diff options
| -rw-r--r-- | .file-metadata | bin | 4780 -> 5403 bytes | |||
| -rwxr-xr-x | configure | 28 | ||||
| -rw-r--r-- | reproduce/src/make/dependencies-python.mk | 15 | ||||
| -rw-r--r-- | reproduce/src/make/dependencies.mk | 9 | ||||
| -rw-r--r-- | tex/dependencies/astropy.tex | 97 | ||||
| -rw-r--r-- | tex/dependencies/cython.tex | 21 | ||||
| -rw-r--r-- | tex/dependencies/gnuastro.tex | 24 | ||||
| -rw-r--r-- | tex/dependencies/matplotlib.tex | 22 | ||||
| -rw-r--r-- | tex/dependencies/mpi4py.tex | 20 | ||||
| -rw-r--r-- | tex/dependencies/numpy.tex | 23 | ||||
| -rw-r--r-- | tex/dependencies/scipy.tex | 34 | ||||
| -rw-r--r-- | tex/src/preamble-biblatex.tex | 3 | ||||
| -rw-r--r-- | tex/src/references.tex | 256 |
13 files changed, 291 insertions, 261 deletions
diff --git a/.file-metadata b/.file-metadata Binary files differindex 0607790..9ca5bd6 100644 --- a/.file-metadata +++ b/.file-metadata @@ -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}, -} |