From 78727050424174fdee340190cdc458e491aaf18c Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Wed, 14 Nov 2018 09:43:04 +0000
Subject: All used software with versions, acknowledged

All the used software are now acknowledged in the template paper along with
their versions. This section is also mentioned in the check list, so users
don't delete it by mistake.
---
 README.md                  |  7 ++++---
 paper.tex                  | 30 ++++++++++++++++++++++++++++++
 tex/preamble-necessary.tex |  1 +
 3 files changed, 35 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 83b4265..7462251 100644
--- a/README.md
+++ b/README.md
@@ -525,8 +525,9 @@ advanced in later stages of your work.
      respective files to remove and parts to fix are discussed here.
 
      - `paper.tex`: Delete the text of the abstract and the paper's main
-       body. Only keep a place holder text to later start writing your own
-       contents.
+       body, *except* the "Acknowledgements" section. This reproduction
+       pipeline was designed by funding from many grants, so its necessary
+       to acknowledge them in your final research.
 
      - `Makefile`: Delete the two lines containing `delete-me` in the
        `foreach` loops. Just make sure the other lines that end in `\` are
@@ -548,7 +549,7 @@ advanced in later stages of your work.
      commit to be sure it works as expected).
 
      ```shell
-     $ make clean            # Clean already built pipeline outputs.
+     $ make clean            # Delete outputs ('make distclean' for all outputs)
      $ make                  # Build the pipeline to ensure everything is fine.
      $ git add -u            # Stage all the changes.
      $ git status            # Make sure everything is fine.
diff --git a/paper.tex b/paper.tex
index 00264e0..0e50b1d 100644
--- a/paper.tex
+++ b/paper.tex
@@ -158,6 +158,36 @@ Zenodo (\url{https://zenodo.org}).
 
 
 
+\section{Acknowledgements}
+\new{Please include the following two paragraphs in the Acknowledgement
+  section of your paper. This reproduction pipeline was developed in
+  parallel with Gnuastro, so it benefited from the same grants. If you
+  don't use any of these packages in the final/customized pipeline, please
+  remove them. }
+
+This research was partly done using GNU Astronomy Utilities (Gnuastro,
+ascl.net/1801.009) version \gnuastroversion, and reproduction pipeline
+\pipelineversion. Work on Gnuastro and the reproduction pipeline has been
+funded by the Japanese Ministry of Education, Culture, Sports, Science, and
+Technology (MEXT) scholarship and its Grant-in-Aid for Scientific Research
+(21244012, 24253003), the European Research Council (ERC) advanced grant
+339659-MUSICOS, European Union’s Horizon 2020 research and innovation
+programme under Marie Sklodowska-Curie grant agreement No 721463 to the
+SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness
+(MINECO) under grant number AYA2016-76219-P.
+
+The following free software tools were also critical component of this
+research (in alphabetical order): {\small CFITSIO} \cfitsioversion, CMake
+\cmakeversion, Git \gitversion, \gnu{Bash} \bashversion, \gnu{Coreutils}
+\coreutilsversion, \gnu{{\small AWK}} \gawkversion, \gnu{Grep}
+\grepversion, \gnu{Libtool} \libtoolversion, \gnu{Make} \makeversion,
+\gnu{Sed} \sedversion, \gnu{Scientific Library} ({\small GSL}) \gslversion,
+    {\small GPL} Ghostscript \ghostscriptversion, Libgit2 \libgitwoversion,
+    Libtiff \libtiffversion, {{\small WCSLIB}} \wcslibversion, and ZLib
+    \zlibversion. We are very grateful to all their creators for freely
+    providing this necessary infrastructure. This research would not be
+    possible without them.
+
 %% Tell BibLaTeX to put the bibliography list here.
 \printbibliography
 
diff --git a/tex/preamble-necessary.tex b/tex/preamble-necessary.tex
index bef5a2f..329352a 100644
--- a/tex/preamble-necessary.tex
+++ b/tex/preamble-necessary.tex
@@ -11,6 +11,7 @@
 % Macros for to help in typing, remove them if you don't need them, but
 % this can help as a demo on how you can simply writing of commonly used
 % words that need special formatting (like software names).
+\newcommand{\gnu}[1]{{\small GNU} #1}
 \newcommand{\snsign}{{\small S}/{\small N}}
 \newcommand{\originsoft}{\textsf{ORIGIN}}
 \newcommand{\sextractor}{\textsf{SE\-xtractor}}
-- 
cgit v1.2.1