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authorMohammad Akhlaghi <mohammad@akhlaghi.org>2022-08-05 20:27:56 +0200
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2022-08-13 22:36:13 +0200
commit79ee52ed1e136fbd2592a5c2a058f73024d8b5b0 (patch)
tree7bb96bf392f45a73cbfe56de75a840ccdfbeb0bd /reproduce/software/bibtex
parentaf723d9c5b36b7b5580d1a00ca9fbe8778237e7c (diff)
IMPORTANT: Software update
SUMMARY: This is a software update to make Maneage more portable and up to date. It does not involve any Maneage infrastructure changes. You should just re-build your project to make sure the updated software haven't removed/changed any of their features that you were using. In particular, for Astrometry.net users, please see the respective note in P.S.2 below. Until now, there have been many updates in the software that are built within Maneage. The last software upadte was almost one year ago. With this commit, the software in the P.S.1 have been updated. A description of notable changes in the software environment is given in P.S.2. This software environment has been tested on an Arch GNU/Linux, Debian, CentOS-7 and macOS. This commit is the merging of 24 individual commits by Raul Infante-Sainz (who put a lot of energy on porting the software below for macOS, and updating citations), Boudewijn Roukema (who helped with memory checking for GCC, and testing on Debian and CentOS), Sepideh Eskandarlou (who tested the environment) and myself. Besides the updates in the core software, the followimg improvements have also been implemented in this commit: - When you run './project shell': - A welcome message is printed that will remind the caller that they have entered a new environment, it will print the location of 'HOME' and the location of the shell startup file. - The 'reproduce/software/shell/bashrc.sh' is loaded as a startup file. This allows you to customize your interactive Maneage shell. A default step has already been placed there that will put the git branch name (in green) within the shell prompt (which was purple). This greatly helps when dealing with directories under Git version control. These settings won't bother with Maneage's default operations: through environment variables we make sure that these './project shell' features will not slow-down the calls to the shell within the non-interactive Make calls. - The host's 'COLORTERM' is passed to the Maneage environment. It is used by some programs that can have color outputs on the terminal. - Updates to citations: - Numpy and Scipy (as requested on their pages): https://numpy.org/citing-numpy and https://scipy.org/citing-scipy - Gnuastro: Added https://arxiv.org/abs/1909.11230 which describes major updates to Gnuastro after 10 releases. - When a software's paper is indexed in the SAO/NASA Astrophysics Data System (ADS), Maneage now use the BibTeX entries provided by ADS. This helps to give a unified format to most software, and more information (like ADS+arXiv hyperlinks in the BibLaTeX compilation of the default bibliography). - We were able to build this version of Maneage on a Debian system from 2010 (+12 years ago!). Only three downgrades were necessary in the "basic" software (not affecting the high-level science software!). A description of the necessary downgrades for such old systems has been added in 'README.md'. P.S.1 List of updated software: Basic software: cURL 7.79.1 --> 7.84.0 Dash 0.5.11.5 --> 0.5.11-057cd65 File 5.41 --> 5.42 GNU AWK 5.1.0 --> 5.1.1 GNU Bash 5.1.8 --> 5.2-rc2 GNU Binutils 2.37 --> 2.39 GNU Compiler Collection (GCC) 11.2.1 --> 12.1.0 GNU Findutils 4.8.0 --> 4.9.0 GNU Gzip 1.11 --> 1.12 GNU Help2man 1.48.5 --> 1.49.2 GNU Integer Set Library (ISL) 0.18 --> 0.24 GNU Libtool 2.4.6 --> 2.4.7 GNU Nano 6.0 --> 6.4 GNU Readline 8.1.1 --> 8.2-rc2 GNU libiconv 0.16 --> 0.17 Git 2.36.0 --> 2.37.1 OpenSSL 3.0.0 --> 3.0.5 PatchELF 0.13 --> 0.15.0 Perl 5.34.0 --> 5.36.0 High-level software: Astrometry.net 0.89 --> 0.91 CFITSIO 4.0.0 --> 4.1.0 CMake 3.21.4 --> 3.24.0 GNU Astronomy Utilities (Gnuastro) 0.16.1 --> 0.18 GPL Ghostscript 9.55.0 --> 9.56.1 HDF5 1.10.5 --> 1.13.1 Libjpeg 9d --> 9e Libtiff 4.3.0 --> 4.4.0 OpenBLAS 0.3.18 --> 0.3.21 PLplot n/a --> 5.15.0 Python 3.10.0 --> 3.10.6 SCAMP 2.6.7 --> 2.10.0 SWarp 2.38.0 --> 2.41.5 Util-Linux 2.37.2 --> 2.38.1 Vim 8.2 --> 9.0 WCSLIB 7.7 --> 7.11 X.org packages (used by graphical software like Ghostscript and LaTeX): Fontconfig 2.13.94 --> 2.14.0 LibX11 1.7.2 --> 1.8 LibXCB 1.14 --> 1.15 XCB-proto 1.14.1 --> 1.15 Xorg-proto 2021.5 --> 2022.1 Python modules: Astropy 5.0 --> 5.1 GalSim 2.3.3 --> 2.3.5 P.S.2: Notable points regarding the software environment: - Two new links from the host's low-level tools are now included in Maneage's build environment: - On GNU/Linux systems, the host's 'ldd' is linked inside the custom environment. This belongs to the GNU C Library (which is not yet installed in Maneage). But helps in checking the linking status of the binaries on GNU/Linux systems. - On macOS: the 'codesign' binary is included, which is used by GNU Emacs on macOS to sign the built executable. - GNU Bison has been moved in basic software (necessary for GNU Binutils). - The Zip and Unzip programs have been moved as high-level software that have to be manually requested when necessary. This is because they are not used by any of the basic software anymore. They were just installed as dependencies of GNU Tar to be close the other compression programs. Also, in the past we would use the original tarballs, and some (for example Numpy) were distributed in Zip format. However, by default, we now use a custom Lzip tarball and don't need Zip or Unzip. This was suggested by Zahra Sharbaf and Raul Infante-Sainz. - Some minor edits in 'reproduce/software/shell/tarball-prepare.sh'. In particular the 'awk' command was effectively just replacing a '_' with '-', so it just uses a simple SED expression instead. - Fixed bug 62700 (https://savannah.nongnu.org/bugs/index.php?62700) by compiling 'xz' with a patched version of the xz source file 'src/liblzma/liblzma.map'. - Astrometry.net doesn't depend on NetPBM any more. NetPBM (and its dependencies) were causing many crashes on macOS and it also a very strange build system that is hard to maintain. Astrometry.net uses it to take images as input. However, it isn't necessary when you provide Astrometry.net with a catalog. Therefore, Raul added some instructions on how to run astrometry from your own custom X-Y catalog. These instruction can be seen on top of the build rule of Astrometry.net in 'reproduce/software/make/high-level.mk'. - h5py has been removed as a dependency of Astropy. It is an optional dependency to write tables into HDF5 format. But since we couldn't get it to build on macOS it has been removed. None of the current Maneage users/developers also use this feature of Astropy! - PLplot is added a new software, but not a default pre-requisite of SCAMP (which can use it to generate figures), because there were many build problems on macOS. Instructions have been added on top of SCAMP on how to add PLplot as a dependency. - With the aim of being able to install Plplot on macOS, we have wrote several lines to fix header problems. However, we didn't succeed. In any case we are leaving these lines in case they are useful in the future. - The '-Wno-nullability-completeness' compiler flag (which is primarily necessary for macOS) is now only added for macOS systems. It was causing many warnings of un-recognized option in GNU/Linux systems. - The 'mkswap' program of Util-Linux has been disabled because it caused crashes on older kernels. Generally, its not necessary for a Maneage project because it needs root permissions to run! - LibXT (of the x.org software) has been added as a dependency of Cairo. - ImageMagick and Lzip were using the host's C++ standard library! But on GNU/Linux we build our own C++ Standard Library with GCC, so with this commit, they properly link with Maneage's C++ standard library. - ImageMagick on macOS couldn't properly link with Maneage's Ghostscript library! This has been fixed using macOS's install_name_tool. - Necessary RAM to build GCC on GNU/Linux systems changed to ~8GB, see https://savannah.nongnu.org/task/?16244#comment12 - Pythran is no longer as prerequisite of Scipy. Until now, Pythran was a prerequisite of Scipy. But we noticed that it is optional and was causing problems on macOS. - The URLs of some of the software have been updated in 'reproduce/software/config/urls.conf'. By default, these are all commented, but they can be useful when searching for new versions or when a project needs custom software that is not (yet) in Maneage.
Diffstat (limited to 'reproduce/software/bibtex')
-rw-r--r--reproduce/software/bibtex/astrometrynet.tex26
-rw-r--r--reproduce/software/bibtex/cython.tex23
-rw-r--r--reproduce/software/bibtex/fftw.tex2
-rw-r--r--reproduce/software/bibtex/gnuastro.tex31
-rw-r--r--reproduce/software/bibtex/healpix.tex9
-rw-r--r--reproduce/software/bibtex/imfit.tex31
-rw-r--r--reproduce/software/bibtex/matplotlib.tex23
-rw-r--r--reproduce/software/bibtex/mpi4py.tex22
-rw-r--r--reproduce/software/bibtex/numpy.tex31
-rw-r--r--reproduce/software/bibtex/scipy.tex41
-rw-r--r--reproduce/software/bibtex/sextractor.tex6
-rw-r--r--reproduce/software/bibtex/tides.tex2
12 files changed, 122 insertions, 125 deletions
diff --git a/reproduce/software/bibtex/astrometrynet.tex b/reproduce/software/bibtex/astrometrynet.tex
index 26d211b..3bedfc3 100644
--- a/reproduce/software/bibtex/astrometrynet.tex
+++ b/reproduce/software/bibtex/astrometrynet.tex
@@ -6,15 +6,19 @@
%% without any warranty.
@ARTICLE{astrometrynet,
- doi = {10.1088/0004-6256/139/5/1782},
- url = {https://doi.org/10.1088%2F0004-6256%2F139%2F5%2F1782},
- year = 2010,
- month = {mar},
- publisher = {{IOP} Publishing},
- volume = {139},
- number = {5},
- pages = {1782},
- author = {Dustin Lang and David W. Hogg and Keir Mierle and Michael Blanton and Sam Roweis},
- title = {{ASTROMETRY}.{NET}: {BLIND} {ASTROMETRIC} {CALIBRATION} {OF} {ARBITRARY} {ASTRONOMICAL} {IMAGES}},
- journal = {AJ}
+ author = {{Lang}, Dustin and {Hogg}, David W. and {Mierle}, Keir and {Blanton}, Michael and {Roweis}, Sam},
+ title = "{Astrometry.net: Blind Astrometric Calibration of Arbitrary Astronomical Images}",
+ journal = {AJ},
+ keywords = {astrometry, catalogs, instrumentation: miscellaneous, methods: data analysis, methods: statistical, techniques: image processing, Astrophysics - Instrumentation and Methods for Astrophysics},
+ year = 2010,
+ month = may,
+ volume = {139},
+ number = {5},
+ pages = {1782-1800},
+ doi = {10.1088/0004-6256/139/5/1782},
+archivePrefix = {arXiv},
+ eprint = {0910.2233},
+ primaryClass = {astro-ph.IM},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2010AJ....139.1782L},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
diff --git a/reproduce/software/bibtex/cython.tex b/reproduce/software/bibtex/cython.tex
index 30a0713..a7df8d5 100644
--- a/reproduce/software/bibtex/cython.tex
+++ b/reproduce/software/bibtex/cython.tex
@@ -6,16 +6,15 @@
%% 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://ui.adsabs.harvard.edu/abs/2011CSE....13b..31B},
- adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+ author = {{Behnel}, Stefan and {Bradshaw}, Robert and {Citro}, Craig and {Dalcin}, Lisandro and {Seljebotn}, Dag Sverre and {Smith}, Kurt},
+ title = "{Cython: The Best of Both Worlds}",
+ journal = {Computing in Science and Engineering},
+ year = 2011,
+ month = mar,
+ volume = {13},
+ number = {2},
+ pages = {31-39},
+ doi = {10.1109/MCSE.2010.118},
+ adsurl = {https://ui.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
index 1186efa..1bca7c2 100644
--- a/reproduce/software/bibtex/fftw.tex
+++ b/reproduce/software/bibtex/fftw.tex
@@ -12,7 +12,7 @@
year = {2005},
volume = {93},
number = {2},
- pages = {216},
+ pages = {216-231},
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
index 018a35b..20efc19 100644
--- a/reproduce/software/bibtex/gnuastro.tex
+++ b/reproduce/software/bibtex/gnuastro.tex
@@ -6,19 +6,20 @@
%% 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://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A},
- adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+ author = {{Akhlaghi}, Mohammad and {Ichikawa}, Takashi},
+ title = "{Noise-based Detection and Segmentation of Nebulous Objects}",
+ journal = {ApJS},
+ keywords = {galaxies: irregular, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies},
+ year = 2015,
+ month = sep,
+ volume = {220},
+ number = {1},
+ eid = {1},
+ pages = {1},
+ doi = {10.1088/0067-0049/220/1/1},
+archivePrefix = {arXiv},
+ eprint = {1505.01664},
+ primaryClass = {astro-ph.IM},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
diff --git a/reproduce/software/bibtex/healpix.tex b/reproduce/software/bibtex/healpix.tex
index 77471c5..2860f72 100644
--- a/reproduce/software/bibtex/healpix.tex
+++ b/reproduce/software/bibtex/healpix.tex
@@ -6,16 +6,15 @@
%% without any warranty.
@ARTICLE{healpix,
- author = {{G{\'o}rski}, K.~M. and {Hivon}, E. and {Banday}, A.~J. and {Wand
- elt}, B.~D. and {Hansen}, F.~K. and {Reinecke}, M. and {Bartelmann}, M.},
+ author = {{G{\'o}rski}, K.~M. and {Hivon}, E. and {Banday}, A.~J. and {Wandelt}, B.~D. and {Hansen}, F.~K. and {Reinecke}, M. and {Bartelmann}, M.},
title = "{HEALPix: A Framework for High-Resolution Discretization and Fast Analysis of Data Distributed on the Sphere}",
journal = {ApJ},
keywords = {Cosmology: Cosmic Microwave Background, Cosmology: Observations, Methods: Statistical, Astrophysics},
- year = "2005",
- month = "Apr",
+ year = 2005,
+ month = apr,
volume = {622},
number = {2},
- pages = {759},
+ pages = {759-771},
doi = {10.1086/427976},
archivePrefix = {arXiv},
eprint = {astro-ph/0409513},
diff --git a/reproduce/software/bibtex/imfit.tex b/reproduce/software/bibtex/imfit.tex
index 167586d..39301a1 100644
--- a/reproduce/software/bibtex/imfit.tex
+++ b/reproduce/software/bibtex/imfit.tex
@@ -6,19 +6,20 @@
%% without any warranty.
@ARTICLE{imfit2015,
- author = {{Erwin}, P.},
- title = "{IMFIT: A Fast, Flexible New Program for Astronomical Image Fitting}",
- journal = {ApJ},
-archivePrefix = "arXiv",
- eprint = {1408.1097},
- primaryClass = "astro-ph.IM",
- keywords = {galaxies: bulges, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric },
- year = 2015,
- month = feb,
- volume = 799,
- eid = {226},
- pages = {226},
- doi = {10.1088/0004-637X/799/2/226},
- adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJ...799..226E},
- adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+ author = {{Erwin}, Peter},
+ title = "{IMFIT: A Fast, Flexible New Program for Astronomical Image Fitting}",
+ journal = {ApJ},
+ keywords = {galaxies: bulges, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies},
+ year = 2015,
+ month = feb,
+ volume = {799},
+ number = {2},
+ eid = {226},
+ pages = {226},
+ doi = {10.1088/0004-637X/799/2/226},
+archivePrefix = {arXiv},
+ eprint = {1408.1097},
+ primaryClass = {astro-ph.IM},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJ...799..226E},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
diff --git a/reproduce/software/bibtex/matplotlib.tex b/reproduce/software/bibtex/matplotlib.tex
index aab2c04..7c2eace 100644
--- a/reproduce/software/bibtex/matplotlib.tex
+++ b/reproduce/software/bibtex/matplotlib.tex
@@ -5,14 +5,17 @@
%% 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},
- publisher = {IEEE COMPUTER SOC},
- doi = {10.1109/MCSE.2007.55},
- year = 2007
+@ARTICLE{matplotlib2007,
+ author = {{Hunter}, John D.},
+ title = "{Matplotlib: A 2D Graphics Environment}",
+ journal = {CiSE},
+ keywords = {Python, Scripting languages, Application development, Scientific programming},
+ year = 2007,
+ month = may,
+ volume = {9},
+ number = {3},
+ pages = {90-95},
+ doi = {10.1109/MCSE.2007.55},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2007CSE.....9...90H},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
diff --git a/reproduce/software/bibtex/mpi4py.tex b/reproduce/software/bibtex/mpi4py.tex
index 598bbda..b8c7b3f 100644
--- a/reproduce/software/bibtex/mpi4py.tex
+++ b/reproduce/software/bibtex/mpi4py.tex
@@ -6,15 +6,15 @@
%% 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 = {AdvWatRes},
- year = 2011,
- month = sep,
- volume = 34,
- pages = {1124},
- doi = {10.1016/j.advwatres.2011.04.013},
- adsurl = {http://ui.adsabs.harvard.edu/abs/2011AdWR...34.1124D},
- adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+ author = {{Dalcin}, Lisandro D. and {Paz}, Rodrigo R. and {Kler}, Pablo A. and {Cosimo}, Alejandro},
+ title = "{Parallel distributed computing using Python}",
+ journal = {Advances in Water Resources},
+ year = 2011,
+ month = sep,
+ volume = {34},
+ number = {9},
+ pages = {1124-1139},
+ doi = {10.1016/j.advwatres.2011.04.013},
+ adsurl = {https://ui.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
index 0dee489..58622da 100644
--- a/reproduce/software/bibtex/numpy.tex
+++ b/reproduce/software/bibtex/numpy.tex
@@ -5,19 +5,20 @@
%% 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://ui.adsabs.harvard.edu/abs/2011CSE....13b..22V},
- adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+@ARTICLE{numpy2020,
+ author = {{Harris}, Charles R. and {Millman}, K. Jarrod and {van der Walt}, St{\'e}fan J. and {Gommers}, Ralf and {Virtanen}, Pauli and {Cournapeau}, David and {Wieser}, Eric and {Taylor}, Julian and {Berg}, Sebastian and {Smith}, Nathaniel J. and {Kern}, Robert and {Picus}, Matti and {Hoyer}, Stephan and {van Kerkwijk}, Marten H. and {Brett}, Matthew and {Haldane}, Allan and {del R{\'\i}o}, Jaime Fern{\'a}ndez and {Wiebe}, Mark and {Peterson}, Pearu and {G{\'e}rard-Marchant}, Pierre and {Sheppard}, Kevin and {Reddy}, Tyler and {Weckesser}, Warren and {Abbasi}, Hameer and {Gohlke}, Christoph and {Oliphant}, Travis E.},
+ title = "{Array programming with NumPy}",
+ journal = {Nature},
+ keywords = {Computer Science - Mathematical Software, Statistics - Computation},
+ year = 2020,
+ month = sep,
+ volume = {585},
+ number = {7825},
+ pages = {357-362},
+ doi = {10.1038/s41586-020-2649-2},
+archivePrefix = {arXiv},
+ eprint = {2006.10256},
+ primaryClass = {cs.MS},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2020Natur.585..357H},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
diff --git a/reproduce/software/bibtex/scipy.tex b/reproduce/software/bibtex/scipy.tex
index 4b1292d..8db9fd6 100644
--- a/reproduce/software/bibtex/scipy.tex
+++ b/reproduce/software/bibtex/scipy.tex
@@ -5,30 +5,19 @@
%% 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},
+@ARTICLE{scipy2020,
+ author = {{Virtanen}, Pauli and {Gommers}, Ralf and {Oliphant}, Travis E. and {Haberland}, Matt and {Reddy}, Tyler and {Cournapeau}, David and {Burovski}, Evgeni and {Peterson}, Pearu and {Weckesser}, Warren and {Bright}, Jonathan and {van der Walt}, St{\'e}fan J. and {Brett}, Matthew and {Wilson}, Joshua and {Millman}, K. Jarrod and {Mayorov}, Nikolay and {Nelson}, Andrew R.~J. and {Jones}, Eric and {Kern}, Robert and {Larson}, Eric and {Carey}, C.~J. and {Polat}, {\.I}lhan and {Feng}, Yu and {Moore}, Eric W. and {VanderPlas}, Jake and {Laxalde}, Denis and {Perktold}, Josef and {Cimrman}, Robert and {Henriksen}, Ian and {Quintero}, E.~A. and {Harris}, Charles R. and {Archibald}, Anne M. and {Ribeiro}, Ant{\^o}nio H. and {Pedregosa}, Fabian and {van Mulbregt}, Paul and {SciPy 1. 0 Contributors}},
+ title = "{SciPy 1.0: fundamental algorithms for scientific computing in Python}",
+ journal = {Nature Methods},
+ keywords = {Computer Science - Mathematical Software, Computer Science - Data Structures and Algorithms, Computer Science - Software Engineering, Physics - Computational Physics},
+ year = 2020,
+ month = feb,
+ volume = {17},
+ pages = {261-272},
+ doi = {10.1038/s41592-019-0686-2},
+archivePrefix = {arXiv},
+ eprint = {1907.10121},
+ primaryClass = {cs.MS},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2020NatMe..17..261V},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
diff --git a/reproduce/software/bibtex/sextractor.tex b/reproduce/software/bibtex/sextractor.tex
index 8905be8..8dbfb48 100644
--- a/reproduce/software/bibtex/sextractor.tex
+++ b/reproduce/software/bibtex/sextractor.tex
@@ -11,10 +11,10 @@
title = "{SExtractor: Software for source extraction.}",
journal = {A\&AS},
keywords = {METHODS: DATA ANALYSIS, TECHNIQUES: IMAGE PROCESSING, GALAXIES: PHOTOMETRY},
- year = "1996",
- month = "Jun",
+ year = 1996,
+ month = jun,
volume = {117},
- pages = {393},
+ pages = {393-404},
doi = {10.1051/aas:1996164},
adsurl = {https://ui.adsabs.harvard.edu/abs/1996A&AS..117..393B},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
diff --git a/reproduce/software/bibtex/tides.tex b/reproduce/software/bibtex/tides.tex
index b97762a..4e69b1a 100644
--- a/reproduce/software/bibtex/tides.tex
+++ b/reproduce/software/bibtex/tides.tex
@@ -13,7 +13,7 @@
month = nov,
volume = 39,
eid = {5},
- pages = {5:1},
+ pages = {1-28},
doi = {10.1145/2382585.2382590},
keywords = {Taylor series method, automatic differentiation, high precision, numerical integration of ODEs, variational equations},
}