deletions | additions       diff --git a/local_build.py b/local_build.py  new file mode 100755  index 0000000..3409580  --- /dev/null  +++ b/local_build.py 
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#!/usr/bin/env python  from __future__ import division, print_function  """  This script generates a file to use for building authorea papers, and then runs  latex on them.  Requires python >= 2.6 (3.x should work, too)  The key assumptions are:  * ``layout.md`` exists in the article (I think it always does in Authorea)  * ``preamble.tex``, ``header.tex``, ``title.tex``, and  ``bibliobgraphy/biblio.bib`` exist (I think these are created normally in a  new Authorea article)  * ``posttitle.tex`` exists. This one you'll have to create, containing  everything you want after the title but before the beginning of the document.  """  import os, re  import subprocess  #lots of dobule-{}'s are here because we use it as a formatting template below  MAIN_TEMPLATE = r"""  {preamblein}  {headerin}  \begin{{document}}  {titlecontent}  \maketitle  \begin{{abstract}}  {abstract}  \end{{abstract}}  {sectioninputs}  \bibliography{{{bibloc}}}{{}}  \end{{document}}  """  FIGURE_TEMPLATE=r"""  \begin{figure}[tb]  \centering  \includegraphics[width=\linewidth]{}    \end{figure}  """.replace('{', '{{').replace('}', '}}').replace('<', '{').replace('>', '}')  WRAPFIGURE_TEMPLATE=r"""  \begin{wrapfigure}  \centering  \includegraphics[width=1\linewidth]{}      \end{wrapfigure}  """.replace('{', '{{').replace('}', '}}').replace('<', '{').replace('>', '}')  FIGURESC_TEMPLATE=r"""  \begin{SCfigure}[50][tb]  \centering  \includegraphics[width=]{}    \end{SCfigure}  """.replace('{', '{{').replace('}', '}}').replace('<', '{').replace('>', '}')  STARTFIG_TEMPLATE=r"""  \begin{figure}[tb]  \centering  \begin{minipage}{\linewidth}  \includegraphics[width=\linewidth]{}    \end{minipage}""".replace('{', '{{').replace('}', '}}').replace('<', '{').replace('>', '}')  ENDFIG_TEMPLATE=r"""\hfill  \begin{minipage}{\linewidth}  \includegraphics[width=\linewidth]{}    \end{minipage}    \end{figure}  """.replace('{', '{{').replace('}', '}}').replace('<', '{').replace('>', '}')  def get_input_string(filename, localdir):  if filename.endswith('.tex'):  filename = filename[:-4]  return r'\input{' + os.path.join(os.path.abspath(localdir), filename) + '}'  def get_figure_string(filename, localdir):  figdir, figfn = os.path.split(filename)  figdir = os.path.join(localdir, figdir)  print('rep', figfn)  figfnbase = os.path.splitext(figfn)[0]  figfn = os.path.join(figdir, figfn)  pdffn = os.path.join(figdir, figfnbase + '.pdf')  epsfn = os.path.join(figdir, figfnbase + '.eps')  figsize = 1  if not os.path.exists(pdffn):  pdffn = None  if not os.path.exists(epsfn):  epsfn = None  if pdffn or epsfn:  figfn = os.path.join(figdir, figfnbase)  figfn = os.path.abspath(figfn)  bigcaption = ''  capfn = os.path.join(figdir, 'caption.tex')  template = FIGURE_TEMPLATE  if os.path.exists(capfn):  caption = r'\caption{ \protect\input{' + os.path.abspath(capfn) + '}}'  captext = open(capfn).read()    m = re.search(r'figsize (\S+)',captext)  if m:  figsize = m.group(1)  m = re.search(r'wrapfig (\S+)\s*(\S*)$',captext,flags = re.MULTILINE)   sc = re.search(r'sidecap (\S+)',captext,flags = re.MULTILINE)   stfig = re.search(r'startfig (\S+)',captext,flags = re.MULTILINE)  endfig = re.search(r'endfig (\S+)',captext,flags = re.MULTILINE)    if m:  template = WRAPFIGURE_TEMPLATE  wrapoptions = m.group(1)  endcap = m.group(2)  elif sc:  template = FIGURESC_TEMPLATE  figwidth = sc.group(1)  elif stfig:  template = STARTFIG_TEMPLATE  figwidth = stfig.group(1)  elif endfig:  template = ENDFIG_TEMPLATE  figwidth = endfig.group(1)  elif re.search(r'%nofig',captext):  template = ''    fullfig = re.search(r'fullfig',captext,flags = re.MULTILINE)  if fullfig:  template = template.replace("{figure}","{figure*}")   bigcap = re.search(r'%bigcap',captext,flags = re.MULTILINE)  if bigcap:  bigcaption = caption  caption = ''   nocap = re.search(r'%nocap',captext,flags = re.MULTILINE)  if nocap:  caption = ''  else:  caption = ''  return template.format(**locals())  def build_authorea_latex(localdir, builddir, latex_exec, bibtex_exec, outname,  usetitle, dobibtex, npostbibcalls, openwith):  if not os.path.exists(builddir):  os.mkdir(builddir)  if not os.path.isdir(builddir):  raise IOError('Requested build directory {0} is a file, not a '  'directory'.format(builddir))  # generate the main tex file as a string  preamblein = get_input_string('preamble', localdir)  headerin = get_input_string('header', localdir)  bibloc = os.path.join(os.path.abspath(localdir), 'bibliography', 'biblio')  abstract = get_input_string('Abstract.tex', localdir)  titlecontent = []  if usetitle:  titlecontent.append(r'\title{'+open(os.path.join(os.path.abspath(localdir), 'title.tex')).read()+'}')  if os.path.exists(os.path.join(os.path.abspath(localdir), 'posttitle.tex')):  titlecontent.append(get_input_string('posttitle', localdir))  titlecontent = '\n'.join(titlecontent)  sectioninputs = []  with open(os.path.join(localdir, 'layout.md')) as f:  for l in f:  ls = l.strip()  if ls == '':  pass  elif ls == 'Abstract.tex':  pass  elif ls.startswith('figures'):  sectioninputs.append(get_figure_string(ls, localdir))  else:  sectioninputs.append(get_input_string(ls, localdir))  sectioninputs = '\n'.join(sectioninputs)  maintexstr = MAIN_TEMPLATE.format(**locals())  #now save that string out as a file  outname = outname if outname.endswith('.tex') else (outname + '.tex')  outtexpath = os.path.join(builddir, outname)  with open(outtexpath, 'w') as f:  f.write(maintexstr)  if outname.endswith('.tex'):  outname = outname[:-4]  #now actually run latex/bibtex  args = [latex_exec, outname + '.tex']  print('\n\RUNNING THIS COMMAND: "{0}"\n'.format(' '.join([latex_exec, outname + '.tex'])))  subprocess.check_call(args, cwd=builddir)  if dobibtex:  args = [bibtex_exec, outname]  print('\n\RUNNING THIS COMMAND: "{0}"\n'.format(' '.join([latex_exec, outname + '.tex'])))  subprocess.check_call(args, cwd=builddir)  for _ in range(npostbibcalls):  args = [latex_exec, outname + '.tex']  print('\n\RUNNING THIS COMMAND: "{0}"\n'.format(' '.join([latex_exec, outname + '.tex'])))  subprocess.check_call(args, cwd=builddir)  #launch the result if necessary  resultfn = outtexpath[:-4] + ('.pdf' if 'pdf' in latex_exec else '.dvi')  if openwith:  args = openwith.split(' ')  args.append(resultfn)  print('\nLaunching as:' + str(args), '\n')  subprocess.check_call(args)  else:  msg = '\nBuild completed. You can see the result in "{0}": "{1}"'  print(msg.format(builddir, resultfn), '\n')  if __name__ == '__main__':  import argparse  parser = argparse.ArgumentParser(description='Local builder for authorea papers.')  parser.add_argument('localdir', nargs='?', default='.',  help='The directory to actually search for the authorea'  ' files in. Default to the current directory.')  parser.add_argument('--build-dir', '-d', default='authorea_build',  help='the directory to build the paper in')  parser.add_argument('--latex', '-l', default='pdflatex',  help='The executable to use for the latex build step.')  parser.add_argument('--bibtex', '-b', default='bibtex',  help='The executable to use for the bibtex build step.')  parser.add_argument('--filename', '-f', default='authorea_paper',  help='The name to use for the output tex file.')  parser.add_argument('--no-bibtex', action='store_false', dest='usebibtex',  help='Provide this to not run bibtex.')  parser.add_argument('--no-title', action='store_false', dest='usetitle',  help='Provide this to skip the title command.')  parser.add_argument('--n-runs-after-bibtex', '-n', type=int, default=3,  help='The number of times to call latex after bibtex.')  parser.add_argument('--open-with', '-o', default=None,  help='An executable to launch the output file with. '  'Default is to not do anything with it.')  args = parser.parse_args()  build_authorea_latex(args.localdir, args.build_dir, args.latex, args.bibtex,  args.filename, args.usetitle, args.usebibtex,  args.n_runs_after_bibtex, args.open_with)  diff --git a/posttitle.tex b/posttitle.tex  new file mode 100644  index 0000000..da30d4d  --- /dev/null  +++ b/posttitle.tex 
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\author{%  Jocelyn Sunseri\,$^{1}$,  and David Ryan Koes\,$^{1}$%  \footnote{To whom correspondence should be addressed.  Email: [email protected]}}  \address{%  $^{1}$Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, 15260}  % Affiliation must include:  % Department name, institution name, full road and district address,  % state, Zip or postal code, country  \history{%  Received XXX, 2016;  Revised XXX, 2016;  Accepted XXX, 2016}  diff --git a/preamble.tex b/preamble.tex  new file mode 100644  index 0000000..4869fbd  --- /dev/null  +++ b/preamble.tex 
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\documentclass[a4,center,fleqn]{NAR}  % Enter dates of publication  \copyrightyear{2016}  \pubdate{XXX}  \pubyear{2016}  \jvolume{VV}  \jissue{II}  \usepackage{graphicx}  \usepackage[space]{grffile}  \usepackage{latexsym}  \usepackage{textcomp}  \usepackage{longtable}  \usepackage{multirow,booktabs}  \usepackage{amsfonts,amsmath,amssymb}  \usepackage{url}  \usepackage{hyperref}  \hypersetup{colorlinks=false,pdfborder={0 0 0}}  %\usepackage{latexml}  %\usepackage[utf8x]{inputenc}  %\usepackage[english]{babel}  \bibliographystyle{nar}