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

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

Fixes #223, #212. Includes PR #224.
This commit is contained in:
Fabien C. Y. Benureau 2020-05-10 09:16:04 +09:00 committed by GitHub
commit 8ab89ab3bb
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GPG Key ID: 4AEE18F83AFDEB23
13 changed files with 93 additions and 60 deletions
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36
.travis.yml
View File

@ -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"
@ -36,16 +21,6 @@ matrix:
- source env/bin/activate
# Mock tests (with mock API)
- os: linux
language: python
python: 3.3
env:
- TO_TEST=TEST_MOCK
- os: linux
language: python
python: 3.4
env:
- TO_TEST=TEST_MOCK
- os: linux
language: python
python: 3.5
@ -63,6 +38,13 @@ matrix:
sudo: true
env:
- TO_TEST=TEST_MOCK
- os: linux
language: python
dist: xenial
python: 3.8
sudo: true
env:
- TO_TEST=TEST_MOCK
# Install tests
@ -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:

4
dev_requirements.txt
View File

@ -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

2
pubs/commands/add_cmd.py
View File

@ -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':

16
pubs/commands/edit_cmd.py
View File

@ -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

2
pubs/commands/list_cmd.py
View File

@ -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()

2
pubs/commands/tag_cmd.py
View File

@ -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()

4
pubs/config/spec.py
View File

@ -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)

21
pubs/pretty.py
View File

@ -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]

12
pubs/utils.py
View File

@ -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)

2
readme.md
View File

@ -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

2
setup.py
View File

@ -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,

10
tests/test_pretty.py
View File

@ -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()

40
tests/test_usecase.py
View File

@ -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)