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-rw-r--r--.file-metadatabin4780 -> 5403 bytes
-rwxr-xr-xconfigure28
-rw-r--r--reproduce/src/make/dependencies-python.mk15
-rw-r--r--reproduce/src/make/dependencies.mk9
-rw-r--r--tex/dependencies/astropy.tex97
-rw-r--r--tex/dependencies/cython.tex21
-rw-r--r--tex/dependencies/gnuastro.tex24
-rw-r--r--tex/dependencies/matplotlib.tex22
-rw-r--r--tex/dependencies/mpi4py.tex20
-rw-r--r--tex/dependencies/numpy.tex23
-rw-r--r--tex/dependencies/scipy.tex34
-rw-r--r--tex/src/preamble-biblatex.tex3
-rw-r--r--tex/src/references.tex256
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
Binary files differ
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},
-}