deletions | additions       diff --git a/Introduction.tex b/Introduction.tex  index 7ea96ef..273d5bc 100644  --- a/Introduction.tex  +++ b/Introduction.tex 
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\section{Introduction}\label{sec:Introduction}  TODO: discuss \TODO{discuss  the HFF survey, the FrontierSN program, and the value of discovering strongly lensed transient events. events.}        diff --git a/LensingModels.tex b/LensingModels.tex  index ccc79dc..d28b410 100644  --- a/LensingModels.tex  +++ b/LensingModels.tex 
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\section{Constraints from Lens Model}\label{sec:LensingModels}  To interpret the observed light curves and the timing of these two  events, we use \textcolor{red}{four} \textcolor{red}{five}  cluster mass models to provide estimates of the magnification and time delays from gravitational  lensing. We identify each by the last name of the principal  investigator of the development team:  diff --git a/Makefile b/Makefile  index cbac1e9..fbabb21 100644  --- a/Makefile  +++ b/Makefile 
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#Generate a pdf file using a modified python script from et_eq  local:   local_build.py local_build_withauthors.py  --build-dir . --filename spock_localbuild --title-input --n-runs-after-bibtex 2 open $(PAPER).pdf  #quick update (single compile)  diff --git a/Observations.tex b/Observations.tex  index 25bfd0f..783aac3 100644  --- a/Observations.tex  +++ b/Observations.tex 
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\citep{Benitez:2000}, and $z=0.92\pm0.05$, derived using the EAZY  program \citep{Brammer:2008}.  Table~\ref{tab:Photometry} Table \TODO{(add a table with photometry)} %~\ref{tab:Photometry}  and Figure~\ref{fig:SpockLCs} Figure~\ref{fig:LightCurves}  present photometry of the \spock\ events  from all available HST observations. The flux was measured on  difference images, first using aperture photometry with a 0\farcs3 
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epochs. All of the aperture and PSF fitting photometry was carried  out using the {\tt PythonPhot} software package \citep{Jones:2015}.  TODO: add a table with photometry.  diff --git a/local_build_withauthors.py b/local_build_withauthors.py  new file mode 100755  index 0000000..79b16e0  --- /dev/null  +++ b/local_build_withauthors.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`` and/or``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.  If it doesn't exist that's ok too, it'll just be ignored.  * Figures are in the ``figures`` directory (where authorea puts them), and in  the correct place in the ``layout.md`` file. A file named 'latexfigopts.json'  can specify a dictionary for additional figure options (see the  `FIGURE_DEFAULTS` below for what options that can be replaced).  """  import os  import subprocess  #lots of dobule-{}'s are here because we use it as a formatting template below  MAIN_TEMPLATE = r"""  {preamblein}  {headerin}  \begin{{document}}  {authorcontent}  {titlecontent}  {sectioninputs}  \bibliography{{{bibloc}}}{{}}  \end{{document}}  """  FIGURE_TEMPLATE = r"""  \begin{}[]  \begin{center}  \includegraphics[width=]{}    \end{center}  \end{}  """.replace('{', '{{').replace('}', '}}').replace('<', '{').replace('>', '}')  FIGURE_DEFAULTS = {'placement': '', 'width': '1\columnwidth', 'figure_env': 'figure'}  def get_input_string(filename, localdir, quotepath=True):  if filename.endswith('.tex'):  filename = filename[:-4]  if quotepath:  quote_chr = '"'  else:  quote_chr = ''  return r'\input{' + quote_chr + os.path.join(localdir, filename) + quote_chr + '}'  def get_figure_string(filename, localdir):  import json  figdir, figfn = os.path.split(filename)  figdir = os.path.join(localdir, figdir)  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')  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)  capfn = os.path.join(figdir, 'caption.tex')  if os.path.exists(capfn):  caption = r'\caption{ \protect\input{' + capfn + '}}'  else:  caption = ''  optsfn = os.path.join(figdir, 'latexfigopts.json')  figopts = FIGURE_DEFAULTS.copy()  if os.path.exists(optsfn):  with open(optsfn) as f:  optsjson = json.load(f)  if not isinstance(optsjson, dict):  raise ValueError('File "{0}" does not have a top-level dict'.format(optsfn))  for k in FIGURE_DEFAULTS.keys():  v = optsjson.pop(k, None)  if v is not None:  figopts[k] = v  if len(optsjson) != 0:  raise ValueError('Entries in "{0}" that were not understood: {1}'.format(optsfn, optsjson))  figopts.update(locals())  return FIGURE_TEMPLATE.format(**figopts)  # if builddir and local dir are the same set the paths used for input/include in  # the output tex file to be relative paths (this helps if sharing the created  # tex file with collaborator who don't use this script) otherwise use absolute  # paths. Alternatively, use the user defined option for whether relative or  # absolute paths are used.  def get_in_path(localdir, builddir, pathtype=None):  """  Figure out the path for a file in ``localdir`` relative to ``builddir``, or  just use an absolute path dependeing on whether ``pathtype`` is 'rel' or  'abs'. Or if it is None, pick relative only if ``localdir`` is the same as  ``builddir``.  """  if pathtype == 'rel':  return os.path.relpath(localdir, builddir)  elif pathtype == 'abs':  return os.path.abspath(localdir)  elif pathtype is None:  if builddir == localdir:  return os.path.relpath(localdir, builddir)  else:  return os.path.abspath(localdir)  else:  raise ValueError('Invalid pathtype: "{0}"'.format(pathtype))  def build_authorea_latex(localdir, builddir, latex_exec, bibtex_exec, outname,  usetitle, dobibtex, npostbibcalls, openwith, titleinput,  dobuild, pathtype):  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  if os.path.exists(os.path.join(localdir, 'preamble.tex')):  preamblein = get_input_string('preamble', get_in_path(localdir, builddir, pathtype))  else:  preamblein = ''  if os.path.exists(os.path.join(localdir, 'header.tex')):  headerin = get_input_string('header', get_in_path(localdir, builddir, pathtype))  else:  headerin = ''  if not headerin and not preamblein:  print("Neither preable nor header found! Proceeding, but that's rather weird")  bibloc = os.path.join(get_in_path(localdir, builddir, pathtype), 'bibliography', 'biblio')  titlecontent = []  if usetitle:  if titleinput:  titlestr = get_input_string('title', get_in_path(localdir, builddir, pathtype))  else:  with open(os.path.join(get_in_path(localdir, builddir, 'abs'), 'title.tex')) as f:  titlestr = f.read()  titlecontent.append(r'\title{' + titlestr + '}')  if os.path.exists(os.path.join(localdir, 'authors.tex')):  authorcontent = get_input_string('authors', get_in_path(localdir, builddir, pathtype))  else:  authorcontent = ""  sectioninputs = []  with open(os.path.join(localdir, 'layout.md')) as f:  for l in f:  ls = l.strip()  if ls == '':  pass  elif ls in ('posttitle.tex', 'title.tex', 'preamble.tex', 'header.tex'):  pass # skip any that have been processed above  elif ls in ('abstract.tex'):  # add abstract to section input  sectioninputs.append(get_input_string('abstract', get_in_path(localdir, builddir, pathtype)))  elif ls.endswith('.html') or ls.endswith('.htm'):  pass # html files aren't latex-able  elif ls.startswith('figures'):  sectioninputs.append(get_figure_string(ls, get_in_path(localdir, builddir, pathtype)))  else:  sectioninputs.append(get_input_string(ls, get_in_path(localdir, builddir, pathtype)))  sectioninputs = '\n'.join(sectioninputs)  if os.path.exists(os.path.join(get_in_path(localdir, builddir, pathtype), 'posttitle.tex')):  titlecontent.append(get_input_string('posttitle', get_in_path(localdir, builddir, pathtype)))  titlecontent = '\n'.join(titlecontent)  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]  if dobuild:  #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')  else:  msg = 'Preprocessing done but skipping build. Main file:"{0}.tex"'  print(msg.format(os.path.join(builddir, outname)))  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('--title-input', action='store_true', dest='titleinput',  help='Provide this to have the title included via the '  '\\input command instead of directly in the '  'generated tex file. This is useful because \\input'  'sometimes prevents the title from being cased '  'correctly.', default=False)  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.')  parser.add_argument('--no-build', action='store_false', dest='dobuild',  help='Only do preprocessing and skip all the build/open steps')  parser.add_argument('--relative-links', action='store_true', dest='rellinks',  help='Always make links (to input files and figures) within '  'the .tex file relative. Default is to do this if '  'localdir and buildir are the same.')  parser.add_argument('--absolute-links', action='store_true', dest='abslinks',  help='Always make links (to input files and figures) within '  'the .tex file absolute. Default is to do this if '  'localdir and buildir are different.')  args = parser.parse_args()  pathtype = None  if args.rellinks and args.abslinks:  raise IOError('You must supply either "--relative-links" OR "--absolute-links".')  else:  if args.rellinks:  pathtype = 'rel'  if args.abslinks:  pathtype = 'abs'  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,  args.titleinput, args.dobuild, pathtype)