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.

1 files changed, 159 insertions, 0 deletions

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.