From 313b936b502d22b6a2ff43f560dee0bb51fd01d0 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Mon, 15 Apr 2019 01:47:58 +0100 Subject: 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). --- tex/dependencies/astropy.tex | 97 ----------------------------------------- tex/dependencies/cython.tex | 21 --------- tex/dependencies/fftw.tex | 19 -------- tex/dependencies/gnuastro.tex | 24 ---------- tex/dependencies/matplotlib.tex | 22 ---------- tex/dependencies/mpi4py.tex | 20 --------- tex/dependencies/numpy.tex | 23 ---------- tex/dependencies/scipy.tex | 34 --------------- tex/src/delete-me-demo.tex | 4 +- tex/src/delete-me.tex | 2 +- tex/src/preamble-biblatex.tex | 2 +- tex/src/preamble-necessary.tex | 2 +- 12 files changed, 5 insertions(+), 265 deletions(-) delete mode 100644 tex/dependencies/astropy.tex delete mode 100644 tex/dependencies/cython.tex delete mode 100644 tex/dependencies/fftw.tex delete mode 100644 tex/dependencies/gnuastro.tex delete mode 100644 tex/dependencies/matplotlib.tex delete mode 100644 tex/dependencies/mpi4py.tex delete mode 100644 tex/dependencies/numpy.tex delete mode 100644 tex/dependencies/scipy.tex (limited to 'tex') diff --git a/tex/dependencies/astropy.tex b/tex/dependencies/astropy.tex deleted file mode 100644 index 450212d..0000000 --- a/tex/dependencies/astropy.tex +++ /dev/null @@ -1,97 +0,0 @@ -%% 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} -} diff --git a/tex/dependencies/cython.tex b/tex/dependencies/cython.tex deleted file mode 100644 index 110cb19..0000000 --- a/tex/dependencies/cython.tex +++ /dev/null @@ -1,21 +0,0 @@ -%% 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} -} diff --git a/tex/dependencies/fftw.tex b/tex/dependencies/fftw.tex deleted file mode 100644 index 60c24a8..0000000 --- a/tex/dependencies/fftw.tex +++ /dev/null @@ -1,19 +0,0 @@ -%% 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{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/tex/dependencies/gnuastro.tex b/tex/dependencies/gnuastro.tex deleted file mode 100644 index 91788c9..0000000 --- a/tex/dependencies/gnuastro.tex +++ /dev/null @@ -1,24 +0,0 @@ -%% 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} -} diff --git a/tex/dependencies/matplotlib.tex b/tex/dependencies/matplotlib.tex deleted file mode 100644 index 8578899..0000000 --- a/tex/dependencies/matplotlib.tex +++ /dev/null @@ -1,22 +0,0 @@ -%% 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 -} diff --git a/tex/dependencies/mpi4py.tex b/tex/dependencies/mpi4py.tex deleted file mode 100644 index 4e0045f..0000000 --- a/tex/dependencies/mpi4py.tex +++ /dev/null @@ -1,20 +0,0 @@ -%% 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} -} diff --git a/tex/dependencies/numpy.tex b/tex/dependencies/numpy.tex deleted file mode 100644 index 0d9028f..0000000 --- a/tex/dependencies/numpy.tex +++ /dev/null @@ -1,23 +0,0 @@ -%% 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} -} diff --git a/tex/dependencies/scipy.tex b/tex/dependencies/scipy.tex deleted file mode 100644 index 60500d2..0000000 --- a/tex/dependencies/scipy.tex +++ /dev/null @@ -1,34 +0,0 @@ -%% 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}, -} diff --git a/tex/src/delete-me-demo.tex b/tex/src/delete-me-demo.tex index abd45f6..67024bb 100644 --- a/tex/src/delete-me-demo.tex +++ b/tex/src/delete-me-demo.tex @@ -20,7 +20,7 @@ %% The displayed WFPC2 image. \node[anchor=south west] (img) at (0,0) {\includegraphics[width=0.5\linewidth] - {tex/pipeline/delete-me-demo/wfpc2.pdf}}; + {tex/build/delete-me-demo/wfpc2.pdf}}; %% Its label \node[anchor=south west] at (0.45\linewidth,0.45\linewidth) @@ -42,7 +42,7 @@ ] \addplot [const plot mark mid, fill=red] table [x index=0, y index=1] - {tex/pipeline/delete-me-demo/wfpc2-hist.txt} + {tex/build/delete-me-demo/wfpc2-hist.txt} \closedcycle; \end{axis} diff --git a/tex/src/delete-me.tex b/tex/src/delete-me.tex index 12fd3b7..552e92a 100644 --- a/tex/src/delete-me.tex +++ b/tex/src/delete-me.tex @@ -26,7 +26,7 @@ %% A particular plot. \addplot+[scatter, only marks] - table {tex/pipeline/delete-me/data.txt}; + table {tex/build/delete-me/data.txt}; \end{axis} \end{tikzpicture} diff --git a/tex/src/preamble-biblatex.tex b/tex/src/preamble-biblatex.tex index b4c02f9..ca54f90 100644 --- a/tex/src/preamble-biblatex.tex +++ b/tex/src/preamble-biblatex.tex @@ -56,7 +56,7 @@ \DeclareFieldFormat[article]{pages}{#1} \DeclareFieldFormat{pages}{\mkfirstpage[{\mkpageprefix[bookpagination]}]{#1}} \addbibresource{tex/src/references.tex} -\addbibresource{tex/pipeline/macros/dependencies-bib.tex} +\addbibresource{tex/build/macros/dependencies-bib.tex} \renewbibmacro{in:}{} \renewcommand*{\bibfont}{\footnotesize} \DefineBibliographyStrings{english}{references = {References}} diff --git a/tex/src/preamble-necessary.tex b/tex/src/preamble-necessary.tex index 2abcb9e..1deb8ec 100644 --- a/tex/src/preamble-necessary.tex +++ b/tex/src/preamble-necessary.tex @@ -24,7 +24,7 @@ %% Values from the analysis. -\input{tex/pipeline/macros/pipeline.tex} +\input{tex/build/macros/project.tex} -- cgit v1.2.1