Packaging, entrypoints and licence

.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
\ No newline at end of file

.gitlab-ci.yml

+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration           #
+#                                                                             #
+# This software is distributed under the terms of the GNU General Public      #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING".   #
+#                                                                             #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization  #
+# or submit itself to any jurisdiction.                                       #
+###############################################################################
 image: python:latest
 
-# Change pip's cache directory to be inside the project directory since we can
-# only cache local items.
-variables:
-  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+pre-commit:
+  stage: build
+  before_script:
+    - pip install pre-commit
+  script:
+    - pre-commit run --all-files
+  variables:
+    PRE_COMMIT_HOME: ${CI_PROJECT_DIR}/.cache/pre-commit
+  cache:
+    paths:
+      - ${PRE_COMMIT_HOME}
 
-# Pip's cache doesn't store the python packages
-# https://pip.pypa.io/en/stable/topics/caching/
-#
-# If you want to also cache the installed packages, you have to install
-# them in a virtualenv and cache it as well.
-cache:
-  paths:
-    - .cache/pip
-    - venv/
 
-build-env:
-  stage: build
-  script: 
+.setup_environment:
+  before_script:
     - python --version ; pip --version  # For debugging
     - pip install virtualenv
     - virtualenv venv
     - source venv/bin/activate
-    - pip install numpy
+    - pip install .
+
 
 extract-and-convert-table-2018-050:
+  extends: .setup_environment
   stage: test
   script:
-    - source venv/bin/activate
-    - python extract_tables_from_source.py -f "TestAnalyses/LHCb-PAPER-2018-050/bfrac-13.tex"
-    - python extract_tables_from_source.py -f "TestAnalyses/LHCb-PAPER-2018-050/Supplementary.tex"
-    - python tex_to_yaml.py --file "ptB.tex" --format "i d stat sys d stat sys"
+    - gethepdata extract_tables -f "TestAnalyses/LHCb-PAPER-2018-050/bfrac-13.tex"
+    - gethepdata extract_tables -f "TestAnalyses/LHCb-PAPER-2018-050/Supplementary.tex"
+    - gethepdata tex_to_yaml --file "ptB.tex" --format "i d stat sys d stat sys"
     - ls *.yaml | grep "ptB.yaml"
-  needs: ["build-env"]
   artifacts:
     when: always
 
 
 extract-and-convert-table-2020-018:
+  extends: .setup_environment
   stage: test
-  needs: ["build-env"]
   script:
-    - source venv/bin/activate
-    - python extract_tables_from_source.py -f "TestAnalyses/LHCb-PAPER-2020-018/main.tex"
-    - python tex_to_yaml.py --file eta_results.tex --format "i d e d e d e"
+    - gethepdata extract_tables -f "TestAnalyses/LHCb-PAPER-2020-018/main.tex"
+    - gethepdata tex_to_yaml --file eta_results.tex --format "i d e d e d e"
     - ls *.yaml | grep "eta_results.yaml"
   artifacts:
     when: always

.pre-commit-config.yaml

+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files
+      - id: no-commit-to-branch
+        args: [--branch, main]
+
+  - repo: https://gitlab.cern.ch/lhcb-core/LbDevTools
+    rev: 2.0.40
+    hooks:
+      - id: lb-add-copyright

README.md

 # HepDataExtractor
 
-Simple python scripts to extract tables from LaTeX papers and convert them to HepData entries
+Simple python tool to extract tables from LaTeX papers and convert them to HepData entries
 
 
 ## Helping to Develop
@@ -12,37 +12,37 @@ Spotted an error? Need something special you think is useable by others? Create
 
 ### I have a LaTeX file with just the tables I want to process
 
-In some ways this is the easiest way to do things! You can simply pass the file to `tex_to_yaml.py` via the command line, e.g.
+In some ways this is the easiest way to do things! You can simply pass the file to `tex_to_yaml` via the command line, e.g.
 
 ```
-python tex_to_yaml.py --file myfile.tex --format "i d stat syst d stat syst"
+gethepdata tex_to_yaml --file myfile.tex --format "i d stat syst d stat syst"
 ```
 
 if you need help with the command line documents, type
 
 ```
-python tex_to_yaml.py --help
+gethepdata tex_to_yaml --help
 ```
 
 
 ### I have a document which I want to process the tables for
 
-Not a problem! The script `extract_tables_from_source.py` extracts all the tables from a document (including recursively by passing only the `main.tex` file). You can call from the command line using
+Not a problem! The command `extract_tables` extracts all the tables from a document (including recursively by passing only the `main.tex` file). You can call from the command line using
 
 ```
-python extract_tables_from_source.py --file /path/to/main.tex
+gethepdata extract_tables --file /path/to/main.tex
 ```
-which will then use the `\label` argument to determine the tex file name. 
+which will then use the `\label` argument to determine the `.tex` file name.
 
 ### My submission is ready! Create the `submission.yaml` file
 
-Once you have all tables in the `.yaml` format, you can run the script `make_submission_yaml_file.py` to create the relevant file suitable for hepdata submission
+Once you have all tables in the `.yaml` format, you can run the command `prepare_submission` to create the relevant file suitable for HepData submission
 
 ```
-python make_submission_yaml_file.py --files *.yaml
+gethepdata prepare_submission --files *.yaml
 ```
 
-This will create the `submission.yaml` based on the *.yaml files produced by the `tex_to_yaml.py` step.
+This will create the `submission.yaml` based on the output of the `tex_to_yaml` step.
 
 
-Original Author: Harvey Turner, Manchester, supervised by Adam Davis and Will Barter. Updated 11 August 2023 by Adam Davis
+Original Author: Harvey Turner, Manchester, supervised by Adam Davis and Will Barter. Updated 11 August 2023 by Adam Davis
\ No newline at end of file

pyproject.toml

+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+
+[project]
+name = "HepDataExtractor"
+dependencies = [
+    "pyyaml",
+    "numpy"
+]
+dynamic = ["version"]
+description = "Simple python tool to extract tables from LaTeX papers and convert them to HepData entries"
+authors = [
+    {name = "Adam Davis"},
+    {name = "Harvey Turner"},
+    {name = "Will Barter"}
+]
+maintainers = [
+    {name = "LHCb Simulation"}
+]
+readme = "README.md"
+classifiers = [
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Programming Language :: Python :: 3"
+]
+
+[project.urls]
+Repository = "https://gitlab.cern.ch/lhcb-simulation/hepdataextractor"
+"Bug Tracker" = "https://gitlab.cern.ch/lhcb-simulation/hepdataextractor/-/issues"
+
+[project.scripts]
+gethepdata = "HepDataExtractor.__main__:parse_args"

src/HepDataExtractor/__init__.py

+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration           #
+#                                                                             #
+# This software is distributed under the terms of the GNU General Public      #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING".   #
+#                                                                             #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization  #
+# or submit itself to any jurisdiction.                                       #
+###############################################################################

src/HepDataExtractor/__main__.py

+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration           #
+#                                                                             #
+# This software is distributed under the terms of the GNU General Public      #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING".   #
+#                                                                             #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization  #
+# or submit itself to any jurisdiction.                                       #
+###############################################################################
+import argparse
+
+from .extract_tables_from_source import main as etfs
+from .make_submission_yaml_file import main as msyf
+from .tex_to_yaml import main as tty
+
+def parse_args():
+    parser = argparse.ArgumentParser()
+    subparsers = parser.add_subparsers(dest="action", required=True)
+
+    # extract_tables_from_source
+    etfs_parser = subparsers.add_parser("extract_tables")
+    etfs_parser.add_argument('-f','--file',type=str,required=True,help='input file to parse')
+    etfs_parser.add_argument('--no_output',action="store_true",help='skip output')
+    etfs_parser.set_defaults(func=etfs)
+
+    # tex_to_yaml
+    tty_parser = subparsers.add_parser("tex_to_yaml")
+    tty_parser.add_argument("--file", type=str,required=True,help='file contains name of data file')
+    tty_parser.add_argument("--format", type=str, required=False,help='''format contains string of data format (not necessary for covariance)
+     A guide: i -- independent variable,
+      d -- dependent variable,
+      stat -- statistical error,
+      sys -- systematic error''')
+    tty_parser.add_argument("--covariance", action="store_true", default=False,help='Flag to say whether the data is a covariance matrix or not') #
+    tty_parser.add_argument("--correlation", action="store_true", default=False,help='Same as covariance, but for a correlation matrix') #
+    tty_parser.add_argument("--qualifiers", type=str, default="None",help='qualifiers contains name of qualifiers file, defaults to "None"')
+    tty_parser.add_argument("--remove", nargs='+', help="list of terms to remove from table")
+    tty_parser.set_defaults(func=tty)
+
+    # make_submission_yaml_file
+    msyf_parser = subparsers.add_parser("prepare_submission",
+        description="Preparation of submission.yaml file for HepData submission. "
+        "Requires the data yaml files produced from tex_to_yaml to be provided")
+    msyf_parser.add_argument('-f','--files',type=str,nargs='+',required=True,help='input yaml file(s) to parse. Note, can pass *.yaml')
+    msyf_parser.set_defaults(func=msyf)
+
+    args = parser.parse_args()
+    args.func(args)

extract_tables_from_source.py → src/HepDataExtractor/extract_tables_from_source.py

+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration           #
+#                                                                             #
+# This software is distributed under the terms of the GNU General Public      #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING".   #
+#                                                                             #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization  #
+# or submit itself to any jurisdiction.                                       #
+###############################################################################
 import sys,os
 
 def extract_tables(sourcefile):
@@ -14,42 +24,36 @@ def extract_tables(sourcefile):
         return tables_in_paper
 
     with open(sourcefile) as f:
-        lines = f.readlines() 
+        lines = f.readlines()
         for i in range(len(lines)):
             if 'begin{table}' in lines[i] or 'begin{sidewaystable}' in lines[i]:
                 # print('starting table')
                 temptable = []
                 j=0
-                while not "\end" in lines[i+j]:
-                    if "\label" in lines[i+j]:
-                        temptablename = lines[i+j].split("\label{")[1].split("}")[0].replace("tab:","")
+                while not r"\end" in lines[i+j]:
+                    if r"\label" in lines[i+j]:
+                        temptablename = lines[i+j].split(r"\label{")[1].split("}")[0].replace("tab:","")
                     if not 'begin{' in lines[i+j]:
                         temptable.append(lines[i+j])
                     j+=1
-                
+
                 tables_in_paper[temptablename]=temptable
-            if '\input' in lines[i]:
+            if r'\input' in lines[i]:
                 #skip commented inputs
-                if "%" in lines[i]: continue 
-                extended_file = lines[i].split("\input{")[1].split("}")[0]+".tex"
+                if "%" in lines[i]: continue
+                extended_file = lines[i].split(r"\input{")[1].split("}")[0]+".tex"
                 #pathological case where people also include .tex in input command
                 if ".tex.tex" in extended_file:
                     extended_file = extended_file.replace(".tex.tex",".tex")
                 path_to_included_file = os.path.join(full_path_to_sourcefile,extended_file)
-                
+
                 extended_dict = extract_tables(path_to_included_file)
-                
+
                 tables_in_paper = tables_in_paper | extended_dict
     return tables_in_paper
 
 
-if '__main__'==__name__:
-    import argparse
-    parser = argparse.ArgumentParser()
-    parser.add_argument('-f','--file',type=str,required=True,help='input file to parse')
-    parser.add_argument('--no_output',action="store_true",help='skip output')
-
-    args = parser.parse_args()
+def main(args):
     print('now parsing',args.file)
 
     tables_in_paper = extract_tables(args.file)
@@ -62,4 +66,4 @@ if '__main__'==__name__:
             f.close()
     else:
         print('here is the output of the tables')
-        print(tables_in_paper)
+        print(tables_in_paper)
\ No newline at end of file

make_submission_yaml_file.py → src/HepDataExtractor/make_submission_yaml_file.py

+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration           #
+#                                                                             #
+# This software is distributed under the terms of the GNU General Public      #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING".   #
+#                                                                             #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization  #
+# or submit itself to any jurisdiction.                                       #
+###############################################################################
 import sys,os
 import argparse
 
@@ -12,7 +22,7 @@ import yaml
 def get_metadata_info_for_yaml(input_yaml):
     """
     Simple wrapper to get the metadata information necessary for the submission.yaml file.
-    Uses safe_substitute on the template in the Templates directory to ensure return even 
+    Uses safe_substitute on the template in the Templates directory to ensure return even
     in the case of error.
     """
     conf = yaml.safe_load(open(input_yaml,'r'))
@@ -33,7 +43,7 @@ def get_metadata_info_for_yaml(input_yaml):
         if 'Covariance' in thing['header']['name'] or 'Correlation' in thing['header']['name']:
             # print('skipping observables addition for correlation/covariance')
             the_dict['special']=str(thing['header']['name'])
-        else: 
+        else:
             observables.append(thing['header']['name'])
     for thing in conf['independent_variables']:
         # print('now appending independent variables',thing['header']['name'])
@@ -45,18 +55,13 @@ def get_metadata_info_for_yaml(input_yaml):
     else:
         vars_sorted = list(OrderedDict.fromkeys(independent_vars))
         # the_dict['description'] = the_dict['special'] + ' for ' +', '.join(vars_sorted)
-    
+
     the_template = Template(open(os.path.dirname(os.path.abspath(__file__))+"/Templates/submission_template.yaml",'r').read())
 
     return the_template.safe_substitute(the_dict)
 
 
-if '__main__'==__name__:
-    parser = argparse.ArgumentParser(description="Preparation of submission.yaml script for hepdata submission.\
-    Requires the data yaml files produced from tex_to_yaml.py to be provided")
-    parser.add_argument('-f','--files',type=str,nargs='+',required=True,help='input yaml file(s) to parse. Note, can pass *.yaml')
-    args = parser.parse_args()
-    
+def main(args):
     for f in args.files:
         if not '.yaml' in f:
             print("You haven't passed valid yaml files! Please try again")
@@ -89,7 +94,7 @@ if '__main__'==__name__:
         submission_file.write('\n')
         submission_file.write("---\n")
         submission_file.write('\n')
-    
-    
+
+
     submission_file.close()
-    print('Done!')
+    print('Done!')
\ No newline at end of file

tex_to_yaml.py → src/HepDataExtractor/tex_to_yaml.py

+###############################################################################
+# (c) Copyright 2024 CERN for the benefit of the LHCb Collaboration           #
+#                                                                             #
+# This software is distributed under the terms of the GNU General Public      #
+# Licence version 3 (GPL Version 3), copied verbatim in the file "COPYING".   #
+#                                                                             #
+# In applying this licence, CERN does not waive the privileges and immunities #
+# granted to it by virtue of its status as an Intergovernmental Organization  #
+# or submit itself to any jurisdiction.                                       #
+###############################################################################
 import argparse
 import numpy as np
 import re
@@ -59,7 +69,7 @@ class value:
         else:
             output = "  - value: " + str(self.x) + "\n"
         return output
-        
+
 class variable:
     """
     Variable class to contain the column header and each value the variable takes, with uncertainties
@@ -90,7 +100,7 @@ def discard(line):
     line = line.strip(" \n\t~{}")
     if line == "":
         return True
-    elif line.startswith("\multicolumn"):
+    elif line.startswith(r"\multicolumn"):
         return False
     elif line[0] == "%" or line[0] == "\\":
         return True
@@ -101,7 +111,7 @@ def extract_header(string):
     """
     Extracts the name and units (if any) from the header of a column and returns a string suitable for yaml
     """
-    string = string.replace("\\xspace", "").replace("\\kern", "").replace("\\,", "").replace("\\!", "").replace("-0.1em", "").strip(" \n\t~\\")
+    string = string.replace(r"\xspace", "").replace(r"\kern", "").replace(r"\,", "").replace(r"\!", "").replace("-0.1em", "").strip(" \n\t~\\")
     if string.startswith("multicolumn"): #Removes leading multicolumn expression from header
         string = string[string.find("}")+1:]
         string = string[string.find("}")+1:]
@@ -122,16 +132,16 @@ def extract_description(string):
     Extract the description field from the caption listed in paper
     """
     temp_string = string.replace("\\n","").replace("\\xspace","").replace("\\","").rstrip().strip()
-    
+
     if 'label' in temp_string:
-        to_rep = re.findall("label\{[tab:]*[a-zA-Z_]*\}",temp_string)
+        to_rep = re.findall(r"label{[tab:]*[a-zA-Z_]*}",temp_string)
         for rep in to_rep:
             temp_string = temp_string.replace(rep,"")
     temp_string = temp_string.replace('caption{',"").replace("}","")
     return temp_string
 
 
-def split_format(string): 
+def split_format(string):
     """
     Splits format string so that each variable is its own string in a list
     """
@@ -143,7 +153,7 @@ def split_format(string):
             temp_list[-1].append(i)
     return temp_list
 
-def format_value(string): 
+def format_value(string):
     """
     Takes string with errors separated by commas and returns value object
     """
@@ -161,7 +171,7 @@ def format_value(string):
             return the_val
 
 
-def write_variables(variable_list, file): 
+def write_variables(variable_list, file):
     """
     Writes variable objects in list to a yaml file
     """
@@ -173,7 +183,7 @@ def write_variables(variable_list, file):
     for i in variable_list:
         if i.is_indep == False:
             file.write(repr(i))
-    
+
 
 def write_description(description,file):
     """
@@ -185,11 +195,11 @@ def remove_phantoms(string): #
     """
     Removes \\phantom{...} from string
     """
-    while "\phantom" in string:
-        x = string.find("\phantom")
+    while r"\phantom" in string:
+        x = string.find(r"\phantom")
         while string[x] != "}":
             x += 1
-        string = string[:string.find("\phantom")] + string[x+1:]
+        string = string[:string.find(r"\phantom")] + string[x+1:]
     return string
 
 def asym_unc(string):
@@ -201,20 +211,7 @@ def asym_unc(string):
 
 
 
-if '__main__'==__name__:
-    parser = argparse.ArgumentParser()
-    parser.add_argument("--file", type=str,required=True,help='file contains name of data file') 
-    parser.add_argument("--format", type=str, required=False,help='format contains string of data format (not necessary for covariance)\n\
-     A guide: i -- independent variable,\
-      d -- dependent variable, \
-      stat -- statistical error,\
-      sys -- systematic error')
-    parser.add_argument("--covariance", action="store_true", default=False,help='Flag to say whether the data is a covariance matrix or not') #
-    parser.add_argument("--correlation", action="store_true", default=False,help='Same as covariance, but for a correlation matrix') #
-    parser.add_argument("--qualifiers", type=str, default="None",help='qualifiers contains name of qualifiers file, defaults to "None"') 
-    parser.add_argument("--remove", nargs='+', help="list of terms to remove from table")
-
-    args = parser.parse_args()
+def main(args):
     description = None
     if args.covariance==False and args.correlation == False and args.format ==None:
         print('Must pass format if not passing a correlation or covariance matrix!')
@@ -234,20 +231,20 @@ if '__main__'==__name__:
     for i in lines:
         if discard(i) == False: #Only valid lines
             if args.covariance == True or args.correlation == True:
-                data_array.append(remove_phantoms(i).replace("\\hline", "").strip(" \n\t~\\").split("&")) #Splits into array by &
+                data_array.append(remove_phantoms(i).replace(r"\hline", "").strip(" \n\t~\\").split("&")) #Splits into array by &
             else:
                 if len(data_array) == 0: #Does not take convert the first line to values, as this contains headers
-                    data_array.append(remove_phantoms(i).replace("\\hline", "").strip(" \n\t~\\").split("&"))
+                    data_array.append(remove_phantoms(i).replace(r"\hline", "").strip(" \n\t~\\").split("&"))
                 else:
-                    line_split = remove_phantoms(i).replace("\\hline", "").strip(" \n\t~\\$").split("&")
-                    if "\pm" in line_split: #Removes items that are just \pm
-                        line_split.remove("\pm")
-                    if " \pm " in line_split:
-                        line_split.remove(" \pm ")
+                    line_split = remove_phantoms(i).replace(r"\hline", "").strip(" \n\t~\\$").split("&")
+                    if r"\pm" in line_split: #Removes items that are just \pm
+                        line_split.remove(r"\pm")
+                    if r" \pm " in line_split:
+                        line_split.remove(r" \pm ")
                     count = 0 #Count iterates in the format string to determine whether each number is a indep value, dep value, sys uncertainty, etc.
                     value_list = [] #List of values extracted from this line
                     for j in line_split: #For item in line split by "&"
-                        temp = j.split("\pm")
+                        temp = j.split(r"\pm")
                         temp = [x.strip(" \n\t~\\$") for x in temp]
                         if len(temp) > 1: #Removes blank characters from temp
                             if "" in temp:
@@ -296,7 +293,7 @@ if '__main__'==__name__:
         else:
             variables.append(variable(True, indep_header, "None"))
             variables.append(variable(True, indep_header, "None"))
-        if args.covariance == True:            
+        if args.covariance == True:
             variables.append(variable(False, "name: Covariance", args.qualifiers))
         else:
             variables.append(variable(False, "name: Correlation", args.qualifiers))
@@ -341,14 +338,14 @@ if '__main__'==__name__:
         for i in range(1,len(data_array)):
             for j in range(len(data_array[i,:])):
                 variables[j].append(data_array[i,j])
-                
+
     output_file = open(args.file.replace(".tex", ".yaml"), "w") #Creates file with same name, but .yaml instead of .tex
-    
+
     write_variables(variables, output_file) #Writes contents of variables list to file
-    output_file.close()   
+    output_file.close()
     #write extra file for description
-    
+
     if description is not None:
         output_description_file = open(args.file.replace('.tex','_description_file.txt'),'w')
         write_description(description, output_description_file)
-        output_description_file.close()
+        output_description_file.close()
\ No newline at end of file