*The main function used when ``cl_utils.py`` is run as a single script from the cl, or when installed as a cl command*

def main(arguments=None):
    """
    *The main function used when ``cl_utils.py`` is run as a single script from the cl, or when installed as a cl command*
    """
    # setup the command-line util settings
    su = tools(
        arguments=arguments,
        docString=__doc__,
        logLevel="WARNING",
        options_first=False,
        projectName="qubits"
    )
    arguments, settings, log, dbConn = su.setup()

    # unpack remaining cl arguments using `exec` to setup the variable names
    # automatically
    for arg, val in arguments.iteritems():
        if arg[0] == "-":
            varname = arg.replace("-", "") + "Flag"
        else:
            varname = arg.replace("<", "").replace(">", "")
        if varname == "import":
            varname = "iimport"
        if isinstance(val, str) or isinstance(val, unicode):
            exec(varname + " = '%s'" % (val,))
        else:
            exec(varname + " = %s" % (val,))
        if arg == "--dbConn":
            dbConn = val
        log.debug('%s = %s' % (varname, val,))

    ## START LOGGING ##
    startTime = times.get_now_sql_datetime()
    log.info(
        '--- STARTING TO RUN THE cl_utils.py AT %s' %
        (startTime,))

    if init:
        from . import workspace
        ws = workspace(
            log=log,
            pathToWorkspace=pathToWorkspace
        )
        ws.setup()
        return

    # IMPORT THE SIMULATION SETTINGS
    (allSettings,
     programSettings,
     limitingMags,
     sampleNumber,
     peakMagnitudeDistributions,
     explosionDaysFromSettings,
     extendLightCurveTail,
     relativeSNRates,
     lowerRedshiftLimit,
     upperRedshiftLimit,
     redshiftResolution,
     restFrameFilter,
     kCorrectionTemporalResolution,
     kCorPolyOrder,
     kCorMinimumDataPoints,
     extinctionType,
     extinctionConstant,
     hostExtinctionDistributions,
     galacticExtinctionDistribution,
     surveyCadenceSettings,
     snLightCurves,
     surveyArea,
     CCSNRateFraction,
     transientToCCSNRateFraction,
     extraSurveyConstraints,
     lightCurvePolyOrder,
     logLevel) = cu.read_in_survey_parameters(
        log,
        pathToSettingsFile=pathToSettingsFile
    )

    logFilePath = pathToOutputDirectory + "/qubits.log"
    del log
    log = _set_up_command_line_tool(
        level=str(logLevel),
        logFilePath=logFilePath
    )

    # dbConn, log = cu.settings(
    #     pathToSettingsFile=pathToSettingsFile,
    #     dbConn=False,
    #     log=True
    # )

    ## START LOGGING ##
    startTime = dcu.get_now_sql_datetime()
    log.info('--- STARTING TO RUN THE qubits AT %s' % (startTime,))

    resultsDict = {}

    pathToOutputPlotDirectory = pathToOutputDirectory + "/plots/"
    dcu.dryx_mkdir(
        log,
        directoryPath=pathToOutputPlotDirectory
    )

    pathToResultsFolder = pathToOutputDirectory + "/results/"
    dcu.dryx_mkdir(
        log,
        directoryPath=pathToResultsFolder
    )

    if not programSettings['Extract Lightcurves from Spectra'] and not programSettings['Generate KCorrection Database'] and not programSettings['Run the Simulation'] and not programSettings['Compile and Plot Results']:
        print "All stages of the simulatation have been switched off. Please switch on at least one stage of the simulation under the 'Programming Settings' in the settings file `%(pathToSettingsFile)s`" % locals()

    # GENERATE THE DATA FOR SIMULATIONS
    if programSettings['Extract Lightcurves from Spectra']:
        log.info('generating the Lightcurves')
        dg.generate_model_lightcurves(
            log=log,
            pathToSpectralDatabase=pathToSpectralDatabase,
            pathToOutputDirectory=pathToOutputDirectory,
            pathToOutputPlotDirectory=pathToOutputPlotDirectory,
            explosionDaysFromSettings=explosionDaysFromSettings,
            extendLightCurveTail=extendLightCurveTail,
            polyOrder=lightCurvePolyOrder
        )
        print "The lightcurve file can be found here: %(pathToOutputDirectory)stransient_light_curves.yaml" % locals()
        print "The lightcurve plots can be found in %(pathToOutputPlotDirectory)s" % locals()

    if programSettings['Generate KCorrection Database']:
        log.info('generating the kcorrection data')
        dg.generate_kcorrection_listing_database(
            log,
            pathToOutputDirectory=pathToOutputDirectory,
            pathToSpectralDatabase=pathToSpectralDatabase,
            restFrameFilter=restFrameFilter,
            temporalResolution=kCorrectionTemporalResolution,
            redshiftResolution=redshiftResolution,
            redshiftLower=lowerRedshiftLimit,
            redshiftUpper=upperRedshiftLimit + redshiftResolution)
        log.info('generating the kcorrection polynomials')
        dg.generate_kcorrection_polynomial_database(
            log,
            pathToOutputDirectory=pathToOutputDirectory,
            restFrameFilter=restFrameFilter,
            kCorPolyOrder=kCorPolyOrder,  # ORDER OF THE POLYNOMIAL TO FIT
            kCorMinimumDataPoints=kCorMinimumDataPoints,
            redshiftResolution=redshiftResolution,
            redshiftLower=lowerRedshiftLimit,
            redshiftUpper=upperRedshiftLimit + redshiftResolution,
            plot=programSettings['Generate KCorrection Plots'])

        print "The k-correction database has been generated here: %(pathToOutputDirectory)sk_corrections" % locals()
        if programSettings['Generate KCorrection Plots']:
            print "The k-correction polynomial plots can also be found in %(pathToOutputDirectory)sk_corrections" % locals()

    if programSettings['Run the Simulation']:
        # CREATE THE OBSERVABLE UNIVERSE!
        log.info('generating the redshift array')
        redshiftArray = u.random_redshift_array(
            log,
            sampleNumber,
            lowerRedshiftLimit,
            upperRedshiftLimit,
            redshiftResolution=redshiftResolution,
            pathToOutputPlotDirectory=pathToOutputPlotDirectory,
            plot=programSettings['Plot Simulation Helper Plots'])
        resultsDict['Redshifts'] = redshiftArray.tolist()

        log.info('generating the SN type array')
        snTypesArray = u.random_sn_types_array(
            log,
            sampleNumber,
            relativeSNRates,
            pathToOutputPlotDirectory=pathToOutputPlotDirectory,
            plot=programSettings['Plot Simulation Helper Plots'])
        resultsDict['SN Types'] = snTypesArray.tolist()

        log.info('generating peak magnitudes for the SNe')
        peakMagnitudesArray = u.random_peak_magnitudes(
            log,
            peakMagnitudeDistributions,
            snTypesArray,
            plot=programSettings['Plot Simulation Helper Plots'])

        log.info('generating the SN host extictions array')
        hostExtinctionArray = u.random_host_extinction(
            log,
            sampleNumber,
            extinctionType,
            extinctionConstant,
            hostExtinctionDistributions,
            plot=programSettings['Plot Simulation Helper Plots'])

        log.info('generating the SN galactic extictions array')
        galacticExtinctionArray = u.random_galactic_extinction(
            log,
            sampleNumber,
            extinctionType,
            extinctionConstant,
            galacticExtinctionDistribution,
            plot=programSettings['Plot Simulation Helper Plots'])

        log.info('generating the raw lightcurves for the SNe')
        rawLightCurveDict = u.generate_numpy_polynomial_lightcurves(
            log,
            snLightCurves=snLightCurves,
            pathToOutputDirectory=pathToOutputDirectory,
            pathToOutputPlotDirectory=pathToOutputPlotDirectory,
            plot=programSettings['Plot Simulation Helper Plots'])

        log.info('generating the k-correction array for the SNe')
        kCorrectionArray = u.build_kcorrection_array(
            log,
            redshiftArray,
            snTypesArray,
            snLightCurves,
            pathToOutputDirectory=pathToOutputDirectory,
            plot=programSettings['Plot Simulation Helper Plots'])

        log.info('generating the observed lightcurves for the SNe')
        observedFrameLightCurveInfo, peakAppMagList = u.convert_lightcurves_to_observered_frame(
            log,
            snLightCurves=snLightCurves,
            rawLightCurveDict=rawLightCurveDict,
            redshiftArray=redshiftArray,
            snTypesArray=snTypesArray,
            peakMagnitudesArray=peakMagnitudesArray,
            kCorrectionArray=kCorrectionArray,
            hostExtinctionArray=hostExtinctionArray,
            galacticExtinctionArray=galacticExtinctionArray,
            restFrameFilter=restFrameFilter,
            pathToOutputDirectory=pathToOutputDirectory,
            pathToOutputPlotDirectory=pathToOutputPlotDirectory,
            polyOrder=lightCurvePolyOrder,
            plot=programSettings['Plot Simulation Helper Plots'])

        log.info('generating the survey observation cadence')
        cadenceDictionary = ss.survey_cadence_arrays(
            log,
            surveyCadenceSettings,
            pathToOutputDirectory=pathToOutputDirectory,
            pathToOutputPlotDirectory=pathToOutputPlotDirectory,
            plot=programSettings['Plot Simulation Helper Plots'])

        log.info('determining if the SNe are discoverable by the survey')
        discoverableList = ss.determine_if_sne_are_discoverable(
            log,
            redshiftArray=redshiftArray,
            limitingMags=limitingMags,
            observedFrameLightCurveInfo=observedFrameLightCurveInfo,
            pathToOutputDirectory=pathToOutputDirectory,
            pathToOutputPlotDirectory=pathToOutputPlotDirectory,
            plot=programSettings['Plot Simulation Helper Plots'])

        log.info(
            'determining the day (if and) when each SN is first discoverable by the survey')
        ripeDayList = ss.determine_when_sne_are_ripe_for_discovery(
            log,
            redshiftArray=redshiftArray,
            limitingMags=limitingMags,
            discoverableList=discoverableList,
            observedFrameLightCurveInfo=observedFrameLightCurveInfo,
            plot=programSettings['Plot Simulation Helper Plots'])

        # log.info('determining the day when each SN is disappears fainter than the survey limiting mags')
        # disappearDayList = determine_when_discovered_sne_disappear(
        #     log,
        #     redshiftArray=redshiftArray,
        #     limitingMags=limitingMags,
        #     ripeDayList=ripeDayList,
        #     observedFrameLightCurveInfo=observedFrameLightCurveInfo,
        #     plot=programSettings['Plot Simulation Helper Plots'])

        log.info('determining if and when each SN is discovered by the survey')
        lightCurveDiscoveryDayList, surveyDiscoveryDayList, snCampaignLengthList = ss.determine_if_sne_are_discovered(
            log,
            limitingMags=limitingMags,
            ripeDayList=ripeDayList,
            cadenceDictionary=cadenceDictionary,
            observedFrameLightCurveInfo=observedFrameLightCurveInfo,
            extraSurveyConstraints=extraSurveyConstraints,
            plot=programSettings['Plot Simulation Helper Plots'])

        resultsDict[
            'Discoveries Relative to Peak Magnitudes'] = lightCurveDiscoveryDayList
        resultsDict[
            'Discoveries Relative to Survey Year'] = surveyDiscoveryDayList
        resultsDict['Campaign Length'] = snCampaignLengthList
        resultsDict['Cadence Dictionary'] = cadenceDictionary
        resultsDict['Peak Apparent Magnitudes'] = peakAppMagList

        now = datetime.now()
        now = now.strftime("%Y%m%dt%H%M%S")
        fileName = pathToOutputDirectory + \
            "/simulation_results_%s.yaml" % (now,)
        stream = file(fileName, 'w')
        yamlContent = dict(allSettings.items() + resultsDict.items())
        yaml.dump(yamlContent, stream, default_flow_style=False)
        stream.close()

        print "The simulation output file can be found here: %(fileName)s. Remember to update your settings file 'Simulation Results File Used for Plots' parameter with this filename before compiling the results." % locals()
        if programSettings['Plot Simulation Helper Plots']:
            print "The simulation helper-plots found in %(pathToOutputPlotDirectory)s" % locals()

    # COMPILE AND PLOT THE RESULTS
    if programSettings['Compile and Plot Results']:
        pathToYamlFile = pathToOutputDirectory + "/" + \
            programSettings['Simulation Results File Used for Plots']
        result_log = r.log_the_survey_settings(log, pathToYamlFile)
        snSurveyDiscoveryTimes, lightCurveDiscoveryTimes, snTypes, redshifts, cadenceDictionary, peakAppMagList, snCampaignLengthList = r.import_results(
            log, pathToYamlFile)
        snRatePlotLink, totalRate, tooFaintRate, shortCampaignRate = r.determine_sn_rate(
            log,
            lightCurveDiscoveryTimes,
            snSurveyDiscoveryTimes,
            redshifts,
            surveyCadenceSettings=surveyCadenceSettings,
            lowerRedshiftLimit=lowerRedshiftLimit,
            upperRedshiftLimit=upperRedshiftLimit,
            redshiftResolution=redshiftResolution,
            surveyArea=surveyArea,
            CCSNRateFraction=CCSNRateFraction,
            transientToCCSNRateFraction=transientToCCSNRateFraction,
            peakAppMagList=peakAppMagList,
            snCampaignLengthList=snCampaignLengthList,
            extraSurveyConstraints=extraSurveyConstraints,
            pathToOutputPlotFolder=pathToOutputPlotDirectory)
        result_log += """
## Results ##

This simulated survey discovered a total of **%s** transients per year. An extra **%s** transients were detected but deemed too faint to constrain a positive transient identification and a further **%s** transients where detected but an observational campaign of more than **%s** days could not be completed to ensure identification. See below for the various output plots.

        """ % (totalRate, tooFaintRate, shortCampaignRate, extraSurveyConstraints["Observable for at least ? number of days"])
        cadenceWheelLink = r.plot_cadence_wheel(
            log,
            cadenceDictionary,
            pathToOutputPlotFolder=pathToOutputPlotDirectory)
        result_log += """%s""" % (cadenceWheelLink,)
        discoveryMapLink = r.plot_sn_discovery_map(
            log,
            snSurveyDiscoveryTimes,
            peakAppMagList,
            snCampaignLengthList,
            redshifts,
            extraSurveyConstraints,
            pathToOutputPlotFolder=pathToOutputPlotDirectory)
        result_log += """%s""" % (discoveryMapLink,)
        ratioMapLink = r.plot_sn_discovery_ratio_map(
            log,
            snSurveyDiscoveryTimes,
            redshifts,
            peakAppMagList,
            snCampaignLengthList,
            extraSurveyConstraints,
            pathToOutputPlotFolder=pathToOutputPlotDirectory)
        result_log += """%s""" % (ratioMapLink,)
        result_log += """%s""" % (snRatePlotLink,)

        now = datetime.now()
        now = now.strftime("%Y%m%dt%H%M%S")
        mdLogPath = pathToResultsFolder + \
            "simulation_result_log_%s.md" % (now,)
        mdLog = open(mdLogPath, 'w')
        mdLog.write(result_log)
        mdLog.close()

        dmd.convert_to_html(
            log=log,
            pathToMMDFile=mdLogPath,
            css="amblin"
        )

        print "Results can be found here: %(pathToResultsFolder)s" % locals()
        html = mdLogPath.replace(".md", ".html")
        print "Open this file in your browser: %(html)s" % locals()

    if "dbConn" in locals() and dbConn:
        dbConn.commit()
        dbConn.close()
    ## FINISH LOGGING ##
    endTime = times.get_now_sql_datetime()
    runningTime = times.calculate_time_difference(startTime, endTime)
    log.info('-- FINISHED ATTEMPT TO RUN THE cl_utils.py AT %s (RUNTIME: %s) --' %
             (endTime, runningTime, ))

    return