@@ 0,0 1,25 @@ 
+syntax: glob
+.DS_Store
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*.pickle
+
+*.Rproj*
+*.Rout
+.RData
+.Rhistory
+
+# pandoc output
+rmarkdown*.{pdf,html,doc,docx,odt}
+paper*.{pdf,html,doc,docx,odt}
+README.{pdf,html,doc,docx,odt}
+
+# graphics
+*.png
+*.pdf
+
+# temp files
+*\~
+bib.keys
+*.swp

          

@@ 0,0 1,339 @@ 
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Lesser General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+  Finally, any free program is threatened constantly by software
+patents.  We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary.  To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License.  The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language.  (Hereinafter, translation is included without limitation in
+the term "modification".)  Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+    a) You must cause the modified files to carry prominent notices
+    stating that you changed the files and the date of any change.
+
+    b) You must cause any work that you distribute or publish, that in
+    whole or in part contains or is derived from the Program or any
+    part thereof, to be licensed as a whole at no charge to all third
+    parties under the terms of this License.
+
+    c) If the modified program normally reads commands interactively
+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
+    announcement including an appropriate copyright notice and a
+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
+    does not normally print such an announcement, your work based on
+    the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works.  But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+    a) Accompany it with the complete corresponding machine-readable
+    source code, which must be distributed under the terms of Sections
+    1 and 2 above on a medium customarily used for software interchange; or,
+
+    b) Accompany it with a written offer, valid for at least three
+    years, to give any third party, for a charge no more than your
+    cost of physically performing source distribution, a complete
+    machine-readable copy of the corresponding source code, to be
+    distributed under the terms of Sections 1 and 2 above on a medium
+    customarily used for software interchange; or,
+
+    c) Accompany it with the information you received as to the offer
+    to distribute corresponding source code.  (This alternative is
+    allowed only for noncommercial distribution and only if you
+    received the program in object code or executable form with such
+    an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it.  For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable.  However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.

          

@@ 0,0 1,38 @@ 
+# Copyright (c) 2013, Phillip Alday
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+python = python
+library ?= /path/to/library
+paper ?= article
+mdflags ?= -f markdown-hard_line_breaks+yaml_metadata_block
+refs ?= $(paper).bib
+
+draft: $(paper).pdf
+	cp $(paper).pdf $(paper)_`hg tip --template "{date|shortdate}_{node|short}"`.pdf
+
+%.pdf: %.md $(refs)
+	pandoc --standalone --template=template.latex --bibliography=$(refs) $*.md -o $*.pdf
+
+%.md: %.Rmd
+	echo 'knitr::knit("$*.Rmd")' | R --vanilla
+
+clean:
+	rm -rf $(paper).{pdf,html,odt,docx}
+
+$(refs): bib.keys
+	$(python) extractbib.py bib.keys $(library) $(refs)
+
+bib.keys: $(paper).md
+	grep @[-:_a-zA-Z0-9]* $(paper).md -oh --color=never | sort  | uniq -u | sed 's/@//g' > bib.keys

          

@@ 0,0 1,58 @@ 
+---
+title: "Effective collaboration with (R)Markdown, pandoc and DVCS"
+date: 22 August 2014
+author: 
+- name: First Author
+  affiliation: |
+     a\footnote{corresponding author: \url{name@university.edu}}
+- name: Second Author
+  affiliation: b
+- name: Third Author
+  affiliation: a,c
+affiliation:
+- symbol: a
+  name: University of Markdown
+- symbol: b
+  name: R State University
+- symbol: c
+  name: Free Culture University 
+abstract: |
+    Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc mollis dui sem, ac condimentum augue eleifend non. Praesent a ante a mi porta congue. Mauris interdum vel neque nec posuere. Pellentesque ante neque, semper et hendrerit vitae, porta quis velit. Nam sodales leo quis dolor malesuada, id mollis neque convallis. Cras mattis eu lacus vel tincidunt. Proin eu ante magna. Curabitur aliquet odio eros, pretium pulvinar dolor hendrerit vitae. Fusce id tempor sem, quis hendrerit mauris. Phasellus porta consectetur augue, vitae euismod magna ornare sodales. Nam rutrum, libero ut maximus bibendum, nisl ante blandit sapien, sed vehicula ante sapien id libero. Donec sed est at quam mattis pellentesque. 
+    \noindent{}**Keywords:** markdown, DVCS, bibtex
+...
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vivamus quis fringilla ligula. In faucibus lacus sed lacus iaculis vestibulum. Cras id sagittis sem, ornare sodales metus. Suspendisse dapibus lacus sit amet urna consectetur, nec porta lectus consequat. Proin eleifend faucibus faucibus. Morbi odio erat, pretium non convallis a, ullamcorper non orci. Donec at elit a nisl viverra feugiat eu eu turpis. Suspendisse ac diam nec ipsum consectetur convallis.
+
+Nulla condimentum sodales gravida. In sit amet ultricies tortor, quis finibus quam. Cras sapien odio, varius et varius quis, dictum id nulla. Quisque fringilla lacus id nisi malesuada dignissim. Phasellus nec scelerisque tortor. Maecenas cursus scelerisque sapien, ut suscipit ex aliquet eget. In vehicula, tellus eget rutrum semper, sem diam posuere mi, ac tincidunt felis tortor sit amet sapien. Nullam fringilla urna sed nisi laoreet, at laoreet quam eleifend. Donec id eros ante. Mauris id mi orci. Aenean malesuada vestibulum ullamcorper. Mauris magna diam, convallis quis lacus eget, condimentum varius erat.
+
+Mauris non massa commodo, porttitor quam in, ullamcorper urna. Proin tempor viverra enim at rhoncus. Nulla quam nunc, commodo vitae eros non, interdum pretium augue. Phasellus mattis mollis nisl. Proin cursus, justo eget lacinia consectetur, ligula mi condimentum lorem, et commodo risus eros et lacus. Donec vitae eleifend ipsum. In ante orci, porttitor et scelerisque eu, ornare consectetur odio. Duis venenatis vehicula tortor sit amet tempus. Curabitur ac lorem elit. Donec viverra imperdiet sapien, vel ultricies quam finibus et. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Pellentesque imperdiet nunc vel eros cursus, in faucibus ipsum commodo. Aliquam tincidunt neque est, nec sollicitudin nisl porttitor vel.
+
+Duis sed aliquet velit. Proin sed ex facilisis, molestie massa id, euismod lorem. Fusce pretium vestibulum nulla at bibendum. Pellentesque aliquam quam ac quam dignissim lobortis. Aenean in velit luctus, iaculis lectus non, accumsan urna. Vivamus aliquam porta lectus sit amet bibendum. Mauris ornare porta sodales. Pellentesque ornare facilisis nisl, at dapibus leo fermentum et.
+
+Aliquam egestas in mauris molestie volutpat. Nam convallis felis leo, ac tristique magna cursus tristique. Morbi nec sagittis ipsum. Praesent nec diam arcu. Curabitur vulputate sodales metus, vel aliquet dui fermentum nec. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Curabitur porta congue volutpat. Aenean accumsan imperdiet mauris, quis ornare tortor tincidunt vitae. Aliquam condimentum varius arcu, a sagittis eros vehicula sit amet. Duis at erat id libero suscipit eleifend et fermentum nulla. Aliquam gravida mattis laoreet.
+
+Etiam erat lorem, posuere non lorem nec, porta sagittis nulla. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Curabitur nisl diam, tincidunt sed diam sit amet, rhoncus aliquam libero. Nam id bibendum nulla. In dictum consequat risus quis ornare. Ut congue arcu nec purus venenatis rhoncus. Aliquam consequat metus in iaculis imperdiet.
+
+Nulla mollis odio urna, quis rhoncus lacus efficitur ac. Vestibulum porta, est vitae gravida lacinia, ex arcu ornare odio, quis maximus nulla mi in mauris. Nunc elementum ornare nunc eget semper. Maecenas venenatis diam eget nulla porttitor tristique. Donec at tempor diam. Integer sollicitudin magna ac sem tempor, in cursus mi ultrices. In sed mauris vel nibh varius gravida sit amet ultrices mi. Quisque lobortis nunc non nunc rhoncus gravida. Nullam cursus, ante mattis interdum sodales, odio augue viverra massa, eget tincidunt nunc neque ac felis. Proin aliquam commodo erat et mollis. Nunc ultrices justo in metus scelerisque ullamcorper. Morbi nec viverra lacus, sit amet blandit erat. Nunc efficitur nulla nibh, et ullamcorper leo consequat in. Vivamus nec ligula viverra dui dapibus imperdiet nec sed eros.
+
+Nam a commodo augue, quis scelerisque sapien. Praesent semper libero nisl, sit amet suscipit neque viverra ut. Maecenas suscipit eleifend massa sed tristique. Curabitur vitae orci vestibulum, rhoncus mi eu, placerat dolor. Donec lobortis sed elit ut efficitur. Phasellus at lobortis enim. Etiam sit amet pulvinar nulla. Donec quis ex bibendum enim rhoncus consectetur a vel nisi. Pellentesque tempor dui vitae lorem aliquam, et sollicitudin dolor luctus. Sed sollicitudin euismod enim sed ultrices.
+
+Aliquam ullamcorper lacus eu metus mattis, in imperdiet felis rhoncus. In ipsum libero, fermentum ac quam tristique, ullamcorper bibendum erat. Proin viverra imperdiet augue sed volutpat. Aliquam auctor arcu id massa ultrices molestie. Morbi et purus purus. Vestibulum a tincidunt risus. In sit amet enim urna. Curabitur sit amet bibendum neque. Phasellus sapien felis, sodales sagittis faucibus in, maximus vitae orci. Cras sed nibh a arcu porta scelerisque. Sed convallis iaculis purus ac elementum. Donec iaculis, tortor id scelerisque iaculis, sem felis faucibus turpis, sed varius arcu ligula a augue. Suspendisse potenti. Donec tempor orci at posuere vehicula.
+
+Morbi accumsan semper ex, ut aliquet turpis consequat eget. Proin vitae rutrum orci. Donec non dui posuere, hendrerit mi et, tincidunt mauris. Donec arcu odio, tristique sit amet sem a, bibendum dignissim nisi. Sed ultrices dolor ac vehicula euismod. Curabitur egestas quam in lorem placerat, id condimentum enim accumsan. Quisque a imperdiet tellus. In vel dui faucibus, lacinia sapien eget, elementum ligula.
+
+Nunc congue non nulla faucibus tempus. Mauris dictum ultrices placerat. Morbi id facilisis nisl. Curabitur feugiat justo at ipsum fermentum fermentum. Suspendisse est dolor, viverra sed lectus at, fermentum hendrerit lacus. Sed mauris nunc, lacinia vitae hendrerit at, fermentum in lectus. Sed mattis leo elementum rhoncus gravida. Nulla facilisi. In sit amet mi non turpis faucibus blandit. Praesent eu elit in velit dignissim egestas nec sed nisi. Integer at scelerisque felis.
+
+Etiam in nisi tincidunt, suscipit arcu elementum, viverra augue. Donec imperdiet lectus ipsum, et pharetra diam blandit at. Nam feugiat justo sapien, id dapibus elit hendrerit in. Morbi semper dolor nibh, nec dapibus justo pellentesque quis. Vestibulum et euismod justo. Donec id congue sapien. Nullam tincidunt viverra leo, id ullamcorper tortor interdum et. Pellentesque viverra, est vel porta euismod, augue quam auctor eros, et hendrerit lacus dui et sem. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Maecenas lorem ante, luctus ut nulla quis, pharetra ultricies ipsum. Nam ac vestibulum ipsum, vel pellentesque dui. Duis volutpat, turpis vel vestibulum maximus, erat nibh mollis turpis, a commodo massa turpis finibus odio. Curabitur mollis eget odio sed condimentum.
+
+Curabitur nec imperdiet libero, vulputate lacinia sapien. Sed nisl diam, ornare ut ultricies et, dapibus a nunc. Vestibulum tristique consequat quam eu pretium. Aliquam quis consequat ex. Aliquam ut erat in tellus tincidunt elementum. Suspendisse convallis ac leo sit amet commodo. Nunc ac nunc eros. Aenean feugiat orci lorem. Duis euismod rutrum sodales. Duis egestas, nisi ut tincidunt convallis, ipsum neque imperdiet leo, non sodales ex erat eu risus. Aenean et mattis ipsum, at vulputate odio. In nec ipsum pellentesque, cursus massa sed, imperdiet mauris. Etiam maximus in magna vel viverra. Pellentesque arcu arcu, placerat luctus risus vel, tincidunt vulputate sapien.
+
+Ut pulvinar enim ante, nec dapibus ligula ultricies a. Morbi semper egestas ultrices. Fusce viverra ex laoreet tincidunt mattis. Nam dignissim faucibus dolor, quis bibendum metus cursus quis. Vivamus lacus orci, hendrerit dapibus venenatis eu, volutpat ac libero. Morbi quis augue nunc. Suspendisse euismod velit nulla, ac hendrerit dui rutrum quis.
+
+Quisque id orci sit amet arcu euismod pharetra at at neque. Proin in metus sem. Pellentesque aliquet luctus enim sed viverra. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Duis sit amet lacus tortor. Aenean varius augue a molestie venenatis. Proin tincidunt sed nibh at tristique. Ut non fringilla mauris. Sed at euismod eros. Nam sit amet urna leo.
+
+Proin molestie porta dui et ullamcorper. Nullam magna elit, tristique vitae tortor malesuada, mattis pharetra tellus. Donec quam massa, accumsan eu pellentesque id, hendrerit sit amet odio. Phasellus imperdiet elit massa, quis sodales sapien vehicula id. In ornare commodo hendrerit. Nullam sodales pulvinar justo, sit amet pellentesque mi iaculis ut. Cras sit amet justo ac velit vulputate tristique eleifend quis leo.
+
+Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Pellentesque dapibus, sapien quis vehicula egestas, leo neque fermentum lorem, ut mollis sem mauris ac augue. Proin ornare ante vel ante elementum, a dignissim ex hendrerit. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Fusce cursus, ex et commodo laoreet, tellus diam fringilla nunc, eget tempor magna elit in nunc. Maecenas quis sapien in augue ornare imperdiet. Nam facilisis, erat quis luctus consequat, augue dolor auctor erat, a fringilla turpis libero vel orci. Nulla vestibulum, eros sit amet mattis sodales, dui est aliquam justo, id vehicula nunc velit pharetra ante. Nullam facilisis imperdiet ante, eu semper sem eleifend quis. Pellentesque tincidunt ex sed ex viverra gravida. Phasellus in lacus diam. Ut et finibus dui.
+
+Fusce ultrices tincidunt lorem, ut tempor leo lacinia non. Sed hendrerit libero leo, id pharetra sapien tristique at. Nulla ut purus placerat, faucibus nunc vel, porta magna. Vivamus ac dapibus lorem, vel varius erat. Duis et purus libero. Vestibulum lobortis pharetra ultrices. Quisque lobortis, arcu facilisis tincidunt consectetur, quam mauris placerat enim, sit amet convallis dolor nisl vitae augue. Curabitur a dui ac purus placerat aliquet. Curabitur sem metus, iaculis in. 
  No newline at end of file

          

@@ 0,0 1,75 @@ 
+#! /usr/bin/env python
+# s. https://gist.github.com/palday/1ff12dd110255541df0f
+# adapted from
+# GitHub Gist https://gist.github.com/tpoisot/7406955
+# don't forget to install bibtexparser: http://bibtexparser.readthedocs.org/en/latest/install.html
+# or with pip:
+# pip install bibtexparser
+
+import sys
+import codecs
+from bibtexparser.bparser import BibTexParser
+
+non_local_fields = ['address',
+                    'annote',
+                    'author',
+                    'booktitle',
+                    'chapter',
+                    'crossref',
+                    'doi',
+                    'edition',
+                    'editor',
+                    'howpublished',
+                    'institution',
+                    'journal',
+                    'key',
+                    'month',
+                    'note',
+                    'number',
+                    'organization',
+                    'pages',
+                    'publisher',
+                    'school',
+                    'series',
+                    'title',
+                    'url',
+                    'volume',
+                    'year',
+                  ]
+
+def dict2bib(ke,di):
+   b = "@"+di['type'].upper()+"{"+ke+",\n"
+   for (k, v) in sorted(di.iteritems()):
+      if k.lower() in non_local_fields:
+         b += '\t' + k + ' = {'+v+'},\n'
+   b += '}\n'
+   return b
+
+if __name__ == "__main__":
+   ## Check the number of arguments
+   if len(sys.argv) != 4:
+      raise ValueError("Wrong number of arguments")
+   else :
+      key_list = sys.argv[1]
+      bib_file = sys.argv[2]
+      out_file = sys.argv[3]
+   ## The three arguments should be strings
+   if not isinstance(key_list, str):
+      raise TypeError("The path to the list of keys should be a string")
+   if not isinstance(bib_file, str):
+      raise TypeError("The path to the bibtex library should be a string")
+   if not isinstance(out_file, str):
+      raise TypeError("The path to the output bibtex file should be a string")
+   ## Step 1 - read the key list
+   keys = [kl.rstrip(":\n") for kl in open(key_list, 'r')]
+   ## Step 2 - read the library file
+   refs = BibTexParser(open(bib_file, 'r').read()).get_entry_dict()
+   ## Step 3 - extract the used entries
+   used_refs = {key: refs[key] for key in keys if key in refs}
+   ## Step 4 - convert the dicts back into bibtex
+   refs_as_bib = [dict2bib(k, v) for (k, v) in used_refs.iteritems()]
+   #print [uk for uk in keys if uk not in used_refs]
+   ## Step 5 - write the output file
+   with codecs.open(out_file, 'w', 'utf-8-sig') as of:
+      of.writelines(refs_as_bib)
+   #print(refs_as_bib)

          

@@ 0,0 1,17 @@ 
+Futhark
+=========
+
+Markdown and DVCS can change the way we collaborate. Even for those pesky journals that require a submission in Word format, you can do the majority of your work in Markdown and then convert to Word via pandoc (and if need be LibreOffice to convert .odt/.docx to .doc). However, a common bibliography is still difficult to pull off. The Makefile and scripts here automagically extract the relevant pandoc references from the specified BibTeX library and create a minimal local BibTeX file that you can include in your repository.
+
+This was inspired by and expands upon the ideas in [this blog post](http://timotheepoisot.fr/2013/11/10/shared-bibtex-file-markdown/).
+
+Requirements:
+- `make`
+-  Mercurial (git version available on GitHub)
+- `pandoc`
+-  Python
+    - currently using Python 2.x because of
+    - [BibTexParser](http://bibtexparser.readthedocs.org/en/latest/install.html)
+
+License:
+My contributions are currently GPLv2, but I am building on the work of others, whose licensing conditions aren't yet clear. The LaTeX template is a modification of the standard pandoc template and is thus subject to [the same restrictions](https://github.com/jgm/pandoc-templates).
  No newline at end of file

          

@@ 0,0 1,65 @@ 
+---
+title: "Effective collaboration with (R)Markdown, pandoc and DVCS"
+date: 22 August 2014
+author:
+- name: First Author
+  affiliation: |
+     a\footnote{corresponding author: \url{name@university.edu}}
+- name: Second Author
+  affiliation: b
+- name: Third Author
+  affiliation: a,c
+affiliation:
+- symbol: a
+  name: University of Markdown
+- symbol: b
+  name: R State University
+- symbol: c
+  name: Free Culture University
+...
+
+
+R is a really great language for statistics and data. `ggplot2` is a great package for pretty graphics.
+```{r, eval=TRUE}
+library(ggplot2)
+```
+
+```{r, fig.cap="Plotting data with a regression line with ggplot"}
+qplot(x=speed,y=dist,data=cars) + geom_smooth(method="lm")
+```
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vivamus quis fringilla ligula. In faucibus lacus sed lacus iaculis vestibulum. Cras id sagittis sem, ornare sodales metus. Suspendisse dapibus lacus sit amet urna consectetur, nec porta lectus consequat. Proin eleifend faucibus faucibus. Morbi odio erat, pretium non convallis a, ullamcorper non orci. Donec at elit a nisl viverra feugiat eu eu turpis. Suspendisse ac diam nec ipsum consectetur convallis.
+
+Nulla condimentum sodales gravida. In sit amet ultricies tortor, quis finibus quam. Cras sapien odio, varius et varius quis, dictum id nulla. Quisque fringilla lacus id nisi malesuada dignissim. Phasellus nec scelerisque tortor. Maecenas cursus scelerisque sapien, ut suscipit ex aliquet eget. In vehicula, tellus eget rutrum semper, sem diam posuere mi, ac tincidunt felis tortor sit amet sapien. Nullam fringilla urna sed nisi laoreet, at laoreet quam eleifend. Donec id eros ante. Mauris id mi orci. Aenean malesuada vestibulum ullamcorper. Mauris magna diam, convallis quis lacus eget, condimentum varius erat.
+
+Mauris non massa commodo, porttitor quam in, ullamcorper urna. Proin tempor viverra enim at rhoncus. Nulla quam nunc, commodo vitae eros non, interdum pretium augue. Phasellus mattis mollis nisl. Proin cursus, justo eget lacinia consectetur, ligula mi condimentum lorem, et commodo risus eros et lacus. Donec vitae eleifend ipsum. In ante orci, porttitor et scelerisque eu, ornare consectetur odio. Duis venenatis vehicula tortor sit amet tempus. Curabitur ac lorem elit. Donec viverra imperdiet sapien, vel ultricies quam finibus et. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Pellentesque imperdiet nunc vel eros cursus, in faucibus ipsum commodo. Aliquam tincidunt neque est, nec sollicitudin nisl porttitor vel.
+
+Duis sed aliquet velit. Proin sed ex facilisis, molestie massa id, euismod lorem. Fusce pretium vestibulum nulla at bibendum. Pellentesque aliquam quam ac quam dignissim lobortis. Aenean in velit luctus, iaculis lectus non, accumsan urna. Vivamus aliquam porta lectus sit amet bibendum. Mauris ornare porta sodales. Pellentesque ornare facilisis nisl, at dapibus leo fermentum et.
+
+Aliquam egestas in mauris molestie volutpat. Nam convallis felis leo, ac tristique magna cursus tristique. Morbi nec sagittis ipsum. Praesent nec diam arcu. Curabitur vulputate sodales metus, vel aliquet dui fermentum nec. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Curabitur porta congue volutpat. Aenean accumsan imperdiet mauris, quis ornare tortor tincidunt vitae. Aliquam condimentum varius arcu, a sagittis eros vehicula sit amet. Duis at erat id libero suscipit eleifend et fermentum nulla. Aliquam gravida mattis laoreet.
+
+Etiam erat lorem, posuere non lorem nec, porta sagittis nulla. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Curabitur nisl diam, tincidunt sed diam sit amet, rhoncus aliquam libero. Nam id bibendum nulla. In dictum consequat risus quis ornare. Ut congue arcu nec purus venenatis rhoncus. Aliquam consequat metus in iaculis imperdiet.
+
+Nulla mollis odio urna, quis rhoncus lacus efficitur ac. Vestibulum porta, est vitae gravida lacinia, ex arcu ornare odio, quis maximus nulla mi in mauris. Nunc elementum ornare nunc eget semper. Maecenas venenatis diam eget nulla porttitor tristique. Donec at tempor diam. Integer sollicitudin magna ac sem tempor, in cursus mi ultrices. In sed mauris vel nibh varius gravida sit amet ultrices mi. Quisque lobortis nunc non nunc rhoncus gravida. Nullam cursus, ante mattis interdum sodales, odio augue viverra massa, eget tincidunt nunc neque ac felis. Proin aliquam commodo erat et mollis. Nunc ultrices justo in metus scelerisque ullamcorper. Morbi nec viverra lacus, sit amet blandit erat. Nunc efficitur nulla nibh, et ullamcorper leo consequat in. Vivamus nec ligula viverra dui dapibus imperdiet nec sed eros.
+
+Nam a commodo augue, quis scelerisque sapien. Praesent semper libero nisl, sit amet suscipit neque viverra ut. Maecenas suscipit eleifend massa sed tristique. Curabitur vitae orci vestibulum, rhoncus mi eu, placerat dolor. Donec lobortis sed elit ut efficitur. Phasellus at lobortis enim. Etiam sit amet pulvinar nulla. Donec quis ex bibendum enim rhoncus consectetur a vel nisi. Pellentesque tempor dui vitae lorem aliquam, et sollicitudin dolor luctus. Sed sollicitudin euismod enim sed ultrices.
+
+Aliquam ullamcorper lacus eu metus mattis, in imperdiet felis rhoncus. In ipsum libero, fermentum ac quam tristique, ullamcorper bibendum erat. Proin viverra imperdiet augue sed volutpat. Aliquam auctor arcu id massa ultrices molestie. Morbi et purus purus. Vestibulum a tincidunt risus. In sit amet enim urna. Curabitur sit amet bibendum neque. Phasellus sapien felis, sodales sagittis faucibus in, maximus vitae orci. Cras sed nibh a arcu porta scelerisque. Sed convallis iaculis purus ac elementum. Donec iaculis, tortor id scelerisque iaculis, sem felis faucibus turpis, sed varius arcu ligula a augue. Suspendisse potenti. Donec tempor orci at posuere vehicula.
+
+Morbi accumsan semper ex, ut aliquet turpis consequat eget. Proin vitae rutrum orci. Donec non dui posuere, hendrerit mi et, tincidunt mauris. Donec arcu odio, tristique sit amet sem a, bibendum dignissim nisi. Sed ultrices dolor ac vehicula euismod. Curabitur egestas quam in lorem placerat, id condimentum enim accumsan. Quisque a imperdiet tellus. In vel dui faucibus, lacinia sapien eget, elementum ligula.
+
+Nunc congue non nulla faucibus tempus. Mauris dictum ultrices placerat. Morbi id facilisis nisl. Curabitur feugiat justo at ipsum fermentum fermentum. Suspendisse est dolor, viverra sed lectus at, fermentum hendrerit lacus. Sed mauris nunc, lacinia vitae hendrerit at, fermentum in lectus. Sed mattis leo elementum rhoncus gravida. Nulla facilisi. In sit amet mi non turpis faucibus blandit. Praesent eu elit in velit dignissim egestas nec sed nisi. Integer at scelerisque felis.
+
+Etiam in nisi tincidunt, suscipit arcu elementum, viverra augue. Donec imperdiet lectus ipsum, et pharetra diam blandit at. Nam feugiat justo sapien, id dapibus elit hendrerit in. Morbi semper dolor nibh, nec dapibus justo pellentesque quis. Vestibulum et euismod justo. Donec id congue sapien. Nullam tincidunt viverra leo, id ullamcorper tortor interdum et. Pellentesque viverra, est vel porta euismod, augue quam auctor eros, et hendrerit lacus dui et sem. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Maecenas lorem ante, luctus ut nulla quis, pharetra ultricies ipsum. Nam ac vestibulum ipsum, vel pellentesque dui. Duis volutpat, turpis vel vestibulum maximus, erat nibh mollis turpis, a commodo massa turpis finibus odio. Curabitur mollis eget odio sed condimentum.
+
+Curabitur nec imperdiet libero, vulputate lacinia sapien. Sed nisl diam, ornare ut ultricies et, dapibus a nunc. Vestibulum tristique consequat quam eu pretium. Aliquam quis consequat ex. Aliquam ut erat in tellus tincidunt elementum. Suspendisse convallis ac leo sit amet commodo. Nunc ac nunc eros. Aenean feugiat orci lorem. Duis euismod rutrum sodales. Duis egestas, nisi ut tincidunt convallis, ipsum neque imperdiet leo, non sodales ex erat eu risus. Aenean et mattis ipsum, at vulputate odio. In nec ipsum pellentesque, cursus massa sed, imperdiet mauris. Etiam maximus in magna vel viverra. Pellentesque arcu arcu, placerat luctus risus vel, tincidunt vulputate sapien.
+
+Ut pulvinar enim ante, nec dapibus ligula ultricies a. Morbi semper egestas ultrices. Fusce viverra ex laoreet tincidunt mattis. Nam dignissim faucibus dolor, quis bibendum metus cursus quis. Vivamus lacus orci, hendrerit dapibus venenatis eu, volutpat ac libero. Morbi quis augue nunc. Suspendisse euismod velit nulla, ac hendrerit dui rutrum quis.
+
+Quisque id orci sit amet arcu euismod pharetra at at neque. Proin in metus sem. Pellentesque aliquet luctus enim sed viverra. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Duis sit amet lacus tortor. Aenean varius augue a molestie venenatis. Proin tincidunt sed nibh at tristique. Ut non fringilla mauris. Sed at euismod eros. Nam sit amet urna leo.
+
+Proin molestie porta dui et ullamcorper. Nullam magna elit, tristique vitae tortor malesuada, mattis pharetra tellus. Donec quam massa, accumsan eu pellentesque id, hendrerit sit amet odio. Phasellus imperdiet elit massa, quis sodales sapien vehicula id. In ornare commodo hendrerit. Nullam sodales pulvinar justo, sit amet pellentesque mi iaculis ut. Cras sit amet justo ac velit vulputate tristique eleifend quis leo.
+
+Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Pellentesque dapibus, sapien quis vehicula egestas, leo neque fermentum lorem, ut mollis sem mauris ac augue. Proin ornare ante vel ante elementum, a dignissim ex hendrerit. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Fusce cursus, ex et commodo laoreet, tellus diam fringilla nunc, eget tempor magna elit in nunc. Maecenas quis sapien in augue ornare imperdiet. Nam facilisis, erat quis luctus consequat, augue dolor auctor erat, a fringilla turpis libero vel orci. Nulla vestibulum, eros sit amet mattis sodales, dui est aliquam justo, id vehicula nunc velit pharetra ante. Nullam facilisis imperdiet ante, eu semper sem eleifend quis. Pellentesque tincidunt ex sed ex viverra gravida. Phasellus in lacus diam. Ut et finibus dui.
+
+Fusce ultrices tincidunt lorem, ut tempor leo lacinia non. Sed hendrerit libero leo, id pharetra sapien tristique at. Nulla ut purus placerat, faucibus nunc vel, porta magna. Vivamus ac dapibus lorem, vel varius erat. Duis et purus libero. Vestibulum lobortis pharetra ultrices. Quisque lobortis, arcu facilisis tincidunt consectetur, quam mauris placerat enim, sit amet convallis dolor nisl vitae augue. Curabitur a dui ac purus placerat aliquet. Curabitur sem metus, iaculis in.
  No newline at end of file

          

@@ 0,0 1,212 @@ 
+\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$lang$,$endif$$if(papersize)$$papersize$,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}
+$if(fontfamily)$
+\usepackage{$fontfamily$}
+$else$
+\usepackage{lmodern}
+$endif$
+$if(linestretch)$
+\usepackage{setspace}
+\setstretch{$linestretch$}
+$endif$
+\usepackage{amssymb,amsmath}
+\usepackage{ifxetex,ifluatex}
+\usepackage{fixltx2e} % provides \textsubscript
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  \usepackage[T1]{fontenc}
+  \usepackage[utf8]{inputenc}
+$if(euro)$
+  \usepackage{eurosym}
+$endif$
+\else % if luatex or xelatex
+  \ifxetex
+    \usepackage{mathspec}
+    \usepackage{xltxtra,xunicode}
+  \else
+    \usepackage{fontspec}
+  \fi
+  \defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
+  \newcommand{\euro}{€}
+$if(mainfont)$
+    \setmainfont{$mainfont$}
+$endif$
+$if(sansfont)$
+    \setsansfont{$sansfont$}
+$endif$
+$if(monofont)$
+    \setmonofont[Mapping=tex-ansi]{$monofont$}
+$endif$
+$if(mathfont)$
+    \setmathfont(Digits,Latin,Greek){$mathfont$}
+$endif$
+\fi
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+% use microtype if available
+\IfFileExists{microtype.sty}{\usepackage{microtype}}{}
+$if(geometry)$
+\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
+$endif$
+$if(natbib)$
+\usepackage{natbib}
+\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
+$endif$
+$if(biblatex)$
+\usepackage{biblatex}
+$if(biblio-files)$
+\bibliography{$biblio-files$}
+$endif$
+$endif$
+$if(listings)$
+\usepackage{listings}
+$endif$
+$if(lhs)$
+\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
+$endif$
+$if(highlighting-macros)$
+$highlighting-macros$
+$endif$
+$if(verbatim-in-note)$
+\usepackage{fancyvrb}
+$endif$
+$if(tables)$
+\usepackage{longtable,booktabs}
+$endif$
+$if(graphics)$
+\usepackage{graphicx}
+\makeatletter
+\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+\makeatother
+% Scale images if necessary, so that they will not overflow the page
+% margins by default, and it is still possible to overwrite the defaults
+% using explicit options in \includegraphics[width, height, ...]{}
+\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+$endif$
+\ifxetex
+  \usepackage[setpagesize=false, % page size defined by xetex
+              unicode=false, % unicode breaks when used with xetex
+              xetex]{hyperref}
+\else
+  \usepackage[unicode=true]{hyperref}
+\fi
+\hypersetup{breaklinks=true,
+            bookmarks=true,
+            pdfauthor={$author-meta$},
+            pdftitle={$title-meta$},
+            colorlinks=true,
+            citecolor=$if(citecolor)$$citecolor$$else$blue$endif$,
+            urlcolor=$if(urlcolor)$$urlcolor$$else$blue$endif$,
+            linkcolor=$if(linkcolor)$$linkcolor$$else$magenta$endif$,
+            pdfborder={0 0 0}}
+\urlstyle{same}  % don't use monospace font for urls
+$if(links-as-notes)$
+% Make links footnotes instead of hotlinks:
+\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
+$endif$
+$if(strikeout)$
+\usepackage[normalem]{ulem}
+% avoid problems with \sout in headers with hyperref:
+\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
+$endif$
+\setlength{\parindent}{0pt}
+\setlength{\parskip}{6pt plus 2pt minus 1pt}
+\setlength{\emergencystretch}{3em}  % prevent overfull lines
+$if(numbersections)$
+\setcounter{secnumdepth}{5}
+$else$
+\setcounter{secnumdepth}{0}
+$endif$
+$if(verbatim-in-note)$
+\VerbatimFootnotes % allows verbatim text in footnotes
+$endif$
+$if(lang)$
+\ifxetex
+  \usepackage{polyglossia}
+  \setmainlanguage{$mainlang$}
+\else
+  \usepackage[$lang$]{babel}
+\fi
+$endif$
+
+\usepackage{authblk}
+
+$if(title)$
+\title{$title$}
+$endif$
+$if(subtitle)$
+\subtitle{$subtitle$}
+$endif$
+
+$for(author)$
+
+$if(author.affiliation)$
+\author[$author.affiliation$]{%
+$else$
+\author{%
+$endif$
+$if(author.name)$
+$author.name$ %
+$else$
+$author$ %
+$endif$
+}
+
+$endfor$
+
+$for(affiliation)$
+\affil[$affiliation.symbol$]{$affiliation.name$}
+$endfor$
+
+
+$if(date)$
+\date{$date$}
+$endif$
+$for(header-includes)$
+$header-includes$
+$endfor$
+
+\begin{document}
+$if(title)$
+\maketitle
+$endif$
+$if(abstract)$
+\begin{abstract}
+$abstract$
+\end{abstract}
+$endif$
+
+$for(include-before)$
+$include-before$
+
+$endfor$
+$if(toc)$
+{
+\hypersetup{linkcolor=black}
+\setcounter{tocdepth}{$toc-depth$}
+\tableofcontents
+}
+$endif$
+$body$
+
+$if(natbib)$
+$if(biblio-files)$
+$if(biblio-title)$
+$if(book-class)$
+\renewcommand\bibname{$biblio-title$}
+$else$
+\renewcommand\refname{$biblio-title$}
+$endif$
+$endif$
+\bibliography{$biblio-files$}
+
+$endif$
+$endif$
+$if(biblatex)$
+\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
+
+$endif$
+$for(include-after)$
+$include-after$
+
+$endfor$
+\end{document}