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).

13 files changed, 291 insertions, 261 deletions

diff --git a/.file-metadata b/.file-metadata
index 0607790..9ca5bd6 100644
--- a/.file-metadata
+++ b/.file-metadata
diff --git a/configure b/configure
index 6760d0b..74c014d 100755
--- a/configure
+++ b/configure
@@ -650,6 +650,9 @@ if ! [ -d $ilidir ]; then mkdir $ilidir; fi
 ipydir=$verdir/python
 if ! [ -d $ipydir ]; then mkdir $ipydir; fi
 
+ictdir=$verdir/cite
+if ! [ -d $ictdir ]; then mkdir $ictdir; fi
+
 itidir=$verdir/tex
 if ! [ -d $itidir ]; then mkdir $itidir; fi
 
@@ -1019,7 +1022,11 @@ fi
 
 
 
-# Put all the names and versions in a human-readable paragraph.
+# Citation of installed software
+#
+# After everything is installed, we'll put all the names and versions in a
+# human-readable paragraph and also prepare the BibTeX citation for the
+# software.
 function prepare_name_version() {
 
     # First see if the (possible) `*' in the input arguments corresponds to
@@ -1065,7 +1072,7 @@ texpkg=$(prepare_name_version $verdir/tex/texlive)
 pkgver=$mtexdir/dependencies.tex
 .local/bin/echo "This research was done with the following free" > $pkgver
 .local/bin/echo "software programs and libraries: $proglibs."   >> $pkgver
-if [ x$pymodules != x ]; then
+if [ x"$pymodules" != x ]; then
     .local/bin/echo "Within Python, the following modules"      >> $pkgver
     echo "were used: $pymodules."                               >> $pkgver
 fi
@@ -1076,6 +1083,23 @@ fi
 .local/bin/echo "infrastructure. This research (and many "      >> $pkgver
 .local/bin/echo "others) would not be possible without them."   >> $pkgver
 
+# Prepare the BibTeX entries for the used software (if there are any).
+hasentry=0
+bibfiles="$ictdir/*"
+for f in $bibfiles; do if [ -f $f ]; then hasentry=1; break; fi; done;
+
+# Make sure we start with an empty file.
+pkgbib=$mtexdir/dependencies-bib.tex
+echo "" > $pkgbib
+
+# Fill it in with all the BibTeX entries in this directory. We'll just
+# avoid writing any comments (usually copyright notices) and also put an
+# empty line after each file's contents to make the output more readable.
+if [ $hasentry = 1 ]; then
+    for f in $bibfiles; do
+        awk '!/^%/{print} END{print ""}' $f >> $pkgbib
+    done
+fi
 
 
 
diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk
index 11c6b1f..7ccf6b3 100644
--- a/reproduce/src/make/dependencies-python.mk
+++ b/reproduce/src/make/dependencies-python.mk
@@ -295,10 +295,8 @@ $(ipydir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \
                    $(ipydir)/h5py                            \
                    $(ipydir)/numpy                           \
                    $(ipydir)/scipy
-        # Since we have two citations in Astropy (with the `,' character
-        # which can be confused in Make), its easier to just re-write the
-        # full version after the build.
 	$(call pybuild, tar xf, $<, astropy-$(astropy-version)) \
+	&& cp $(dtexdir)/astropy.tex $(ictdir)/                 \
 	&& echo "Astropy $(astropy-version) \citep{astropy2013,astropy2018}" > $@
 
 $(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.gz \
@@ -336,6 +334,7 @@ $(ipydir)/cycler: $(tdir)/cycler-$(cycler-version).tar.gz \
 $(ipydir)/cython: $(tdir)/cython-$(cython-version).tar.gz \
                   $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, Cython-$(cython-version)) \
+	&& cp $(dtexdir)/cython.tex $(ictdir)/                \
 	&& echo "Cython $(cython-version) \citep{cython2011}" > $@
 
 $(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \
@@ -389,7 +388,8 @@ $(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz   \
                       $(ipydir)/numpy                                   \
                       $(ipydir)/pyparsing                               \
                       $(ipydir)/python-dateutil
-	$(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version))       \
+	$(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version)) \
+	&& cp $(dtexdir)/matplotlib.tex $(ictdir)/                    \
 	&& echo "Matplotlib $(matplotlib-version) \citep{matplotlib2007}" > $@
 
 # Currently mpi4py doesn't build because of some conflict with OpenMPI:
@@ -404,7 +404,8 @@ $(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz   \
 $(ipydir)/mpi4py: $(tdir)/mpi4py-$(mpi4py-version).tar.gz    \
                   $(ipydir)/setuptools                       \
                   $(ilidir)/openmpi
-	$(call pybuild, tar xf, $<, mpi4py-$(mpi4py-version))    \
+	$(call pybuild, tar xf, $<, mpi4py-$(mpi4py-version)) \
+	&& cp $(dtexdir)/mpi4py.tex $(ictdir)/                \
 	&& echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@
 
 $(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
@@ -420,6 +421,7 @@ $(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
 	conf="$$(pwd)/reproduce/config/pipeline/dependency-numpy-scipy.cfg"; \
 	$(call pybuild, unzip, $<, numpy-$(numpy-version),$$conf,            \
 	                Numpy $(numpy-version))                              \
+	&& cp $(dtexdir)/numpy.tex $(ictdir)/                                \
 	&& echo "Numpy $(numpy-version) \citep{numpy2011}" > $@
 
 $(ibidir)/pip3: $(tdir)/pip-$(pip-version).tar.gz \
@@ -465,7 +467,8 @@ $(ipydir)/scipy: $(tdir)/scipy-$(scipy-version).tar.gz \
 	  export LDFLAGS="$(LDFLAGS) -shared";                               \
 	fi;                                                                  \
 	conf="$$(pwd)/reproduce/config/pipeline/dependency-numpy-scipy.cfg"; \
-	$(call pybuild, tar xf, $<, scipy-$(scipy-version),$$conf)           \
+	$(call pybuild, tar xf, $<, scipy-$(scipy-version),$$conf)           \
+	&& cp $(dtexdir)/scipy.tex $(ictdir)/                                \
 	&& echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@
 
 $(ipydir)/secretstorage: $(tdir)/secretstorage-$(secretstorage-version).tar.gz \
diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk
index ae1daa7..67ce490 100644
--- a/reproduce/src/make/dependencies.mk
+++ b/reproduce/src/make/dependencies.mk
@@ -37,6 +37,7 @@ include reproduce/config/pipeline/dependency-versions.mk
 
 lockdir = $(BDIR)/locks
 ddir    = $(BDIR)/dependencies
+dtexdir = $(shell pwd)/tex/dependencies
 tdir    = $(BDIR)/dependencies/tarballs
 idir    = $(BDIR)/dependencies/installed
 ibdir   = $(BDIR)/dependencies/installed/bin
@@ -44,6 +45,7 @@ ildir   = $(BDIR)/dependencies/installed/lib
 ibidir  = $(BDIR)/dependencies/installed/version-info/bin
 ilidir  = $(BDIR)/dependencies/installed/version-info/lib
 itidir  = $(BDIR)/dependencies/installed/version-info/tex
+ictdir  = $(BDIR)/dependencies/installed/version-info/cite
 ipydir  = $(BDIR)/dependencies/installed/version-info/python
 
 # Define the top-level programs to build (installed in `.local/bin').
@@ -604,9 +606,10 @@ $(ibidir)/gnuastro: $(tdir)/gnuastro-$(gnuastro-version).tar.lz \
 ifeq ($(static_build),yes)
 	staticopts="--enable-static=yes --enable-shared=no";
 endif
-	$(call gbuild, $<, gnuastro-$(gnuastro-version), static,     \
-	               $$staticopts, -j$(numthreads),                \
-	               make check -j$(numthreads))                   \
+	$(call gbuild, $<, gnuastro-$(gnuastro-version), static, \
+	               $$staticopts, -j$(numthreads),            \
+	               make check -j$(numthreads))               \
+	&& cp $(dtexdir)/gnuastro.tex $(ictdir)/                 \
 	&& echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@
 
 $(ibidir)/unzip: $(tdir)/unzip-$(unzip-version).tar.gz
diff --git a/tex/dependencies/astropy.tex b/tex/dependencies/astropy.tex
new file mode 100644
index 0000000..f77799e
--- /dev/null
+++ b/tex/dependencies/astropy.tex
@@ -0,0 +1,97 @@
+%% Copyright (C) 2019, Mohammad Akhlaghi.
+%%
+%% 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{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}
+}
+
+
+
+
+
+@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}
+}
\ No newline at end of file
diff --git a/tex/dependencies/cython.tex b/tex/dependencies/cython.tex
new file mode 100644
index 0000000..de30273
--- /dev/null
+++ b/tex/dependencies/cython.tex
@@ -0,0 +1,21 @@
+%% Copyright (C) 2019, Raul Infante-Sainz.
+%%
+%% 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{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}
+}
\ No newline at end of file
diff --git a/tex/dependencies/gnuastro.tex b/tex/dependencies/gnuastro.tex
new file mode 100644
index 0000000..6195145
--- /dev/null
+++ b/tex/dependencies/gnuastro.tex
@@ -0,0 +1,24 @@
+%% Copyright (C) 2019, Mohammad Akhlaghi.
+%%
+%% 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{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}
+}
\ No newline at end of file
diff --git a/tex/dependencies/matplotlib.tex b/tex/dependencies/matplotlib.tex
new file mode 100644
index 0000000..630ebc9
--- /dev/null
+++ b/tex/dependencies/matplotlib.tex
@@ -0,0 +1,22 @@
+%% Copyright (C) 2019, Raul Infante-Sainz.
+%%
+%% 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{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
+}
\ No newline at end of file
diff --git a/tex/dependencies/mpi4py.tex b/tex/dependencies/mpi4py.tex
new file mode 100644
index 0000000..e238c78
--- /dev/null
+++ b/tex/dependencies/mpi4py.tex
@@ -0,0 +1,20 @@
+%% Copyright (C) 2019, Raul Infante-Sainz.
+%%
+%% 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{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}
+}
\ No newline at end of file
diff --git a/tex/dependencies/numpy.tex b/tex/dependencies/numpy.tex
new file mode 100644
index 0000000..fb54b8f
--- /dev/null
+++ b/tex/dependencies/numpy.tex
@@ -0,0 +1,23 @@
+%% Copyright (C) 2019, Raul Infante-Sainz.
+%%
+%% 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{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}
+}
\ No newline at end of file
diff --git a/tex/dependencies/scipy.tex b/tex/dependencies/scipy.tex
new file mode 100644
index 0000000..4527a7c
--- /dev/null
+++ b/tex/dependencies/scipy.tex
@@ -0,0 +1,34 @@
+%% Copyright (C) 2019, Raul Infante-Sainz.
+%%
+%% 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{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{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},
+}
\ No newline at end of file
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
-}
-
-
-
-
-
-@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},
-}