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-rw-r--r--reproduce/software/config/checksums.conf12
-rwxr-xr-xreproduce/software/config/software_acknowledge_context.sh112
-rw-r--r--reproduce/software/config/urls.conf159
-rw-r--r--reproduce/software/config/versions.conf93
4 files changed, 327 insertions, 49 deletions
diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index e23df9f..2da488b 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -38,7 +38,7 @@ libiconv-checksum = 365dac0b34b4255a0066e8033a8b3db4bdb94b9b57a9dca17ebf2d779139
libtool-checksum = a6eef35f3cbccf2c9e2667f44a476ebc80ab888725eb768e91a3a6c33b8c931afc46eb23efaee76c8696d3e4eed74ab1c71157bcb924f38ee912c8a90a6521a4
libunistring-checksum = 01dcab6e05ea4c33572bf96cc0558bcffbfc0e62fc86410cef06c1597a0073d5750525fe2dee4fdb39c9bd704557fcbab864f9645958108a2e07950bc539fe54
libxml2-checksum = cb7784ba4e72e942614e12e4f83f4ceb275f3d738b30e3b5c1f25edf8e9fa6789e854685974eed95b362049dbf6c8e7357e0327d64c681ed390534ac154e6810
-lzip-checksum = e3331bbf0166541332182a9a28c2e08f522735ef668a06dfa26055251d5142a09227d97e6ae50b38c0b8805479a307a9e55c81b120d5befad2fde44676261843
+lzip-checksum = e2e229899002072322a5bf7fb7ef37ff7cc2d0ded7d6525679ac29cec5c1534de89f76bc01e15c3d76584099957d596b9e5b32d3f9cbfc6bc8d6370fc67d7d96
m4-checksum = a92cad4441b3fd7c033837389ca3499494523d364a5fda043d92c517051510f1758b3b837f0477f42d2258a179ab79a4993e5d1694ef2673db6d96d1faff84fe
make-checksum = ddf0fdcb9ee1b182ef294c5da70c1275288c99bef60e63a25c0abed2ddd44aba1770be4aab1db8cac81e5f624576f2127c5d825a1824e1c7a49df4f16445526b
metastore-checksum = b2a5fdde9de5ddc1e6c368d5da1b2e97e4fdbaa138a7be281ccb40a81dd4a9bb1849d36b2d5d3f01205079bace60441f82a7002097ff3a7037340a35b0f1574a
@@ -80,7 +80,7 @@ atlas-checksum = bf17306f09f2aa973cb776e2c9eacfb2409ad4d95d19802e1c4e0597d0a099f
autoconf-checksum = c25e834251bfc2befe822614caf1c80d7e1314a83e7173304abc235fd15a958b8db9fbc801e8ad98328dfd6d9dbc425bfbbefec500fa268992ae7bbf4fa5bc35
automake-checksum = 47b0120a59e3e020529a6ce750297d7de1156fd2be38db5d101e50120f11b40c28741ecd5eacf2790a9e25386713dcf7717339cfa5d7943d0dbf47c417383448
bison-checksum = 00d2b37187b93100ec4b220ce2752d12ccf68f9d0d39b380d375d36dd8a22aa1d6e60156918f95e4493f9531c5d42d8fad38fd807307b491c1ca7ca4177823d9
-boost-checksum = 4378e20f18db9f186ac0f38ad98c522526e0fe48a8deb968c41325e3f69e733be3298505e91ea713e79a9d9e741305fa879d289f74e6276e0ec7286f03be87fc
+boost-checksum = 2844dddd3357e76909f2f3d008f686949f8b54aed29e1c650e18becd0b50701a273bb3754f1a4e56c0c056693b27c354c9ba54ddbec92599e192c2f6736fe3be
cairo-checksum = 9eb27c4cf01c0b8b56f2e15e651f6d4e52c99d0005875546405b64f1132aed12fbf84727273f493d84056a13105e065009d89e94a8bfaf2be2649e232b82377f
cdsclient-checksum = 2d7abf0079189b9dd19cb8919061445fd19ea9f7dfd54e8ceee26b743218cf62ab00eba0147abe82d9294223927f04b4cc3328620dfc9184a7049f8d515b29e4
cfitsio-checksum = c0502699e266928dd25abe57730dc4b357ccc9023789fe745324ae01aa688516aceaf37321ee578f0430111d9718f0fec0dc5b54c07f935529560f00b32ce1e3
@@ -88,7 +88,7 @@ cmake-checksum = f09440681e0c414f5ca669f3aeba6666d09e0642f30a2e12c3199e7fb3da95a
eigen-checksum = 34cf600914cce719d61511577ef9cd26fbdcb7a6fad1d0ab8396f98b887fac6a5577d3967e84a8f56225cc50de38f3b91f34f447d14312028383e32b34ea1972
expat-checksum = 514ff2ef3c93af0b1715b7a08732db33c13a113c4c72422716a22ee26c09235deed71ec55510cee24c33bcd6b2347602bd71ce70a432d5583fb63765ff9e0e09
fftw-checksum = ab918b742a7c7dcb56390a0a0014f517a6dff9a2e4b4591060deeb2c652bf3c6868aa74559a422a276b853289b4b701bdcbd3d4d8c08943acf29167a7be81a38
-flex-checksum = e9785f3d620a204b7d20222888917dc065c2036cae28667065bf7862dfa1b25235095a12fd04efdbd09bfd17d3452e6b9ef953a8c1137862ff671c97132a082e
+flex-checksum = b4ef58d4a1d66b213e2f59df06959decf46d26b253cdc3f51cd26e2e2b505461ef23dafa974dd2005b1f0cafa5a83fe9258baf78004b2fdae6dfc299bc17bfd1
freetype-checksum = 02f0f4211f9cee5b5e46ebe61190482fca5b41bc26be06fcf0d2d717e9fb119229308398c420eeea476fa2511ca2d52948f1a3242efad30ca82ed0b07cd50e3a
gdb-checksum = b4161df5adfce3eb51b3b3fc6072b2ef9f612f5e0f95b25bc57382812854836e9d1b24807c68cc8987e37e90112c6d75ffc1de3ea67a9f92858b4ce1af85c479
ghostscript-checksum = acee64fae78771bffa19b0b2bfaba3c345b420f93ceb4fc9df5fb705f785c8ed720fde2aef53546fac6aca2f7366c64c68a6e373a71999a42dc71aadc9aa782f
@@ -104,15 +104,17 @@ libffi-checksum = 980ca30a8d76f963fca722432b1fe5af77d7a4e4d2eac5144fbc5374d4c596
libgit2-checksum = 0879c162e2e1dc00eadfbda22cd1f9d3a95b4ec2b653c108983f37c2f695140882de4d50d7cbc04ced247125a4e9fe6df16130e1267891aecdb2411d920db5c6
libjpeg-checksum = 74ea5af3545657d4ac03f8f7933913112cc2d982f0e379d0e5647f1acac21931468e53806297c30ebe180c7bcf84919a0ac20a4195afb03db03060d57904ef6c
libnsl-checksum = a3c8f674357674b7ed4b26c05adde607f39be8d6dc9ff715448e1fcc5fc23d11fbb4ce85a6e493b79bdb0bb450dc3ffb1fb480715779f738d7bc016fae91621d
+libpaper-checksum = 3bf6ebb0af89931d2f72ea4a09a7fa958b2facda5f238983ec7bac39652e08614b33f0de3af74a03457b2a4203eee4950bf18a4b726e79aa64093ace6a1fb0bc
libpng-checksum = 59e8c1059013497ae616a14c3abbe239322d3873c6ded0912403fc62fb260561768230b6ab997e2cccc3b868c09f539fd13635616b9fa0dd6279a3f63ec7e074
libtiff-checksum = d213e5db09fd56b8977b187c5a756f60d6e3e998be172550c2892dbdb4b2a8e8c750202bc863fe27d0d1c577ab9de1710d15e9f6ed665aadbfd857525a81eea8
-libtirpc-checksum = 392f391f9fc1bd68d81dc44e4058831a64b32790b5c8c37338b0ab416fad2ae4d16389e632596734dba09780347918cc65c6f134e0c1afd09e81ec250785ed23
+libtirpc-checksum = bcb6b5c062c1301aa1246ec93ae0a5c1d221b8421126d020863517cb814b43ed038fb6c0c2faf4e68ff133b69abefe4f4d42bfc870671da6c27ca941a30b155a
missfits-checksum = 32727f5eb30573a1cedacb8900e2536867e4815059eee32e64e3db65be9291b8a91b9f45b2c9f3cf6fc2a8cc448012ea3d502bdd9dee516008e17d5086aee795
netpbm-checksum = 064720f8a9d0a502488e1af4daecdbf3936910996507ca6f311073a0ad842346692a148eb1ddf7b717f7b108f60500246cb4b83f4d3665f5fc285a84ae1d63d6
-openblas-checksum = 91b3074eb922453bf843158b4281cde65db9e8bbdd7590e75e9e6cdcb486157f7973f2936f327bb3eb4f1702ce0ba51ae6729d8d4baf2d986c50771e8f696df0
+openblas-checksum = 64a5f983b2f6e02cdb6e0f14433498cc5daa1ccfb49246f7a2dcd38f9982fa608f2abea069fe0e35012af8c1441c43d1f6418eaccd40795f5002fed1c36ce05d
openmpi-checksum = 760716974cb6b25ad820184622e1ee7926bc6fda87db6b574f76792bc1ca99522e52195866c14b7cb2df5a4981efdaf9f71d2c5533cc0e8e45c2c4b3b74cbacc
openssh-checksum = e280fa2d56f550efd37c5d2477670326261aa8b94d991f9eb17aad90e0c6c9c939efa90fe87d33260d0f709485cb05c379f0fd1bd44fc0d5190298b6398c9982
patch-checksum = 75d4e1544484da12185418cd4a1571994398140a91ac606fa08dd067004187dad77d1413f0eb3319b3fe4df076714615c98b29df06af052bb65960fa8b0c86bf
+pcre-checksum = abac4c4f9df9e61d7d7761a9c50843882611752e1df0842a54318f358c28f5953025eba2d78997d21ee690756b56cc9f1c04a5ed591dd60654cc78ba16d9ecfb
pixman-checksum = 1b0205dbe9d9185c68813ce577a889f3c83e83fbd9955c3a72d411c3b476e6be93fc246b5b6ef4ee17e2bb8eb6fb5559e01dff7feb6a6c4c6314f980e960d690
python-checksum = c25a72ad792f7c1b4c2f79faebbe9608d04b04b2fe58ab804cb4732cdaa75ea93d175f5e52b38e91cb6ae0559ea6b645d802c8b6a869584e8bb9b5018367ce3d
R-checksum = 17513e9f4dd27c61c11f7aa45227aeeeefb375bf5d4e193b471724f379a1b2da33e127cbe91aa175cbbbb048b892047e2f610280585c8159242a6c94790b07f9
diff --git a/reproduce/software/config/software_acknowledge_context.sh b/reproduce/software/config/software_acknowledge_context.sh
new file mode 100755
index 0000000..b0ede85
--- /dev/null
+++ b/reproduce/software/config/software_acknowledge_context.sh
@@ -0,0 +1,112 @@
+#!/usr/bin/env sh
+
+# Surrounding text for software acknowledgement and citation. The list of
+# names, versions and citations of the software are written by an automatic
+# script. However, through this file, users have the option to specify the
+# text surrounding those lists.
+#
+# We recommend to leave these values untouched at first, after building
+# your PDF, you can see how they surround the list of software you used in
+# your project to make a smoothly readable English text. Afterwards, please
+# feel free to modify them as you wish.
+#
+# Copyright (C) 2020 Boud Roukema <boud@cosmo.torun.pl>
+# Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# This script 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 script 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.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+# WARNING:
+# In contrast to most configure files in maneage, this configure file is
+# technically a shell script, to be called by 'configure.sh', so the
+# variables defined here must follow 'shell' syntax, not 'make' syntax.
+
+# These variables will be exported to the 'configure.sh' script - so
+# descriptive, unique names should be used, to reduce the chance of
+# conflicts between identically named variables.
+
+# COMMENT:
+# Sentences have a tendancy to become very long. To avoid making the
+# variable values too long (and thus making this file hard to read), one
+# method is to break the sentence into smaller components and build the
+# full sentence gradually, similar to what we have done with 'str' in the
+# examples below. Each time, the value of 'str' is re-written by appending
+# its previous value with the rest of the sentence.
+
+# COMMENT:
+# As of 2020-06-10, the general issue of how to best cite software within
+# maneage, especially a full list of software in the Acknowledgments
+# section, remains wide open. See
+# https://savannah.nongnu.org/task/index.php?15318 for some technical
+# aspects of software citation.
+
+
+
+
+
+# Add your definitions of the LaTeX text here.
+#
+# To override a default but generate no text, use a string of non-zero
+# length such as "{}" that will have only minor effects in LaTeX.
+
+# An introduction to the software acknowledgement.
+thank_software_introduce=
+
+# The text to be used before listing C/C++ programs and libraries.
+thank_progs_libs=
+
+# The text to be used before listing Python modules.
+thank_python=
+
+# The text to be used before listing LaTeX packages.
+thank_latex=
+
+# Concluding remarks.
+thank_software_conclude=
+
+
+
+
+
+# Defaults
+# --------
+#
+# These are the default values which are only written into the variable if
+# you don't specify a value above
+if [ "x$thank_software_introduce" = "x" ]; then
+ thank_software_introduce=""
+fi
+
+if [ "x$thank_progs_libs" = "x" ]; then
+ str="This research was done with the following free software"
+ str="$str programs and libraries:"
+ thank_progs_libs="$str"
+fi
+
+if [ "x$thank_python" = "x" ]; then
+ thank_python="Within Python, the following modules were used:"
+fi
+
+if [ "x$thank_latex" = "x" ]; then
+ str="The \LaTeX{} source of the paper was compiled to make the"
+ str="$str PDF using the following packages:"
+ thank_latex="$str"
+fi
+
+if [ "x${thank_software_conclude}" = "x" ]; then
+ str="We are very grateful to all their creators for freely "
+ str="$str providing this necessary infrastructure. This research "
+ str="$str (and many other projects) would not be possible without "
+ str="$str them."
+ thank_software_conclude="$str"
+fi
diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf
new file mode 100644
index 0000000..dc5a9d8
--- /dev/null
+++ b/reproduce/software/config/urls.conf
@@ -0,0 +1,159 @@
+# Optional URLs of software to use for downloading their source
+#
+# If un-commented the URLs of this file will be used. Otherwise default
+# servers (primarily on 'zenodo.org') will be checked for the tarball.
+#
+# Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020 Raul Infante-Sainz <infantesainz@gmail.com>
+#
+# Copying and distribution of this file, with or without modification, are
+# permitted in any medium without royalty provided the copyright notice and
+# this notice are preserved. This file is offered as-is, without any
+# warranty.
+
+
+
+
+
+# Basic/low-level programs and libraires (installed in any case)
+# --------------------------------------------------------------
+#bash-url = http://akhlaghi.org/maneage-software
+#binutils-url = http://ftp.gnu.org/gnu/binutils
+#bzip2-url = http://akhlaghi.org/maneage-software
+#cert-url = http://akhlaghi.org/maneage-software
+#coreutils-url = http://ftp.gnu.org/gnu/coreutils
+#curl-url = https://curl.haxx.se/download
+#dash-url = http://akhlaghi.org/maneage-software
+#diffutils-url = http://ftp.gnu.org/gnu/diffutils
+#file-url = ftp://ftp.astron.com/pub/file
+#findutils-url = http://ftp.gnu.org/gnu/findutils
+#flock-url = http://akhlaghi.org/src
+#gawk-url = http://ftp.gnu.org/gnu/gawk
+#gcc-url = http://ftp.gnu.org/gnu/gcc/gcc-$(gcc-version)
+#gettext-url = https://ftp.gnu.org/gnu/gettext
+#git-url = http://mirrors.edge.kernel.org/pub/software/scm/git
+#gmp-url = https://gmplib.org/download/gmp
+#grep-url = http://ftp.gnu.org/gnu/grep
+#gzip-url = http://akhlaghi.org/src
+#isl-url = ftp://gcc.gnu.org/pub/gcc/infrastructure
+#libbsd-url = http://libbsd.freedesktop.org/releases
+#libiconv-url = https://ftp.gnu.org/pub/gnu/libiconv
+#libtool-url = http://ftp.gnu.org/gnu/libtool
+#libunistring-url = http://ftp.gnu.org/gnu/libunistring
+#libxml2-url = ftp://xmlsoft.org/libxml2
+#lzip-url = http://akhlaghi.org/src
+#m4-url = http://akhlaghi.org/maneage-software
+#make-url = http://akhlaghi.org/src
+#metastore-url = http://akhlaghi.org/maneage-software
+#mpc-url = http://ftp.gnu.org/gnu/mpc
+#mpfr-url = http://www.mpfr.org/mpfr-current
+#ncurses-url = http://ftp.gnu.org/gnu/ncurses
+#openssl-url = http://www.openssl.org/source
+#patchelf-url = http://nixos.org/releases/patchelf/patchelf-$(patchelf-version)
+#perl-url = $(shell echo https://www.cpan.org/src/$$(echo $(perl-version) | sed -e's/\./ /g' | awk '{printf("%d.0", $$1)}'))
+#pkgconfig-url = http://pkg-config.freedesktop.org/releases
+#readline-url = http://ftp.gnu.org/gnu/readline
+#sed-url = http://ftp.gnu.org/gnu/sed
+#tar-url = http://ftp.gnu.org/gnu/tar
+#texinfo-url = http://ftp.gnu.org/gnu/texinfo
+#unzip-url = $(shell echo ftp://ftp.info-zip.org/pub/infozip/src/unzip$$(echo $(unzip-version) | sed -e's/\.//').tgz)
+#wget-url = http://ftp.gnu.org/gnu/wget
+#which-url = http://ftp.gnu.org/gnu/which
+#xz-url = http://tukaani.org/xz
+#zip-url = $(shell echo ftp://ftp.info-zip.org/pub/infozip/src/zip$$(echo $(zip-version) | sed -e's/\.//').tgz)
+#zlib-url = http://www.zlib.net
+
+
+
+
+
+# Optional/high-level programs and libraries
+# ------------------------------------------
+#
+# These are programs and libraries that are optional, The ones in
+# `reproduce/software/config/TARGETS.conf' will be built as
+# part of a project. To specify a software there, just remove the
+# `-url' suffix from the list below.
+#apachelog4cxx-url = http://akhlaghi.org/maneage-software
+#apr-url = https://www-us.apache.org/dist/apr
+#apr-util-url = https://www-us.apache.org/dist/apr
+#astrometrynet-url = http://astrometry.net/downloads
+#atlas-url = https://sourceforge.net/projects/math-atlas/files/Stable/$(atlas-version)/atlas$(atlas-version).tar.bz2/download
+#autoconf-url = http://akhlaghi.org/maneage-software
+#automake-url = http://ftp.gnu.org/gnu/automake
+#bison-url = http://ftp.gnu.org/gnu/bison
+#boost-url = $(shell vstr=$$(echo $(boost-version) | sed -e's/\./_/g'); echo https://dl.bintray.com/boostorg/release/$(boost-version)/source)
+#cairo-url = https://www.cairographics.org/releases
+#cdsclient-url = http://cdsarc.u-strasbg.fr/ftp/pub/sw
+#cfitsio-url = https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c
+#cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv/cmake-$(cmake-version).tar.gz)
+#eigen-url = http://bitbucket.org/eigen/eigen/get/$(eigen-version).tar.gz
+#expat-url = $(shell vstr=$$(echo $(expat-version) | sed -e's/\./_/g'); echo https://github.com/libexpat/libexpat/releases/download/R_$$vstr/expat-$(expat-version).tar.lz)
+#fftw-url = ftp://ftp.fftw.org/pub/fftw
+#flex-url = https://github.com/westes/flex/files/981163
+#freetype-url = https://download.savannah.gnu.org/releases/freetype
+#gdb-url = http://ftp.gnu.org/gnu/gdb
+#ghostscript-url = $(shell v=$$(echo $(ghostscript-version) | sed -e's/\.//'); echo https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs$$v)
+#gnuastro-url = http://ftp.gnu.org/gnu/gnuastro
+#gsl-url = http://ftp.gnu.org/gnu/gsl
+#hdf5-url = $(shell majorver=$$(echo $(hdf5-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$$majorver/hdf5-$(hdf5-version)/src)
+#healpix-url = http://akhlaghi.org/maneage-software
+#help2man-url = http://ftp.gnu.org/gnu/help2man
+#imagemagick-url = http://akhlaghi.org/maneage-software
+#imfit-url = http://www.mpe.mpg.de/~erwin/resources/imfit
+#lapack-url = http://www.netlib.org/lapack
+#libffi-url = ftp://sourceware.org/pub/libffi
+#libgit2-url = https://github.com/libgit2/libgit2/archive
+#libjpeg-url = http://ijg.org/files
+#libnsl-url = http://akhlaghi.org/maneage-software
+#ibpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/
+#libpng-url = https://download.sourceforge.net/libpng
+#libtiff-url = https://download.osgeo.org/libtiff
+#libtirpc-url = https://downloads.sourceforge.net/libtirpc
+#minizip-url =
+#missfits-url = https://www.astromatic.net/download/missfits
+#netpbm-url = http://akhlaghi.org/maneage-software
+#openblas-url = https://github.com/xianyi/OpenBLAS/archive
+#openmpi-url = $(shell majorver=$$(echo $(openmpi-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://download.open-mpi.org/release/open-mpi/v$$majorver)
+#openssh-url = https://artfiles.org/openbsd/OpenSSH/portable
+#patch-url = http://ftp.gnu.org/gnu/patch
+#pixman-url = https://www.cairographics.org/releases
+#python-url = https://www.python.org/ftp/python/$(python-version)
+#R-url = $(shell majver=$$(echo $(R-version) | sed -e's/\./ /g' | awk '{print $$1}'); echo https://cran.r-project.org/src/base/R-$$majver)
+#rpcsvc-proto-url = https://github.com/thkukuk/rpcsvc-proto/releases/download
+#scamp-url = http://akhlaghi.org/maneage-software
+#scons-url = https://sourceforge.net/projects/scons/files/scons/$(scons-version)/scons-$(scons-version).tar.gz/download
+#sextractor-url = http://akhlaghi.org/maneage-software
+#swarp-url = https://www.astromatic.net/download/swarp
+#swig-url = https://sourceforge.net/projects/swig/files/swig/swig-$(swig-version)
+#tides-url = http://akhlaghi.org/maneage-software
+#valgrind-url = https://sourceware.org/pub/valgrind
+#wcslib-url = ftp://ftp.atnf.csiro.au/pub/software/wcslib
+#xlsxio-url = https://github.com/brechtsanders/xlsxio/archive
+#yaml-url = pyyaml.org/download/libyaml
+
+
+
+
+
+# Python packages
+# ---------------
+#
+# Similar to optional programs and libraries above.
+#
+# IMPORTANT: Python packages are usually distributed on servers like
+# 'https://pypi.org'. You can search for your package here and add the link
+# to the tarball here for your desired software. The links in PyPi don't
+# contain the names of the software, but only have hashes. So we aren't
+# including them by default here. But adding them is trivial for a certain
+# version. For example if you search "Numpy" and click on the "Download
+# files" menu, you can download the source '.zip' file. For version 1.18.5,
+# (with full filename of 'numpy-1.18.5.zip') the link will be like this.
+#
+# numpy-url = https://files.pythonhosted.org/packages/01/1b/d3ddcabd5817be02df0e6ee20d64f77ff6d0d97f83b77f65e98c8a651981/numpy-1.18.5.zip
+#
+# Hence, if the version changes, the checksum, and its two top host
+# directories also change. This is why we aren't putting any URL here by
+# default, if you need to add one, simply follow the numpy example above.
+# But be sure to send us a link to the tarball so we upload it to Maneage's
+# backup servers.
diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 1a4172a..b395e0f 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -14,6 +14,8 @@
# Basic/low-level programs and libraires (installed in any case)
# --------------------------------------------------------------
+#
+# CLASS:BASIC (important identifier, don't modify this line)
bash-version = 5.0.11
binutils-version = 2.32
coreutils-version = 8.31
@@ -22,6 +24,7 @@ dash-version = 0.5.10.2
diffutils-version = 3.7
file-version = 5.36
findutils-version = 4.7.0
+flock-version = 0.2.3
gawk-version = 5.0.1
gcc-version = 9.2.0
gettext-version = 0.20.2
@@ -35,8 +38,8 @@ libiconv-version = 1.16
libtool-version = 2.4.6
libunistring-version = 0.9.10
libxml2-version = 2.9.9
-lzip-version = 1.20
-m4-version = 1.4.18
+lzip-version = 1.22-rc2
+m4-version = 1.4.18-patched
make-version = 4.3
metastore-version = 1.1.2-23-fa9170b
mpc-version = 1.1.0
@@ -56,6 +59,14 @@ xz-version = 5.2.4
zip-version = 3.0
zlib-version = 1.2.11
+# Version-dependent build
+# -----------------------
+#
+# When updating the version of these programs/libraries, please look into
+# the build rule first: In one way or another, the version string becomes
+# necessary during their build and must be accounted for.
+bzip2-version = 1.0.6
+
@@ -67,6 +78,8 @@ zlib-version = 1.2.11
# `reproduce/software/config/TARGETS.conf' will be built as
# part of a project. To specify a software there, just remove the
# `-version' suffix from the list below.
+#
+# CLASS:HIGHLEVEL (important identifier, don't modify this line.)
apachelog4cxx-version = 0.10.0-603-014954db
apr-version = 1.7.0
apr-util-version = 1.6.1
@@ -75,7 +88,7 @@ atlas-version = 3.10.3
autoconf-version = 2.69.200-babc
automake-version = 1.16.1
bison-version = 3.4.2
-boost-version = 1.71.0
+boost-version = 1.73.0
cairo-version = 1.16.0
cdsclient-version = 3.84
cfitsio-version = 3.47
@@ -83,8 +96,7 @@ cmake-version = 3.17.0
eigen-version = 3.3.7
expat-version = 2.2.9
fftw-version = 3.3.8
-flex-version = 2.6.4
-flock-version = 0.2.3
+flex-version = 2.6.4-91-ga631f5d
freetype-version = 2.9
gdb-version = 8.3
ghostscript-version = 9.50
@@ -98,14 +110,16 @@ imfit-version = 1.6.1
libffi-version = 3.2.1
libjpeg-version = v9b
libnsl-version = 1.2.0-4a062cf
+libpaper-version = 1.1.28
libpng-version = 1.6.37
libtiff-version = 4.0.10
-libtirpc-version = 1.1.4
+libtirpc-version = 1.2.6
missfits-version = 2.8.0
-openblas-version = 0.3.5
+openblas-version = 0.3.10
openmpi-version = 4.0.1
openssh-version = 8.0p1
patch-version = 2.7.6
+pcre-version = 8.44
pixman-version = 0.38.0
python-version = 3.7.4
R-version = 3.6.2
@@ -119,6 +133,29 @@ tides-version = 2.0
xlsxio-version = 0.2.21
yaml-version = 0.2.2
+# Version-dependent build
+# -----------------------
+lapack-version = 3.8.0
+libgit2-version = 0.28.2
+wcslib-version = 6.4
+
+# Netpbm's questions in the configure steps maybe change with different or
+# new versions.
+netpbm-version = 10.86.99
+
+# Minizip is installed with the same `zlib' tarball, and they have the same
+# version.
+minizip-version = $(zlib-version)
+
+# From version 1.2 OpenSSL may not need a manual addition, as described in
+# its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't
+# cause problems, put it back in the list of "Basic/low-level" tools.
+openssl-version = 1.1.1a
+
+# Version 3.15.0 needs two patches, please check if they are necessary on
+# any future release.
+valgrind-version = 3.15.0
+
@@ -131,6 +168,8 @@ yaml-version = 0.2.2
# IMPORTANT: If you intend to change the version of any of the Python
# modules/libraries below, please fix the hash strings of the respective
# URL in `reproduce/software/make/python.mk'.
+#
+# CLASS:PYTHON (important identifier, don't modify this line.)
asn1crypto-version = 0.24.0
asteval-version = 0.9.16
astropy-version = 4.0
@@ -151,7 +190,6 @@ flake8-version = 3.7.8
future-version = 0.18.1
galsim-version = 2.2.1
h5py-version = 2.9.0
-healpy-version = installed-with-healpix
html5lib-version = 1.0.1
idna-version = 2.8
jeepney-version = 0.4
@@ -184,42 +222,9 @@ soupsieve-version = 1.8
sympy-version = 1.4
uncertainties-version = 3.1.2
urllib3-version = 1.24.1
-virtualenv-version = 16.4.0
webencodings-version = 0.5.1
-
-
-
-
-# Special programs and libraries
-# ------------------------------
-#
-# When updating the version of these libraries, please look into the build
-# rule first: In one way or another, the version string becomes necessary
-# during their build and must be accounted for.
+# Special Python modules:
#
-# Special notes:
-# - `netpbm' questions in the configure steps maybe change with different
-# or new versions.
-
-# Basic/low-level
-bzip2-version = 1.0.6
-
-# Optional/high-level
-lapack-version = 3.8.0
-libgit2-version = 0.28.2
-netpbm-version = 10.86.99
-wcslib-version = 6.4
-
-# Minizip is installed with the same `zlib' tarball, and they have the same
-# version.
-minizip-version = $(zlib-version)
-
-# From version 1.2 OpenSSL may not need a manual addition, as described in
-# its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't
-# cause problems, put it back in the list of "Basic/low-level" tools.
-openssl-version = 1.1.1a
-
-# Version 3.15.0 needs two patches, please check if they are necessary on
-# any future release.
-valgrind-version = 3.15.0
+# Healpy: When any Python module is requested, healpix will also build its
+# Python module Healpy.