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.

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},
 }