Merge pubs updates

changelog.md

@@ -7,6 +7,8 @@
 
 ### Implemented enhancements
 
+- Possibily to exclude bibtext field when adding references ([#273](https://github.com/pubs/pubs/pull/273) by [Mitsuhiro Nakamura](https://github.com/m15a))
+- Less ambiguous tag display for tags with space ([#265](https://github.com/pubs/pubs/pull/265) by [Florian Richoux](https://github.com/richoux))
 - 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))

pubs/commands/add_cmd.py

@@ -116,6 +116,9 @@ def command(conf, args):
         if bibentry is None:
             ui.error('invalid bibfile {}.'.format(bibfile))
 
+    # exclude bibtex fields if specified
+    utils.remove_bibtex_fields(bibentry, conf['main']['exclude_bibtex_fields'])
+
     # citekey
 
     citekey = args.citekey

pubs/commands/edit_cmd.py

@@ -6,7 +6,7 @@ from .. import color
 
 from ..uis import get_ui
 from ..endecoder import EnDecoder
-from ..utils import resolve_citekey
+from ..utils import resolve_citekey, remove_bibtex_fields
 from ..completion import CiteKeyCompletion
 from ..events import ModifyEvent
 
@@ -59,6 +59,9 @@ def command(conf, args):
                 ui.info(("The metadata of paper '{}' was successfully "
                          "edited.".format(color.dye_out(citekey, 'citekey'))))
             else:
+                # exclude bibtex fields if specified
+                remove_bibtex_fields(content, conf['main']['exclude_bibtex_fields'])
+
                 new_paper = Paper.from_bibentry(content,
                                                 metadata=paper.metadata)
                 if rp.rename_paper(new_paper, old_citekey=paper.citekey):

pubs/commands/export_cmd.py

@@ -5,7 +5,7 @@ import argparse
 from .. import repo
 from ..uis import get_ui
 from .. import endecoder
-from ..utils import resolve_citekey_list
+from ..utils import resolve_citekey_list, remove_bibtex_fields
 from ..endecoder import BIBFIELD_ORDER
 from ..completion import CiteKeyCompletion, CommaSeparatedListCompletion
 
@@ -53,6 +53,9 @@ def command(conf, args):
     for p in papers:
         bib[p.citekey] = p.bibdata
 
+    # exclude bibtex fields if specified
+    remove_bibtex_fields(bib, conf['main']['exclude_bibtex_fields'])
+
     exporter = endecoder.EnDecoder()
     bibdata_raw = exporter.encode_bibdata(bib, args.ignore_fields)
     ui.message(bibdata_raw)

pubs/commands/import_cmd.py

@@ -11,6 +11,7 @@ from .. import content
 from ..paper import Paper
 from ..uis import get_ui
 from ..content import system_path, read_text_file
+from ..utils import remove_bibtex_fields
 from ..command_utils import add_doc_copy_arguments
 
 
@@ -21,7 +22,7 @@ _IGNORING_MSG = " Ignoring it."
 def parser(subparsers, conf):
     parser = subparsers.add_parser(
         'import',
-        help='import paper(s) to the repository.')
+        help='import paper(s) to the repository')
     parser.add_argument(
         'bibpath',
         help=("path to bibtex, bibtexml or bibyaml file, or a directory "
@@ -40,7 +41,7 @@ def parser(subparsers, conf):
     return parser
 
 
-def many_from_path(ui, bibpath, ignore=False):
+def many_from_path(ui, bibpath, exclude_bibtex_fields=[], ignore=False):
     """Extract list of papers found in bibliographic files in path.
 
     The behavior is to:
@@ -62,7 +63,10 @@ def many_from_path(ui, bibpath, ignore=False):
     biblist = []
     for filepath in all_files:
         try:
-            biblist.append(coder.decode_bibdata(read_text_file(filepath)))
+            bibentry = coder.decode_bibdata(read_text_file(filepath))
+            # exclude bibtex fields if specified
+            remove_bibtex_fields(bibentry, exclude_bibtex_fields)
+            biblist.append(bibentry)
         except coder.BibDecodingError:
             error = "Could not parse bibtex at {}.".format(filepath)
             if ignore:
@@ -100,7 +104,9 @@ def command(conf, args):
 
     rp = repo.Repository(conf)
     # Extract papers from bib
-    papers = many_from_path(ui, bibpath, ignore=args.ignore_malformed)
+    papers = many_from_path(ui, bibpath,
+        exclude_bibtex_fields=conf['main']['exclude_bibtex_fields'],
+        ignore=args.ignore_malformed)
     keys = args.keys or papers.keys()
     for k in keys:
         p = papers[k]

pubs/commands/statistics_cmd.py

@@ -6,7 +6,7 @@ from .. import color
 def parser(subparsers, conf):
     parser = subparsers.add_parser(
         'statistics',
-        help="show statistics on the repository.")
+        help="show statistics on the repository")
     return parser
 
 

pubs/commands/tag_cmd.py

@@ -87,7 +87,7 @@ def command(conf, args):
     rp = Repository(conf)
 
     if citekeyOrTag is None:
-        ui.message(color.dye_out(' '.join(sorted(rp.get_tags())), 'tag'))
+        ui.message(color.dye_out(', '.join(sorted(rp.get_tags())), 'tag'))
     else:
         not_citekey = False
         try:
@@ -97,7 +97,7 @@ def command(conf, args):
         if not not_citekey:
             p = rp.pull_paper(citekeyOrTag)
             if tags is None:
-                ui.message(color.dye_out(' '.join(sorted(p.tags)), 'tag'))
+                ui.message(color.dye_out(', '.join(sorted(p.tags)), 'tag'))
             else:
                 add_tags, remove_tags = _tag_groups(_parse_tag_seq(tags))
                 for tag in add_tags:

pubs/config/spec.py

@@ -56,6 +56,11 @@ normalize_citekey = boolean(default=False)
 #
 citekey_format = string(default='{{author_last_name:l}}{{year}}{{short_title:l}}')
 
+# which bibliographic fields to exclude from bibtex files. By default, none.
+# Please note that excluding critical fields such as `title` or `author`
+# will break many commands of pubs.
+exclude_bibtex_fields = force_list(default=list())
+
 [formating]
 
 # Enable bold formatting, if the terminal supports it.

pubs/pretty.py

@@ -78,7 +78,7 @@ def paper_oneliner(p, citekey_only=False, max_authors=3):
                                else 'NOEXT'),
                 'tag')
         tags = '' if len(p.tags) == 0 else '| {}'.format(
-            ','.join(color.dye_out(t, 'tag') for t in sorted(p.tags)))
+            ', '.join(color.dye_out(t, 'tag') for t in sorted(p.tags)))
         return '[{citekey}] {descr}{doc} {tags}'.format(
             citekey=color.dye_out(p.citekey, 'citekey'),
             descr=bibdesc, tags=tags, doc=doc_str)

pubs/utils.py

@@ -87,3 +87,9 @@ def standardize_doi(doi):
     new_doi = match.group(0)
 
     return new_doi
+
+def remove_bibtex_fields(bibentry, fields):
+    for item in bibentry.values():
+        for field in fields:
+            if field in item:
+                del item[field]

readme.md

@@ -187,3 +187,5 @@ You can access the self-documented configuration by using `pubs conf`, and all t
 - [Jonáš Kulhánek](https://github.com/jkulhanek)
 - [Dominik Stańczak](https://github.com/StanczakDominik)
 - [Gustavo José de Sousa](https://github.com/guludo)
+- [Florian Richoux](https://github.com/richoux)
+- [Mitsuhiro Nakamura](https://github.com/m15a)

tests/str_fixtures.py

@@ -138,6 +138,9 @@ edit_cmd = "vim"
 # the full python stack is printed.
 debug = False
 
+# which bibliographic fields to exclude from bibtex files.
+exclude_bibtex_fields =
+
 [formating]
 
 # Enable bold formatting, if the terminal supports it.

tests/test_usecase.py

@@ -437,6 +437,18 @@ class TestAdd(URLContentTestCase):
             self.execute_cmds(cmds)
         self.assertEqual(cm.exception.code, 1)
 
+    def test_add_excludes_bibtex_fields(self):
+        self.execute_cmds(['pubs init'])
+        config = conf.load_conf()
+        config['main']['exclude_bibtex_fields'] = ['abstract', 'publisher']
+        conf.save_conf(config)
+        self.execute_cmds(['pubs add data/pagerank.bib'])
+        with FakeFileOpen(self.fs)(self.default_pubs_dir + '/bib/Page99.bib', 'r') as buf:
+            out = endecoder.EnDecoder().decode_bibdata(buf.read())
+        for bib in out.values():
+            self.assertFalse('abstract' in bib or 'publisher' in bib)
+            self.assertTrue('title' in bib and 'author' in bib)
+
 
 class TestList(DataCommandTestCase):
 
@@ -590,7 +602,7 @@ class TestTag(DataCommandTestCase):
                 'pubs list',
                 ]
         correct = ['',
-                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) | network,search\n' +
+                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) | network, search\n' +
                    '[Turing1950] Turing, Alan M "Computing machinery and intelligence" Mind (1950) \n',
                    ]
         out = self.execute_cmds(cmds)
@@ -738,9 +750,9 @@ class TestUsecase(DataCommandTestCase):
                    '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) [pdf] \n',
                    '\n',
                    '',
-                   'network search\n',
+                   'network, search\n',
                    'info: Assuming search to be a tag.\n'
-                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) [pdf] | network,search\n',
+                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) [pdf] | network, search\n',
                   ]
 
         cmds = ['pubs init -p /paper_first',
@@ -785,7 +797,7 @@ class TestUsecase(DataCommandTestCase):
                    '',
                    '',
                    '',
-                   'search network\n',
+                   'search, network\n',
                   ]
 
         cmds = ['pubs init -p paper_first/',
@@ -798,7 +810,7 @@ class TestUsecase(DataCommandTestCase):
         out = self.execute_cmds(cmds)
 
         def clean(s):
-            return set(s.strip().split(' '))
+            return set(s.strip().split(', '))
 
         self.assertEqual(clean(correct[2]), clean(out[2]))
         self.assertEqual(clean(correct[4]), clean(out[4]))
@@ -829,6 +841,22 @@ class TestUsecase(DataCommandTestCase):
                 ]
         self.execute_cmds(cmds)
 
+    def test_editor_excludes_bibtex_field(self):
+        cmds = ['pubs init',
+                'pubs add data/pagerank.bib',
+                ]
+        self.execute_cmds(cmds)
+        config = conf.load_conf()
+        config['main']['exclude_bibtex_fields'] = ['author']
+        conf.save_conf(config)
+        cmds = [('pubs edit Page99', ['@misc{Page99, title="TTT", author="auth"}', 'n'])]
+        self.execute_cmds(cmds)
+        with FakeFileOpen(self.fs)(self.default_pubs_dir + '/bib/Page99.bib', 'r') as buf:
+            out = endecoder.EnDecoder().decode_bibdata(buf.read())
+        for bib in out.values():
+            self.assertFalse('author' in bib)
+            self.assertTrue('title' in bib)
+
     def test_add_aborts(self):
         with self.assertRaises(FakeSystemExit):
             cmds = ['pubs init',
@@ -879,7 +907,7 @@ class TestUsecase(DataCommandTestCase):
         meta = str_fixtures.turing_meta
 
         line = '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n'
-        line1 = re.sub('\n', '| AI,computer\n', line)
+        line1 = re.sub('\n', '| AI, computer\n', line)
 
         cmds = ['pubs init',
                 'pubs add data/pagerank.bib',
@@ -908,6 +936,19 @@ class TestUsecase(DataCommandTestCase):
             fixtures.page_bibentry, ignore_fields=['author', 'title'])
         self.assertEqual(outs[2], expected + os.linesep)
 
+    def test_export_excludes_bibtex_field(self):
+        cmds = ['pubs init',
+                'pubs add data/pagerank.bib'
+                ]
+        self.execute_cmds(cmds)
+        config = conf.load_conf()
+        config['main']['exclude_bibtex_fields'] = ['url']
+        conf.save_conf(config)
+        outs = self.execute_cmds(['pubs export Page99'])
+        for bib in endecoder.EnDecoder().decode_bibdata(outs[0]).values():
+            self.assertFalse('url' in bib)
+            self.assertTrue('title' in bib and 'author' in bib)
+
     def test_import(self):
         cmds = ['pubs init',
                 'pubs import data/',
@@ -970,6 +1011,18 @@ class TestUsecase(DataCommandTestCase):
         outs = self.execute_cmds(cmds)
         self.assertEqual(1 + 1, len(outs[-1].split('\n')))
 
+    def test_import_excludes_bibtex_field(self):
+        self.execute_cmds(['pubs init'])
+        config = conf.load_conf()
+        config['main']['exclude_bibtex_fields'] = ['abstract']
+        conf.save_conf(config)
+        self.execute_cmds(['pubs import data/ Page99'])
+        with FakeFileOpen(self.fs)(self.default_pubs_dir + '/bib/Page99.bib', 'r') as buf:
+            out = endecoder.EnDecoder().decode_bibdata(buf.read())
+        for bib in out.values():
+            self.assertFalse('abstract' in bib)
+            self.assertTrue('title' in bib and 'author' in bib)
+
     def test_update(self):
         cmds = ['pubs init',
                 'pubs add data/pagerank.bib',