Prepare arxiv latex submission tarball (package all files into one directory with bib, figure files, etc).

package.py

"""Package a paper written in latex for arxiv.
 
Rationale
---------

You may have figures and bibliography included from somewhere else in your file system with absolute paths.
This script makes a subdirectory package-mylatexfile.tex/ which contains the latex file, figures, .bib, input files referenced in the tex file
in the subdirectory, pdflatex mylatexfile.tex should work and not touch any files outside the subdirectory.
the subdirectory can then by tarred and uploaded to arxiv.
 
Synopsis::

    python3 package.py mylatexfile.tex

"""

import shutil
import sys
import os
import codecs

filename = sys.argv[1]
outdir = 'package-%s/' % filename
if not os.path.exists(outdir): os.mkdir(outdir)
#l = open(filename).readlines()
outfile = codecs.open(outdir + filename, 'w', encoding='latin1')
file_ids = {}

def handle_resource(filepath):
	if filepath not in file_ids:
		filename = os.path.basename(filepath)
		if filename.count('.') > 1: # remove additional "."
			prefix, suffix = filename.rsplit('.', maxsplit=1)
			prefix = prefix.replace('.', '_')
			filename = '%s.%s' % (prefix, suffix)
		
		# if we have same name already from a different folder
		if filename in file_ids.values():
			# add a number to it
			prefix, suffix = filename.rsplit('.', maxsplit=1)
			prefix = prefix.replace('.', '_')
			filename = '%s.%s' % (prefix, suffix)
			for i in range(100):
				filenameplus = '%s%d.%s' % (prefix, i, suffix)
				if filenameplus not in file_ids.values():
					filename = filenameplus
					break
		
		file_ids[filepath] = filename
	
	filename = file_ids[filepath]
	outfilename = outdir + filename
	print('copying resource %s from %s' % (filename, filepath))
	shutil.copyfile(filepath, outfilename)
	return filename
def handle_command(cmd, l, filepostfix = ''):
	i = l.index(r'\%s{' % cmd) + len(r'\%s{' % cmd)
	n = l[i:].index('}')
	filename = handle_resource(l[i:i+n] + filepostfix)
	l = '%s%s%s' % (l[:i], filename, l[i+n:])
	return l
def handle_command_multiple(cmd, l, filepostfix = ''):
	i = l.index(r'\%s{' % cmd) + len(r'\%s{' % cmd)
	n = l[i:].index('}')
	filenames = []
	for li in l[i:i+n].split(','):
		lout = handle_resource(li + filepostfix)
		filenames.append(lout.replace(filepostfix, ''))
	l = '%s%s%s' % (l[:i], ','.join(filenames), l[i+n:])
	return l

for l in codecs.open(filename, 'r', encoding='latin1'):
	l = l.replace(r'\altaffiltext', r'\altaffiliation')
	if l.startswith('\\includegraphics'):
		before, after = l.split('{', 1)
		filepath, post = after.split("}", 1)
		realfilepath = filepath.replace('\\lyxdot ', '.')
		if os.path.exists(realfilepath + '.pdf'):
			realfilepath = realfilepath + '.pdf'
		elif os.path.exists(realfilepath + '.eps'):
			realfilepath = realfilepath + '.eps'
		elif os.path.exists(realfilepath + '.png'):
			realfilepath = realfilepath + '.png'
		filename = handle_resource(realfilepath)
		l = '%s{%s}%s' % (before, filename.replace('.pdf', ''), post)
	if '}\\includegraphics' in l:
		i = l.index('}\\includegraphics')
		ll = l[i:]
		before, after = ll.split('{', 1)
		filepath, post = after.split("}", 1)
		realfilepath = filepath.replace('\\lyxdot ', '.')
		if os.path.exists(realfilepath + '.pdf'):
			realfilepath = realfilepath + '.pdf'
		elif os.path.exists(realfilepath + '.eps'):
			realfilepath = realfilepath + '.eps'
		elif os.path.exists(realfilepath + '.png'):
			realfilepath = realfilepath + '.png'
		filename = handle_resource(realfilepath)
		l = l[:i] + '%s{%s}%s' % (before, filename.replace('.pdf', ''), post)
	if '\\input{' in l:
		l = handle_command('input', l)
	if '\\include{' in l:
		l = handle_command('include', l, filepostfix = '.tex')
	if '\\bibliography{' in l:
		l = handle_command_multiple('bibliography', l, filepostfix='.bib')
	
	# copy over styles if they exist
	if l.startswith('\\documentclass'):
		before, after = l.split('{', 1)
		filepath, post = after.split("}", 1)
		realfilepath = filepath + '.cls'
		if os.path.exists(realfilepath):
			_ = handle_resource(realfilepath)
	if l.startswith('\\bibliographystyle'):
		before, after = l.split('{', 1)
		filepath, post = after.split("}", 1)
		realfilepath = filepath + '.bst'
		if os.path.exists(realfilepath):
			_ = handle_resource(realfilepath)
	
	outfile.write(l)
outfile.close()