Merge pull request #227 from pubs/feat/remove_prompt

Feat/remove prompt

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 `max_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)
 

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"""

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) [{}]"
+        to_remove_str = '\n'.join(pretty.paper_oneliner(rp.pull_paper(key),
-            " (this will also delete associated documents)?")
+                                                        max_authors=conf['main']['max_authors'])
-            .format(', '.join([color.dye_out(c, 'citekey') for c in args.citekeys])))
+                                  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')))

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,
+                bibstr, common_strings=True, customization=customizations,
-                homogenize_fields=True).get_entry_dict()
+                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):

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)])
 

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}
+}

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},
+}

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.stdout = _fake_stdio(additional_out=old_stdout if verbose else None)
-        sys.stderr = _fake_stdio(additional_out=old_stderr if False 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:

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},

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']['title'] = r"{E}l Ni{\~n}o"
-        latexenc_paper.bibentry['Doe2013']['author'][0] = "Erd\H{o}s, Paul"
+        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))
 

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',