Imported recent work in master, minor conflict fixed in paper.mk

Only two conflicts came up in the newly added comments of 'paper.mk' in the
Maneage branch. It happened because in this project we don't use
'pdflatex', but 'latex' alone.

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.