Merge pull request #225 from pubs/feat/212_n_authors

Add a max_authors option in the configuration, and fix test failures.

Fixes #223, #212. Includes PR #224.

.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:

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

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, 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':

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

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, max_authors=conf['main']['max_authors'])
             for p in papers))
 
     rp.close()

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, max_authors=conf['main']['max_authors'])
                                  for p in papers_list))
 
         rp.close()

pubs/config/spec.py

@@ -27,6 +27,10 @@ edit_cmd = string(default='')
 # Which default extension to use when creating a note file.
 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.'.
+max_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)

pubs/pretty.py

@@ -23,19 +23,24 @@ def person_repr(p):
         ' '.join(p.lineage(abbr=True))] if s)
 
 
-def short_authors(bibdata):
+def short_authors(bibdata, max_authors=3):
+    """
+    :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 len(authors) < 3:
-            return ' and '.join(authors)
+        if 0 < max_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)
+        return authors_str
     except KeyError:  # When no author is defined
         return ''
 
 
-def bib_oneliner(bibdata):
-    authors = short_authors(bibdata)
+def bib_oneliner(bibdata, max_authors=3):
+    authors = short_authors(bibdata, max_authors=max_authors)
     journal = ''
     if 'journal' in bibdata:
         journal = ' ' + bibdata['journal']
@@ -60,11 +65,11 @@ def bib_desc(bib_data):
     return s
 
 
-def paper_oneliner(p, citekey_only=False):
+def paper_oneliner(p, citekey_only=False, max_authors=3):
     if citekey_only:
         return p.citekey
     else:
-        bibdesc = bib_oneliner(p.get_unicode_bibdata())
+        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]

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, max_authors=conf['main']['max_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)

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
 

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,

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_max_authors(self):
+        decoder = endecoder.EnDecoder()
+        bibdata = decoder.decode_bibdata(bibtex_raw0)
+        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'], 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'], max_authors=max_authors)), line)
+
 if __name__ == '__main__':
     unittest.main()

tests/test_usecase.py

@@ -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):
@@ -1079,7 +1088,8 @@ 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):
@@ -1145,5 +1155,23 @@ class TestCache(DataCommandTestCase):
         self.assertEqual(line1, out[4])
 
 
+class TestConfigChange(DataCommandTestCase):
+
+    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 max_authors in [1, 2, 3]:
+            self.update_config({'main': {'max_authors': max_authors}})
+            self.execute_cmds([('pubs list', None, line_al, None)])
+
+        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)])
+
+
+
 if __name__ == '__main__':
     unittest.main(verbosity=2)