<commit_before>"""
An entry point for the PyFBA command
"""

import os
import sys
import argparse
import PyFBA
from .citation import cite_me_please
from .fluxes import measure_fluxes
from .gapfill_from_roles import gapfill_from_roles

def full_help():
    """
    Just return the help text
    :return: The help
    """

    return f"""
Welcome to PyFBA version {PyFBA.__version__}

Please use one of these commands with their appropriate flags. Use pyfba <command> -h for more help

gapfill_roles\tGapfill Flux Balance Analysis from a list of functional roles
fluxes\tGiven a set of reactions that form a model, report the fluxes through those reactions

help\tThis help menu
version\tPrint the version and exit

citations\tGet the citations for PyFBA and the work that it is built upon
    """


def run():
    """
    Run the appropriate pyfba command
    """


    if sys.argv[1] == 'help' or sys.argv[1] == '-h' or sys.argv[1] == '--help': 
        print(full_help())
        sys.exit(0)
    elif 'version' in sys.argv[1] or '-v' in sys.argv[1]:
        print(PyFBA.__version__)
        sys.exit(0)
    elif 'citation' in sys.argv[1] or 'cite' in sys.argv[1]:<commit_msg>Checking for no options!<commit_after>"""
An entry point for the PyFBA command
"""

import os
import sys
import argparse
import PyFBA
from .citation import cite_me_please
from .fluxes import measure_fluxes
from .gapfill_from_roles import gapfill_from_roles

def full_help():
    """
    Just return the help text
    :return: The help
    """

    return f"""
Welcome to PyFBA version {PyFBA.__version__}

Please use one of these commands with their appropriate flags. Use pyfba <command> -h for more help

gapfill_roles\tGapfill Flux Balance Analysis from a list of functional roles
fluxes\tGiven a set of reactions that form a model, report the fluxes through those reactions

help\tThis help menu
version\tPrint the version and exit

citations\tGet the citations for PyFBA and the work that it is built upon
    """


def run():
    """
    Run the appropriate pyfba command
    """

    if len(sys.argv) == 1 or sys.argv[1] == 'help' or sys.argv[1] == '-h' or sys.argv[1] == '--help':
        print(full_help())
        sys.exit(0)
    elif 'version' in sys.argv[1] or '-v' in sys.argv[1]:
        print(PyFBA.__version__)
        sys.exit(0)
    elif 'citation' in sys.argv[1] or 'cite' in sys.argv[1]:
{'fraction_non_alphanumeric': 0.09651699538396978, 'fraction_numerical': 0.007973143096936634, 'mean_word_length': 3.3743119266055044, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '610985', 'n_tokens_mistral': 788, 'n_tokens_neox': 750, 'n_words': 293}