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	diff --git a/bin/rivet-cmphistos b/bin/rivet-cmphistos
	--- a/bin/rivet-cmphistos
	+++ b/bin/rivet-cmphistos
	@@ -1,491 +1,495 @@
	#! /usr/bin/env python

	"""\
	Generate histogram comparison plots

	USAGE:
	%(prog)s [options] yodafile1[:'PlotOption1=Value':'PlotOption2=Value':...] [path/to/yodafile2 ...] [PLOT:Key1=Val1:...]

	where the plot options are described in the make-plots manual in the HISTOGRAM
	section.

	ENVIRONMENT:
	* RIVET_ANALYSIS_PATH: list of paths to be searched for plugin
	analysis libraries at runtime
	* RIVET_DATA_PATH: list of paths to be searched for data files
	"""

	from __future__ import print_function
	import rivet, yoda, sys, os
	rivet.util.check_python_version()
	rivet.util.set_process_name(os.path.basename(__file__))


	class Plot(dict):
	"A tiny Plot object to help writing out the head in the .dat file"
	def __repr__(self):
	return "# BEGIN PLOT\n" + "\n".join("%s=%s" % (k,v) for k,v in self.items()) + "\n# END PLOT\n\n"


	def sanitiseString(s):
	#s = s.replace('_','\\_')
	#s = s.replace('^','\\^{}')
	#s = s.replace('$','\\$')
	s = s.replace('#','\\#')
	s = s.replace('%','\\%')
	return s


	def getHistos(filelist):
	"""Loop over all input files. Only use the first occurrence of any REF-histogram
	and the first occurrence in each MC file for every MC-histogram."""
	refhistos, mchistos = {}, {}
	for infile in filelist:
	mchistos.setdefault(infile, {})
	analysisobjects = yoda.read(infile, patterns=args.PATHPATTERNS, unpatterns=args.PATHUNPATTERNS)
	#print(analysisobjects)
	for path, ao in analysisobjects.items():
	## We can't plot non-histograms yet
	# TODO: support counter plotting with a faked x (or y) position and forced plot width/height
	if ao.type not in ("Counter",
	"Histo1D",
	"Histo2D",
	"Profile1D",
	"Profile2D",
	"Scatter1D",
	"Scatter2D",
	"Scatter3D"):
	continue

	## Make a path object and ensure the path is in standard form
	try:
	aop = rivet.AOPath(path)
	except Exception as e:
	#print(e)
	print("Found analysis object with non-standard path structure:", path, "... skipping")
	continue

	## We don't plot data objects with path components hidden by an underscore prefix
	if aop.istmp() or aop.israw():
	continue

	## Add it to the ref or mc paths, if this path isn't already known
	basepath = aop.basepath(keepref=False)
	if aop.isref() and basepath not in refhistos:
	ao.path = aop.varpath(keepref=False, defaultvarid=0)
	refhistos[basepath] = ao
	else: #if basepath not in mchistos[infile]:
	mchistos[infile].setdefault(basepath, {})[aop.varid(0)] = ao

	return refhistos, mchistos


	def getRivetRefData(anas=None):
	"Find all Rivet reference data files"
	refhistos = {}
	rivet_data_dirs = rivet.getAnalysisRefPaths()
	dirlist = []
	for d in rivet_data_dirs:
	if anas is None:
	import glob
	dirlist.append(glob.glob(os.path.join(d, '*.yoda')))
	else:
	dirlist.append([os.path.join(d, a+'.yoda') for a in anas])
	for filelist in dirlist:
	# TODO: delegate to getHistos?
	for infile in filelist:
	analysisobjects = yoda.read(infile, patterns=args.PATHPATTERNS, unpatterns=args.PATHUNPATTERNS)
	for path, ao in analysisobjects.items():
	aop = rivet.AOPath(ao.path)
	if aop.isref():
	ao.path = aop.basepath(keepref=False)
	refhistos[ao.path] = ao
	return refhistos


	def parseArgs(args):
	"""Look at the argument list and split it at colons, in order to separate
	the file names from the plotting options. Store the file names and
	file specific plotting options."""
	filelist = []
	plotoptions = {}
	for a in args:
	asplit = a.split(':')
	path = asplit[0]
	filelist.append(path)
	plotoptions[path] = []
	has_title = False
	for i in range(1, len(asplit)):
	## Add 'Title' if there is no = sign before math mode
	if '=' not in asplit[i] or ('$' in asplit[i] and asplit[i].index('$') < asplit[i].index('=')):
	asplit[i] = 'Title=%s' % asplit[i]
	if asplit[i].startswith('Title='):
	has_title = True
	plotoptions[path].append(asplit[i])
	if path != "PLOT" and not has_title:
	plotoptions[path].append('Title=%s' % sanitiseString(os.path.basename( os.path.splitext(path)[0] )) )
	return filelist, plotoptions


	def setStyle(ao, istyle, variation=False):
	"""Set default plot styles (color and line width) colors borrowed from Google Ngrams"""
	# LINECOLORS = ['{[HTML]{EE3311}}', # red (Google uses 'DC3912')
	# '{[HTML]{3366FF}}', # blue
	# '{[HTML]{109618}}', # green
	# '{[HTML]{FF9900}}', # orange
	# '{[HTML]{990099}}'] # lilac
	LINECOLORS = ['red', 'blue', 'green', 'orange', 'lilac']
	LINESTYLES = ['solid', 'dashed', 'dashdotted', 'dotted']

	if args.STYLE == 'talk':
	ao.setAnnotation('LineWidth', '1pt')
	if args.STYLE == 'bw':
	LINECOLORS = ['black!90',
	'black!50',
	'black!30']

	jc = istyle % len(LINECOLORS)
	c = LINECOLORS[jc]
	js = (istyle // len(LINECOLORS)) % len(LINESTYLES)
	s = LINESTYLES[js]

	## If plotting a variation (i.e. band), fade the colour
	if variation:
	c += "!30"

	ao.setAnnotation('LineStyle', '%s' % s)
	ao.setAnnotation('LineColor', '%s' % c)


	def setOptions(ao, options):
	"Set arbitrary annotations"
	for opt in options:
	key, val = opt.split('=', 1)
	ao.setAnnotation(key, val)


	# TODO: move to rivet.utils
	def mkoutdir(outdir):
	"Function to make output directories"
	if not os.path.exists(outdir):
	try:
	os.makedirs(outdir)
	except:
	msg = "Can't make output directory '%s'" % outdir
	raise Exception(msg)
	if not os.access(outdir, os.W_OK):
	msg = "Can't write to output directory '%s'" % outdir
	raise Exception(msg)


	def mkOutput(hpath, aos, plot=None, special=None):
	"""
	Make the .dat file string. We can't use "yoda.writeFLAT(anaobjects, 'foobar.dat')"
	because the PLOT and SPECIAL blocks don't have a corresponding analysis object.
	"""
	output = ''

	if plot is not None:
	output += str(plot)

	if special is not None:
	output += "\n"
	output += "# BEGIN SPECIAL %s\n" % hpath
	output += special
	output += "# END SPECIAL\n\n"

	from io import StringIO
	sio = StringIO()
	yoda.writeFLAT(aos, sio)
	output += sio.getvalue()

	return output


	def writeOutput(output, h):
	"Choose output file name and dir"
	if args.HIER_OUTPUT:
	hparts = h.strip("/").split("/", 1)
	ana = "_".join(hparts[:-1]) if len(hparts) > 1 else "ANALYSIS"
	outdir = os.path.join(args.OUTDIR, ana)
	outfile = '%s.dat' % hparts[-1].replace("/", "_")
	else:
	hparts = h.strip("/").split("/")
	outdir = args.OUTDIR
	outfile = '%s.dat' % "_".join(hparts)
	mkoutdir(outdir)
	outfilepath = os.path.join(outdir, outfile)
	f = open(outfilepath, 'w')
	f.write(output)
	f.close()


	#--------------------------------------------------------------------------------------------


	if __name__ == '__main__':

	## Command line parsing
	import argparse
	parser = argparse.ArgumentParser(description=__doc__)

	parser.add_argument("ARGS", nargs="*")
	parser.add_argument('-o', '--outdir', dest='OUTDIR',
	default='.', help='write data files into this directory')
	parser.add_argument("--hier-out", action="store_true", dest="HIER_OUTPUT", default=False,
	help="write output dat files into a directory hierarchy which matches the analysis paths")
	parser.add_argument('--plotinfodir', dest='PLOTINFODIRS', action='append',
	default=['.'], help='directory which may contain plot header information (in addition '
	'to standard Rivet search paths)')
	parser.add_argument("--no-rivet-refs", dest="RIVETREFS", action="store_false",
	default=True, help="don't use Rivet reference data files")
	# parser.add_argument("--refid", dest="REF_ID",
	# default="REF", help="ID of reference data set (file path for non-REF data)")
	parser.add_argument("--reftitle", dest="REFTITLE",
	default='Data', help="Reference data legend entry")
	parser.add_argument("--pwd", dest="PATH_PWD", action="store_true", default=False,
	help="append the current directory (pwd) to the analysis/data search paths (cf. $RIVET_ANALYSIS/DATA_PATH)")
	parser.add_argument("-v", "--verbose", dest="VERBOSE", action="store_true", default=False,
	help="produce debug output to the terminal")

	stygroup = parser.add_argument_group("Plot style")
	stygroup.add_argument("--linear", action="store_true", dest="LINEAR",
	default=False, help="plot with linear scale")
	stygroup.add_argument("--errs", "--mcerrs", "--mc-errs", action="store_true", dest="MC_ERRS",
	default=False, help="show vertical error bars on the MC lines")
	stygroup.add_argument("--no-ratio", action="store_false", dest="RATIO",
	default=True, help="disable the ratio plot")
	stygroup.add_argument("--rel-ratio", action="store_true", dest="RATIO_DEVIATION",
	default=False, help="show the ratio plots scaled to the ref error")
	stygroup.add_argument("--no-plottitle", action="store_true", dest="NOPLOTTITLE",
	default=False, help="don't show the plot title on the plot "
	"(useful when the plot description should only be given in a caption)")
	stygroup.add_argument("--style", dest="STYLE", default="default",
	help="change plotting style: default\|bw\|talk")
	stygroup.add_argument("-c", "--config", dest="CONFIGFILES", action="append", default=["~/.make-plots"],
	help="additional plot config file(s). Settings will be included in the output configuration.")
	+ stygroup.add_argument("--remove-options", help="remove options label from legend", dest="REMOVE_OPTIONS",
	+ action="store_true", default=False)

	selgroup = parser.add_argument_group("Selective plotting")
	# selgroup.add_argument("--show-single", dest="SHOW_SINGLE", choices=("no", "ref", "mc", "all"),
	# default="mc", help="control if a plot file is made if there is only one dataset to be plotted "
	# "[default=%(default)s]. If the value is 'no', single plots are always skipped, for 'ref' and 'mc', "
	# "the plot will be written only if the single plot is a reference plot or an MC "
	# "plot respectively, and 'all' will always create single plot files.\n The 'ref' and 'all' values "
	# "should be used with great care, as they will also write out plot files for all reference "
	# "histograms without MC traces: combined with the -R/--rivet-refs flag, this is a great way to "
	# "write out several thousand irrelevant reference data histograms!")
	# selgroup.add_argument("--show-mc-only", "--all", action="store_true", dest="SHOW_IF_MC_ONLY",
	# default=False, help="make a plot file even if there is only one dataset to be plotted and "
	# "it is an MC one. Deprecated and will be removed: use --show-single instead, which overrides this.")
	# # selgroup.add_argument("-l", "--histogram-list", dest="HISTOGRAMLIST",
	# # default=None, help="specify a file containing a list of histograms to plot, in the format "
	# # "/ANALYSIS_ID/histoname, one per line, e.g. '/DELPHI_1996_S3430090/d01-x01-y01'.")
	selgroup.add_argument("-m", "--match", action="append",
	help="only write out histograms whose $path/$name string matches these regexes. The argument "
	"may also be a text file.",
	dest="PATHPATTERNS")
	selgroup.add_argument("-M", "--unmatch", action="append",
	help="exclude histograms whose $path/$name string matches these regexes",
	dest="PATHUNPATTERNS")

	args = parser.parse_args()

	## Add pwd to search paths
	if args.PATH_PWD:
	rivet.addAnalysisLibPath(os.path.abspath("."))
	rivet.addAnalysisDataPath(os.path.abspath("."))

	## Split the input file names and the associated plotting options
	## given on the command line into two separate lists
	filelist, plotoptions = parseArgs(args.ARGS)

	## Remove the PLOT dummy file from the file list
	if "PLOT" in filelist:
	filelist.remove("PLOT")

	## Check that the files exist
	for f in filelist:
	if not os.access(f, os.R_OK):
	print("Error: cannot read from %s" % f)
	sys.exit(1)

	## Read the .plot files
	plotdirs = args.PLOTINFODIRS + [os.path.abspath(os.path.dirname(f)) for f in filelist]
	plotparser = rivet.mkStdPlotParser(plotdirs, args.CONFIGFILES)

	## Create a list of all histograms to be plotted, and identify if they are 2D histos (which need special plotting)
	try:
	refhistos, mchistos = getHistos(filelist)
	except IOError as e:
	print("File reading error: ", e.strerror)
	exit(1)
	hpaths, h2ds = [], []
	for aos in mchistos.values():
	for p in aos.keys():
	ps = rivet.stripOptions(p)
	if ps and ps not in hpaths:
	hpaths.append(ps)
	firstaop = aos[p][sorted(aos[p].keys())[0]]
	# TODO: Would be nicer to test via isHisto and dim or similar, or yoda.Scatter/Histo/Profile base classes
	if type(firstaop) in (yoda.Histo2D, yoda.Profile2D) and ps not in h2ds:
	h2ds.append(ps)

	## Take reference data from the Rivet search paths, if there is not already
	if args.RIVETREFS:
	try:
	refhistos2 = getRivetRefData()
	except IOError as e:
	print("File reading error: ", e.strerror)
	exit(1)
	refhistos2.update(refhistos)
	refhistos = refhistos2

	## Purge unmatched ref data entries to save memory
	keylist = list(refhistos.keys()) # can't modify for-loop target
	for refhpath in keylist:
	if refhpath not in hpaths:
	del refhistos[refhpath]


	## Now loop over all MC histograms and plot them
	# TODO: factorize much of this into a rivet.utils mkplotfile(mchists, refhist, kwargs, is2d=False) function
	for hpath in hpaths:
	#print('Currently looking at', hpath)

	## The analysis objects to be plotted
	anaobjects = []
	## List of histos to be drawn, to sync the legend and plotted lines
	mainlines = []
	varlines = []
	## Is this a 2D histo?
	is2d = (hpath in h2ds)
	## Will we be drawing a ratio plot?
	showratio = args.RATIO and not is2d


	## A Plot object to represent the PLOT section in the .dat file
	plot = Plot()
	if not is2d:
	plot['Legend'] = '1'
	plot['LogY'] = '1'
	headers = plotparser.getHeaders(hpath)
	if headers:
	plot.update(headers)
	# for key, val in headers.items():
	# plot[key] = val
	if "PLOT" in plotoptions:
	for key_val in plotoptions["PLOT"]:
	key, val = [s.strip() for s in key_val.split("=", 1)]
	if 'ReplaceOption' in key_val:
	opt_group = key_val.split("=", 2)
	key, val = "=".join(opt_group[:2]), opt_group[2]
	plot[key] = val
	+ if args.REMOVE_OPTIONS:
	+ plot['RemoveOptions'] = '1'
	if args.LINEAR:
	plot['LogY'] = '0'
	if args.NOPLOTTITLE:
	plot['Title'] = ''
	if showratio and args.RATIO_DEVIATION:
	plot['RatioPlotMode'] = 'deviation'
	if args.STYLE == 'talk':
	plot['PlotSize'] = '8,6'
	elif args.STYLE == 'bw' and showratio:
	plot['RatioPlotErrorBandColor'] = 'black!10'


	## Get a special object, if there is one for this path
	special = plotparser.getSpecial(hpath)


	## Handle reference data histogram, if there is one
	ratioreference, hasdataref = None, False
	if hpath in refhistos:
	hasdataref = True
	refdata = refhistos[hpath]
	refdata.setAnnotation('Title', args.REFTITLE)
	if not is2d:
	refdata.setAnnotation('ErrorBars', '1')
	refdata.setAnnotation('PolyMarker', '*')
	refdata.setAnnotation('ConnectBins', '0')
	if showratio:
	ratioreference = hpath
	## For 1D
	anaobjects.append(refdata)
	mainlines.append(hpath)
	## For 2D
	if is2d:
	s = mkOutput(hpath, [refdata], plot, special)
	writeOutput(s, hpath)


	## Loop over the MC files to plot all instances of the histogram
	styleidx = 0
	for infile in filelist:
	if infile in mchistos:
	for xpath in sorted(mchistos[infile]):
	if rivet.stripOptions(xpath) != hpath:
	continue
	hmcs = mchistos[infile][xpath]
	## For now, just plot all the different variation histograms (reversed, so [0] is on top)
	# TODO: calculate and plot an appropriate error band, somehow...
	for i in sorted(hmcs.keys(), reverse=True):
	iscanonical = (str(i) == "0")
	hmc = hmcs[i]
	## Default linecolor, linestyle
	if not is2d:
	setStyle(hmc, styleidx, not iscanonical)
	if args.MC_ERRS:
	hmc.setAnnotation('ErrorBars', '1')
	## Plot defaults from .plot files
	histopts = plotparser.getHistogramOptions(hpath)
	if histopts:
	for key, val in histargs.items():
	hmc.setAnnotation(key, val)
	## Command line plot options
	setOptions(hmc, plotoptions[infile])
	## Set path attribute
	fullpath = "/"+infile+xpath
	if not iscanonical:
	fullpath += "["+str(i)+"]"
	hmc.setAnnotation('Path', fullpath)
	## Add object / path to appropriate lists
	#if hmc.hasAnnotation("Title"):
	# hmc.setAnnotation("Title", hmc.annotation("Title") +
	# rivet.extractOptionString(xpath))
	anaobjects.append(hmc)
	if iscanonical:
	mainlines.append(fullpath)
	else:
	varlines.append(fullpath)
	if showratio and ratioreference is None and iscanonical:
	ratioreference = fullpath
	## For 2D, plot each histo now (since overlay makes no sense)
	if is2d:
	s = mkOutput(hpath, [hmc], plot, special)
	writeOutput(s, fullpath)
	styleidx += 1


	## Finally render the combined plots; only show the first one if it's 2D
	# TODO: Only show the first MC one if 2D?
	if is2d:
	anaobjects = anaobjects[:1]
	## Add final attrs to Plot
	if not plot.has_key('DrawOnly'):
	plot['DrawOnly'] = ' '.join(varlines + mainlines).strip()
	if not plot.has_key('LegendOnly'):
	plot['LegendOnly'] = ' '.join(mainlines).strip()
	if showratio and not plot.has_key('RatioPlot') and len(varlines + mainlines) > 1:
	plot['RatioPlot'] = '1'
	if showratio and plot.has_key('RatioPlot') and plot['RatioPlot'] == '1' and len(varlines + mainlines) > 0:
	if not plot.has_key('RatioPlotReference'):
	plot['RatioPlotReference'] = ratioreference
	if not hasdataref and "RatioPlotYLabel" not in plot:
	if plot.get('RatioPlotMode', '') == 'deviation':
	plot['RatioPlotYLabel'] = 'Deviation' #r'$\text{MC}-\text{MC}_\text{ref}$'
	else:
	plot['RatioPlotYLabel'] = 'Ratio' #r'$\text{MC}/\text{MC}_\text{ref}$'


	## Make the output and write to file
	o = mkOutput(hpath, anaobjects, plot, special)
	writeOutput(o, hpath)
	diff --git a/bin/rivet-mkhtml b/bin/rivet-mkhtml
	--- a/bin/rivet-mkhtml
	+++ b/bin/rivet-mkhtml
	@@ -1,506 +1,510 @@
	#! /usr/bin/env python

	"""\
	%(prog)s [options] <yodafile1> [<yodafile2> <yodafile3>...] [PLOT:Key1=Val1:...]

	Make web pages from histogram files written out by Rivet. You can specify
	multiple Monte Carlo YODA files to be compared in the same syntax as for
	rivet-cmphistos, i.e. including plotting options.

	Reference data, analysis metadata, and plot style information should be found
	automatically (if not, set the RIVET_ANALYSIS_PATH or similar variables
	appropriately).

	Any existing output directory will be overwritten.

	ENVIRONMENT:
	* RIVET_ANALYSIS_PATH: list of paths to be searched for analysis plugin libraries
	* RIVET_DATA_PATH: list of paths to be searched for data files
	"""

	from __future__ import print_function

	import rivet, sys, os
	rivet.util.check_python_version()
	rivet.util.set_process_name(os.path.basename(__file__))

	import glob, shutil
	from subprocess import Popen,PIPE


	import argparse
	parser = argparse.ArgumentParser(usage=__doc__)
	parser.add_argument("YODAFILES", nargs="+", help="data files to compare")
	parser.add_argument("-o", "--outputdir", dest="OUTPUTDIR",
	default="./rivet-plots", help="directory for Web page output")
	parser.add_argument("-c", "--config", dest="CONFIGFILES", action="append", default=["~/.make-plots"],
	help="plot config file(s) to be used with rivet-cmphistos")
	parser.add_argument("-n", "--num-threads", metavar="NUMTHREADS", dest="NUMTHREADS", type=int,
	default=None, help="request make-plots to use a specific number of threads")
	parser.add_argument("--ignore-missing", dest="IGNORE_MISSING", action="store_true",
	default=False, help="ignore missing YODA files")
	parser.add_argument("-i", "--ignore-unvalidated", dest="IGNORE_UNVALIDATED", action="store_true",
	default=False, help="ignore unvalidated analyses")
	# parser.add_argument("--ref", "--refid", dest="REF_ID",
	# default=None, help="ID of reference data set (file path for non-REF data)")
	parser.add_argument("--dry-run", help="don't actually do any plotting or HTML building", dest="DRY_RUN",
	action="store_true", default=False)
	parser.add_argument("--no-cleanup", dest="NO_CLEANUP", action="store_true", default=False,
	help="keep plotting temporary directory")
	parser.add_argument("--no-subproc", dest="NO_SUBPROC", action="store_true", default=False,
	help="don't use subprocesses to render the plots in parallel -- useful for debugging")
	parser.add_argument("--pwd", dest="PATH_PWD", action="store_true", default=False,
	help="append the current directory (pwd) to the analysis/data search paths (cf. $RIVET_ANALYSIS_PATH)")

	stygroup = parser.add_argument_group("Style options")
	stygroup.add_argument("-t", "--title", dest="TITLE",
	default="Plots from Rivet analyses", help="title to be displayed on the main web page")
	stygroup.add_argument("--reftitle", dest="REFTITLE",
	default="Data", help="legend entry for reference data")
	stygroup.add_argument("--no-plottitle", dest="NOPLOTTITLE", action="store_true",
	default=False, help="don't show the plot title on the plot "
	"(useful when the plot description should only be given in a caption)")
	stygroup.add_argument("-s", "--single", dest="SINGLE", action="store_true",
	default=False, help="display plots on single webpage.")
	stygroup.add_argument("--no-ratio", dest="SHOW_RATIO", action="store_false",
	default=True, help="don't draw a ratio plot under each main plot.")
	stygroup.add_argument("--errs", "--mcerrs", "--mc-errs", dest="MC_ERRS", action="store_true",
	default=False, help="plot error bars.")
	stygroup.add_argument("--offline", dest="OFFLINE", action="store_true",
	default=False, help="generate HTML that does not use external URLs.")
	stygroup.add_argument("--pdf", dest="VECTORFORMAT", action="store_const", const="PDF",
	default="PDF", help="use PDF as the vector plot format.")
	stygroup.add_argument("--ps", dest="VECTORFORMAT", action="store_const", const="PS",
	default="PDF", help="use PostScript as the vector plot format. DEPRECATED")
	stygroup.add_argument("--booklet", dest="BOOKLET", action="store_true",
	default=False, help="create booklet (currently only available for PDF with pdftk or pdfmerge).")
	stygroup.add_argument("--font", dest="OUTPUT_FONT", choices="palatino,cm,times,helvetica,minion".split(","),
	default="palatino", help="choose the font to be used in the plots")
	stygroup.add_argument("--palatino", dest="OUTPUT_FONT", action="store_const", const="palatino", default="palatino",
	help="use Palatino as font (default). DEPRECATED: Use --font")
	stygroup.add_argument("--cm", dest="OUTPUT_FONT", action="store_const", const="cm", default="palatino",
	help="use Computer Modern as font. DEPRECATED: Use --font")
	stygroup.add_argument("--times", dest="OUTPUT_FONT", action="store_const", const="times", default="palatino",
	help="use Times as font. DEPRECATED: Use --font")
	stygroup.add_argument("--helvetica", dest="OUTPUT_FONT", action="store_const", const="helvetica", default="palatino",
	help="use Helvetica as font. DEPRECATED: Use --font")
	stygroup.add_argument("--minion", dest="OUTPUT_FONT", action="store_const", const="minion", default="palatino",
	help="use Adobe Minion Pro as font. DEPRECATED: Use --font")
	+stygroup.add_argument("--remove-options", help="remove options label from legend", dest="REMOVE_OPTIONS",
	+ action="store_true", default=False)

	selgroup = parser.add_argument_group("Selective plotting")
	selgroup.add_argument("-m", "--match", action="append", dest="PATHPATTERNS", default=[],
	help="only write out histograms whose $path/$name string matches any of these regexes")
	selgroup.add_argument("-M", "--unmatch", action="append", dest="PATHUNPATTERNS", default=[],
	help="exclude histograms whose $path/$name string matches any of these regexes")
	selgroup.add_argument("--ana-match", action="append", dest="ANAPATTERNS", default=[],
	help="only write out histograms from analyses whose name matches any of these regexes")
	selgroup.add_argument("--ana-unmatch", action="append", dest="ANAUNPATTERNS", default=[],
	help="exclude histograms from analyses whose name matches any of these regexes")

	vrbgroup = parser.add_argument_group("Verbosity control")
	vrbgroup.add_argument("-v", "--verbose", help="add extra debug messages", dest="VERBOSE",
	action="store_true", default=False)

	args = parser.parse_args()
	yodafiles = args.YODAFILES

	## Add pwd to search paths
	if args.PATH_PWD:
	rivet.addAnalysisLibPath(os.path.abspath("."))
	rivet.addAnalysisDataPath(os.path.abspath("."))


	## Check that there are some arguments!
	if not yodafiles:
	print("Error: You need to specify some YODA files to be plotted!")
	sys.exit(1)


	## Make output directory
	if not args.DRY_RUN:
	if os.path.exists(args.OUTPUTDIR) and not os.path.realpath(args.OUTPUTDIR)==os.getcwd():
	import shutil
	shutil.rmtree(args.OUTPUTDIR)
	try:
	os.makedirs(args.OUTPUTDIR)
	except:
	print("Error: failed to make new directory '%s'" % args.OUTPUTDIR)
	sys.exit(1)

	## Get set of analyses involved in the runs
	plotarg = None
	analyses = set()
	blocked_analyses = set()
	import yoda
	for yodafile in yodafiles:
	if yodafile.startswith("PLOT:"):
	plotarg = yodafile
	continue
	yodafilepath = os.path.abspath(yodafile.split(":")[0])
	if not os.access(yodafilepath, os.R_OK):
	print("Error: cannot read from %s" % yodafilepath)
	if args.IGNORE_MISSING:
	continue
	else:
	sys.exit(2)

	try:
	## Note: we use -m/-M flags here as well as when calling rivet-cmphistos, to potentially speed this initial loading
	analysisobjects = yoda.read(yodafilepath, patterns=args.PATHPATTERNS, unpatterns=args.PATHUNPATTERNS)
	except IOError as e:
	print("File reading error: ", e.strerror)
	sys.exit(1)

	for path, ao in analysisobjects.items():
	## Make a path object and ensure the path is in standard form
	try:
	aop = rivet.AOPath(path)
	except Exception as e:
	#print(e)
	print("Found analysis object with non-standard path structure:", path, "... skipping")
	continue

	## We don't plot data objects with path components hidden by an underscore prefix
	if aop.istmp() or aop.israw():
	continue

	## Identify analysis/histo name parts
	analysis = "ANALYSIS"
	if aop.basepathparts(keepref=False):
	analysis = rivet.stripOptions(aop.basepathparts(keepref=False)[0]) #< TODO: for compatibility with rivet-cmphistos... generalise?
	#analysis = "_".join(aop.dirnameparts(keepref=False)[:-1]) #< TODO: would this be nicer? Currently incompatible with rivet-cmphistos

	## Optionally veto on analysis name pattern matching
	if analysis in analyses.union(blocked_analyses):
	continue
	import re
	matched = True
	if args.ANAPATTERNS:
	matched = False
	for patt in args.ANAPATTERNS:
	if re.match(patt, analysis) is not None:
	matched = True
	break
	if matched and args.ANAUNPATTERNS:
	for patt in args.ANAUNPATTERNS:
	if re.match(patt, analysis) is not None:
	matched = False
	break
	if matched:
	analyses.add(analysis)
	else:
	blocked_analyses.add(analysis)


	## Sort analyses: group ascending by analysis name (could specialise grouping by collider), then
	## descending by year, and finally descending by bibliographic archive ID code (INSPIRE first).
	def anasort(name):
	rtn = (1, name)
	if name.startswith("MC"):
	rtn = (99999999, name)
	else:
	stdparts = name.split("_")
	try:
	year = int(stdparts[1])
	rtn = (0, stdparts[0], -year, 0)
	idcode = (0 if stdparts[2][0] == "I" else 1e10) - int(stdparts[2][1:])
	rtn = (0, stdparts[0], -year, idcode)
	if len(stdparts) > 3:
	rtn += stdparts[3:]
	except:
	pass
	return rtn

	analyses = sorted(analyses, key=anasort)

	## Uncomment to test analysis ordering on index page
	# print(analyses)
	# sys.exit(0)


	## Run rivet-cmphistos to get plain .dat files from .yoda
	## We do this here since it also makes the necessary directories
	ch_cmd = ["rivet-cmphistos"]
	if args.MC_ERRS:
	ch_cmd.append("--mc-errs")
	if not args.SHOW_RATIO:
	ch_cmd.append("--no-ratio")
	if args.NOPLOTTITLE:
	ch_cmd.append("--no-plottitle")
	+if args.REMOVE_OPTIONS:
	+ ch_cmd.append("--remove-options")
	# if args.REF_ID is not None:
	# ch_cmd.append("--refid=%s" % os.path.abspath(args.REF_ID))
	if args.REFTITLE:
	ch_cmd.append("--reftitle=%s" % args.REFTITLE )
	if args.PATHPATTERNS:
	for patt in args.PATHPATTERNS:
	ch_cmd += ["-m", patt] #"'"+patt+"'"]
	if args.PATHUNPATTERNS:
	for patt in args.PATHUNPATTERNS:
	ch_cmd += ["-M", patt] #"'"+patt+"'"]
	ch_cmd.append("--hier-out")
	# TODO: Need to be able to override this: provide a --plotinfodir cmd line option?
	ch_cmd.append("--plotinfodir=%s" % os.path.abspath("../"))
	for af in yodafiles:
	yodafilepath = os.path.abspath(af.split(":")[0])
	if af.startswith("PLOT:"):
	yodafilepath = "PLOT"
	elif not os.access(yodafilepath, os.R_OK):
	continue
	newarg = yodafilepath
	if ":" in af:
	newarg += ":" + af.split(":", 1)[1]
	# print(newarg)
	ch_cmd.append(newarg)

	## Pass rivet-mkhtml -c args to rivet-cmphistos
	for configfile in args.CONFIGFILES:
	configfile = os.path.abspath(os.path.expanduser(configfile))
	if os.access(configfile, os.R_OK):
	ch_cmd += ["-c", configfile]

	if args.VERBOSE:
	ch_cmd.append("--verbose")
	print("Calling rivet-cmphistos with the following command:")
	print(" ".join(ch_cmd))

	## Run rivet-cmphistos in a subdir, after fixing any relative paths in Rivet env vars
	if not args.DRY_RUN:
	for var in ("RIVET_ANALYSIS_PATH", "RIVET_DATA_PATH", "RIVET_REF_PATH", "RIVET_INFO_PATH", "RIVET_PLOT_PATH"):
	if var in os.environ:
	abspaths = [os.path.abspath(p) for p in os.environ[var].split(":")]
	os.environ[var] = ":".join(abspaths)
	subproc = Popen(ch_cmd, cwd=args.OUTPUTDIR, stdout=PIPE, stderr=PIPE)
	out, err = subproc.communicate()
	retcode = subproc.returncode
	if args.VERBOSE or retcode != 0:
	print('Output from rivet-cmphistos:\n', out)
	if err :
	print('Errors from rivet-cmphistos:\n', err)
	if retcode != 0:
	print('Crash in rivet-cmphistos code = ', retcode, ' exiting')
	exit(retcode)



	## Write web page containing all (matched) plots
	## Make web pages first so that we can load it locally in
	## a browser to view the output before all plots are made
	if not args.DRY_RUN:

	style = '''<style>
	html { font-family: sans-serif; }
	img { border: 0; }
	a { text-decoration: none; font-weight: bold; }
	</style>
	'''

	## Include MathJax configuration
	script = ''
	if not args.OFFLINE:
	script = '''\
	<script type="text/x-mathjax-config">
	MathJax.Hub.Config({
	tex2jax: {inlineMath: [["$","$"]]}
	});
	</script>
	<script type="text/javascript"
	src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
	</script>
	'''

	## A helper function for metadata LaTeX -> HTML conversion
	from rivet.util import htmlify

	## A timestamp HTML fragment to be used on each page:
	import datetime
	timestamp = '<p>Generated at %s</p>\n' % datetime.datetime.now().strftime("%A, %d. %B %Y %I:%M%p")

	index = open(os.path.join(args.OUTPUTDIR, "index.html"), "w")
	index.write('<html>\n<head>\n<title>%s</title>\n%s</head>\n<body>' % (args.TITLE, style + script))
	if args.BOOKLET and args.VECTORFORMAT == "PDF":
	index.write('<h2><a href="booklet.pdf">%s</a></h2>\n\n' % args.TITLE)
	else:
	index.write('<h2>%s</h2>\n\n' % args.TITLE)

	if args.SINGLE:
	## Write table of contents
	index.write('<ul>\n')
	for analysis in analyses:
	summary = analysis
	ana = rivet.AnalysisLoader.getAnalysis(analysis)
	if ana:
	summary = "%s (%s)" % (ana.summary(), analysis)
	if args.IGNORE_UNVALIDATED and ana.status() != "VALIDATED":
	continue
	index.write('<li><a href="#%s">%s</a>\n' % (analysis, htmlify(summary)) )
	index.write('</ul>\n')

	for analysis in analyses:
	references = []
	summary = htmlify(analysis)
	description, inspireid, spiresid = None, None, None

	if analysis.find("_I") > 0:
	inspireid = analysis[analysis.rfind('_I')+2:len(analysis)]
	elif analysis.find("_S") > 0:
	spiresid = analysis[analysis.rfind('_S')+2:len(analysis)]

	ana = rivet.AnalysisLoader.getAnalysis(analysis)
	if ana:
	if ana.summary():
	summary = htmlify("%s (%s)" % (ana.summary(), analysis))
	references = ana.references()
	description = htmlify(ana.description())
	spiresid = ana.spiresId()
	if args.IGNORE_UNVALIDATED and ana.status().upper() != "VALIDATED":
	continue

	try:
	# a, s = (analysis.encode("utf-8"), summary.encode("utf-8"))
	if args.SINGLE:
	index.write('\n<h3 style="clear:left; padding-top:2em;"><a name="%s">%s</a></h3>\n' % (analysis.encode("utf-8"), summary.encode("utf-8")))
	else:
	index.write('\n<h3><a href="%s/index.html" style="text-decoration:none;">%s</a></h3>\n' % (analysis.encode("utf-8"), summary.encode("utf-8")))
	except UnicodeEncodeError as ue:
	print("Unicode error in analysis description for " + analysis + ": " + str(ue))

	reflist = []
	if inspireid:
	reflist.append('<a href="http://inspire-hep.net/record/%s">Inspire</a>' % inspireid)
	reflist.append('<a href="http://hepdata.net/record/ins%s">HepData</a>' % inspireid)
	elif spiresid:
	# elif ana.spiresId():
	reflist.append('<a href="http://inspire-hep.net/search?p=find+key+%s">Inspire</a>' % spiresid)
	reflist.append('<a href="http://hepdata.cedar.ac.uk/view/irn%s">HepData</a>' % spiresid)
	reflist += references
	index.write('<p>%s</p>\n' % " \| ".join(reflist))

	if description:
	try:
	index.write('<p style="font-size:smaller;">%s</p>\n' % description)
	except UnicodeEncodeError as ue:
	print("Unicode error in analysis description for " + analysis + ": " + str(ue))

	anapath = os.path.join(args.OUTPUTDIR, analysis)
	if not args.SINGLE:
	if not os.path.exists(anapath):
	os.makedirs(anapath)
	anaindex = open(os.path.join(anapath, "index.html"), 'w')
	anaindex.write('<html>\n<head>\n<title>%s – %s</title>\n%s</head>\n<body>\n' %
	(htmlify(args.TITLE), analysis, style + script))
	anaindex.write('<h3>%s</h3>\n' % htmlify(analysis))
	anaindex.write('<p><a href="../index.html">Back to index</a></p>\n')
	if description:
	try:
	anaindex.write('<p>\n %s\n</p>\n' % description)
	except UnicodeEncodeError as ue:
	print("Unicode error in analysis description for " + analysis + ": " + str(ue))
	else:
	anaindex = index

	datfiles = glob.glob("%s/*.dat" % anapath)
	#print(datfiles)

	anaindex.write('<div style="float:none; overflow:auto; width:100%">\n')
	for datfile in sorted(datfiles):
	obsname = os.path.basename(datfile).replace(".dat", "")
	pngfile = obsname+".png"
	vecfile = obsname+"."+args.VECTORFORMAT.lower()
	srcfile = obsname+".dat"
	if args.SINGLE:
	pngfile = os.path.join(analysis, pngfile)
	vecfile = os.path.join(analysis, vecfile)
	srcfile = os.path.join(analysis, srcfile)

	anaindex.write(' <div style="float:left; font-size:smaller; font-weight:bold;">\n')
	anaindex.write(' <a href="#%s-%s">⚓</a><a href="%s">&#8984</a> %s:<br/>\n' %
	(analysis, obsname, srcfile, os.path.splitext(vecfile)[0]) )
	anaindex.write(' <a name="%s-%s"><a href="%s">\n' % (analysis, obsname, vecfile) )
	anaindex.write(' <img src="%s">\n' % pngfile )
	anaindex.write(' </a></a>\n')
	anaindex.write(' </div>\n')
	anaindex.write('</div>\n')

	if not args.SINGLE:
	anaindex.write('<div style="float:none">%s</body>\n</html></div>\n' % timestamp)
	anaindex.close()
	index.write('<br>%s</body>\n</html>' % timestamp)
	index.close()

	# http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
	def which(program):
	import os
	def is_exe(fpath):
	return os.path.isfile(fpath) and os.access(fpath, os.X_OK)

	fpath, fname = os.path.split(program)
	if fpath:
	if is_exe(program):
	return program
	else:
	for path in os.environ["PATH"].split(os.pathsep):
	path = path.strip('"')
	exe_file = os.path.join(path, program)
	if is_exe(exe_file):
	return exe_file

	return None

	## Run make-plots on all generated .dat files
	# sys.exit(0)
	mp_cmd = ["make-plots"]
	if args.NUMTHREADS:
	mp_cmd.append("--num-threads=%d" % args.NUMTHREADS)
	if args.NO_CLEANUP:
	mp_cmd.append("--no-cleanup")
	if args.NO_SUBPROC:
	mp_cmd.append("--no-subproc")
	if args.VECTORFORMAT == "PDF":
	mp_cmd.append("--pdfpng")
	elif args.VECTORFORMAT == "PS":
	mp_cmd.append("--pspng")
	if args.OUTPUT_FONT:
	mp_cmd.append("--font=%s" % args.OUTPUT_FONT)
	# if args.OUTPUT_FONT.upper() == "PALATINO":
	# mp_cmd.append("--palatino")
	# if args.OUTPUT_FONT.upper() == "CM":
	# mp_cmd.append("--cm")
	# elif args.OUTPUT_FONT.upper() == "TIMES":
	# mp_cmd.append("--times")
	# elif args.OUTPUT_FONT.upper() == "HELVETICA":
	# mp_cmd.append("--helvetica")
	# elif args.OUTPUT_FONT.upper() == "MINION":
	# mp_cmd.append("--minion")
	datfiles = []
	for analysis in analyses:
	anapath = os.path.join(args.OUTPUTDIR, analysis)
	#print(anapath)
	anadatfiles = glob.glob("%s/*.dat" % anapath)
	datfiles += sorted(anadatfiles)
	if datfiles:
	mp_cmd += datfiles
	if args.VERBOSE:
	mp_cmd.append("--verbose")
	print("Calling make-plots with the following options:")
	print(" ".join(mp_cmd))
	if not args.DRY_RUN:
	Popen(mp_cmd).wait()
	if args.BOOKLET and args.VECTORFORMAT=="PDF":
	if which("pdftk") is not None:
	bookletcmd = ["pdftk"]
	for analysis in analyses:
	anapath = os.path.join(args.OUTPUTDIR, analysis)
	bookletcmd += sorted(glob.glob("%s/*.pdf" % anapath))
	bookletcmd += ["cat", "output", "%s/booklet.pdf" % args.OUTPUTDIR]
	print(bookletcmd)
	Popen(bookletcmd).wait()
	elif which("pdfmerge") is not None:
	bookletcmd = ["pdfmerge"]
	for analysis in analyses:
	anapath = os.path.join(args.OUTPUTDIR, analysis)
	bookletcmd += sorted(glob.glob("%s/*.pdf" % anapath))
	bookletcmd += ["%s/booklet.pdf" % args.OUTPUTDIR]
	print(bookletcmd)
	Popen(bookletcmd).wait()
	else:
	print("Neither pdftk nor pdfmerge available --- not booklet output possible")

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