def init(app, config_file):
global metadata
config = topicexplorer.config.read(config_file)
try:
filename = config.get('bibtex', 'path')
except ConfigParserError:
model_path = config.get('main', 'path')
filename = os.path.join(model_path, 'library.bib')
print("Loading Bibtex metadata from", filename)
bib = parse_file(filename)
metadata = dict()
for entry in bib.entries:
key = '/' + bib.entries[entry].fields.get('file', '').replace(
':pdf', '')[1:]
if 'C$\\backslash$:' in key:
key = key.replace('C$\\backslash$:', '')
key = key[1:]
key = os.path.normpath(key)
key = os.path.basename(key)
try:
citation = pybtex.format_from_file(filename,
style='plain',
output_backend='text',
citations=[entry])[3:]
metadata[key] = citation
except PybtexError:
metadata[key] = filename
def init(viewer, config, args):
global metadata
try:
filename = args.bibtex or config.get('bibtex', 'path')
except ConfigParser.Error:
model_path = config.get('main','path')
filename = os.path.join(model_path, 'library.bib')
print "Loading Bibtex metadata from", filename
bib = parse_file(filename)
metadata = dict()
for entry in bib.entries:
key = '/' + bib.entries[entry].fields.get('file','').replace(':pdf','')[1:]
if 'C$\\backslash$:' in key:
key = key.replace('C$\\backslash$:', '')
key = key[1:]
key = os.path.normpath(key)
key = os.path.basename(key)
try:
citation = pybtex.format_from_file(
filename, style='plain', output_backend='text', citations=[entry])[3:]
metadata[key] = citation
except PybtexError:
metadata[key] = filename
def print(self, filename=None, output_format="text"):
"""Print all citations that were used for running simulations.
Parameters
----------
filename : str, optional
Filename to which to print citations. If None, citations are printed to the
terminal.
"""
citations = ""
citations_file = os.path.join(pybamm.root_dir(), "pybamm",
"CITATIONS.txt")
if output_format == "text":
citations = pybtex.format_from_file(
citations_file,
"plain",
citations=self._papers_to_cite,
output_backend="plaintext",
)
elif output_format == "bibtex":
for key in self._papers_to_cite:
citations += self._all_citations[key] + "\n"
else:
raise pybamm.OptionError(
"Output format {} not recognised."
"It should be 'text' or 'bibtex'.".format(output_format))
if filename is None:
print(citations)
else:
with open(filename, "w") as f:
f.write(citations)
def generate_ps_doc(parameter_set_dict):
"""
Generates docstring of parameter_sets.py from the given dictionary
"""
output_list = [DOC_INTRO]
citations_file = os.path.join(pybamm.root_dir(), "pybamm", "CITATIONS.txt")
for ps_chemistry in sorted(parameter_set_dict.keys()):
output_list.append("")
ps_citations = parameter_set_dict[ps_chemistry]
chem_name = ps_chemistry.capitalize().replace("_", "-") + " " + "parameter sets"
output_list.append(chem_name)
dashes = "-" * len(ps_chemistry) + "-" * 15
output_list.append(dashes)
for ps_name, ps_citation in sorted(ps_citations):
citations = pybtex.format_from_file(
citations_file,
style="plain",
output_backend="plaintext",
citations=ps_citation,
nocite=True,
)
# Remove citation labels "[3]"
citations = re.split(r"(?:^|\n)\[\d+\]\s", citations)
# Remove empty strings
citations = filter(bool, citations)
fmt_citations = []
for citation in citations:
# Break line at the first space before 80 characters
citation_parts = re.findall(r"(.{1,79})(?:\s|$)", citation)
# first_line = citation.split('\n')
indent_citation_parts = []
for idx, citation_part in enumerate(citation_parts):
if idx == 0:
citation_part = "- " + citation_part
else:
citation_part = " " + citation_part
indent_citation_parts.append(" " * 7 + citation_part)
# Join to create a single citation paragraph
citation = "\n".join(indent_citation_parts)
fmt_citations.append(citation)
fmt_citations = "\n".join(fmt_citations)
ps_doc = f" * {ps_name:} :\n{fmt_citations}"
output_list.append(ps_doc)
output = "\n".join(output_list)
output += "\n"
return output
from pybtex import format_from_file
with open('references.bib') as bib_file:
s_formatted = format_from_file(
bib_file,
style='unsrt',
abbreviate_names=True,
output_backend='text',
capfirst=False,
)
print(s_formatted.replace('Csadorf', 'csadorf'))
class YearSortingStyle(SortingStyle):
def sorting_key(self, entry):
if entry.type in ('book', 'inbook'):
author_key = self.author_editor_key(entry)
elif 'author' in entry.persons:
author_key = self.persons_key(entry.persons['author'])
else:
author_key = ''
return (-int(entry.fields.get('year', '')), author_key,
entry.fields.get('title', ''))
register_plugin('pybtex.style.sorting', 'year_author_title', YearSortingStyle)
markdown = pybtex.format_from_file(sys.argv[1],
style='plain',
output_backend='markdown',
sorting_style='year_author_title',
abbreviate_names=True)
markdown = re.sub('(\[\d+\])', '\n\\1', markdown)
# markdown, _ = re.subn(r'\\textbf \\underline N\\., Sonnenschein', '**<u>N., Sonnenschein</u>**', markdown)
markdown, _ = re.subn(r'\\\\textbf.*underline.*Sonnenschein',
'**<u>N. Sonnenschein</u>**', markdown)
markdown, _ = re.subn(r'\\\\textbf.*Sonnenschein', '**N. Sonnenschein**',
markdown)
markdown, _ = re.subn(r'\\\\emph\s*', '', markdown)
print(markdown)
# print(re.sub(r'\\textbf \\underline N\., Sonnenschein\.', '!@#$', markdown))