Move files

This commit is contained in:
Andras Schmelczer 2022-07-04 19:31:15 +02:00
commit 00cc8225c5
56 changed files with 31 additions and 49 deletions

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from .chunk import chunk
from .clean import clean
from .config_file import ConfigFile, ParseError
from .evaluate_ranking import evaluate_ranking
from .get_sentences import get_sentences
from .language import english_name_of_language, is_english, predict_language
from .logger import get_logger
from .match_names import match_names
from .parallel_map import WorkerException, parallel_map, threaded_parallel_map
from .unchunk import unchunk
from .unique import unique

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from typing import Iterable, List, TypeVar
T = TypeVar("T")
def chunk(values: Iterable[T], chunk_size: int) -> Iterable[T]:
assert chunk_size >= 1
result: List[T] = []
for v in values:
result.append(v)
if len(result) == chunk_size:
yield result
result = []
if len(result) > 0:
yield result

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import html
import re
import unicodedata
import unidecode
from .data import left_regular_punctuations, right_regular_punctuations
from .external.pylatexenc.latex2text import LatexNodes2Text
from .logger import get_logger
logger = get_logger("clean")
latex = LatexNodes2Text()
joined_left_punctuations = "".join(left_regular_punctuations).replace("]", r"\]")
joined_right_punctuations = "".join(right_regular_punctuations).replace("[", r"\[")
def clean(
text: str,
ignore_xml: bool = False,
ignore_latex: bool = False,
remove_brackets: bool = False,
convert_to_ascii: bool = False,
) -> str:
if not ignore_xml:
text = re.sub(r"<[^>]*>", " ", text)
text = html.unescape(text)
if not ignore_latex:
text = text.replace("%", "\\%") # escape LaTeX comments before parsing as LaTeX
try:
text = latex.latex_to_text(text, tolerant_parsing=True, strict_braces=False)
text = text.replace("%s", " ")
except:
logger.exception("Latex parsing error")
if convert_to_ascii:
text = unicodedata.normalize("NFKD", text)
try:
text.encode("ASCII", errors="strict")
except UnicodeEncodeError:
text = "".join([c for c in text if not unicodedata.combining(c)])
text = unidecode.unidecode(text)
text = re.sub(
r"\b[a-zA-Z](?:[\t ]+[a-zA-Z]\b)+", lambda m: re.sub(r"[\t ]", "", m[0]), text
) # A R T I C L E => ARTICLE
if remove_brackets:
text = re.sub(r"\[[^\]]*\]", " ", text)
# fix hypens: break- word => break-word
text = re.sub(r"(\S)-\s+", r"\1-", text)
text = re.sub(r"\s+-(\S)", r"-\1", text)
# collapse whitespace
text = re.sub(r"\s+", " ", text)
# fix punctuation
text = re.sub(rf" ([{joined_left_punctuations}])", r"\1", text)
text = re.sub(rf"([{joined_right_punctuations}]) ", r"\1", text)
text = text.strip()
return text

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from .config_file import ConfigFile
from .parse_error import ParseError

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import os
from pathlib import Path
from typing import Dict, Iterable, Tuple, Union
from ..logger import get_logger
from .parse_error import ParseError
from .pattern import pattern
ENVIRONMENT_VARIABLE_KEY_PREFIX = "ENV"
logger = get_logger("ConfigFile")
class ConfigFile:
def __init__(self, path: Union[Path, str]) -> None:
if not isinstance(path, Path):
path = Path(path)
if not path.exists():
raise FileNotFoundError(path.absolute())
self._path = path
self._key_values: Dict[str, str] = {}
self._parse()
def _parse(self):
with open(self._path, encoding="utf-8") as f:
lines: str = f.read()
matches = pattern.findall(lines)
for key, *values in matches:
try:
value = next(v for v in values if v)
except StopIteration:
raise ParseError(
f"Cannot parse config file ({self._path.absolute()}), error at key `{key}`"
)
already_exists = key in self._key_values
if already_exists and not value.startswith(
f"{ENVIRONMENT_VARIABLE_KEY_PREFIX}:"
):
raise KeyError(
f"Key `{key}` has been already defined and its value is `{self._key_values[key]}`"
)
if value.startswith(f"{ENVIRONMENT_VARIABLE_KEY_PREFIX}:"):
_, value = value.split(":")
if value not in os.environ:
issue = f'The value of `{key}` contains the "{ENVIRONMENT_VARIABLE_KEY_PREFIX}` prefix but `{value}` is not defined as an environment variable'
if already_exists:
logger.warning(
f"{issue}, using the default value defined above (`{self._key_values[key]}`)"
)
continue
else:
raise KeyError(
f"{issue} and no default value has been provided"
)
else:
value = os.environ[value]
self._key_values[key] = value
def __getattr__(self, key: str) -> str:
if key in self._key_values:
return self._key_values[key]
raise KeyError(
f"Key `{key}` is not found in configuration file ({self._path.absolute()})"
)
__getitem__ = __getattr__
def __iter__(self) -> Iterable[Tuple[str, str]]:
return iter(self._key_values)
def __len__(self) -> int:
return len(self._key_values)
def keys(self):
return self._key_values.keys()
def values(self):
return self._key_values.values()
def items(self):
return self._key_values.items()
def __repr__(self):
return f"{type(self).__name__}(path={self._path}) {self._key_values}"

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class ParseError(Exception):
pass

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import re
pattern = re.compile(
r"""
(?:^|\n) # new key-value pairs must start on a new line
\s* # leading whitespace is allowed
(?!\#) # the key cannot start with a `#` symbol
(\w+?) # then comes the key
\s*=\s* # the key and value are separated by an equal sign
(?: # then comes the value
"([^"]*)" # the value can be surrounded by quotes: "value"
| '([^']*)' # the value can be surrounded by quotes: 'value'
| `([^`]*)` # the value can be surrounded by quotes: `value`
| ([^#\n]*?) # or it is bare, in that case, the trailing whitespace is ignored
)
\s*(?:\#.*)? # comments can be added with the `#` symbol
(?=\n|$) # a key-value pairs are separated by new lines
""",
flags=re.UNICODE | re.VERBOSE,
)

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from .american_spellings import american_spellings
from .punctuations import (
left_regular_punctuations,
right_regular_punctuations,
sentence_ending_punctuations,
)

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sentence_ending_punctuations = [".", "?", "!", ":", ";"]
# punctuations that usually have no space between them and the character to their left
left_regular_punctuations = [
*sentence_ending_punctuations,
",",
"'",
"%",
")",
"}",
"]",
]
# punctuations that usually have no space between them and the character to their right
right_regular_punctuations = [
"(",
"{",
"[",
"$",
"€",
"#",
]

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from .draw_f1_iso_lines import draw_f1_iso_lines
from .evaluate_ranking import evaluate_ranking

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from typing import Optional
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.axes import Axes
def draw_f1_iso_lines(
resolution: int = 1000,
min: float = 0.2,
max: float = 0.8,
steps: int = 4,
axes: Optional[Axes] = None,
) -> None:
if axes is None:
axes = plt.axes()
for f_score in np.linspace(min, max, num=steps):
x = np.linspace(f_score / (2 - f_score), 1, num=resolution)
y = f_score * x / (2 * x - f_score)
axes.plot(x[y >= 0], y[y >= 0], color="gray", alpha=0.2)
axes.annotate(
f"f1={f_score:0.1f}",
backgroundcolor="w",
xy=(0.9, y[int(resolution * 0.9)] + 0.02),
)

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from pathlib import Path
from typing import Dict, List, Optional, Union
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from sklearn.metrics import average_precision_score, precision_recall_curve
from ..unique import unique
from .draw_f1_iso_lines import draw_f1_iso_lines
def evaluate_ranking(
expected: List[Union[str, float]],
actual_scores: List[float],
target_recall: float,
title: Optional[str] = "",
disable_interpolation: bool = False,
axes: Optional[plt.Axes] = None,
output_svg: Optional[Path] = None,
reverse_order: bool = False,
plot: bool = True,
) -> Dict[Union[str, float], float]:
assert 0 <= target_recall <= 1
if plot and axes is None:
fig = plt.figure(figsize=(20, 10))
fig.patch.set_facecolor("white")
ax = plt.axes()
else:
ax = axes
classes = sorted(unique(expected), reverse=reverse_order)
str_classes = [str(c) for c in classes]
with matplotlib.rc_context({"font.size": 20}):
if plot:
ax.set_xmargin(0)
draw_f1_iso_lines(axes=ax)
results: Dict[Union[str, float], float] = {}
for i in range(len(classes) - 1):
binarized_expected = [
(v < classes[i]) if reverse_order else (v > classes[i])
for v in expected
]
precision, recall, _ = precision_recall_curve(
binarized_expected, actual_scores
)
if not disable_interpolation:
for j in range(1, len(precision)):
precision[j] = max(precision[j - 1], precision[j])
closest_recall_index = np.argmin(np.abs(recall - target_recall))
precision_at_closest_recall = precision[closest_recall_index]
average_precision = average_precision_score(
binarized_expected, actual_scores
)
results[classes[i]] = precision_at_closest_recall
if plot:
ax.plot(
recall,
precision,
label=f"{'|'.join(str_classes[:i + 1])} ↔ {'|'.join(str_classes[i+1:])} (P@{target_recall:.2f}={precision_at_closest_recall:.2f}, AP={average_precision:.2f})",
)
if plot:
ax.legend(loc="upper right")
ax.axvline(x=target_recall, linestyle="--", color="#55c6bb", linewidth=2.0)
if title is None:
title = "Ranking evaluation"
ax.set_title(f'{title} ({" < ".join(str_classes)})', pad=20)
ax.set_xlabel("Recall")
ax.set_ylabel("Precision")
ax.set_xticks([target_recall] + sorted(ax.get_xticks()))
if plot and output_svg is None:
if axes is None:
plt.show()
elif output_svg:
plt.savefig(output_svg, format="svg")
return results

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https://github.com/phfaist/pylatexenc

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#
# The MIT License (MIT)
#
# Copyright (c) 2015 Philippe Faist
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
"""
Utilities for LaTeX to/from Unicode Text conversion.
Main Site:
https://github.com/phfaist/pylatexenc/
"""
from .version import version_str as _version_str
__version__ = _version_str

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# -*- coding: utf-8 -*-
#
# The MIT License (MIT)
#
# Copyright (c) 2019 Philippe Faist
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# Internal module. Internal API may move, disappear or otherwise change at any
# time and without notice.
try:
# Python >= 3.3
from collections.abc import MutableMapping
except ImportError:
from collections import MutableMapping
import bisect
import warnings
# ------------------------------------------------------------------------------
def pylatexenc_deprecated_ver(ver, msg, stacklevel=2):
warnings.warn(
"Deprecated (pylatexenc {}): {} ".format(ver, msg.strip()),
DeprecationWarning,
stacklevel=stacklevel + 1,
)
def pylatexenc_deprecated_2(msg, stacklevel=2):
warnings.warn(
(
"Deprecated (pylatexenc 2.0): {} "
"[see https://pylatexenc.readthedocs.io/en/latest/new-in-pylatexenc-2/]"
).format(msg.strip()),
DeprecationWarning,
stacklevel=stacklevel + 1,
)
# ------------------------------------------------------------------------------
class LazyDict(MutableMapping):
r"""
A lazy dictionary that loads its data when it is first queried.
This is used to store the legacy
:py:data:`pylatexenc.latexwalker.default_macro_dict` as well as
:py:data:`pylatexenc.latex2text.default_macro_dict` etc. Such that these
"dictionaries" are still exposed at the module-level, but the data is loaded
only if they are actually queried.
"""
def __init__(self, generate_dict_fn):
self._full_dict = None
self._generate_dict_fn = generate_dict_fn
def _ensure_instance(self):
if self._full_dict is not None:
return
self._full_dict = self._generate_dict_fn()
def __getitem__(self, key):
self._ensure_instance()
return self._full_dict.__getitem__(key)
def __setitem__(self, key, val):
self._ensure_instance()
return self._full_dict.__setitem__(key, val)
def __delitem__(self, key):
self._ensure_instance()
return self._full_dict.__delitem__(key)
def __iter__(self):
self._ensure_instance()
return iter(self._full_dict)
def __len__(self):
self._ensure_instance()
return len(self._full_dict)
def copy(self):
self._ensure_instance()
return self._full_dict.copy()
def clear(self):
self._ensure_instance()
return self._full_dict.clear()
# ------------------------------------------------------------------------------
class LineNumbersCalculator(object):
r"""
Utility to calculate line numbers.
"""
def __init__(self, s):
super(LineNumbersCalculator, self).__init__()
def find_all_new_lines(x):
# first line starts at the beginning of the string
yield 0
k = 0
while k < len(x):
k = x.find("\n", k)
if k == -1:
return
k += 1
# s[k] is the character after the newline, i.e., the 0-th column
# of the new line
yield k
self._pos_new_lines = list(find_all_new_lines(s))
def pos_to_lineno_colno(self, pos, as_dict=False):
r"""
Return the line and column number corresponding to the given `pos`.
Return a tuple `(lineno, colno)` giving line number and column number.
Line numbers start at 1 and column number start at zero, i.e., the
beginning of the document (`pos=0`) has line and column number `(1,0)`.
If `as_dict=True`, then a dictionary with keys 'lineno', 'colno' is
returned instead of a tuple.
"""
# find line number in list
# line_no is the index of the last item in self._pos_new_lines that is <= pos.
line_no = bisect.bisect_right(self._pos_new_lines, pos) - 1
assert line_no >= 0 and line_no < len(self._pos_new_lines)
col_no = pos - self._pos_new_lines[line_no]
# 1+... so that line and column numbers start at 1
if as_dict:
return {"lineno": 1 + line_no, "colno": col_no}
return (1 + line_no, col_no)

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# -*- coding: utf-8 -*-
#
# The MIT License (MIT)
#
# Copyright (c) 2018 Philippe Faist
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
import argparse
import fileinput
import logging
import sys
from .. import latexwalker
from ..latex2text import LatexNodes2Text, _strict_latex_spaces_predef
from ..version import version_str
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
parser = argparse.ArgumentParser(prog="latex2text", add_help=False)
codegroup = parser.add_argument_group("Input options")
codegroup.add_argument(
"--code",
"-c",
action="store",
default=None,
metavar="LATEX_CODE",
help="Convert the given LATEX_CODE to unicode text instead of reading "
"from FILE or standard input. You cannot specify FILEs if you use this "
"option, and any standard input is ignored.",
)
codegroup.add_argument(
"files",
metavar="FILE",
nargs="*",
help="Input files to read LaTeX code from. If no FILE(s) is/are specified, "
"LaTeX code is read from standard input unless --code is specified",
)
group = parser.add_argument_group("LatexWalker options")
group.add_argument(
"--parser-keep-inline-math",
action="store_const",
const=True,
dest="parser_keep_inline_math",
default=None,
help=argparse.SUPPRESS,
)
group.add_argument(
"--no-parser-keep-inline-math",
action="store_const",
const=False,
dest="parser_keep_inline_math",
help=argparse.SUPPRESS,
)
group.add_argument(
"--tolerant-parsing",
action="store_const",
const=True,
dest="tolerant_parsing",
default=True,
)
group.add_argument(
"--no-tolerant-parsing",
action="store_const",
const=False,
dest="tolerant_parsing",
help="Tolerate syntax errors when parsing, and attempt to continue (default yes)",
)
# I'm not sure this flag is useful and if it should be exposed at all.
# Accept it, but make it hidden.
parser.add_argument(
"--strict-braces",
action="store_const",
const=True,
dest="strict_braces",
default=False,
help=argparse.SUPPRESS,
)
parser.add_argument(
"--no-strict-braces",
action="store_const",
const=False,
dest="strict_braces",
# help="Report errors for mismatching LaTeX braces (default no)"
help=argparse.SUPPRESS,
)
group = parser.add_argument_group("LatexNodes2Text options")
group.add_argument(
"--text-keep-inline-math",
action="store_const",
const=True,
dest="text_keep_inline_math",
default=None,
help=argparse.SUPPRESS,
)
group.add_argument(
"--no-text-keep-inline-math",
action="store_const",
const=False,
dest="text_keep_inline_math",
help=argparse.SUPPRESS,
)
group.add_argument(
"--math-mode",
action="store",
dest="math_mode",
choices=["text", "with-delimiters", "verbatim", "remove"],
default="text",
help="How to handle chunks of math mode LaTeX code. 'text' = convert "
"to text like the rest; 'with-delimiters' = same as 'text' but retain "
"the original math mode delimiters; 'verbatim' = keep verbatim LaTeX code; "
"'remove' = remove from input entirely",
)
group.add_argument(
"--fill-text",
dest="fill_text",
action="store",
nargs="?",
default=-1,
help="Attempt to wrap text to the given width, or 80 columns if option is "
"specified with no argument",
)
group.add_argument(
"--keep-comments",
action="store_const",
const=True,
dest="keep_comments",
default=False,
)
group.add_argument(
"--no-keep-comments",
action="store_const",
const=False,
dest="keep_comments",
help="Keep LaTeX comments in text output (default no)",
)
class ListWithHiddenItems(list):
def __init__(self, thelist, hiddenitems):
super(ListWithHiddenItems, self).__init__(thelist)
self.hiddenitems = hiddenitems
def __contains__(self, value):
return (
super(ListWithHiddenItems, self).__contains__(value)
or value in self.hiddenitems
)
strict_latex_spaces_choices = ListWithHiddenItems(
# the list
["off", "on"]
+ list(k for k in _strict_latex_spaces_predef.keys() if k != "default"),
# hidden items: Value is accepted, but not shown in list of choices
["default"],
)
group.add_argument(
"--strict-latex-spaces",
choices=strict_latex_spaces_choices,
dest="strict_latex_spaces",
default="macros",
help="How to handle whitespace. See documentation for the class "
"LatexNodes2Text().",
)
group.add_argument(
"--keep-braced-groups",
action="store_const",
const=True,
dest="keep_braced_groups",
default=False,
)
group.add_argument(
"--no-keep-braced-groups",
action="store_const",
const=False,
dest="keep_braced_groups",
help="Keep LaTeX {braced groups} in text output (default no)",
)
group.add_argument(
"--keep-braced-groups-minlen",
type=int,
default=2,
dest="keep_braced_groups_minlen",
help="Only apply --keep-braced-groups to groups that contain at least "
"this many characters",
)
group = parser.add_argument_group("General options")
group.add_argument(
"-q",
"--quiet",
dest="logging_level",
action="store_const",
const=logging.ERROR,
default=logging.INFO,
help="Suppress warning messages",
)
group.add_argument(
"-v",
"--verbose",
dest="logging_level",
action="store_const",
const=logging.DEBUG,
help="Verbose output",
)
group.add_argument(
"--version",
action="version",
version="pylatexenc {}".format(version_str),
help="Show version information and exit",
)
group.add_argument(
"--help", action="help", help="Show this help information and exit"
)
args = parser.parse_args(argv)
logging.basicConfig()
logging.getLogger().setLevel(args.logging_level)
logger = logging.getLogger(__name__)
if (
args.parser_keep_inline_math is not None
or args.text_keep_inline_math is not None
):
logger.warning(
"Options --parser-keep-inline-math and --text-keep-inline-math are "
"deprecated and no longer have any effect. Please use "
"--math-mode=... instead."
)
latex = ""
if args.code:
if args.files:
logger.error(
"Cannot specify both FILEs and --code option. "
"Use --help option for more information."
)
sys.exit(1)
latex = args.code
else:
for line in fileinput.input(files=args.files):
latex += line
if args.fill_text != -1:
if args.fill_text is not None and len(args.fill_text):
fill_text = int(args.fill_text)
else:
fill_text = True
else:
fill_text = None
lw = latexwalker.LatexWalker(
latex, tolerant_parsing=args.tolerant_parsing, strict_braces=args.strict_braces
)
(nodelist, pos, len_) = lw.get_latex_nodes()
ln2t = LatexNodes2Text(
math_mode=args.math_mode,
keep_comments=args.keep_comments,
strict_latex_spaces=args.strict_latex_spaces,
keep_braced_groups=args.keep_braced_groups,
keep_braced_groups_minlen=args.keep_braced_groups_minlen,
fill_text=fill_text,
)
print(ln2t.nodelist_to_text(nodelist))
def run_main():
try:
main()
except SystemExit:
raise
except: # lgtm [py/catch-base-exception]
import pdb
import traceback
traceback.print_exc()
pdb.post_mortem()
if __name__ == "__main__":
main()
# run_main() # debug

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