Dependency BibTeX entries included only when necessary

Until now, there was a single `tex/src/references.tex' file that housed the
BibTex entries for everything (software and non-software).

Since we have started to include the BibTeX entry for more software, it
will be hard to manage the large (sometime unused) BibTeX entries of the
software in the middle of the non-software related citations in the text of
the paper.

Therefore, with this commit, a `tex/dependencies' directory has been made
which has a separate BibTeX entry file for each software that needs
one. After the software is built, this file is copied to the new
`.local/version-info/cite' directory. At the end, the configure script will
concatenate all the files in this directory into one file which will later
be used with `tex/src/references.tex' by BibLaTeX.

This greatly simplifies managing of citations. Allowing us to focus on the
software-building and paper-writing citations separately/cleanly (and thus
be more efficient in both).

2 files changed, 9 insertions, 250 deletions

diff --git a/tex/src/preamble-biblatex.tex b/tex/src/preamble-biblatex.tex
index 6358fb1..602c5a1 100644
--- a/tex/src/preamble-biblatex.tex
+++ b/tex/src/preamble-biblatex.tex
@@ -48,7 +48,7 @@
     url=false,
     dashed=false,
     eprint=false,
-    maxbibnames=4,
+    maxbibnames=2,
     minbibnames=1,
     hyperref=true,
     maxcitenames=2,
@@ -59,6 +59,7 @@
 \DeclareFieldFormat[article]{pages}{#1}
 \DeclareFieldFormat{pages}{\mkfirstpage[{\mkpageprefix[bookpagination]}]{#1}}
 \addbibresource{tex/src/references.tex}
+\addbibresource{tex/pipeline/macros/dependencies-bib.tex}
 \renewbibmacro{in:}{}
 \renewcommand*{\bibfont}{\footnotesize}
 \DefineBibliographyStrings{english}{references = {References}}
diff --git a/tex/src/references.tex b/tex/src/references.tex
index 641089e..de4682f 100644
--- a/tex/src/references.tex
+++ b/tex/src/references.tex
@@ -1,84 +1,12 @@
-%% References used in the template paper.
+%% Copyright (C) 2018-2019, Mohammad Akhlaghi.
 %
-%% Original author:
-%%     Mohammad Akhlaghi <mohammad@akhlaghi.org>
-%% Contributing author(s):
-%%     Your name <your@email.address>
-%% Copyright (C) 2018-2019, Your Name.
+%% Non-software BibTeX entries. The software-specific BibTeX entries are
+%% stored in a `*.tex' file under the `tex/dependencies' directory.
 %
-%% This template 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 3 of the License, or (at your
-%% option) any later version.
-%
-%% This template 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 Template.  If not, see <https://www.gnu.org/licenses/>.
-
-@ARTICLE{astropy2018,
-   author = {{Astropy Collaboration} and {Price-Whelan}, A.~M. and {Sip{\H o}cz}, B.~M. and
-	{G{\"u}nther}, H.~M. and {Lim}, P.~L. and {Crawford}, S.~M. and
-	{Conseil}, S. and {Shupe}, D.~L. and {Craig}, M.~W. and {Dencheva}, N. and
-	{Ginsburg}, A. and {VanderPlas}, J.~T. and {Bradley}, L.~D. and
-	{P{\'e}rez-Su{\'a}rez}, D. and {de Val-Borro}, M. and {Aldcroft}, T.~L. and
-	{Cruz}, K.~L. and {Robitaille}, T.~P. and {Tollerud}, E.~J. and
-	{Ardelean}, C. and {Babej}, T. and {Bach}, Y.~P. and {Bachetti}, M. and
-	{Bakanov}, A.~V. and {Bamford}, S.~P. and {Barentsen}, G. and
-	{Barmby}, P. and {Baumbach}, A. and {Berry}, K.~L. and {Biscani}, F. and
-	{Boquien}, M. and {Bostroem}, K.~A. and {Bouma}, L.~G. and {Brammer}, G.~B. and
-	{Bray}, E.~M. and {Breytenbach}, H. and {Buddelmeijer}, H. and
-	{Burke}, D.~J. and {Calderone}, G. and {Cano Rodr{\'{\i}}guez}, J.~L. and
-	{Cara}, M. and {Cardoso}, J.~V.~M. and {Cheedella}, S. and {Copin}, Y. and
-	{Corrales}, L. and {Crichton}, D. and {D'Avella}, D. and {Deil}, C. and
-	{Depagne}, {\'E}. and {Dietrich}, J.~P. and {Donath}, A. and
-	{Droettboom}, M. and {Earl}, N. and {Erben}, T. and {Fabbro}, S. and
-	{Ferreira}, L.~A. and {Finethy}, T. and {Fox}, R.~T. and {Garrison}, L.~H. and
-	{Gibbons}, S.~L.~J. and {Goldstein}, D.~A. and {Gommers}, R. and
-	{Greco}, J.~P. and {Greenfield}, P. and {Groener}, A.~M. and
-	{Grollier}, F. and {Hagen}, A. and {Hirst}, P. and {Homeier}, D. and
-	{Horton}, A.~J. and {Hosseinzadeh}, G. and {Hu}, L. and {Hunkeler}, J.~S. and
-	{Ivezi{\'c}}, {\v Z}. and {Jain}, A. and {Jenness}, T. and {Kanarek}, G. and
-	{Kendrew}, S. and {Kern}, N.~S. and {Kerzendorf}, W.~E. and
-	{Khvalko}, A. and {King}, J. and {Kirkby}, D. and {Kulkarni}, A.~M. and
-	{Kumar}, A. and {Lee}, A. and {Lenz}, D. and {Littlefair}, S.~P. and
-	{Ma}, Z. and {Macleod}, D.~M. and {Mastropietro}, M. and {McCully}, C. and
-	{Montagnac}, S. and {Morris}, B.~M. and {Mueller}, M. and {Mumford}, S.~J. and
-	{Muna}, D. and {Murphy}, N.~A. and {Nelson}, S. and {Nguyen}, G.~H. and
-	{Ninan}, J.~P. and {N{\"o}the}, M. and {Ogaz}, S. and {Oh}, S. and
-	{Parejko}, J.~K. and {Parley}, N. and {Pascual}, S. and {Patil}, R. and
-	{Patil}, A.~A. and {Plunkett}, A.~L. and {Prochaska}, J.~X. and
-	{Rastogi}, T. and {Reddy Janga}, V. and {Sabater}, J. and {Sakurikar}, P. and
-	{Seifert}, M. and {Sherbert}, L.~E. and {Sherwood-Taylor}, H. and
-	{Shih}, A.~Y. and {Sick}, J. and {Silbiger}, M.~T. and {Singanamalla}, S. and
-	{Singer}, L.~P. and {Sladen}, P.~H. and {Sooley}, K.~A. and
-	{Sornarajah}, S. and {Streicher}, O. and {Teuben}, P. and {Thomas}, S.~W. and
-	{Tremblay}, G.~R. and {Turner}, J.~E.~H. and {Terr{\'o}n}, V. and
-	{van Kerkwijk}, M.~H. and {de la Vega}, A. and {Watkins}, L.~L. and
-	{Weaver}, B.~A. and {Whitmore}, J.~B. and {Woillez}, J. and
-	{Zabalza}, V. and {Astropy Contributors}},
-    title = "{The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package}",
-  journal = {AJ},
-archivePrefix = "arXiv",
-   eprint = {1801.02634},
- primaryClass = "astro-ph.IM",
- keywords = {methods: data analysis, methods: miscellaneous, methods: statistical, reference systems },
-     year = 2018,
-    month = sep,
-   volume = 156,
-      eid = {123},
-    pages = {123},
-      doi = {10.3847/1538-3881/aabc4f},
-   adsurl = {http://adsabs.harvard.edu/abs/2018AJ....156..123A},
-  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
-
-
-
-
+%% Copying and distribution of this file, with or without modification,
+%% are permitted in any medium without royalty provided the copyright
+%% notice and this notice are preserved.  This file is offered as-is,
+%% without any warranty.
 
 @ARTICLE{bacon17,
    author = {{Bacon}, R. and {Conseil}, S. and {Mary}, D. and {Brinchmann}, J. and
@@ -103,173 +31,3 @@ archivePrefix = "arXiv",
    adsurl = {http://adsabs.harvard.edu/abs/2017A\%26A...608A...1B},
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
-
-
-
-
-
-@ARTICLE{gnuastro,
-   author = {{Akhlaghi}, M. and {Ichikawa}, T.},
-    title = "{Noise-based Detection and Segmentation of Nebulous Objects}",
-  journal = {ApJS},
-archivePrefix = "arXiv",
-   eprint = {1505.01664},
- primaryClass = "astro-ph.IM",
- keywords = {galaxies: irregular, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric},
-     year = 2015,
-    month = sep,
-   volume = 220,
-      eid = {1},
-    pages = {1},
-      doi = {10.1088/0067-0049/220/1/1},
-   adsurl = {http://adsabs.harvard.edu/abs/2015ApJS..220....1A},
-  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
-
-
-
-
-
-@ARTICLE{astropy2013,
-   author = {{Astropy Collaboration} and {Robitaille}, T.~P. and {Tollerud}, E.~J. and
-	{Greenfield}, P. and {Droettboom}, M. and {Bray}, E. and {Aldcroft}, T. and
-	{Davis}, M. and {Ginsburg}, A. and {Price-Whelan}, A.~M. and
-	{Kerzendorf}, W.~E. and {Conley}, A. and {Crighton}, N. and
-	{Barbary}, K. and {Muna}, D. and {Ferguson}, H. and {Grollier}, F. and
-	{Parikh}, M.~M. and {Nair}, P.~H. and {Unther}, H.~M. and {Deil}, C. and
-	{Woillez}, J. and {Conseil}, S. and {Kramer}, R. and {Turner}, J.~E.~H. and
-	{Singer}, L. and {Fox}, R. and {Weaver}, B.~A. and {Zabalza}, V. and
-	{Edwards}, Z.~I. and {Azalee Bostroem}, K. and {Burke}, D.~J. and
-	{Casey}, A.~R. and {Crawford}, S.~M. and {Dencheva}, N. and
-	{Ely}, J. and {Jenness}, T. and {Labrie}, K. and {Lim}, P.~L. and
-	{Pierfederici}, F. and {Pontzen}, A. and {Ptak}, A. and {Refsdal}, B. and
-	{Servillat}, M. and {Streicher}, O.},
-    title = "{Astropy: A community Python package for astronomy}",
-  journal = {A\&A},
-archivePrefix = "arXiv",
-   eprint = {1307.6212},
- primaryClass = "astro-ph.IM",
- keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools},
-     year = 2013,
-    month = oct,
-   volume = 558,
-      eid = {A33},
-    pages = {A33},
-      doi = {10.1051/0004-6361/201322068},
-   adsurl = {http://adsabs.harvard.edu/abs/2013A\%26A...558A..33A},
-  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
-
-
-
-
-
-@ARTICLE{cython2011,
-   author = {{Behnel}, S. and {Bradshaw}, R. and {Citro}, C. and {Dalcin}, L. and
-	{Seljebotn}, D.~S. and {Smith}, K.},
-    title = "{Cython: The Best of Both Worlds}",
-  journal = {CiSE},
-     year = 2011,
-    month = mar,
-   volume = 13,
-   number = 2,
-    pages = {31},
-      doi = {10.1109/MCSE.2010.118},
-   adsurl = {http://adsabs.harvard.edu/abs/2011CSE....13b..31B},
-  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
-
-
-
-
-
-@ARTICLE{mpi4py2011,
-   author = {{Dalcin}, L.~D. and {Paz}, R.~R. and {Kler}, P.~A. and {Cosimo}, A.
-	},
-    title = "{Parallel distributed computing using Python}",
-  journal = {Advances in Water Resources},
-     year = 2011,
-    month = sep,
-   volume = 34,
-    pages = {1124},
-      doi = {10.1016/j.advwatres.2011.04.013},
-   adsurl = {http://adsabs.harvard.edu/abs/2011AdWR...34.1124D},
-  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
-
-
-
-
-
-@ARTICLE{scipy2011,
-author={K. J. {Millman} and M. {Aivazis}},
-journal={CiSE},
-title={Python for Scientists and Engineers},
-year={2011},
-volume={13},
-number={2},
-pages={9},
-keywords={Special issues and sections;Computer languages;Programming;Scientific computing;Numerical models;Programming languages;Python;Scientific computing;interactive research;Python libraries;Python tools},
-doi={10.1109/MCSE.2011.36},
-ISSN={1521-9615},
-month={March},
-}
-
-
-
-
-
-@ARTICLE{numpy2011,
-   author = {{van der Walt}, S. and {Colbert}, S.~C. and {Varoquaux}, G.},
-    title = "{The NumPy Array: A Structure for Efficient Numerical Computation}",
-  journal = {CiSE},
-archivePrefix = "arXiv",
-   eprint = {1102.1523},
- primaryClass = "cs.MS",
-     year = 2011,
-    month = mar,
-   volume = 13,
-   number = 2,
-    pages = {22},
-      doi = {10.1109/MCSE.2011.37},
-   adsurl = {http://adsabs.harvard.edu/abs/2011CSE....13b..22V},
-  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
-
-
-
-
-
-@Article{matplotlib2007,
-  Author    = {Hunter, J. D.},
-  Title     = {Matplotlib: A 2D graphics environment},
-  Journal   = {CiSE},
-  Volume    = {9},
-  Number    = {3},
-  Pages     = {90},
-  abstract  = {Matplotlib is a 2D graphics package used for Python
-  for application development, interactive scripting, and
-  publication-quality image generation across user
-  interfaces and operating systems.},
-  publisher = {IEEE COMPUTER SOC},
-  doi       = {10.1109/MCSE.2007.55},
-  year      = 2007
-}
-
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-
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-@ARTICLE{scipy2007,
-author={T. E. {Oliphant}},
-journal={CiSE},
-title={Python for Scientific Computing},
-year={2007},
-volume={9},
-number={3},
-pages={10},
-keywords={high level languages;Python;scientific computing;steering language;scientific codes;high-level language;Scientific computing;High level languages;Libraries;Writing;Application software;Embedded software;Software standards;Standards development;Internet;Prototypes;Python;computer languages;scientific programming;scientific computing},
-doi={10.1109/MCSE.2007.58},
-ISSN={1521-9615},
-month={May},
-}