New architecture to separate software-building and analysis steps

Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.

Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.

Also, some of the software versions were also updated after some checks
with their webpages.

This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).

8 files changed, 260 insertions, 0 deletions

diff --git a/reproduce/software/bibtex/astropy.tex b/reproduce/software/bibtex/astropy.tex
new file mode 100644
index 0000000..450212d
--- /dev/null
+++ b/reproduce/software/bibtex/astropy.tex
@@ -0,0 +1,97 @@
+%% Copyright (C) 2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%%
+%% 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}
+}
diff --git a/reproduce/software/bibtex/cython.tex b/reproduce/software/bibtex/cython.tex
new file mode 100644
index 0000000..110cb19
--- /dev/null
+++ b/reproduce/software/bibtex/cython.tex
@@ -0,0 +1,21 @@
+%% Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
+%%
+%% 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}
+}
diff --git a/reproduce/software/bibtex/fftw.tex b/reproduce/software/bibtex/fftw.tex
new file mode 100644
index 0000000..60c24a8
--- /dev/null
+++ b/reproduce/software/bibtex/fftw.tex
@@ -0,0 +1,19 @@
+%% Copyright (C) 2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%%
+%% 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{fftw,
+   author = {M. {Frigo} and S. G. {Johnson}},
+  journal = {IEEE Proc.},
+    title = {The Design and Implementation of FFTW3},
+     year = {2005},
+   volume = {93},
+   number = {2},
+    pages = {216},
+      doi = {10.1109/JPROC.2004.840301},
+     ISSN = {0018-9219},
+    month = {Feb},
+}
diff --git a/reproduce/software/bibtex/gnuastro.tex b/reproduce/software/bibtex/gnuastro.tex
new file mode 100644
index 0000000..91788c9
--- /dev/null
+++ b/reproduce/software/bibtex/gnuastro.tex
@@ -0,0 +1,24 @@
+%% Copyright (C) 2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%%
+%% 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}
+}
diff --git a/reproduce/software/bibtex/matplotlib.tex b/reproduce/software/bibtex/matplotlib.tex
new file mode 100644
index 0000000..8578899
--- /dev/null
+++ b/reproduce/software/bibtex/matplotlib.tex
@@ -0,0 +1,22 @@
+%% Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
+%%
+%% 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
+}
diff --git a/reproduce/software/bibtex/mpi4py.tex b/reproduce/software/bibtex/mpi4py.tex
new file mode 100644
index 0000000..4e0045f
--- /dev/null
+++ b/reproduce/software/bibtex/mpi4py.tex
@@ -0,0 +1,20 @@
+%% Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
+%%
+%% 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}
+}
diff --git a/reproduce/software/bibtex/numpy.tex b/reproduce/software/bibtex/numpy.tex
new file mode 100644
index 0000000..0d9028f
--- /dev/null
+++ b/reproduce/software/bibtex/numpy.tex
@@ -0,0 +1,23 @@
+%% Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
+%%
+%% 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}
+}
diff --git a/reproduce/software/bibtex/scipy.tex b/reproduce/software/bibtex/scipy.tex
new file mode 100644
index 0000000..60500d2
--- /dev/null
+++ b/reproduce/software/bibtex/scipy.tex
@@ -0,0 +1,34 @@
+%% Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
+%%
+%% 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},
+}