def test_Bib_update_content_bib_info(entries):
bib1 = bm.Bib(entries['jones_minimal'])
bib1.bibcode = 'bibcode1'
bib2 = bm.Bib(entries['jones_minimal'])
bib1.update_content(bib2)
# bibcode gets updated to None since it's bibtex info:
assert bib1.bibcode is None
def test_Bib_not_equal_both_no_author():
b1 = bm.Bib('''@MISC{1978windEnergyReport,
title = "{Wind energy systems: Program summary}",
year = 1978,
}''')
b2 = bm.Bib('''@MISC{1979NewWindEnergyReport,
title = "{New wind energy systems: Program summary}",
year = 1979,
}''')
assert b2 != b1
def test_Bib_equal_no_year():
b1 = bm.Bib('''@Misc{JonesEtal2001scipy,
author = {Eric Jones},
title = {SciPy},
}''')
b2 = bm.Bib('''@Misc{JonesEtalScipy_noyear,
author = {Eric Jones},
title = {SciPy},
}''')
assert b1 == b2
def test_Bib_lower_than_both_no_author():
b1 = bm.Bib('''@MISC{1978windEnergyReport,
title = "{Wind energy systems: Program summary}",
year = 1978,
}''')
b2 = bm.Bib('''@MISC{1979windEnergyReport,
title = "{Wind energy systems: Program summary}",
year = 1979,
}''')
assert b2 > b1
def test_Bib_meta():
e = '''@Misc{JonesEtal2001scipy,
author = {Eric Jones},
title = {SciPy},
year = {2001},
}'''
bib = bm.Bib(e)
assert bib.meta() == ''
bib = bm.Bib(e, freeze=True, pdf='file.pdf')
assert bib.meta() == 'freeze\npdf: file.pdf\n'
def test_Bib_equal_no_author():
b1 = bm.Bib('''@MISC{1978windEnergyReport,
title = "{Wind energy systems: Program summary}",
year = 1978,
}''')
b2 = bm.Bib('''@Misc{ZJones2001Scipy,
author = {Eric ZJones},
title = {SciPy},
year = 2001,
}''')
assert b1 != b2
def test_Bib_lower_than_no_year():
b1 = bm.Bib('''@Misc{JonesEtal2001scipy,
author = {Eric Jones},
title = {SciPy},
year = {2001},
}''')
b2 = bm.Bib('''@Misc{JonesEtalScipy_noyear,
author = {Eric Jones},
title = {SciPy},
}''')
assert b1 < b2
def test_Bib_update_content_keep_meta(entries):
bib1 = bm.Bib(entries['jones_minimal'])
bib1.bibcode = 'bibcode1'
bib1.pdf = 'pdf1'
bib1.freeze = True
bib1.tags = ['tag']
bib2 = bm.Bib(entries['jones_minimal'])
bib1.update_content(bib2)
# pdf, freeze, and tags remeain as in bib1 since they are None in bib2:
assert bib1.pdf == 'pdf1'
assert bib1.freeze is True
assert bib1.tags == ['tag']
def test_merge_bibs_no_titles(capfd, mock_init):
e1 = """@Misc{Jones2001scipy,
author = {Eric Jones},
year = {2001},
}"""
e2 = """@Misc{Oliphant2001scipy,
author = {Travis Oliphant},
year = {2001},
}"""
bibs = [bm.Bib(e1), bm.Bib(e2)]
bm.merge(new=bibs)
captured = capfd.readouterr()
assert captured.out == "\nMerged 2 new entries.\n"
def test_Bib_update_content(entries):
bib1 = bm.Bib(entries['jones_minimal'])
bib1.bibcode = 'bibcode1'
bib1.pdf = 'pdf1'
bib1.freeze = True
bib2 = bm.Bib(entries['jones_minimal'])
bib2.pdf = 'pdf2'
bib1.update_content(bib2)
# bibcode gets updated to None since it's bibtex info:
assert bib1.bibcode is None
# pdf gets updated since it's not None:
assert bib1.pdf == 'pdf2'
# freeze does not get updated, since it's not bibtex and is None:
assert bib1.freeze is True
def test_Bib_update_content_update_meta(entries):
bib1 = bm.Bib(entries['jones_minimal'])
bib1.bibcode = 'bibcode1'
bib1.pdf = 'pdf1'
bib1.tags = ['tag1']
bib2 = bm.Bib(entries['jones_minimal'])
bib2.pdf = 'pdf2'
bib2.freeze = True
bib1.tags = ['tag2']
bib1.update_content(bib2)
# pdf, freeze, and tags get updated since they are not None:
assert bib1.pdf == 'pdf2'
assert bib1.freeze is True
assert bib1.tags == ['tag2']
def test_display_bibs_meta_shown(capfd, mock_init):
e1 = '''@Misc{JonesEtal2001scipy,
author = {Eric Jones},
title = {SciPy},
year = {2001},
}'''
e2 = '''@Misc{Jones2001,
author = {Travis Oliphant},
title = {tools for Python},
year = {2001},
}'''
bibs = [bm.Bib(e1), bm.Bib(e2, freeze=True, pdf='file.pdf')]
bm.display_bibs(["DATABASE:\n", "NEW:\n"], bibs, meta=True)
captured = capfd.readouterr()
assert captured.out == '\x1b[0m\x1b[?7h\x1b[0;38;5;248;3m\r\n::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::\r\n\x1b[0mDATABASE:\r\n\x1b[0;38;5;248;3m\x1b[0;38;5;34;1;4m@Misc\x1b[0m{\x1b[0;38;5;142mJonesEtal2001scipy\x1b[0m,\x1b[0;38;5;250m\r\n \x1b[0;38;5;33mauthor\x1b[0;38;5;250m \x1b[0m=\x1b[0;38;5;250m \x1b[0;38;5;130m{Eric Jones}\x1b[0m,\x1b[0;38;5;250m\r\n \x1b[0;38;5;33mtitle\x1b[0;38;5;250m \x1b[0m=\x1b[0;38;5;250m \x1b[0;38;5;130m{SciPy}\x1b[0m,\x1b[0;38;5;250m\r\n \x1b[0;38;5;33myear\x1b[0;38;5;250m \x1b[0m=\x1b[0;38;5;250m \x1b[0;38;5;130m{2001}\x1b[0m,\x1b[0;38;5;250m\r\n \x1b[0m}\x1b[0;38;5;250m\r\n\x1b[0m\r\nNEW:\r\n\x1b[0;38;5;248;3mfreeze\r\npdf: file.pdf\r\n\x1b[0;38;5;34;1;4m@Misc\x1b[0m{\x1b[0;38;5;142mJones2001\x1b[0m,\x1b[0;38;5;250m\r\n \x1b[0;38;5;33mauthor\x1b[0;38;5;250m \x1b[0m=\x1b[0;38;5;250m \x1b[0;38;5;130m{Travis Oliphant}\x1b[0m,\x1b[0;38;5;250m\r\n \x1b[0;38;5;33mtitle\x1b[0;38;5;250m \x1b[0m=\x1b[0;38;5;250m \x1b[0;38;5;130m{tools for Python}\x1b[0m,\x1b[0;38;5;250m\r\n \x1b[0;38;5;33myear\x1b[0;38;5;250m \x1b[0m=\x1b[0;38;5;250m \x1b[0;38;5;130m{2001}\x1b[0m,\x1b[0;38;5;250m\r\n \x1b[0m}\x1b[0;38;5;250m\r\n\x1b[0m\r\n\x1b[0m'
def test_display_bibs(capfd, mock_init):
e1 = '''@Misc{JonesEtal2001scipy,
author = {Eric Jones},
title = {SciPy},
year = {2001},
}'''
e2 = '''@Misc{Jones2001,
author = {Travis Oliphant},
title = {tools for Python},
year = {2001},
}'''
bibs = [bm.Bib(e1), bm.Bib(e2)]
bm.display_bibs(["DATABASE:\n", "NEW:\n"], bibs)
captured = capfd.readouterr()
assert captured.out == '\x1b[0m\x1b[?7h\x1b[0;38;5;248;3m\r\n::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::\r\n\x1b[0mDATABASE:\r\n\x1b[0;38;5;34;1;4m@Misc\x1b[0m{\x1b[0;38;5;142mJonesEtal2001scipy\x1b[0m,\x1b[0m\r\n \x1b[0;38;5;33mauthor\x1b[0m \x1b[0m=\x1b[0m \x1b[0;38;5;130m{\x1b[0;38;5;130mEric Jones\x1b[0;38;5;130m}\x1b[0m,\x1b[0m\r\n \x1b[0;38;5;33mtitle\x1b[0m \x1b[0m=\x1b[0m \x1b[0;38;5;130m{\x1b[0;38;5;130mSciPy\x1b[0;38;5;130m}\x1b[0m,\x1b[0m\r\n \x1b[0;38;5;33myear\x1b[0m \x1b[0m=\x1b[0m \x1b[0;38;5;130m{\x1b[0;38;5;130m2001\x1b[0;38;5;130m}\x1b[0m,\x1b[0m\r\n \x1b[0m}\x1b[0m\r\n\x1b[0m\r\n\x1b[0mNEW:\r\n\x1b[0;38;5;34;1;4m@Misc\x1b[0m{\x1b[0;38;5;142mJones2001\x1b[0m,\x1b[0m\r\n \x1b[0;38;5;33mauthor\x1b[0m \x1b[0m=\x1b[0m \x1b[0;38;5;130m{\x1b[0;38;5;130mTravis Oliphant\x1b[0;38;5;130m}\x1b[0m,\x1b[0m\r\n \x1b[0;38;5;33mtitle\x1b[0m \x1b[0m=\x1b[0m \x1b[0;38;5;130m{\x1b[0;38;5;130mtools for Python\x1b[0;38;5;130m}\x1b[0m,\x1b[0m\r\n \x1b[0;38;5;33myear\x1b[0m \x1b[0m=\x1b[0m \x1b[0;38;5;130m{\x1b[0;38;5;130m2001\x1b[0;38;5;130m}\x1b[0m,\x1b[0m\r\n \x1b[0m}\x1b[0m\r\n\x1b[0m\r\n\x1b[0m\x1b[0m'
def test_Bib_minimal(entries):
# Minimal entry (key, author, title, and year):
bib = bm.Bib(entries['jones_minimal'])
assert bib.content == entries['jones_minimal']
assert bib.key == "JonesEtal2001scipy"
assert bib.authors == [
u.Author(last='Jones', first='Eric', von='', jr=''),
u.Author(last='Oliphant', first='Travis', von='', jr=''),
u.Author(last='Peterson', first='Pearu', von='', jr='')
]
assert bib.sort_author == u.Sort_author(last='jones',
first='e',
von='',
jr='',
year=2001,
month=13)
assert bib.year == 2001
assert bib.title == "SciPy: Open source scientific tools for Python"
assert bib.doi == None
assert bib.bibcode == None
assert bib.adsurl == None
assert bib.eprint == None
assert bib.isbn == None
assert bib.month == 13
assert bib.pdf is None
assert bib.freeze is None
def test_guess_name_no_bibcode():
bib = bm.Bib('''@ARTICLE{Raftery1995BIC,
author = {{Raftery}, A.~E},
title = "{Bayesian Model Selection in Social Research}",
year = 1995,
}''')
assert pm.guess_name(bib) == 'Raftery1995.pdf'
def test_Bib_published_non_ads():
# Does not have adsurl:
entry = '''@ARTICLE{DoeEtal2020,
author = {{Doe}, J. and {Perez}, J. and {Dupont}, J.},
title = "What Have the Astromomers ever Done for Us?",
year = 2020,}'''
bib = bm.Bib(entry)
assert bib.published() == -1
def test_guess_name_no_author_no_year():
bib = bm.Bib('''@ARTICLE{Raftery1995BIC,
title = "{Bayesian Model Selection in Social Research}",
}''')
with pytest.raises(ValueError,
match='Could not guess a good filename since entry does not '
'have author nor year fields'):
pm.guess_name(bib)
def test_Bib_month(month_in, month_out):
e = '''@Misc{JonesEtal2001scipy,
author = {Eric Jones},
title = {SciPy},
year = {2001},
''' + month_in + '}'
bib = bm.Bib(e)
assert bib.month == month_out
def test_guess_name_bibcode_no_pages():
bib = bm.Bib('''@BOOK{Chase1986jttJANAF,
author = {{Chase}, M.~W.},
title = "{JANAF thermochemical tables}",
year = "1986",
adsurl = {https://ui.adsabs.harvard.edu/abs/1986jtt..book.....C},
}''')
assert pm.guess_name(bib) == 'Chase1986_jtt_book.pdf'
def test_guess_name_bibcode_no_volume():
bib = bm.Bib('''@PHDTHESIS{Payne1925phdStellarAtmospheres,
author = {{Payne}, Cecilia Helena},
title = "{Stellar Atmospheres; a Contribution to the Observational Study of High Temperature in the Reversing Layers of Stars.}",
year = "1925",
adsurl = {https://ui.adsabs.harvard.edu/abs/1925PhDT.........1P},
}''')
assert pm.guess_name(bib) == 'Payne1925_PhDT_1.pdf'
def test_guess_name_non_ascii():
bib = bm.Bib('''@ARTICLE{HuangEtal2014jqsrtCO2,
author = {{Huang (黄新川)}, Xinchuan and {Gamache}, Robert R.},
title = "{Reliable infrared line lists for 13 CO$_{2}$}",
year = "2014",
adsurl = {https://ui.adsabs.harvard.edu/abs/2014JQSRT.147..134H},
}''')
assert pm.guess_name(bib) == 'Huang2014_JQSRT_147_134.pdf'
def test_guess_name_non_letter_characters():
bib = bm.Bib(r'''@ARTICLE{GarciaMunoz2007pssHD209458bAeronomy,
author = {{Garc{\'\i}a-Mu{\~n}oz}, A.},
title = "{Physical and chemical aeronomy of HD 209458b}",
year = "2007",
adsurl = {https://ui.adsabs.harvard.edu/abs/2007P&SS...55.1426G},
}''')
assert pm.guess_name(bib) == 'GarciaMunoz2007_PSS_55_1426.pdf'
def test_guess_name_blanks():
bib = bm.Bib('''@MISC{AASteamHendrickson2018aastex62,
author = {{AAS Journals Team}, and {Hendrickson}, Amy},
title = "{Aasjournals/Aastex60: Version 6.2 Official Release}",
year = "2018",
adsurl = {https://ui.adsabs.harvard.edu/abs/2018zndo...1209290T},
}''')
assert pm.guess_name(bib) == 'AASJournalsTeam2018_zndo_12_9290.pdf'
def test_search_title_entry_without_title(mock_init_sample, entries):
# Multiple-title querries act with AND logic:
bib = bm.Bib(entries['jones_no_title'])
bm.merge(new=[bib])
matches = bm.search(title=['HD 209458b', 'atmospheric circulation'])
assert len(matches) == 1
keys = [m.key for m in matches]
assert 'ShowmanEtal2009apjRadGCM' in keys
def test_guess_name_arxiv_arxiv():
bib = bm.Bib('''@ARTICLE{AndraeEtal2010arxivChiSquareStats,
author = {{Andrae}, Rene and {Schulze-Hartung}, Tim and {Melchior}, Peter},
title = "{Dos and don'ts of reduced chi-squared}",
year = "2010",
adsurl = {https://ui.adsabs.harvard.edu/abs/2010arXiv1012.3754A},
}''')
assert pm.guess_name(bib, arxiv=True) == \
'Andrae2010_arXiv_1012_3754.pdf'
def test_Bib_published_arxiv():
# Has 'arXiv' adsurl:
entry = '''@ARTICLE{DoeEtal2020,
author = {{Doe}, J. and {Perez}, J. and {Dupont}, J.},
title = "What Have the Astromomers ever Done for Us?",
adsurl = {http://adsabs.harvard.edu/abs/2016arXiv0123.0045S},
year = 2020,}'''
bib = bm.Bib(entry)
assert bib.published() == 0
def test_Bib_published_peer_reviewed():
# Has adsurl field, no 'arXiv' in it:
entry = '''@ARTICLE{DoeEtal2020,
author = {{Doe}, J. and {Perez}, J. and {Dupont}, J.},
title = "What Have the Astromomers ever Done for Us?",
adsurl = {http://adsabs.harvard.edu/abs/2016Natur.123...45S},
year = 2020,}'''
bib = bm.Bib(entry)
assert bib.published() == 1
def test_Bib_month_invalid(month):
e = '''@Misc{JonesEtal2001scipy,
author = {Eric Jones},
title = {SciPy},
year = {2001},
''' + f'month = {month}' + ',}'
value = f'{month.lower()}'
with pytest.raises(ValueError, match=fr"Invalid month value \({value}\)"):
bib = bm.Bib(e)
def test_guess_name_with_bibcode():
bib = bm.Bib('''@ARTICLE{FortneyEtal2008apjTwoClasses,
author = {{Fortney}, J.~J. and {Lodders}, K. and {Marley}, M.~S. and
{Freedman}, R.~S.},
title = "{A Unified Theory for the Atmospheres of the Hot and Very Hot Jupiters: Two Classes of Irradiated Atmospheres}",
year = "2008",
adsurl = {https://ui.adsabs.harvard.edu/abs/2008ApJ...678.1419F},
}''')
assert pm.guess_name(bib) == 'Fortney2008_ApJ_678_1419.pdf'
def test_Bib_warning_month(month):
e = '''@Misc{JonesEtal2001scipy,
author = {Eric Jones},
title = {SciPy},
year = {2001},
''' + f'month = {month}' + ',}'
with pytest.warns(Warning) as record:
bib = bm.Bib(e)
assert str(record[0].message) == \
f"Invalid month value '{month}' for entry 'JonesEtal2001scipy'"
