(pretty.paper_oneliner(p, n_authors=conf['main']['n_authors'])
                                  for p in papers_list))
 
         rp.close()
diff --git a/pubs/config/spec.py b/pubs/config/spec.py
index a31d1b4..4aba92b 100644
--- a/pubs/config/spec.py
+++ b/pubs/config/spec.py
@@ -27,7 +27,8 @@ edit_cmd = string(default='')
 # Which default extension to use when creating a note file.
 note_extension = string(default='txt')
 
-# How many authors to display in
+# How many authors to display when displaying a citation. If there are more
+# authors, only the first author is diplayed followed by 'et al.'.
 n_authors = integer(default=3)
 
 # If true debug mode is on which means exceptions are not catched and
diff --git a/pubs/utils.py b/pubs/utils.py
index eda7480..a7aceb1 100644
--- a/pubs/utils.py
+++ b/pubs/utils.py
@@ -33,7 +33,7 @@ def resolve_citekey(repo, citekey, ui=None, exit_on_fail=True):
                      "citekeys:".format(citekey))
             for c in citekeys:
                 p = repo.pull_paper(c)
-                ui.message('    {}'.format(pretty.paper_oneliner(p)))
+                ui.message('    {}'.format(pretty.paper_oneliner(p, n_authors=conf['main']['n_authors'])))
             if exit_on_fail:
                 ui.exit()
     return citekey
@@ -73,11 +73,11 @@ def standardize_doi(doi):
     """
 
     doi_regexes = (
-        '(10\.\d{4,9}/[-._;()/:A-z0-9\>\<]+)',
-        '(10.1002/[^\s]+)',
-        '(10\.\d{4}/\d+-\d+X?(\d+)\d+<[\d\w]+:[\d\w]*>\d+.\d+.\w+;\d)',
-        '(10\.1021/\w\w\d+\+)',
-        '(10\.1207/[\w\d]+\&\d+_\d+)')
+        r'(10\.\d{4,9}/[-._;()/:A-z0-9\>\<]+)',
+        r'(10.1002/[^\s]+)',
+        r'(10\.\d{4}/\d+-\d+X?(\d+)\d+<[\d\w]+:[\d\w]*>\d+.\d+.\w+;\d)',
+        r'(10\.1021/\w\w\d+\+)',
+        r'(10\.1207/[\w\d]+\&\d+_\d+)')
     doi_pattern = re.compile('|'.join(doi_regexes))
 
     match = doi_pattern.search(doi)

From 7bd475378c3c63300a25b8ed7fd231f7307e8209 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Tue, 5 May 2020 17:39:12 +0900
Subject: [PATCH 09/45] support for non-standard bibtex types, fix #210 #218

---
 pubs/endecoder.py                              | 16 ++++++++--------
 .../{collection.bib => three_articles.bib}     |  0
 .../non_standard_collection.bib                |  9 +++++++++
 .../non_standard_software.bib                  |  7 +++++++
 tests/fake_env.py                              |  4 ++--
 tests/test_usecase.py                          | 18 +++++++++++++++++-
 6 files changed, 43 insertions(+), 11 deletions(-)
 rename tests/data/{collection.bib => three_articles.bib} (100%)
 create mode 100644 tests/data_non_standard/non_standard_collection.bib
 create mode 100644 tests/data_non_standard/non_standard_software.bib

diff --git a/pubs/endecoder.py b/pubs/endecoder.py
index 346af3a..e289ddc 100644
--- a/pubs/endecoder.py
+++ b/pubs/endecoder.py
@@ -119,18 +119,18 @@ class EnDecoder(object):
                 keyword for keyword in entry['keyword'])
         return entry
 
-    def decode_bibdata(self, bibdata):
+    def decode_bibdata(self, bibstr):
         """Decodes bibdata from string.
 
         If the decoding fails, returns a BibDecodingError.
         """
-        if len(bibdata) == 0:
+        if len(bibstr) == 0:
             error_msg = 'parsing error: the provided string has length zero.'
-            raise self.BibDecodingError(error_msg, bibdata)
+            raise self.BibDecodingError(error_msg, bibstr)
         try:
             entries = bp.bparser.BibTexParser(
-                bibdata, common_strings=True, customization=customizations,
-                homogenize_fields=True).get_entry_dict()
+                bibstr, common_strings=True, customization=customizations,
+                homogenize_fields=True, ignore_nonstandard_types=False).get_entry_dict()
             # Remove id from bibtexparser attribute which is stored as citekey
             for e in entries:
                 entries[e].pop(BP_ID_KEY)
@@ -147,13 +147,13 @@ class EnDecoder(object):
                 return entries
             else:
                 raise self.BibDecodingError(('no valid entry found in the provided data: '
-                                            ' {}').format(bibdata), bibdata)
+                                            ' {}').format(bibstr), bibstr)
         except (pyparsing.ParseException, pyparsing.ParseSyntaxException) as e:
             error_msg = self._format_parsing_error(e)
-            raise self.BibDecodingError(error_msg, bibdata)
+            raise self.BibDecodingError(error_msg, bibstr)
         except bibtexparser.bibdatabase.UndefinedString as e:
             error_msg = 'parsing error: undefined string in provided data: {}'.format(e)
-            raise self.BibDecodingError(error_msg, bibdata)
+            raise self.BibDecodingError(error_msg, bibstr)
 
     @classmethod
     def _format_parsing_error(cls, e):
diff --git a/tests/data/collection.bib b/tests/data/three_articles.bib
similarity index 100%
rename from tests/data/collection.bib
rename to tests/data/three_articles.bib
diff --git a/tests/data_non_standard/non_standard_collection.bib b/tests/data_non_standard/non_standard_collection.bib
new file mode 100644
index 0000000..0dbd1f2
--- /dev/null
+++ b/tests/data_non_standard/non_standard_collection.bib
@@ -0,0 +1,9 @@
+@collection{Geometric_phases,
+ title = {Geometric phases in physics},
+ editor = {Shapere, Alfred and Wilczek, Frank},
+ year = {1989},
+ series = {Advanced Series in Mathematical Physics},
+ volume = {5},
+ publisher = {World Scientific},
+ isbn = {9789971506216}
+}
diff --git a/tests/data_non_standard/non_standard_software.bib b/tests/data_non_standard/non_standard_software.bib
new file mode 100644
index 0000000..87ecd7b
--- /dev/null
+++ b/tests/data_non_standard/non_standard_software.bib
@@ -0,0 +1,7 @@
+@software{hadoop,
+  author = {{Apache Software Foundation}},
+  title = {Hadoop},
+  url = {https://hadoop.apache.org},
+  version = {0.20.2},
+  date = {2010-02-19},
+}
diff --git a/tests/fake_env.py b/tests/fake_env.py
index 6d790a3..41d22d7 100644
--- a/tests/fake_env.py
+++ b/tests/fake_env.py
@@ -43,8 +43,8 @@ def capture(f, verbose=False):
     """
     def newf(*args, **kwargs):
         old_stderr, old_stdout = sys.stderr, sys.stdout
-        sys.stdout = _fake_stdio(additional_out=old_stderr if verbose else None)
-        sys.stderr = _fake_stdio(additional_out=old_stderr if False else None)
+        sys.stdout = _fake_stdio(additional_out=old_stdout if verbose else None)
+        sys.stderr = _fake_stdio(additional_out=old_stderr if verbose else None)
         try:
             return f(*args, **kwargs), _get_fake_stdio_ucontent(sys.stdout), _get_fake_stdio_ucontent(sys.stderr)
         finally:
diff --git a/tests/test_usecase.py b/tests/test_usecase.py
index b0044fa..f213d11 100644
--- a/tests/test_usecase.py
+++ b/tests/test_usecase.py
@@ -1091,6 +1091,22 @@ class TestUsecase(DataCommandTestCase):
         actual = self.execute_cmds(cmds, capture_output=True)
         self.assertEqual(correct, actual)
 
+    def test_add_non_standard(self):
+        """Test that non-standard bibtex are correctly added"""
+        self.fs.add_real_directory(os.path.join(self.rootpath, 'data_non_standard'), read_only=False)
+        correct = ['Initializing pubs in /pubs\n',
+                   'added to pubs:\n[Geometric_phases]  "Geometric phases in physics" (1989) \n',
+                   'added to pubs:\n[hadoop] Foundation, Apache Software "Hadoop" \n',
+                  ]
+        cmds = ['pubs init -p /pubs',
+                'pubs add data_non_standard/non_standard_collection.bib',
+                'pubs add data_non_standard/non_standard_software.bib',
+                # 'pubs list',
+               ]
+        actual = self.execute_cmds(cmds, capture_output=True)
+        self.assertEqual(correct, actual)
+
+
     @mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
     def test_readme(self, reqget):
         """Test that the readme example work."""
@@ -1099,7 +1115,7 @@ class TestUsecase(DataCommandTestCase):
         self.fs.add_real_file(os.path.join(self.rootpath, 'data/pagerank.pdf'), target_path='data/Knuth1995.pdf')
 
         cmds = ['pubs init',
-                'pubs import data/collection.bib',
+                'pubs import data/three_articles.bib',
                 'pubs add data/pagerank.bib -d data/pagerank.pdf',
                 #'pubs add -D 10.1007/s00422-012-0514-6 -d data/pagerank.pdf',
                 'pubs add -I 978-0822324669 -d data/oyama2000the.pdf',

From 4a27faf3ab132c8cb8385928f19db954230926a2 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Tue, 5 May 2020 17:51:19 +0900
Subject: [PATCH 10/45] update changelog

---
 changelog.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/changelog.md b/changelog.md
index 52dadd9..fe627c4 100644
--- a/changelog.md
+++ b/changelog.md
@@ -5,8 +5,14 @@
 
 [Full Changelog](https://github.com/pubs/pubs/compare/v0.8.3...master)
 
+### Implemented enhancements
+
+- Added support for non-standard bibtex types, e.g. @collection, @software, etc. ([#226](https://github.com/pubs/pubs/pull/226)
+- The number of displayed authors in listings is now configurable, as the `n_authors` value in the `main` section of the configuration. ([#225](https://github.com/pubs/pubs/pull/225)
+
 ### Fixed bugs
 
+- Tests don't run on python 2.7 or <=3.4. They may still work, but support will not be tested and will eventually be dropped. ([#223](https://github.com/pubs/pubs/pull/223)
 
 ## [v0.8.3](https://github.com/pubs/pubs/compare/v0.8.2...v0.8.3) (2019-08-12)
 

From 90b61089b150a5162255dbbeac6c70048fdd6ed0 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Fri, 8 May 2020 11:42:02 +0900
Subject: [PATCH 11/45] improve remove prompt (see #153)

---
 pubs/commands/remove_cmd.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/pubs/commands/remove_cmd.py b/pubs/commands/remove_cmd.py
index 0b7f9e0..cad1fda 100644
--- a/pubs/commands/remove_cmd.py
+++ b/pubs/commands/remove_cmd.py
@@ -2,6 +2,7 @@ from __future__ import unicode_literals
 
 from .. import repo
 from .. import color
+from .. import pretty
 from ..uis import get_ui
 from ..utils import resolve_citekey_list
 from ..p3 import ustr, u_maybe
@@ -25,11 +26,15 @@ def command(conf, args):
     rp = repo.Repository(conf)
 
     keys = resolve_citekey_list(repo=rp, citekeys=args.citekeys, ui=ui, exit_on_fail=True)
+    plural = 's' if len(keys) > 1 else ''
 
     if force is None:
-        are_you_sure = (("Are you sure you want to delete the publication(s) [{}]"
-            " (this will also delete associated documents)?")
-            .format(', '.join([color.dye_out(c, 'citekey') for c in args.citekeys])))
+        to_remove_str = '\n'.join(pretty.paper_oneliner(rp.pull_paper(key),
+                                                        n_authors=conf['main']['n_authors'])
+                                  for key in keys)
+        are_you_sure = (("Are you sure you want to delete the following publication{}"
+            " (this will also delete associated documents)?:\n{}\n")
+            .format(plural, to_remove_str))
         sure = ui.input_yn(question=are_you_sure, default='n')
     if force or sure:
         failed = False  # Whether something failed
@@ -42,11 +47,12 @@ def command(conf, args):
         if failed:
             ui.exit()  # Exit with nonzero error code
         else:
-            ui.message('The publication(s) [{}] were removed'.format(
+
+            ui.message('The publication{} {} were removed'.format(plural,
                 ', '.join([color.dye_out(c, 'citekey') for c in keys])))
 
         # FIXME: print should check that removal proceeded well.
     else:
-        ui.message('The publication(s) [{}] were {} removed'.format(
+        ui.message('The publication{} {} were {} removed'.format(plural,
             ', '.join([color.dye_out(c, 'citekey') for c in keys]),
             color.dye_out('not','bold')))

From 04b25a22c83638a6ea9f0599215bd0a1a6d81c7f Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Sun, 10 May 2020 08:53:11 +0900
Subject: [PATCH 12/45] renamed n_authors into max_authors

---
 pubs/commands/add_cmd.py  |  2 +-
 pubs/commands/list_cmd.py |  2 +-
 pubs/commands/tag_cmd.py  |  2 +-
 pubs/config/spec.py       |  2 +-
 pubs/pretty.py            | 20 +++++++-------------
 pubs/utils.py             |  2 +-
 tests/test_pretty.py      | 10 +++++-----
 tests/test_usecase.py     | 10 +++++-----
 8 files changed, 22 insertions(+), 28 deletions(-)

diff --git a/pubs/commands/add_cmd.py b/pubs/commands/add_cmd.py
index 74e5a46..9e9dd0d 100644
--- a/pubs/commands/add_cmd.py
+++ b/pubs/commands/add_cmd.py
@@ -147,7 +147,7 @@ def command(conf, args):
         doc_add = conf['main']['doc_add']
 
     rp.push_paper(p)
-    ui.message('added to pubs:\n{}'.format(pretty.paper_oneliner(p, n_authors=conf['main']['n_authors'])))
+    ui.message('added to pubs:\n{}'.format(pretty.paper_oneliner(p, max_authors=conf['main']['max_authors'])))
     if docfile is not None:
         rp.push_doc(p.citekey, docfile, copy=(doc_add in ('copy', 'move')))
         if doc_add == 'move' and content.content_type(docfile) != 'url':
diff --git a/pubs/commands/list_cmd.py b/pubs/commands/list_cmd.py
index a382544..24e533b 100644
--- a/pubs/commands/list_cmd.py
+++ b/pubs/commands/list_cmd.py
@@ -54,7 +54,7 @@ def command(conf, args):
         papers = sorted(papers, key=date_added)
     if len(papers) > 0:
         ui.message('\n'.join(
-            pretty.paper_oneliner(p, citekey_only=args.citekeys, n_authors=conf['main']['n_authors'])
+            pretty.paper_oneliner(p, citekey_only=args.citekeys, max_authors=conf['main']['max_authors'])
             for p in papers))
 
     rp.close()
diff --git a/pubs/commands/tag_cmd.py b/pubs/commands/tag_cmd.py
index 90d6d9c..78357c3 100644
--- a/pubs/commands/tag_cmd.py
+++ b/pubs/commands/tag_cmd.py
@@ -117,7 +117,7 @@ def command(conf, args):
                     len(p.tags.intersection(excluded)) == 0):
                     papers_list.append(p)
 
-            ui.message('\n'.join(pretty.paper_oneliner(p, n_authors=conf['main']['n_authors'])
+            ui.message('\n'.join(pretty.paper_oneliner(p, max_authors=conf['main']['max_authors'])
                                  for p in papers_list))
 
         rp.close()
diff --git a/pubs/config/spec.py b/pubs/config/spec.py
index 4aba92b..6921bae 100644
--- a/pubs/config/spec.py
+++ b/pubs/config/spec.py
@@ -29,7 +29,7 @@ note_extension = string(default='txt')
 
 # How many authors to display when displaying a citation. If there are more
 # authors, only the first author is diplayed followed by 'et al.'.
-n_authors = integer(default=3)
+max_authors = integer(default=3)
 
 # If true debug mode is on which means exceptions are not catched and
 # the full python stack is printed.
diff --git a/pubs/pretty.py b/pubs/pretty.py
index 369c3e4..6b12fb6 100644
--- a/pubs/pretty.py
+++ b/pubs/pretty.py
@@ -23,30 +23,24 @@ def person_repr(p):
         ' '.join(p.lineage(abbr=True))] if s)
 
 
-def short_authors(bibdata, n_authors=3):
+def short_authors(bibdata, max_authors=3):
     """
-    :param n_authors:  number of authors to display completely. Additional authors will be
+    :param max_authors:  number of authors to display completely. Additional authors will be
                        represented by 'et al.'.
     """
     try:
         authors = [p for p in bibdata['author']]
-        if 0 < n_authors < len(authors):
+        if 0 < max_authors < len(authors):
             authors_str = '{} et al.'.format(authors[0])
         else:
             authors_str = ' and '.join(authors)
-
-        # if n_authors > 0:
-        #     authors = authors[:n_authors]
-        # authors_str = ' and '.join(authors)
-        # if 0 < n_authors < len(bibdata['author']):
-        #     authors_str += ' et al.'
         return authors_str
     except KeyError:  # When no author is defined
         return ''
 
 
-def bib_oneliner(bibdata, n_authors=3):
-    authors = short_authors(bibdata, n_authors=n_authors)
+def bib_oneliner(bibdata, max_authors=3):
+    authors = short_authors(bibdata, max_authors=max_authors)
     journal = ''
     if 'journal' in bibdata:
         journal = ' ' + bibdata['journal']
@@ -71,11 +65,11 @@ def bib_desc(bib_data):
     return s
 
 
-def paper_oneliner(p, citekey_only=False, n_authors=3):
+def paper_oneliner(p, citekey_only=False, max_authors=3):
     if citekey_only:
         return p.citekey
     else:
-        bibdesc = bib_oneliner(p.get_unicode_bibdata(), n_authors=n_authors)
+        bibdesc = bib_oneliner(p.get_unicode_bibdata(), max_authors=max_authors)
         doc_str = ''
         if p.docpath is not None:
             doc_extension = os.path.splitext(p.docpath)[1]
diff --git a/pubs/utils.py b/pubs/utils.py
index a7aceb1..9b93aa3 100644
--- a/pubs/utils.py
+++ b/pubs/utils.py
@@ -33,7 +33,7 @@ def resolve_citekey(repo, citekey, ui=None, exit_on_fail=True):
                      "citekeys:".format(citekey))
             for c in citekeys:
                 p = repo.pull_paper(c)
-                ui.message('    {}'.format(pretty.paper_oneliner(p, n_authors=conf['main']['n_authors'])))
+                ui.message('    {}'.format(pretty.paper_oneliner(p, max_authors=conf['main']['max_authors'])))
             if exit_on_fail:
                 ui.exit()
     return citekey
diff --git a/tests/test_pretty.py b/tests/test_pretty.py
index cc9f4f4..b73edfd 100644
--- a/tests/test_pretty.py
+++ b/tests/test_pretty.py
@@ -28,15 +28,15 @@ class TestPretty(unittest.TestCase):
         line = 'Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web."'
         self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'])), line)
 
-    def test_oneliner_n_authors(self):
+    def test_oneliner_max_authors(self):
         decoder = endecoder.EnDecoder()
         bibdata = decoder.decode_bibdata(bibtex_raw0)
-        for n_authors in [1, 2, 3]:
+        for max_authors in [1, 2, 3]:
             line = 'Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999)'
-            self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'], n_authors=n_authors)), line)
-        for n_authors in [-1, 0, 4, 5, 10]:
+            self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'], max_authors=max_authors)), line)
+        for max_authors in [-1, 0, 4, 5, 10]:
             line = 'Page, Lawrence and Brin, Sergey and Motwani, Rajeev and Winograd, Terry "The PageRank Citation Ranking: Bringing Order to the Web." (1999)'
-            self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'], n_authors=n_authors)), line)
+            self.assertEqual(color.undye(pretty.bib_oneliner(bibdata['Page99'], max_authors=max_authors)), line)
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/tests/test_usecase.py b/tests/test_usecase.py
index b0044fa..a591485 100644
--- a/tests/test_usecase.py
+++ b/tests/test_usecase.py
@@ -1157,18 +1157,18 @@ class TestCache(DataCommandTestCase):
 
 class TestConfigChange(DataCommandTestCase):
 
-    def test_n_authors_default(self):
+    def test_max_authors_default(self):
         line_al   = '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
         line_full = '[Page99] Page, Lawrence and Brin, Sergey and Motwani, Rajeev and Winograd, Terry "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
 
         self.execute_cmds(['pubs init', 'pubs add data/pagerank.bib'])
 
-        for n_authors in [1, 2, 3]:
-            self.update_config({'main': {'n_authors': n_authors}})
+        for max_authors in [1, 2, 3]:
+            self.update_config({'main': {'max_authors': max_authors}})
             self.execute_cmds([('pubs list', None, line_al, None)])
 
-        for n_authors in [-1, 0, 4, 5, 10]:
-            self.update_config({'main': {'n_authors': n_authors}})
+        for max_authors in [-1, 0, 4, 5, 10]:
+            self.update_config({'main': {'max_authors': max_authors}})
             self.execute_cmds([('pubs list', None, line_full, None)])
 
 

From 76f5156a2152fee8ef972e5c734d7f1db6c91b2d Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Sun, 10 May 2020 09:06:15 +0900
Subject: [PATCH 13/45] pin ddt version to 1.3.1

because of https://github.com/datadriventests/ddt/issues/83
---
 dev_requirements.txt | 4 +++-
 setup.py             | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/dev_requirements.txt b/dev_requirements.txt
index 1891f81..f6555a6 100644
--- a/dev_requirements.txt
+++ b/dev_requirements.txt
@@ -20,6 +20,8 @@ six
 # those are the additional packages required to run the tests
 pyfakefs
 certifi
-ddt
+# FIXME: remove strict version when https://github.com/datadriventests/ddt/issues/83 is fixed.
+#        (also remove in setup.py)
+ddt==1.3.1
 mock
 pytest # optional (python setup.py test works without it), but possible nonetheless
diff --git a/setup.py b/setup.py
index d7fe2dd..a8eb7de 100644
--- a/setup.py
+++ b/setup.py
@@ -61,7 +61,7 @@ setup(
     ],
 
     test_suite='tests',
-    tests_require=['pyfakefs>=3.4', 'mock', 'ddt', 'certifi'],
+    tests_require=['pyfakefs>=3.4', 'mock', 'ddt==1.3.1', 'certifi'],
 
     # in order to avoid 'zipimport.ZipImportError: bad local file header'
     zip_safe=False,

From c9aa8ddd41bb13835e4a5c0d694ec7b6a0e85b7c Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Sun, 10 May 2020 09:53:04 +0900
Subject: [PATCH 14/45] fix side-effects of merge, and deprecation warnings

---
 changelog.md                |  2 +-
 pubs/color.py               |  2 +-
 pubs/commands/remove_cmd.py |  2 +-
 pubs/filebroker.py          |  2 +-
 tests/str_fixtures.py       | 20 ++++++++++----------
 tests/test_queries.py       |  8 ++++----
 6 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/changelog.md b/changelog.md
index fe627c4..f7aeafb 100644
--- a/changelog.md
+++ b/changelog.md
@@ -8,7 +8,7 @@
 ### Implemented enhancements
 
 - Added support for non-standard bibtex types, e.g. @collection, @software, etc. ([#226](https://github.com/pubs/pubs/pull/226)
-- The number of displayed authors in listings is now configurable, as the `n_authors` value in the `main` section of the configuration. ([#225](https://github.com/pubs/pubs/pull/225)
+- The number of displayed authors in listings is now configurable, as the `max_authors` value in the `main` section of the configuration. ([#225](https://github.com/pubs/pubs/pull/225)
 
 ### Fixed bugs
 
diff --git a/pubs/color.py b/pubs/color.py
index 86e8622..0e41cf9 100644
--- a/pubs/color.py
+++ b/pubs/color.py
@@ -144,7 +144,7 @@ def setup(conf, force_colors=False):
 
 
 # undye
-undye_re = re.compile('\x1b\[[;\d]*[A-Za-z]')
+undye_re = re.compile('\x1b\\[[;\d]*[A-Za-z]')
 
 def undye(s):
     """Purge string s of color"""
diff --git a/pubs/commands/remove_cmd.py b/pubs/commands/remove_cmd.py
index cad1fda..e09039c 100644
--- a/pubs/commands/remove_cmd.py
+++ b/pubs/commands/remove_cmd.py
@@ -30,7 +30,7 @@ def command(conf, args):
 
     if force is None:
         to_remove_str = '\n'.join(pretty.paper_oneliner(rp.pull_paper(key),
-                                                        n_authors=conf['main']['n_authors'])
+                                                        max_authors=conf['main']['max_authors'])
                                   for key in keys)
         are_you_sure = (("Are you sure you want to delete the following publication{}"
             " (this will also delete associated documents)?:\n{}\n")
diff --git a/pubs/filebroker.py b/pubs/filebroker.py
index f48ba93..7043f4c 100644
--- a/pubs/filebroker.py
+++ b/pubs/filebroker.py
@@ -16,7 +16,7 @@ def filter_filename(filename, ext):
     """ Return the filename without the extension if the extension matches ext.
         Otherwise return None
     """
-    pattern = '.*\{}$'.format(ext)
+    pattern = '.*\\{}$'.format(ext)
     if re.match(pattern, filename) is not None:
         return u_maybe(filename[:-len(ext)])
 
diff --git a/tests/str_fixtures.py b/tests/str_fixtures.py
index 1372a80..d2fbfec 100644
--- a/tests/str_fixtures.py
+++ b/tests/str_fixtures.py
@@ -1,7 +1,7 @@
 from __future__ import unicode_literals
 
 
-bibtex_external0 = """
+bibtex_external0 = r"""
 @techreport{Page99,
      number = {1999-66},
       month = {November},
@@ -17,7 +17,7 @@ institution = {Stanford InfoLab},
 }
 """
 
-bibtex_external_alt = """
+bibtex_external_alt = r"""
 @techreport{Page99,
      number = {1999-66},
       month = {November},
@@ -33,7 +33,7 @@ institution = {Stanford InfoLab},
 }
 """
 
-bibtex_raw0 = """@techreport{
+bibtex_raw0 = r"""@techreport{
     Page99,
     author = "Page, Lawrence and Brin, Sergey and Motwani, Rajeev and Winograd, Terry",
     publisher = "Stanford InfoLab",
@@ -50,12 +50,12 @@ bibtex_raw0 = """@techreport{
 
 """
 
-metadata_raw0 = """docfile: docsdir://Page99.pdf
+metadata_raw0 = r"""docfile: docsdir://Page99.pdf
 tags: [search, network]
 added: '2013-11-14 13:14:20'
 """
 
-turing_bib = """@article{turing1950computing,
+turing_bib = r"""@article{turing1950computing,
   title={Computing machinery and intelligence},
   author={Turing, Alan M},
   journal={Mind},
@@ -75,7 +75,7 @@ added: '2013-11-14 13:14:20'
 """
 
 # Should not parse (see #113)
-bibtex_no_citekey = """@Manual{,
+bibtex_no_citekey = r"""@Manual{,
     title = {R: A Language and Environment for Statistical Computing},
     author = {{R Core Team}},
     organization = {R Foundation for Statistical Computing},
@@ -85,7 +85,7 @@ bibtex_no_citekey = """@Manual{,
 }
 """
 
-bibtex_month = """@inproceedings{Goyal2017,
+bibtex_month = r"""@inproceedings{Goyal2017,
  author = {Goyal, Anirudh and Sordoni, Alessandro and C{\^{o}}t{\'{e}}, Marc-Alexandre and Ke, Nan Rosemary and Bengio, Yoshua},
  title = {Z-Forcing: Training Stochastic Recurrent Networks},
  year = {2017},
@@ -94,15 +94,15 @@ bibtex_month = """@inproceedings{Goyal2017,
 }
 """
 
-not_bibtex = """@misc{this looks,
+not_bibtex = r"""@misc{this looks,
   like = a = bibtex file but
     , is not a real one!
 
 """
 
-bibtex_with_latex = """@article{kjaer2018large,
+bibtex_with_latex = r"""@article{kjaer2018large,
   title={A large impact crater beneath Hiawatha Glacier in northwest Greenland},
-  author={Kj{\\ae}r, Kurt H and Larsen, Nicolaj K and Binder, Tobias and Bj{\\o}rk, Anders A and Eisen, Olaf and Fahnestock, Mark A and Funder, Svend and Garde, Adam A and Haack, Henning and Helm, Veit and others},
+  author={Kj{\ae}r, Kurt H and Larsen, Nicolaj K and Binder, Tobias and Bj{\o}rk, Anders A and Eisen, Olaf and Fahnestock, Mark A and Funder, Svend and Garde, Adam A and Haack, Henning and Helm, Veit and others},
   journal={Science advances},
   volume={4},
   number={11},
diff --git a/tests/test_queries.py b/tests/test_queries.py
index 207c4fc..a0ca6c7 100644
--- a/tests/test_queries.py
+++ b/tests/test_queries.py
@@ -200,8 +200,8 @@ class TestFilterPaper(unittest.TestCase):
 
     def test_latex_enc(self):
         latexenc_paper = doe_paper.deepcopy()
-        latexenc_paper.bibentry['Doe2013']['title'] = "{E}l Ni{\~n}o"
-        latexenc_paper.bibentry['Doe2013']['author'][0] = "Erd\H{o}s, Paul"
+        latexenc_paper.bibentry['Doe2013']['title'] = r"{E}l Ni{\~n}o"
+        latexenc_paper.bibentry['Doe2013']['author'][0] = r"Erd\H{o}s, Paul"
         self.assertTrue(get_paper_filter(['title:El'])(latexenc_paper))
         self.assertTrue(get_paper_filter(['title:Niño'])(latexenc_paper))
         self.assertTrue(get_paper_filter(['author:erdős'])(latexenc_paper))
@@ -209,12 +209,12 @@ class TestFilterPaper(unittest.TestCase):
 
     def test_normalize_unicode(self):
         latexenc_paper = doe_paper.deepcopy()
-        latexenc_paper.bibentry['Doe2013']['title'] = "{E}l Ni{\~n}o"
+        latexenc_paper.bibentry['Doe2013']['title'] = r"{E}l Ni{\~n}o"
         self.assertTrue(get_paper_filter(['title:Nin\u0303o'])(latexenc_paper))
 
     def test_strict(self):
         latexenc_paper = doe_paper.deepcopy()
-        latexenc_paper.bibentry['Doe2013']['title'] = "El Ni{\~n}o"
+        latexenc_paper.bibentry['Doe2013']['title'] = r"El Ni{\~n}o"
         self.assertFalse(get_paper_filter(
             ['title:Nin\u0303o'], strict=True)(latexenc_paper))
 

From 21518f3a75987ecfd5ddc30e1206ca93abddffbc Mon Sep 17 00:00:00 2001
From: beuerle <beuerle@users.noreply.github.com>
Date: Tue, 26 May 2020 17:31:36 +0200
Subject: [PATCH 15/45] fix missing conf argument for resolve_citekey

---
 pubs/commands/doc_cmd.py    | 8 ++++----
 pubs/commands/edit_cmd.py   | 2 +-
 pubs/commands/export_cmd.py | 2 +-
 pubs/commands/note_cmd.py   | 2 +-
 pubs/commands/remove_cmd.py | 2 +-
 pubs/commands/rename_cmd.py | 2 +-
 pubs/commands/tag_cmd.py    | 2 +-
 pubs/commands/url_cmd.py    | 2 +-
 pubs/utils.py               | 6 +++---
 9 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/pubs/commands/doc_cmd.py b/pubs/commands/doc_cmd.py
index d1a44df..2bb6f9c 100644
--- a/pubs/commands/doc_cmd.py
+++ b/pubs/commands/doc_cmd.py
@@ -71,7 +71,7 @@ def command(conf, args):
     # ui.exit()
 
     if args.action == 'add':
-        citekey = resolve_citekey(rp, args.citekey[0], ui=ui, exit_on_fail=True)
+        citekey = resolve_citekey(rp, conf, args.citekey[0], ui=ui, exit_on_fail=True)
         paper = rp.pull_paper(citekey)
 
         if paper.docpath is not None and not args.force:
@@ -98,7 +98,7 @@ def command(conf, args):
 
     elif args.action == 'remove':
 
-        for key in resolve_citekey_list(rp, args.citekeys, ui=ui, exit_on_fail=True):
+        for key in resolve_citekey_list(rp, conf, args.citekeys, ui=ui, exit_on_fail=True):
             paper = rp.pull_paper(key)
 
             # if there is no document (and the user cares) -> inform + continue
@@ -126,7 +126,7 @@ def command(conf, args):
                 color.dye_err(args.path[0], 'filepath')))
             ui.exit(1)
 
-        for key in resolve_citekey_list(rp, args.citekeys, ui=ui, exit_on_fail=True):
+        for key in resolve_citekey_list(rp, conf, args.citekeys, ui=ui, exit_on_fail=True):
             try:
                 paper = rp.pull_paper(key)
                 doc = paper.docpath
@@ -143,7 +143,7 @@ def command(conf, args):
 
     elif args.action == 'open':
         with_command = args.cmd
-        citekey = resolve_citekey(rp, args.citekey[0], ui=ui, exit_on_fail=True)
+        citekey = resolve_citekey(rp, conf, args.citekey[0], ui=ui, exit_on_fail=True)
         paper = rp.pull_paper(citekey)
 
         if paper.docpath is None:
diff --git a/pubs/commands/edit_cmd.py b/pubs/commands/edit_cmd.py
index d4ad366..5ea7679 100644
--- a/pubs/commands/edit_cmd.py
+++ b/pubs/commands/edit_cmd.py
@@ -30,7 +30,7 @@ def command(conf, args):
     meta = args.meta
 
     rp = repo.Repository(conf)
-    citekey = resolve_citekey(rp, args.citekey, ui=ui, exit_on_fail=True)
+    citekey = resolve_citekey(rp, conf, args.citekey, ui=ui, exit_on_fail=True)
     paper = rp.pull_paper(citekey)
 
     coder = EnDecoder()
diff --git a/pubs/commands/export_cmd.py b/pubs/commands/export_cmd.py
index 2bbe01d..b316efc 100644
--- a/pubs/commands/export_cmd.py
+++ b/pubs/commands/export_cmd.py
@@ -46,7 +46,7 @@ def command(conf, args):
     if len(args.citekeys) < 1:
         papers = rp.all_papers()
     else:
-        for key in resolve_citekey_list(repo=rp, citekeys=args.citekeys, ui=ui, exit_on_fail=True):
+        for key in resolve_citekey_list(rp, conf, args.citekeys, ui=ui, exit_on_fail=True):
             papers.append(rp.pull_paper(key))
 
     bib = {}
diff --git a/pubs/commands/note_cmd.py b/pubs/commands/note_cmd.py
index 9466566..04c7eba 100644
--- a/pubs/commands/note_cmd.py
+++ b/pubs/commands/note_cmd.py
@@ -23,7 +23,7 @@ def command(conf, args):
 
     ui = get_ui()
     rp = repo.Repository(conf)
-    citekey = resolve_citekey(rp, args.citekey, ui=ui, exit_on_fail=True)
+    citekey = resolve_citekey(rp, conf, args.citekey, ui=ui, exit_on_fail=True)
     notepath = rp.databroker.real_notepath(citekey, rp.conf['main']['note_extension'])
     if args.append is None:
         ui.edit_file(notepath, temporary=False)
diff --git a/pubs/commands/remove_cmd.py b/pubs/commands/remove_cmd.py
index 0b7f9e0..3982dba 100644
--- a/pubs/commands/remove_cmd.py
+++ b/pubs/commands/remove_cmd.py
@@ -24,7 +24,7 @@ def command(conf, args):
     force = args.force
     rp = repo.Repository(conf)
 
-    keys = resolve_citekey_list(repo=rp, citekeys=args.citekeys, ui=ui, exit_on_fail=True)
+    keys = resolve_citekey_list(rp, conf, args.citekeys, ui=ui, exit_on_fail=True)
 
     if force is None:
         are_you_sure = (("Are you sure you want to delete the publication(s) [{}]"
diff --git a/pubs/commands/rename_cmd.py b/pubs/commands/rename_cmd.py
index af14c4f..3461250 100644
--- a/pubs/commands/rename_cmd.py
+++ b/pubs/commands/rename_cmd.py
@@ -26,7 +26,7 @@ def command(conf, args):
     rp = repo.Repository(conf)
 
     # TODO: here should be a test whether the new citekey is valid
-    key = resolve_citekey(repo=rp, citekey=args.citekey, ui=ui, exit_on_fail=True)
+    key = resolve_citekey(rp, conf, args.citekey, ui=ui, exit_on_fail=True)
     paper = rp.pull_paper(key)
     rp.rename_paper(paper, args.new_citekey)
     ui.message("The '{}' citekey has been renamed into '{}'".format(
diff --git a/pubs/commands/tag_cmd.py b/pubs/commands/tag_cmd.py
index 78357c3..485d785 100644
--- a/pubs/commands/tag_cmd.py
+++ b/pubs/commands/tag_cmd.py
@@ -89,7 +89,7 @@ def command(conf, args):
     else:
         not_citekey = False
         try:
-            citekeyOrTag = resolve_citekey(repo=rp, citekey=citekeyOrTag, ui=ui, exit_on_fail=True)
+            citekeyOrTag = resolve_citekey(rp, conf, citekeyOrTag, ui=ui, exit_on_fail=True)
         except SystemExit:
             not_citekey = True
         if not not_citekey:
diff --git a/pubs/commands/url_cmd.py b/pubs/commands/url_cmd.py
index 7ac7b7f..224da7f 100644
--- a/pubs/commands/url_cmd.py
+++ b/pubs/commands/url_cmd.py
@@ -22,7 +22,7 @@ def command(conf, args):
     ui = get_ui()
     rp = repo.Repository(conf)
 
-    for key in resolve_citekey_list(rp, args.citekey, ui=ui, exit_on_fail=False):
+    for key in resolve_citekey_list(rp, conf, args.citekey, ui=ui, exit_on_fail=False):
         try:
             paper = rp.pull_paper(key)
             url = paper.bibdata['url']
diff --git a/pubs/utils.py b/pubs/utils.py
index 9b93aa3..e7878f5 100644
--- a/pubs/utils.py
+++ b/pubs/utils.py
@@ -7,7 +7,7 @@ from . import color
 from . import pretty
 
 
-def resolve_citekey(repo, citekey, ui=None, exit_on_fail=True):
+def resolve_citekey(repo, conf, citekey, ui=None, exit_on_fail=True):
     """Check that a citekey exists, or autocompletes it if not ambiguous.
         :returns found citekey
     """
@@ -39,12 +39,12 @@ def resolve_citekey(repo, citekey, ui=None, exit_on_fail=True):
     return citekey
 
 
-def resolve_citekey_list(repo, citekeys, ui=None, exit_on_fail=True):
+def resolve_citekey_list(repo, conf, citekeys, ui=None, exit_on_fail=True):
     shutdown = False
     keys = []
     for key in citekeys:
         try:
-            keys.append(resolve_citekey(repo, key, ui, exit_on_fail))
+            keys.append(resolve_citekey(repo, conf, key, ui=ui, exit_on_fail=exit_on_fail))
         except SystemExit:
             shutdown = exit_on_fail
 

From e8700d7db1f26b276fb2961fea4638ddb897a0c0 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Tue, 2 Jun 2020 18:55:24 +0900
Subject: [PATCH 16/45] added test for ambiguous citkeys

* also reworked the test code to allow to capture output even
  when pubs throws an error.
* empty tags are not added to the metadata anymore (does not affect
  existing instances)
---
 pubs/commands/tag_cmd.py  |  4 ++-
 pubs/utils.py             |  7 +++---
 tests/fake_env.py         | 25 +-----------------
 tests/test_note_append.py |  2 +-
 tests/test_usecase.py     | 53 ++++++++++++++++++++++++++-------------
 5 files changed, 45 insertions(+), 46 deletions(-)

diff --git a/pubs/commands/tag_cmd.py b/pubs/commands/tag_cmd.py
index 485d785..c12bf8f 100644
--- a/pubs/commands/tag_cmd.py
+++ b/pubs/commands/tag_cmd.py
@@ -55,7 +55,9 @@ def _parse_tag_seq(s):
             if last != 0:
                 raise ValueError('could not match tag expression')
         else:
-            tags.append(s[last:(m.start())])
+            tag = s[last:(m.start())]
+            if len(tag) > 0:
+                tags.append(s[last:(m.start())])
         last = m.start()
     if last == len(s):
         raise ValueError('could not match tag expression')
diff --git a/pubs/utils.py b/pubs/utils.py
index e7878f5..120edfd 100644
--- a/pubs/utils.py
+++ b/pubs/utils.py
@@ -29,11 +29,12 @@ def resolve_citekey(repo, conf, citekey, ui=None, exit_on_fail=True):
     elif citekey not in citekeys:
         if ui is not None:
             citekeys = sorted(citekeys)
-            ui.error("Be more specific; '{}' matches multiples "
-                     "citekeys:".format(citekey))
+            msg = ["Be more specific; '{}' matches multiples citekeys:".format(citekey)]
             for c in citekeys:
                 p = repo.pull_paper(c)
-                ui.message('    {}'.format(pretty.paper_oneliner(p, max_authors=conf['main']['max_authors'])))
+                paper_str = pretty.paper_oneliner(p, max_authors=conf['main']['max_authors'])
+                msg.append('    {}'.format(paper_str))
+            ui.error('\n'.join(msg))
             if exit_on_fail:
                 ui.exit()
     return citekey
diff --git a/tests/fake_env.py b/tests/fake_env.py
index 41d22d7..1d1865f 100644
--- a/tests/fake_env.py
+++ b/tests/fake_env.py
@@ -9,7 +9,7 @@ import dotdot
 
 from pyfakefs import fake_filesystem, fake_filesystem_unittest
 
-from pubs.p3 import input, _fake_stdio, _get_fake_stdio_ucontent
+from pubs.p3 import input
 from pubs import content, filebroker, uis
 
 # code for fake fs
@@ -29,29 +29,6 @@ original_exception_handler = uis.InputUI.handle_exception
 locale.setlocale(locale.LC_ALL, '')
 
 
-# capture output
-
-def capture(f, verbose=False):
-    """Capture the stdout and stderr output.
-
-    Useful for comparing the output with the expected one during tests.
-
-    :param f:        The function to capture output from.
-    :param verbose:  If True, print call will still display their outputs.
-                     If False, they will be silenced.
-
-    """
-    def newf(*args, **kwargs):
-        old_stderr, old_stdout = sys.stderr, sys.stdout
-        sys.stdout = _fake_stdio(additional_out=old_stdout if verbose else None)
-        sys.stderr = _fake_stdio(additional_out=old_stderr if verbose else None)
-        try:
-            return f(*args, **kwargs), _get_fake_stdio_ucontent(sys.stdout), _get_fake_stdio_ucontent(sys.stderr)
-        finally:
-            sys.stderr, sys.stdout = old_stderr, old_stdout
-    return newf
-
-
 # Test helpers
 
 # automating input
diff --git a/tests/test_note_append.py b/tests/test_note_append.py
index c3009f2..32eebee 100644
--- a/tests/test_note_append.py
+++ b/tests/test_note_append.py
@@ -46,7 +46,7 @@ class TestNoteAppend(DataCommandTestCase):
         #   * Pass the command split into a command and its args to
         #     execute_cmdsplit, which is called by execute_cmds:
         cmd_split = ['pubs', 'note', 'Page99', '-a', 'xxx yyy']
-        self.execute_cmdsplit(cmd_split, expected_out=None, expected_err=None)
+        self.execute_cmd_capture(cmd_split, expected_out=None, expected_err=None)
         note_lines.append('xxx yyy')
         self.assertFileContentEqual(fin_notes, self._get_note_content(note_lines))
 
diff --git a/tests/test_usecase.py b/tests/test_usecase.py
index 891d9cc..ba94559 100644
--- a/tests/test_usecase.py
+++ b/tests/test_usecase.py
@@ -17,6 +17,7 @@ import dotdot
 import fake_env
 import mock_requests
 
+
 from pubs import pubs_cmd, color, content, uis, p3, endecoder
 from pubs.config import conf
 
@@ -118,14 +119,12 @@ class CommandTestCase(fake_env.TestFakeFs):
                 input.as_global()
                 try:
                     if capture_output:
-                        actual_out = self.execute_cmdsplit(
-                            actual_cmd.split(), expected_out, expected_err)
+                        actual_out = self.execute_cmd_capture(actual_cmd.split(), expected_out, expected_err)
                         outs.append(color.undye(actual_out))
                     else:
                         pubs_cmd.execute(actual_cmd.split())
                 except fake_env.FakeInput.UnexpectedInput:
-                    self.fail('Unexpected input asked by command: {}.'.format(
-                        actual_cmd))
+                    self.fail('Unexpected input asked by command: {}.'.format(actual_cmd))
             return outs
         except SystemExit as exc:
             exc_class, exc, tb = sys.exc_info()
@@ -145,21 +144,25 @@ class CommandTestCase(fake_env.TestFakeFs):
             pass
         return s
 
-    def execute_cmdsplit(self, actual_cmdlist, expected_out, expected_err):
-        """Run a single command, which has been split into a list containing cmd and args"""
-        capture_wrap = fake_env.capture(pubs_cmd.execute,
-                                        verbose=PRINT_OUTPUT)
-        _, stdout, stderr = capture_wrap(actual_cmdlist)
-        actual_out = self.normalize(stdout)
-        actual_err = self.normalize(stderr)
+    def execute_cmd_capture(self, cmd, expected_out, expected_err):
+        """Run a single command, captures the output and and stderr and compare it to the expected ones"""
+        sys_stdout, sys_stderr = sys.stdout, sys.stderr
+        sys.stdout = p3._fake_stdio(additional_out=sys_stdout if PRINT_OUTPUT else None)
+        sys.stderr = p3._fake_stdio(additional_out=sys_stderr if PRINT_OUTPUT else None)
+
+        try:
+            pubs_cmd.execute(cmd)
+        finally:
+            # capturing output even if exception was raised.
+            self.captured_stdout = self.normalize(p3._get_fake_stdio_ucontent(sys.stdout))
+            self.captured_stderr = self.normalize(p3._get_fake_stdio_ucontent(sys.stderr))
+            sys.stderr, sys.stdout = sys_stderr, sys_stdout
+
         if expected_out is not None:
-            self.assertEqual(p3.u_maybe(actual_out), p3.u_maybe(expected_out))
+            self.assertEqual(p3.u_maybe(self.captured_stdout), p3.u_maybe(expected_out))
         if expected_err is not None:
-            self.assertEqual(p3.u_maybe(actual_err), p3.u_maybe(expected_err))
-        return actual_out
-
-    def tearDown(self):
-        pass
+            self.assertEqual(p3.u_maybe(self.captured_stderr), p3.u_maybe(expected_err))
+        return self.captured_stdout
 
     def update_config(self, config_update, path=None):
         """Allow to set the config parameters. Must have done a `pubs init` beforehand."""
@@ -624,6 +627,7 @@ class TestTag(DataCommandTestCase):
         with self.assertRaises(FakeSystemExit):
             self.execute_cmds(cmds)
 
+
 class TestURL(DataCommandTestCase):
 
     def setUp(self):
@@ -1126,6 +1130,21 @@ class TestUsecase(DataCommandTestCase):
         self.execute_cmds(cmds, capture_output=True)
 #        self.assertEqual(correct, self.execute_cmds(cmds, capture_output=True))
 
+    def test_ambiguous_citekey(self):
+        cmds = ['pubs init',
+                'pubs add data/pagerank.bib',
+                'pubs add data/pagerank.bib', # now we have Page99 and Page99a
+                'pubs edit Page',
+                ]
+        output = '\n'.join(["error: Be more specific; 'Page' matches multiples citekeys:",
+                            "    [Page99] Page, Lawrence et al. \"The PageRank Citation Ranking: Bringing Order to the Web.\" (1999) ",
+                            "    [Page99a] Page, Lawrence et al. \"The PageRank Citation Ranking: Bringing Order to the Web.\" (1999) \n"])
+
+        with self.assertRaises(FakeSystemExit):
+            self.execute_cmds(cmds)
+
+        self.assertEqual(self.captured_stderr, output)
+
 
 
 @ddt.ddt

From 54facc4085053cbb31d4eb712f91d6a715ab5e0b Mon Sep 17 00:00:00 2001
From: beuerle <beuerle@users.noreply.github.com>
Date: Mon, 25 May 2020 13:59:40 +0200
Subject: [PATCH 17/45] fix statistics cmd; count papers w/ tag, not w/o

---
 pubs/commands/statistics_cmd.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pubs/commands/statistics_cmd.py b/pubs/commands/statistics_cmd.py
index e3b6583..a606fa0 100644
--- a/pubs/commands/statistics_cmd.py
+++ b/pubs/commands/statistics_cmd.py
@@ -22,7 +22,7 @@ def command(conf, args):
     else:
         doc_count = sum([0 if p.docpath is None else 1 for p in papers])
         tag_count = len(list(rp.get_tags()))
-        papers_with_tags = sum([0 if p.tags else 1 for p in papers])
+        papers_with_tags = sum([1 if p.tags else 0 for p in papers])
 
         ui.message(color.dye_out('Repository statistics:', 'bold'))
         ui.message('Total papers: {}, {} ({}) have a document attached'.format(

From d11f44327617e9a69c27bf0d8c196bfd2f13330a Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Fri, 5 Jun 2020 13:22:54 +0900
Subject: [PATCH 18/45] explicit move/copy dialog in add; update changelog

---
 changelog.md             | 42 ++++++++--------------------------------
 pubs/commands/add_cmd.py | 19 ++++++++++--------
 pubs/commands/doc_cmd.py |  1 +
 pubs/repo.py             | 13 +++++++++----
 readme.md                |  1 +
 tests/test_usecase.py    |  7 ++++---
 6 files changed, 34 insertions(+), 49 deletions(-)

diff --git a/changelog.md b/changelog.md
index f7aeafb..3c056a7 100644
--- a/changelog.md
+++ b/changelog.md
@@ -7,12 +7,17 @@
 
 ### Implemented enhancements
 
-- Added support for non-standard bibtex types, e.g. @collection, @software, etc. ([#226](https://github.com/pubs/pubs/pull/226)
-- The number of displayed authors in listings is now configurable, as the `max_authors` value in the `main` section of the configuration. ([#225](https://github.com/pubs/pubs/pull/225)
+- Added support for non-standard bibtex types, e.g. @collection, @software, etc. ([#226](https://github.com/pubs/pubs/pull/226))
+- The number of displayed authors in listings is now configurable, as the `max_authors` value in the `main` section of the configuration. ([#225](https://github.com/pubs/pubs/pull/225))
+- More explicit add command dialogs when copying and moving documents.
+- Empty tags are not added to papers anymore.
 
 ### Fixed bugs
 
-- Tests don't run on python 2.7 or <=3.4. They may still work, but support will not be tested and will eventually be dropped. ([#223](https://github.com/pubs/pubs/pull/223)
+- Tests don't run on python 2.7 or <=3.4. They may still work, but support will not be tested and will eventually be dropped. ([#223](https://github.com/pubs/pubs/pull/223))
+- Fixed the reported number of paper with a tag in the statistic command ([#232](https://github.com/pubs/pubs/pull/232)  by [beuerle](https://github.com/beuerle))
+- Fixed a crash when resolving citekeys introduced by [#225](https://github.com/pubs/pubs/pull/225) ([#233](https://github.com/pubs/pubs/pull/233)  by [beuerle](https://github.com/beuerle))
+
 
 ## [v0.8.3](https://github.com/pubs/pubs/compare/v0.8.2...v0.8.3) (2019-08-12)
 
@@ -44,7 +49,6 @@ A hotfix release. All users of 0.8.0 are urged to upgrade.
 ### Fixed bugs
 
 - Fix adding paper with DOIs, ISBNs or arXiv references. [(#165)](https://github.com/pubs/pubs/pull/165)
-
 - Fix statistics command when there is not yet any paper in the repository. [(#164)](https://github.com/pubs/pubs/pull/164)
 
 
@@ -55,69 +59,39 @@ A long overdue feature release. Add supports for arXiv bibtex fetching, and many
 ### Implemented enhancements
 
 - Adds `move`, and `link` options for handling of documents during `import` (copy being the default). Makes `copy` the default for document handling during `add`. [(#159)](https://github.com/pubs/pubs/pull/159)
-
 - Support for downloading arXiv reference from their ID ([#146](https://github.com/pubs/pubs/issues/146) by [joe-antognini](https://github.com/joe-antognini))
-
 - Better feedback when an error is encountered while adding a reference from a DOI, ISBN or arXiv ID [#155](https://github.com/pubs/pubs/issues/155)
-
 - Better dialog after editing paper [(#142)](https://github.com/pubs/pubs/issues/142)
-
 - Add a command to open urls ([#139](https://github.com/pubs/pubs/issues/139) by [ksunden](https://github.com/ksunden))
-
 - More robust cache on version change [(#138)](https://github.com/pubs/pubs/issues/138)
-
 - Allow utf8 citekeys [(#133)](https://github.com/pubs/pubs/issues/133)
-
 - Adds tag list completion in `pubs add -t ` [(#130)](https://github.com/pubs/pubs/issues/130)
-
 - Wider Travis coverage ([#107](https://github.com/pubs/pubs/issues/107) and [#108](https://github.com/pubs/pubs/issues/108))
-
 - Uses bibtexparser bwriter instead of internal encoder and adds `--ignore-fields` option to export. [(#106)](https://github.com/pubs/pubs/issues/106)
-
 - Configurable alias descriptions ([#104](https://github.com/pubs/pubs/issues/104) by [wflynny](https://github.com/wflynny))
-
 - Support year ranges in query [(#102)](https://github.com/pubs/pubs/issues/102)
-
 - Tests can now be run with `python setup.py test` [#155](https://github.com/pubs/pubs/issues/155)
 
 ### Fixed bugs
 
 - [[#144]](https://github.com/pubs/pubs/issues/144) More robust handling of the `doc_add` options [(#159)](https://github.com/pubs/pubs/pull/159)
-
 - [[#149]](https://github.com/pubs/pubs/issues/149) More robust handling of parsing and citekey errors [(#87)](https://github.com/pubs/pubs/pull/87)
-
 - [[#148]](https://github.com/pubs/pubs/issues/148) Fix compatibility with Pyfakefs 3.7 [(#151)](https://github.com/pubs/pubs/pull/151)
-
 - [[#95]](https://github.com/pubs/pubs/issues/95) Error message when editor is missing [(#141)](https://github.com/pubs/pubs/issues/141)
-
 - Fixes tests for printing help on `--help` and without argument. [(#137)](https://github.com/pubs/pubs/issues/137)
-
 - [[#126]](https://github.com/pubs/pubs/issues/126) Removes journal customization [(#127)](https://github.com/pubs/pubs/issues/127)
-
 - Fixes Travis failure on installing python3 for OSX [(#125)](https://github.com/pubs/pubs/issues/125)
-
 - [[#119]](https://github.com/pubs/pubs/issues/119) Removes link and DOI customization. [(#124)](https://github.com/pubs/pubs/issues/124)
-
 - [[#122]](https://github.com/pubs/pubs/issues/122) Fixes common strings [(#123)](https://github.com/pubs/pubs/issues/123)
-
 - [[#28]](https://github.com/pubs/pubs/issues/28) allow utf8 in citekeys [(#120)](https://github.com/pubs/pubs/issues/120)
-
 - Fixes field orders to use 'url' and fixes broken test. [(#118)](https://github.com/pubs/pubs/issues/118)
-
 - [[#25]](https://github.com/pubs/pubs/issues/25) Fix bibtex testcase [(#117)](https://github.com/pubs/pubs/issues/117)
-
 - [[#103]](https://github.com/pubs/pubs/issues/103) Fixes unicode comparison [(#116)](https://github.com/pubs/pubs/issues/116)
-
 - [[#95]](https://github.com/pubs/pubs/issues/95) robust handling of DOIs ([#105](https://github.com/pubs/pubs/issues/105) by [wflynny](https://github.com/wflynny))
-
 - [[#99]](https://github.com/pubs/pubs/issues/99) Print help when no subcommand is provided ([#100](https://github.com/pubs/pubs/issues/100) by [wflynny](https://github.com/wflynny))
-
 - Fix defaults not used in config. [(#97)](https://github.com/pubs/pubs/issues/97)
-
 - Fixes content not read from urls because of call to `os.abspath` [(#96)](https://github.com/pubs/pubs/issues/96)
-
 - [[#93]](https://github.com/pubs/pubs/issues/93) actually save the modifications on `edit -m`. [(#94)](https://github.com/pubs/pubs/issues/94)
-
 - [[#88]](https://github.com/pubs/pubs/issues/88) Adds proper escaping for
 arguments in alias plugin. [(#91)](https://github.com/pubs/pubs/issues/91)
 
diff --git a/pubs/commands/add_cmd.py b/pubs/commands/add_cmd.py
index 9e9dd0d..ada5e7c 100644
--- a/pubs/commands/add_cmd.py
+++ b/pubs/commands/add_cmd.py
@@ -6,6 +6,7 @@ from .. import p3
 from .. import bibstruct
 from .. import content
 from .. import repo
+from .. import color
 from .. import paper
 from .. import templates
 from .. import apis
@@ -149,13 +150,15 @@ def command(conf, args):
     rp.push_paper(p)
     ui.message('added to pubs:\n{}'.format(pretty.paper_oneliner(p, max_authors=conf['main']['max_authors'])))
     if docfile is not None:
-        rp.push_doc(p.citekey, docfile, copy=(doc_add in ('copy', 'move')))
-        if doc_add == 'move' and content.content_type(docfile) != 'url':
-            content.remove_file(docfile)
-
-        if doc_add == 'move':
-            ui.message('{} was moved to the pubs repository.'.format(docfile))
-        elif doc_add == 'copy':
-            ui.message('{} was copied to the pubs repository.'.format(docfile))
+        rp.push_doc_paper(p, docfile, copy=(doc_add in ('copy', 'move')))
+
+        if doc_add in ('move', 'copy'):
+            if doc_add == 'move' and content.content_type(docfile) != 'url':
+                content.remove_file(docfile)
+
+            docpath = content.system_path(rp.databroker.real_docpath(p.docpath))
+            verb = 'moved' if doc_add == 'move' else 'copied'
+            ui.message('{} was {} to {} inside the pubs repository.'.format(color.dye_out(docfile, 'filepath'), verb,
+                                                                            color.dye_out(docpath, 'filepath')))
 
     rp.close()
diff --git a/pubs/commands/doc_cmd.py b/pubs/commands/doc_cmd.py
index 2bb6f9c..95e314e 100644
--- a/pubs/commands/doc_cmd.py
+++ b/pubs/commands/doc_cmd.py
@@ -92,6 +92,7 @@ def command(conf, args):
         if not args.link and args.move:
             content.remove_file(document)
 
+        # FIXME: coherence with add command, the destination location should be given when copying/moving.
         ui.message('{} added to {}'.format(
             color.dye_out(document, 'filepath'),
             color.dye_out(paper.citekey, 'citekey')))
diff --git a/pubs/repo.py b/pubs/repo.py
index 4b341a4..e97e022 100644
--- a/pubs/repo.py
+++ b/pubs/repo.py
@@ -182,17 +182,22 @@ class Repository(object):
             events.RenameEvent(paper, old_citekey).send()
             return True
 
+
     def push_doc(self, citekey, docfile, copy=None):
         p = self.pull_paper(citekey)
+        return self.push_doc_paper(p, docfile, copy=copy)
+
+    def push_doc_paper(self, paper, docfile, copy=None):
+        """Same as push_doc, only the Paper instance is provided rather than the citekey"""
         if copy is None:
             copy = self.conf['main']['doc_add'] in ('copy', 'move')
         if copy:
-            docfile = self.databroker.add_doc(citekey, docfile)
+            docfile = self.databroker.add_doc(paper.citekey, docfile)
         else:
             docfile = system_path(docfile)
-        p.docpath = docfile
-        self.push_paper(p, overwrite=True, event=False)
-        events.DocAddEvent(citekey).send()
+        paper.docpath = docfile
+        self.push_paper(paper, overwrite=True, event=False)
+        events.DocAddEvent(paper.citekey).send()
 
     def unique_citekey(self, base_key, bibentry):
         """Create a unique citekey for a given base key.
diff --git a/readme.md b/readme.md
index aa4c691..7bc2a40 100644
--- a/readme.md
+++ b/readme.md
@@ -183,3 +183,4 @@ You can access the self-documented configuration by using `pubs conf`, and all t
 - [Shane Stone](https://github.com/shanewstone)
 - [Amlesh Sivanantham](http://github.com/zamlz)
 - [DV Klopfenstein](http://github.com/dvklopfenstein)
+- [beuerle](https://github.com/beuerle)
diff --git a/tests/test_usecase.py b/tests/test_usecase.py
index ba94559..9219657 100644
--- a/tests/test_usecase.py
+++ b/tests/test_usecase.py
@@ -12,6 +12,7 @@ import ddt
 import certifi
 import mock
 from pyfakefs.fake_filesystem import FakeFileOpen
+import pytest
 
 import dotdot
 import fake_env
@@ -26,7 +27,7 @@ import fixtures
 
 
 # makes the tests very noisy
-PRINT_OUTPUT   = False
+PRINT_OUTPUT   = True #False
 CAPTURE_OUTPUT = True
 
 
@@ -733,7 +734,7 @@ class TestUsecase(DataCommandTestCase):
     def test_first(self):
         correct = ['Initializing pubs in /paper_first\n',
                    'added to pubs:\n[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
-                   'data/pagerank.pdf was copied to the pubs repository.\n',
+                   'data/pagerank.pdf was copied to /paper_first/doc/Page99.pdf inside the pubs repository.\n',
                    '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) [pdf] \n',
                    '\n',
                    '',
@@ -1085,7 +1086,7 @@ class TestUsecase(DataCommandTestCase):
                               target_path=os.path.join('data', 'no-ext'))
         correct = ['Initializing pubs in /pubs\n',
                    'added to pubs:\n[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
-                   'data/no-ext was copied to the pubs repository.\n',
+                   'data/no-ext was copied to /pubs/doc/Page99 inside the pubs repository.\n',
                    '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) [NOEXT] \n',
                   ]
         cmds = ['pubs init -p /pubs',

From d0608697bb762bf3442f472f94fd3184be9ec9cc Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Sat, 7 Nov 2020 16:45:47 -0800
Subject: [PATCH 19/45] Add pytest to test requirements as none optional.

---
 dev_requirements.txt | 2 +-
 setup.py             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/dev_requirements.txt b/dev_requirements.txt
index f6555a6..b9879c5 100644
--- a/dev_requirements.txt
+++ b/dev_requirements.txt
@@ -24,4 +24,4 @@ certifi
 #        (also remove in setup.py)
 ddt==1.3.1
 mock
-pytest # optional (python setup.py test works without it), but possible nonetheless
+pytest
diff --git a/setup.py b/setup.py
index a8eb7de..18c64cf 100644
--- a/setup.py
+++ b/setup.py
@@ -61,7 +61,7 @@ setup(
     ],
 
     test_suite='tests',
-    tests_require=['pyfakefs>=3.4', 'mock', 'ddt==1.3.1', 'certifi'],
+    tests_require=['pyfakefs>=3.4', 'mock', 'ddt==1.3.1', 'certifi', 'pytest'],
 
     # in order to avoid 'zipimport.ZipImportError: bad local file header'
     zip_safe=False,

From c21659eb98418d7cbc89849b2347218d9f0dd9d7 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Sat, 7 Nov 2020 17:27:58 -0800
Subject: [PATCH 20/45] Update dependencies and test to drop python 3.5
 support.

The reason for dropping python 3.5 support is that it is not compatible
with the feedparser dependency. The version is anyway not supported any
more (security fixes stopped on 2020/09).
---
 .travis.yml | 5 -----
 setup.py    | 3 +--
 2 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 9f84fc9..3792177 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -21,11 +21,6 @@ matrix:
         - source env/bin/activate
 
     # Mock tests (with mock API)
-    - os: linux
-      language: python
-      python: 3.5
-      env:
-        - TO_TEST=TEST_MOCK
     - os: linux
       language: python
       python: 3.6
diff --git a/setup.py b/setup.py
index 18c64cf..f5e45d2 100644
--- a/setup.py
+++ b/setup.py
@@ -45,16 +45,15 @@ setup(
         },
 
     include_package_data=True,
-
     install_requires=['pyyaml', 'bibtexparser>=1.0', 'python-dateutil', 'six',
                       'requests', 'configobj', 'beautifulsoup4', 'feedparser'],
     extras_require={'autocompletion': ['argcomplete'],
                     },
 
+    python_requires='>=3.6',
     classifiers=[
         'Development Status :: 4 - Beta',
         'License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)',
-        'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
         'Intended Audience :: Developers',
         'Intended Audience :: Science/Research',

From f1fd60679bddf94ad5ad48cb2cc83bac3f140526 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Sat, 7 Nov 2020 17:30:21 -0800
Subject: [PATCH 21/45] Adds python 3.9 to build matrix.

---
 .travis.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 3792177..a03b5d2 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,7 +5,7 @@ matrix:
     # Full tests (with online API)
     - os: linux
       language: python
-      python: 3.7
+      python: 3.9
       dist: xenial
       sudo: true
       env:
@@ -40,6 +40,13 @@ matrix:
       sudo: true
       env:
         - TO_TEST=TEST_MOCK
+    - os: linux
+      language: python
+      dist: xenial
+      python: 3.9
+      sudo: true
+      env:
+        - TO_TEST=TEST_MOCK
 
 
     # Install tests
@@ -53,7 +60,7 @@ matrix:
       language: python
       dist: xenial
       sudo: true
-      python: 3.8
+      python: 3.9
       env:
         - TO_TEST=INSTALL
       if: type = cron

From e6d0754a8d2c22be92af4d2b0bd23b945546d95f Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Tue, 12 Jan 2021 11:41:35 +0900
Subject: [PATCH 22/45] Fix #249: ~ expansion in filebroker.DocBroker

---
 pubs/filebroker.py       |  2 +-
 tests/test_filebroker.py | 10 ++++++++++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/pubs/filebroker.py b/pubs/filebroker.py
index 7043f4c..7c052b3 100644
--- a/pubs/filebroker.py
+++ b/pubs/filebroker.py
@@ -154,7 +154,7 @@ class DocBroker(object):
 
     def __init__(self, directory, scheme='docsdir', subdir='doc'):
         self.scheme = scheme
-        self.docdir = os.path.join(directory, subdir)
+        self.docdir = os.path.expanduser(os.path.join(directory, subdir))
         if not check_directory(self.docdir, fail=False):
             os.mkdir(system_path(self.docdir))
 
diff --git a/tests/test_filebroker.py b/tests/test_filebroker.py
index f8560a9..1f09008 100644
--- a/tests/test_filebroker.py
+++ b/tests/test_filebroker.py
@@ -71,6 +71,16 @@ class TestFileBroker(fake_env.TestFakeFs):
 
 class TestDocBroker(fake_env.TestFakeFs):
 
+    def test_expanduser(self):
+        """Test that real_docpath expand the user ~"""
+
+        self.fs.add_real_directory(os.path.join(self.rootpath, 'data'), read_only=False)
+        fb = filebroker.FileBroker('~/testrepo', create = True)
+        docb = filebroker.DocBroker('~/testrepo')
+        self.assertTrue(os.path.isabs(docb.docdir))
+        self.assertTrue(os.path.isabs(docb.real_docpath('docsdir://abc')))
+
+
     def test_doccopy(self):
 
         self.fs.add_real_directory(os.path.join(self.rootpath, 'data'), read_only=False)

From 89429a8c24d0aef444de614f2a102feeb14b615f Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Sat, 16 Jan 2021 12:22:05 +0900
Subject: [PATCH 23/45] update changelog

---
 changelog.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/changelog.md b/changelog.md
index 3c056a7..1c712f3 100644
--- a/changelog.md
+++ b/changelog.md
@@ -14,6 +14,7 @@
 
 ### Fixed bugs
 
+- Note path correctly expand user '~' ([#250](https://github.com/pubs/pubs/pull/250))
 - Tests don't run on python 2.7 or <=3.4. They may still work, but support will not be tested and will eventually be dropped. ([#223](https://github.com/pubs/pubs/pull/223))
 - Fixed the reported number of paper with a tag in the statistic command ([#232](https://github.com/pubs/pubs/pull/232)  by [beuerle](https://github.com/beuerle))
 - Fixed a crash when resolving citekeys introduced by [#225](https://github.com/pubs/pubs/pull/225) ([#233](https://github.com/pubs/pubs/pull/233)  by [beuerle](https://github.com/beuerle))

From 0777a99d3037ddedc4f9631704d123de1146b787 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jon=C3=A1=C5=A1=20Kulh=C3=A1nek?= <jonas.kulhanek@live.com>
Date: Fri, 7 Aug 2020 10:54:45 +0200
Subject: [PATCH 24/45] Allow passing named arguments to custom commands.

This allows passing named arguments to custom commands. An example would be `pubs search keyword --ignore-author` and the corresponding alias would redirect the call to the custom script like follows: `search = !"$DOTFILES/pubs/scripts/search.py" "$@"`.
---
 pubs/plugs/alias/alias.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pubs/plugs/alias/alias.py b/pubs/plugs/alias/alias.py
index fd9cae2..5bee03d 100644
--- a/pubs/plugs/alias/alias.py
+++ b/pubs/plugs/alias/alias.py
@@ -1,5 +1,6 @@
 import shlex
 import subprocess
+import argparse
 from pipes import quote as shell_quote
 
 from ...plugins import PapersPlugin
@@ -19,7 +20,7 @@ class Alias(object):
     def parser(self, parser):
         self.parser = parser
         p = parser.add_parser(self.name, help=self.description)
-        p.add_argument('arguments', nargs='*',
+        p.add_argument('arguments', nargs=argparse.REMAINDER,
                        help="arguments to be passed to %s" % self.name)
         return p
 

From 2e939dbc1b1cebef11bfc78d07e3d84b0780cfa9 Mon Sep 17 00:00:00 2001
From: Jonas Kulhanek <jonas.kulhanek@live.com>
Date: Thu, 26 Nov 2020 11:46:14 +0100
Subject: [PATCH 25/45] Add tests for alias

---
 tests/test_plug_alias.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/tests/test_plug_alias.py b/tests/test_plug_alias.py
index 63086f7..d91f677 100644
--- a/tests/test_plug_alias.py
+++ b/tests/test_plug_alias.py
@@ -1,7 +1,7 @@
 import shlex
 import unittest
-
 import dotdot
+import argparse
 
 import pubs
 from pubs import config
@@ -61,6 +61,19 @@ class AliasTestCase(unittest.TestCase):
             shlex.split(self.subprocess.called.splitlines()[-1])[1:],
             args)
 
+    def testShellAliasNamedArguments(self):
+        parser = argparse.ArgumentParser()
+        parser.add_argument('--test2')
+        subparsers = parser.add_subparsers(title='commands', dest='command')
+
+        alias = Alias.create_alias('test', '!echo "$@"')
+        alias.parser(subparsers)
+        args = ['test', '2', '--option', '3']
+        args = parser.parse_args(args)
+
+        self.assertEqual(args.command, 'test')
+        self.assertListEqual(args.arguments, ['2', '--option', '3'])
+
 
 class AliasPluginTestCase(unittest.TestCase):
 

From 1130a9343d14e808725b5224513611bf7d1329a3 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Sat, 16 Jan 2021 12:46:17 +0900
Subject: [PATCH 26/45] fix deprecation warning in color.py

---
 pubs/color.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pubs/color.py b/pubs/color.py
index 0e41cf9..7a3ad64 100644
--- a/pubs/color.py
+++ b/pubs/color.py
@@ -144,7 +144,7 @@ def setup(conf, force_colors=False):
 
 
 # undye
-undye_re = re.compile('\x1b\\[[;\d]*[A-Za-z]')
+undye_re = re.compile('\x1b\\[[;\\d]*[A-Za-z]')
 
 def undye(s):
     """Purge string s of color"""

From 5d6010394d81926c622c8e08752583427bb15654 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dominik=20Sta=C5=84czak?= <stanczakdominik@gmail.com>
Date: Wed, 15 Jul 2020 09:17:58 +0200
Subject: [PATCH 27/45] Add note on using commas in alias descriptions

On my installation, using commas in docstring descriptions causes a `error: unsupported operand type(s) for %: 'list' and 'dict'` error. Wrapping the description in a string solves that.
---
 pubs/config/spec.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/pubs/config/spec.py b/pubs/config/spec.py
index 6921bae..c98df99 100644
--- a/pubs/config/spec.py
+++ b/pubs/config/spec.py
@@ -99,6 +99,11 @@ active = force_list(default=list('alias'))
 # command = !pubs list -k | wc -l
 # description = lists number of pubs in repo
 
+# To use commas in the description, wrap them in a "" string. For example:
+# [[[hellocount]]]
+# command = !pubs list -k | wc -l; echo "hello!"
+# description = "lists number of pubs in repo, greets the user afterward"
+
 [[git]]
 # The git plugin will commit changes to the repository in a git repository
 # created at the root of the pubs directory. All detected changes will be

From a8ec3f41e6c3f03693e6feb7cd24ca0c6309eb05 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dominik=20Sta=C5=84czak?= <stanczakdominik@gmail.com>
Date: Sat, 7 Nov 2020 18:57:23 +0100
Subject: [PATCH 28/45] Adjust for conciseness

---
 pubs/config/spec.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pubs/config/spec.py b/pubs/config/spec.py
index c98df99..b691f80 100644
--- a/pubs/config/spec.py
+++ b/pubs/config/spec.py
@@ -100,8 +100,6 @@ active = force_list(default=list('alias'))
 # description = lists number of pubs in repo
 
 # To use commas in the description, wrap them in a "" string. For example:
-# [[[hellocount]]]
-# command = !pubs list -k | wc -l; echo "hello!"
 # description = "lists number of pubs in repo, greets the user afterward"
 
 [[git]]

From dc2bc9c0e5d1025f72fbf5930ffd87f16ad24b2e Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Sat, 16 Jan 2021 13:06:18 +0900
Subject: [PATCH 29/45] update changelog and contributors

---
 changelog.md | 2 ++
 readme.md    | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/changelog.md b/changelog.md
index 1c712f3..0a25116 100644
--- a/changelog.md
+++ b/changelog.md
@@ -7,6 +7,7 @@
 
 ### Implemented enhancements
 
+- Allow passing named arguments to custom commands ([#241](https://github.com/pubs/pubs/pull/241) by [jkulhanek](https://github.com/jkulhanek))
 - Added support for non-standard bibtex types, e.g. @collection, @software, etc. ([#226](https://github.com/pubs/pubs/pull/226))
 - The number of displayed authors in listings is now configurable, as the `max_authors` value in the `main` section of the configuration. ([#225](https://github.com/pubs/pubs/pull/225))
 - More explicit add command dialogs when copying and moving documents.
@@ -14,6 +15,7 @@
 
 ### Fixed bugs
 
+- Note on comma in alias descriptions ([#240](https://github.com/pubs/pubs/pull/240) [StanczakDominik](https://github.com/StanczakDominik))
 - Note path correctly expand user '~' ([#250](https://github.com/pubs/pubs/pull/250))
 - Tests don't run on python 2.7 or <=3.4. They may still work, but support will not be tested and will eventually be dropped. ([#223](https://github.com/pubs/pubs/pull/223))
 - Fixed the reported number of paper with a tag in the statistic command ([#232](https://github.com/pubs/pubs/pull/232)  by [beuerle](https://github.com/beuerle))
diff --git a/readme.md b/readme.md
index 7bc2a40..e4de268 100644
--- a/readme.md
+++ b/readme.md
@@ -184,3 +184,5 @@ You can access the self-documented configuration by using `pubs conf`, and all t
 - [Amlesh Sivanantham](http://github.com/zamlz)
 - [DV Klopfenstein](http://github.com/dvklopfenstein)
 - [beuerle](https://github.com/beuerle)
+- [Jonáš Kulhánek](https://github.com/jkulhanek)
+- [Dominik Stańczak](https://github.com/StanczakDominik)

From c363e13cbf55ac930cc28d9c95dedcc2b8d4ae8b Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Sun, 17 Jan 2021 14:38:04 -0800
Subject: [PATCH 30/45] Fix collision of entry type key with valid field name
 'type'.

Fixes #252.
---
 pubs/bibstruct.py       |  2 +-
 tests/test_endecoder.py | 14 ++++++++++++++
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/pubs/bibstruct.py b/pubs/bibstruct.py
index a8312b0..d3e6614 100644
--- a/pubs/bibstruct.py
+++ b/pubs/bibstruct.py
@@ -7,7 +7,7 @@ from .p3 import ustr, uchr
 
 # Citekey stuff
 
-TYPE_KEY = 'type'
+TYPE_KEY = 'ENTRYTYPE'
 
 CONTROL_CHARS = ''.join(map(uchr, list(range(0, 32)) + list(range(127, 160))))
 CITEKEY_FORBIDDEN_CHARS = '@\'\\,#}{~%/ '  # '/' is OK for bibtex but forbidden
diff --git a/tests/test_endecoder.py b/tests/test_endecoder.py
index d9ade7f..eaa95e4 100644
--- a/tests/test_endecoder.py
+++ b/tests/test_endecoder.py
@@ -57,6 +57,12 @@ class TestEnDecode(unittest.TestCase):
 
         self.assertEqual(bibraw1, bibraw2)
 
+    def test_decode_bibtex_preserves_type_field(self):
+        """Test that multiple encode/decode step preserve data"""
+        decoder = endecoder.EnDecoder()
+        entry = decoder.decode_bibdata(bibtex_raw0)
+        self.assertEqual(entry['Page99']['type'], "technical report")
+
     def test_endecode_bibtex_BOM(self):
         """Test that bibtexparser if fine with BOM-prefixed data"""
         decoder = endecoder.EnDecoder()
@@ -179,6 +185,14 @@ class TestEnDecode(unittest.TestCase):
         with self.assertRaises(decoder.BibDecodingError):
             decoder.decode_bibdata("@misc{I am not a correct bibtex{{}")
 
+    def test_endecode_preserves_type(self):
+        decoder = endecoder.EnDecoder()
+        entry = decoder.decode_bibdata(bibtex_raw0)
+
+        bibraw1 = decoder.encode_bibdata(
+            entry, ignore_fields=['title', 'note', 'abstract', 'journal'])
+
+
 
 if __name__ == '__main__':
     unittest.main()

From 7c5cbf4267acc53eda55c844e4ce055afb29bf5f Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Tue, 19 Jan 2021 12:56:57 -0800
Subject: [PATCH 31/45] Minor: remove unused partial test.

---
 tests/test_endecoder.py | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/tests/test_endecoder.py b/tests/test_endecoder.py
index eaa95e4..858213f 100644
--- a/tests/test_endecoder.py
+++ b/tests/test_endecoder.py
@@ -185,14 +185,6 @@ class TestEnDecode(unittest.TestCase):
         with self.assertRaises(decoder.BibDecodingError):
             decoder.decode_bibdata("@misc{I am not a correct bibtex{{}")
 
-    def test_endecode_preserves_type(self):
-        decoder = endecoder.EnDecoder()
-        entry = decoder.decode_bibdata(bibtex_raw0)
-
-        bibraw1 = decoder.encode_bibdata(
-            entry, ignore_fields=['title', 'note', 'abstract', 'journal'])
-
-
 
 if __name__ == '__main__':
     unittest.main()

From 16ae70d7736c6d93fd64be30436246f016f39f0a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gustavo=20Jos=C3=A9=20de=20Sousa?=
 <guludo@users.noreply.github.com>
Date: Thu, 21 Jan 2021 12:07:20 -0300
Subject: [PATCH 32/45] Update links for argcomplete

The location for argcomplete's documentation has been changed to https://kislyuk.github.io/argcomplete .
---
 readme.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/readme.md b/readme.md
index e4de268..19f38fc 100644
--- a/readme.md
+++ b/readme.md
@@ -147,7 +147,7 @@ The second starts with a bang: `!`, and is treated as a shell command. If other
 
 ## Autocompletion
 
-For autocompletion to work, you need the [argcomplete](https://argcomplete.readthedocs.io) Python package, and Bash 4.2 or newer. For activating *bash* or *tsch* completion, consult the [argcomplete documentation](https://argcomplete.readthedocs.io/en/latest/#global-completion).
+For autocompletion to work, you need the [argcomplete](https://kislyuk.github.io/argcomplete) Python package, and Bash 4.2 or newer. For activating *bash* or *tsch* completion, consult the [argcomplete documentation](https://kislyuk.github.io/argcomplete/#global-completion).
 
 For *zsh* completion, the global activation is not supported but bash completion compatibility can be used for pubs. For that, add the following to your `.zshrc`:
   ```shell

From 0eeec091bf4ed7821fecf3b27efbc3ba8eb9ca45 Mon Sep 17 00:00:00 2001
From: Gustavo Sousa <gustavo.jo.sousa@gmail.com>
Date: Thu, 21 Jan 2021 12:59:29 -0300
Subject: [PATCH 33/45] Detect HTTPS links in content_type()

This allows downloading files provided via https links.
---
 pubs/content.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pubs/content.py b/pubs/content.py
index b1e403b..e06b72e 100644
--- a/pubs/content.py
+++ b/pubs/content.py
@@ -114,7 +114,7 @@ def write_file(filepath, data, mode='w'):
 
 def content_type(path):
     parsed = urlparse(path)
-    if parsed.scheme == 'http':
+    if parsed.scheme in ('http', 'https'):
         return 'url'
     else:
         return 'file'

From 96cce2cab5b4f3016bbcf7b08c2bd4fd8108d3e1 Mon Sep 17 00:00:00 2001
From: "Fabien C. Y. Benureau" <fabien@benureau.com>
Date: Fri, 22 Jan 2021 10:05:32 +0900
Subject: [PATCH 34/45] update contributors

---
 readme.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/readme.md b/readme.md
index 19f38fc..cf1fdff 100644
--- a/readme.md
+++ b/readme.md
@@ -186,3 +186,4 @@ You can access the self-documented configuration by using `pubs conf`, and all t
 - [beuerle](https://github.com/beuerle)
 - [Jonáš Kulhánek](https://github.com/jkulhanek)
 - [Dominik Stańczak](https://github.com/StanczakDominik)
+- [Gustavo José de Sousa](https://github.com/guludo)

From 1865e64ce37e1d1178cfd64a0a0705b4d7946124 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Sun, 24 Jan 2021 17:54:33 -0800
Subject: [PATCH 35/45] Update ddt dependency after upstream bug fix.

---
 dev_requirements.txt | 4 +---
 setup.py             | 2 +-
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/dev_requirements.txt b/dev_requirements.txt
index b9879c5..0b107fb 100644
--- a/dev_requirements.txt
+++ b/dev_requirements.txt
@@ -20,8 +20,6 @@ six
 # those are the additional packages required to run the tests
 pyfakefs
 certifi
-# FIXME: remove strict version when https://github.com/datadriventests/ddt/issues/83 is fixed.
-#        (also remove in setup.py)
-ddt==1.3.1
+ddt>=1.4.1
 mock
 pytest
diff --git a/setup.py b/setup.py
index f5e45d2..011ad68 100644
--- a/setup.py
+++ b/setup.py
@@ -60,7 +60,7 @@ setup(
     ],
 
     test_suite='tests',
-    tests_require=['pyfakefs>=3.4', 'mock', 'ddt==1.3.1', 'certifi', 'pytest'],
+    tests_require=['pyfakefs>=3.4', 'mock', 'ddt>=1.4.1', 'certifi', 'pytest'],
 
     # in order to avoid 'zipimport.ZipImportError: bad local file header'
     zip_safe=False,

From 741392658984deabddf0a6612e3cdd6bbee449ab Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Mon, 25 Jan 2021 21:37:45 -0800
Subject: [PATCH 36/45] Add github test workflow.

---
 .github/workflows/tests.yaml | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 .github/workflows/tests.yaml

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
new file mode 100644
index 0000000..fbad0e9
--- /dev/null
+++ b/.github/workflows/tests.yaml
@@ -0,0 +1,30 @@
+name: Pubs tests
+
+on: [push, pull_request]
+
+jobs:
+  unit-test:
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r dev_requirements.txt
+      - name: Test with pytest (mock API mode)
+        env:
+          PUBS_TESTS_MODE: MOCK
+        run: pytest
+      - name: Test with pytest (online API mode)
+        env:
+          PUBS_TESTS_MODE: COLLECT
+        run: pytest

From 526ed05c4133c2cd383ffd6ed9cddc02eb32fe51 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Mon, 25 Jan 2021 22:05:34 -0800
Subject: [PATCH 37/45] PEP8 and cosmetic changes.

---
 pubs/plugs/git/git.py | 32 ++++++++++++++++++--------------
 tests/test_git.py     |  3 +--
 2 files changed, 19 insertions(+), 16 deletions(-)

diff --git a/pubs/plugs/git/git.py b/pubs/plugs/git/git.py
index 5be9221..3bff3d6 100644
--- a/pubs/plugs/git/git.py
+++ b/pubs/plugs/git/git.py
@@ -16,11 +16,13 @@ GITIGNORE = """# files or directories for the git plugin to ignore
 
 
 class GitPlugin(PapersPlugin):
-    """The git plugin creates a git repository in the pubs directory and commit the changes
-    to the pubs repository everytime a paper is modified.
+    """Make the pubs repository also a git repository.
 
-    It also add the `pubs git` subcommand, so git commands can be executed in the git repository
-    from the command line.
+    The git plugin creates a git repository in the pubs directory
+    and commit the changes to the pubs repository.
+
+    It also add the `pubs git` subcommand, so git commands can be executed
+    in the git repository from the command line.
     """
 
     name = 'git'
@@ -28,10 +30,10 @@ class GitPlugin(PapersPlugin):
 
     def __init__(self, conf, ui):
         self.ui = ui
-        self.pubsdir     = os.path.expanduser(conf['main']['pubsdir'])
-        self.manual      = conf['plugins'].get('git', {}).get('manual', False)
+        self.pubsdir = os.path.expanduser(conf['main']['pubsdir'])
+        self.manual = conf['plugins'].get('git', {}).get('manual', False)
         self.force_color = conf['plugins'].get('git', {}).get('force_color', True)
-        self.quiet   = conf['plugins'].get('git', {}).get('quiet', True)
+        self.quiet = conf['plugins'].get('git', {}).get('quiet', True)
         self.list_of_changes = []
         self._gitinit()
 
@@ -72,17 +74,18 @@ class GitPlugin(PapersPlugin):
         """
         colorize = ' -c color.ui=always' if self.force_color else ''
         git_cmd = 'git -C {}{} {}'.format(self.pubsdir, colorize, cmd)
-        #print(git_cmd)
         p = Popen(git_cmd, stdin=PIPE, stdout=PIPE, stderr=STDOUT, shell=True)
         output, err = p.communicate(input_stdin)
         p.wait()
 
         if p.returncode != 0:
-            raise RuntimeError('The git plugin encountered an error when running the git command:\n' +
-                '{}\n\nReturned output:\n{}\n'.format(git_cmd, output.decode('utf-8')) +
-                'If needed, you may fix the state of the {} git repository '.format(self.pubsdir) +
-                'manually.\nIf relevant, you may submit a bug report at ' +
-                'https://github.com/pubs/pubs/issues')
+            raise RuntimeError((
+                'The git plugin encountered an error when running the git command:\n'
+                '{}\n\n'
+                'Returned output:\n{}\n'
+                'If needed, you may fix the state of the {} git repository manually.\n'
+                'If relevant, you may submit a bug report at https://github.com/pubs/pubs/issues'
+            ).format(git_cmd, output.decode('utf-8'), self.pubsdir))
         elif command:
             self.ui.message(output.decode('utf-8'), end='')
         elif not self.quiet:
@@ -97,10 +100,11 @@ def paper_change_event(event):
         git = GitPlugin.get_instance()
         if not git.manual:
             event_desc = event.description
-            for a, b in [('\\','\\\\'), ('"','\\"'), ('$','\\$'), ('`','\\`')]:
+            for a, b in [('\\', '\\\\'), ('"', '\\"'), ('$', '\\$'), ('`', '\\`')]:
                 event_desc = event_desc.replace(a, b)
             git.list_of_changes.append(event_desc)
 
+
 @PostCommandEvent.listen()
 def git_commit(event):
     if GitPlugin.is_loaded():
diff --git a/tests/test_git.py b/tests/test_git.py
index 9eb60f8..192c042 100644
--- a/tests/test_git.py
+++ b/tests/test_git.py
@@ -31,7 +31,7 @@ class TestGitPlugin(sand_env.SandboxedCommandTestCase):
         self.execute_cmds([('pubs rename Page99a ABC',)])
         hash_c = git_hash(self.default_pubs_dir)
 
-        self.execute_cmds([('pubs remove ABC', ['y']),])
+        self.execute_cmds([('pubs remove ABC', ['y'])])
         hash_d = git_hash(self.default_pubs_dir)
 
         self.execute_cmds([('pubs doc add testrepo/doc/Page99.pdf Page99',)])
@@ -101,6 +101,5 @@ class TestGitPlugin(sand_env.SandboxedCommandTestCase):
         self.assertNotEqual(hash_l, hash_m)
 
 
-
 if __name__ == '__main__':
     unittest.main()

From fd2227b5482a080a0c74c1b4cb4e7aaec7914dbb Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Mon, 25 Jan 2021 22:18:47 -0800
Subject: [PATCH 38/45] Fix git plugin tests.

Add fake author info to environment while running the tests to avoid
failure of the git commit commands.
---
 .github/workflows/tests.yaml |  7 +++++++
 tests/test_git.py            | 14 +++++++++++++-
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index fbad0e9..fb2b8e0 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -20,6 +20,13 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r dev_requirements.txt
+      - name: Configure git author (fix issue with environment variable)
+        run: |
+          # Manually sets some git user and email to avoid failure of the test
+          # (For some reason the environment variables set in the test are not
+          # taken into account by git on the runner.)
+          git config --global user.name "Pubs test"
+          git config --global user.email "unittest@pubs.org"
       - name: Test with pytest (mock API mode)
         env:
           PUBS_TESTS_MODE: MOCK
diff --git a/tests/test_git.py b/tests/test_git.py
index 192c042..d9926ba 100644
--- a/tests/test_git.py
+++ b/tests/test_git.py
@@ -1,5 +1,6 @@
-import unittest
+import os
 import subprocess
+import unittest
 
 import sand_env
 
@@ -16,12 +17,22 @@ class TestGitPlugin(sand_env.SandboxedCommandTestCase):
 
     def setUp(self, nsec_stat=True):
         super(TestGitPlugin, self).setUp()
+        # Backup environment variables and set git author
+        self.env_backup = os.environ.copy()
+        os.environ['GIT_AUTHOR_NAME'] = "Pubs test"
+        os.environ['GIT_AUTHOR_EMAIL'] = "unittest@pubs.org"
+        # Setup pubs repository
         self.execute_cmds([('pubs init',)])
         conf = config.load_conf(path=self.default_conf_path)
         conf['plugins']['active'] = ['git']
         config.save_conf(conf, path=self.default_conf_path)
 
+    def tearDown(self):
+        super().tearDown()
+        os.environ = self.env_backup
+
     def test_git(self):
+        print(self.default_pubs_dir)
         self.execute_cmds([('pubs add data/pagerank.bib',)])
         hash_a = git_hash(self.default_pubs_dir)
 
@@ -72,6 +83,7 @@ class TestGitPlugin(sand_env.SandboxedCommandTestCase):
         # self.assertEqual(hash_i, hash_j)
 
     def test_manual(self):
+        print(self.default_pubs_dir)
         conf = config.load_conf(path=self.default_conf_path)
         conf['plugins']['active'] = ['git']
         conf['plugins']['git']['manual'] = True

From 745db24eaf76762a3c500fe3a88919c1baf1dec7 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Mon, 25 Jan 2021 23:05:19 -0800
Subject: [PATCH 39/45] Add install test to github action with cron trigger.

The install test is only run when the cron event is the trigger.
---
 .github/workflows/tests.yaml | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index fb2b8e0..28dbaeb 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -1,9 +1,15 @@
 name: Pubs tests
 
-on: [push, pull_request]
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 8 * * *'
+
 
 jobs:
   unit-test:
+    name: Run unit tests
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest]
@@ -35,3 +41,20 @@ jobs:
         env:
           PUBS_TESTS_MODE: COLLECT
         run: pytest
+
+  install-test:
+    name: Test installation
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    if: github.event_name == 'cron'
+
+    steps:
+      - uses: actions/setup-python@v2
+      - name: install test
+        run: |
+          pip install -U pip
+          pip install pubs
+          pubs --help
+          pip uninstall -y pubs

From d89cc30862872a373492d855e4a0be6f47a989d5 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Mon, 25 Jan 2021 23:14:53 -0800
Subject: [PATCH 40/45] Remove travis configuration.

---
 .travis.yml | 89 -----------------------------------------------------
 1 file changed, 89 deletions(-)
 delete mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index a03b5d2..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,89 +0,0 @@
-# list of environments to test
-matrix:
-  include:
-
-    # Full tests (with online API)
-    - os: linux
-      language: python
-      python: 3.9
-      dist: xenial
-      sudo: true
-      env:
-        - TO_TEST=TEST_FULL
-    - os: osx
-      language: generic
-      python: ">=3.6"
-      env:
-        - TO_TEST=TEST_FULL
-      before_install:
-        - brew outdated python3 || brew install python3 || brew upgrade python3
-        - python3 -m venv env
-        - source env/bin/activate
-
-    # Mock tests (with mock API)
-    - os: linux
-      language: python
-      python: 3.6
-      env:
-        - TO_TEST=TEST_MOCK
-    - os: linux
-      language: python
-      dist: xenial
-      python: 3.7
-      sudo: true
-      env:
-        - TO_TEST=TEST_MOCK
-    - os: linux
-      language: python
-      dist: xenial
-      python: 3.8
-      sudo: true
-      env:
-        - TO_TEST=TEST_MOCK
-    - os: linux
-      language: python
-      dist: xenial
-      python: 3.9
-      sudo: true
-      env:
-        - TO_TEST=TEST_MOCK
-
-
-    # Install tests
-    - os: linux
-      language: python
-      python: 2.7
-      env:
-        - TO_TEST=INSTALL
-      if: type = cron
-    - os: linux
-      language: python
-      dist: xenial
-      sudo: true
-      python: 3.9
-      env:
-        - TO_TEST=INSTALL
-      if: type = cron
-    - os: osx
-      language: generic
-      python: 2.7
-      env:
-        - TO_TEST=INSTALL
-      if: type = cron
-    - os: osx
-      language: generic
-      python: ">=3.6"
-      env:
-        - TO_TEST=INSTALL
-      if: type = cron
-
-  allow_failures:
-    - python: 2.7
-
-# command to run tests
-script:
-  - python --version
-  - if [ "$TO_TEST" = "TEST_MOCK" ] ||
-       [ "$TO_TEST" = "TEST_FULL" ]; then PUBS_TESTS_MODE=MOCK    python setup.py test; fi
-  - if [ "$TO_TEST" = "TEST_FULL" ]; then PUBS_TESTS_MODE=COLLECT python setup.py test; fi
-  - if [ "$TO_TEST" = "INSTALL" ]; then pip install -U pip && pip install pubs && pubs --help && pip uninstall -y pubs; fi

From 427af1b4b3379e505d065e18a559798f92f337cb Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Wed, 27 Jan 2021 23:13:40 -0800
Subject: [PATCH 41/45] Use correct event name in workflow.

---
 .github/workflows/tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index 28dbaeb..af0312e 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -48,7 +48,7 @@ jobs:
       matrix:
         os: [macos-latest, ubuntu-latest]
     runs-on: ${{ matrix.os }}
-    if: github.event_name == 'cron'
+    if: github.event_name == 'schedule'
 
     steps:
       - uses: actions/setup-python@v2

From 6e31a98c1898dee6837c44249cb10f9f5c210f10 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Fri, 29 Jan 2021 21:08:35 -0800
Subject: [PATCH 42/45] Minor: forgotten print.

---
 tests/test_git.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_git.py b/tests/test_git.py
index d9926ba..d25e6e7 100644
--- a/tests/test_git.py
+++ b/tests/test_git.py
@@ -32,7 +32,6 @@ class TestGitPlugin(sand_env.SandboxedCommandTestCase):
         os.environ = self.env_backup
 
     def test_git(self):
-        print(self.default_pubs_dir)
         self.execute_cmds([('pubs add data/pagerank.bib',)])
         hash_a = git_hash(self.default_pubs_dir)
 

From a6b63ccafad160051c5f273072b135582fd10c69 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Fri, 29 Jan 2021 21:12:25 -0800
Subject: [PATCH 43/45] Changelog update.

---
 changelog.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/changelog.md b/changelog.md
index 0a25116..ca05610 100644
--- a/changelog.md
+++ b/changelog.md
@@ -7,6 +7,7 @@
 
 ### Implemented enhancements
 
+- Migration from Travis CI to Github actions ([#260](https://github.com/pubs/pubs/pull/260))
 - Allow passing named arguments to custom commands ([#241](https://github.com/pubs/pubs/pull/241) by [jkulhanek](https://github.com/jkulhanek))
 - Added support for non-standard bibtex types, e.g. @collection, @software, etc. ([#226](https://github.com/pubs/pubs/pull/226))
 - The number of displayed authors in listings is now configurable, as the `max_authors` value in the `main` section of the configuration. ([#225](https://github.com/pubs/pubs/pull/225))
@@ -15,6 +16,7 @@
 
 ### Fixed bugs
 
+- Fixed collision when entry uses `type` field ([#252](https://github.com/pubs/pubs/pull/252))
 - Note on comma in alias descriptions ([#240](https://github.com/pubs/pubs/pull/240) [StanczakDominik](https://github.com/StanczakDominik))
 - Note path correctly expand user '~' ([#250](https://github.com/pubs/pubs/pull/250))
 - Tests don't run on python 2.7 or <=3.4. They may still work, but support will not be tested and will eventually be dropped. ([#223](https://github.com/pubs/pubs/pull/223))

From 29e8fecfa9c7bdd991ef231a8fb1d250d9ebd8a9 Mon Sep 17 00:00:00 2001
From: Olivier Mangin <olivier@mangin.com>
Date: Tue, 2 Feb 2021 22:03:33 -0800
Subject: [PATCH 44/45] Minor readme fixes.

---
 readme.md | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/readme.md b/readme.md
index cf1fdff..446a8ad 100644
--- a/readme.md
+++ b/readme.md
@@ -20,19 +20,19 @@ is supposed to do: help us do science, so now we are mostly doing that.
 ## Installation
 
 You can install the latest stable version of `pubs` through Pypi, with:
-  ```
+  ```shell
   pip install pubs
   ```
 
 Alternatively, you can:
 
   - install the latest development version with pip:
-    ```
+    ```shell
     pip install --upgrade git+https://github.com/pubs/pubs
     ```
 
   - clone the repository and install it manually:
-    ```
+    ```shell
     git clone https://github.com/pubs/pubs
     cd pubs
     python setup.py install [--user]
@@ -44,32 +44,32 @@ Arch Linux users can also use the [pubs-git](https://aur.archlinux.org/packages/
 ## Getting started
 
 Create your library (by default, goes to `~/.pubs/`).
-  ```
+  ```shell
   pubs init
   ```
 
 Import existing data from bibtex (pubs will try to automatically copy documents defined as 'file' in bibtex):
-  ```
+  ```shell
   pubs import path/to/collection.bib
   ```
 
 or for a .bib file containing a single reference:
-  ```
+  ```shell
   pubs add reference.bib -d article.pdf
   ```
 
 pubs can also automatically retrieve the bibtex from a doi:
-  ```
+  ```shell
   pubs add -D 10.1007/s00422-012-0514-6 -d article.pdf
   ```
 
 or an ISBN (dashes are ignored):
-  ```
+  ```shell
   pubs add -I 978-0822324669 -d article.pdf
   ```
 
 or an arXiv id (automatically downloading arXiv article is in the works):
-  ```
+  ```shell
   pubs add -X math/9501234 -d article.pdf
   ```
 
@@ -79,7 +79,7 @@ or an arXiv id (automatically downloading arXiv article is in the works):
 If you use latex, you can automatize references, by running `pubs export > references.bib` each time you update your library, which also fits well as a `makefile` rule.
 
 This ensures that your reference file is always up-to-date; you can cite a paper in your manuscript a soon as you add it in pubs. This means that if you have, for instance, a DOI on a webpage, you only need to do:
-  ```
+  ```shell
   pubs add -D 10.1007/s00422-012-0514-6
   ```
 
@@ -89,12 +89,12 @@ and then add `\cite{Loeb_2012}` in your manuscript. After exporting the bibliogr
 ## Document management
 
 You can attach a document to a reference:
-  ```
+  ```shell
   pubs doc add Loeb2012_downloaded.pdf Loeb_2012
   ```
 
 And open your documents automatically from the command line:
-  ```
+  ```shell
   pubs doc open Loeb_2012
   pubs doc open --with lp Loeb_2012  # Opens the document with `lp` to actually print it.
   ```
@@ -114,18 +114,18 @@ You can then also conveniently interact with the git repository by using `pubs g
 ## Multiple pubs Repositories
 
 You may want to have different pubs repositories, for different projects. To create an alternate repository:
-  ```
+  ```shell
   pubs --config /path/to/config init --pubsdir /path/to/desired_repository_directory
   ```
 The configuration file and repository will be automatically created.
 
 Then you can add papers to the new repository:
-  ```
+  ```shell
   pubs --config /path/to/config add -D 10.1007/s00422-012-0514-6
   ```
 
 A useful thing might be to define an alias in your shell:
-  ```
+  ```shell
   alias pubs2="pubs --config /path/to/config"
   ```
 and then use `pubs2` as you would use `pubs` directly.  Note that you cannot use the alias plugin below to do this.
@@ -141,8 +141,8 @@ You can add custom commands to pubs by defining aliases in your configuration fi
   count = !pubs list -k "$@" | wc -l
   ```
 
-The first command defines a new subcommand: `pubs open --with evince` will be executed when `pubs evince` is typed.
-The second starts with a bang: `!`, and is treated as a shell command. If other arguments are provided they are passed to the shell command as in a script. In the example above the `count` alias can take arguments that are be passed to the `pubs list -k` command, hence enabling filters like `pubs count year:2012`.
+The first configuration line defines a new subcommand: `pubs open --with evince` will be executed when `pubs evince` is typed.
+The second starts with a bang: `!`, which means that it is treated as a shell command. If other arguments are provided they are passed to the shell command as in a script. In the example above the `count` alias can take arguments that are passed over to the `pubs list -k` command, hence enabling filters like `pubs count year:2012`.
 
 
 ## Autocompletion

From cb61ff6fc8cf7ec944e69586d20e34f299c1fbae Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= <dev@schuetz-co.de>
Date: Sat, 27 Feb 2021 12:59:56 +0100
Subject: [PATCH 45/45] preserve case of field 'type'

Non-standard types such as "Diplomarbeit" should not be converted to
lowercase.
---
 pubs/endecoder.py       | 1 -
 tests/test_endecoder.py | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/pubs/endecoder.py b/pubs/endecoder.py
index e289ddc..6c88bd7 100644
--- a/pubs/endecoder.py
+++ b/pubs/endecoder.py
@@ -51,7 +51,6 @@ def customizations(record):
     """
 
     # record = bp.customization.convert_to_unicode(record) # transform \& into & ones, messing-up latex
-    record = bp.customization.type(record)
     record = bp.customization.author(record)
     record = bp.customization.editor(record)
     record = bp.customization.keyword(record)
diff --git a/tests/test_endecoder.py b/tests/test_endecoder.py
index 858213f..3e81e8e 100644
--- a/tests/test_endecoder.py
+++ b/tests/test_endecoder.py
@@ -61,7 +61,7 @@ class TestEnDecode(unittest.TestCase):
         """Test that multiple encode/decode step preserve data"""
         decoder = endecoder.EnDecoder()
         entry = decoder.decode_bibdata(bibtex_raw0)
-        self.assertEqual(entry['Page99']['type'], "technical report")
+        self.assertEqual(entry['Page99']['type'], "Technical Report")
 
     def test_endecode_bibtex_BOM(self):
         """Test that bibtexparser if fine with BOM-prefixed data"""