Imported recent updates in Maneage, minor conflicts fixed

Some very minor conflicts came up and were easily corrected. They were
mostly in parts that are also shared with the demonstration in the core
Maneage branch.

1 files changed, 44 insertions, 41 deletions

diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 7998345..0a9e21e 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -16,24 +16,24 @@
 # --------------------------------------------------------------
 #
 # CLASS:BASIC (important identifier, don't modify this line)
-bash-version = 5.0.11
-binutils-version = 2.32
-coreutils-version = 8.31
-curl-version = 7.65.3
+bash-version = 5.0.18
+binutils-version = 2.35
+coreutils-version = 8.32
+curl-version = 7.71.1
 dash-version = 0.5.10.2
 diffutils-version = 3.7
-file-version = 5.36
+file-version = 5.39
 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
-git-version = 2.26.2
-gmp-version = 6.1.2
-grep-version = 3.3
+gawk-version = 5.1.0
+gcc-version = 10.2.0
+gettext-version = 0.21
+git-version = 2.28.0
+gmp-version = 6.2.0
+grep-version = 3.4
 gzip-version = 1.10
 isl-version = 0.18
-libbsd-version = 0.9.1
+libbsd-version = 0.10.0
 libiconv-version = 1.16
 libtool-version = 2.4.6
 libunistring-version = 0.9.10
@@ -44,18 +44,18 @@ make-version = 4.3
 metastore-version = 1.1.2-23-fa9170b
 mpc-version = 1.1.0
 mpfr-version = 4.0.2
-ncurses-version = 6.1
+ncurses-version = 6.2
 patchelf-version = 0.10
-perl-version = 5.30.0
+perl-version = 5.32.0
 pkgconfig-version = 0.29.2
 readline-version = 8.0
-sed-version = 4.7
+sed-version = 4.8
 tar-version = 1.32
-texinfo-version = 6.6
+texinfo-version = 6.7
 unzip-version = 6.0
 wget-version = 1.20.3
 which-version = 2.21
-xz-version = 5.2.4
+xz-version = 5.2.5
 zip-version = 3.0
 zlib-version = 1.2.11
 
@@ -83,35 +83,34 @@ bzip2-version = 1.0.6
 apachelog4cxx-version = 0.10.0-603-014954db
 apr-version = 1.7.0
 apr-util-version = 1.6.1
-astrometrynet-version = 0.77
+astrometrynet-version = 0.80
 atlas-version = 3.10.3
 autoconf-version = 2.69.200-babc
-automake-version = 1.16.1
-bison-version = 3.6
+automake-version = 1.16.2
+bison-version = 3.7
 boost-version = 1.73.0
 cairo-version = 1.16.0
 cdsclient-version = 3.84
-cfitsio-version = 3.47
-cmake-version = 3.17.0
+cfitsio-version = 3.48
+cmake-version = 3.18.1
 eigen-version = 3.3.7
 expat-version = 2.2.9
 fftw-version = 3.3.8
 flex-version = 2.6.4-91-ga631f5d
-freetype-version = 2.9
-gdb-version = 8.3
-ghostscript-version = 9.50
+freetype-version = 2.10.2
+gdb-version = 9.2
+ghostscript-version = 9.52
 ghostscript-fonts-gnu-version = 6.0
 ghostscript-fonts-std-version = 8.11
-gnuastro-version = 0.11
+gnuastro-version = 0.12
 gperf-version = 3.1
 gsl-version = 2.6
-hdf5-version = 1.10.5
 healpix-version = 3.50
 help2man-version = 1.47.11
 imagemagick-version = 7.0.8-67
 imfit-version = 1.6.1
 libffi-version = 3.2.1
-libidn-version = 1.35
+libidn-version = 1.36
 libjpeg-version = v9b
 libnsl-version = 1.2.0-4a062cf
 libpaper-version = 1.1.28
@@ -120,13 +119,13 @@ libtiff-version = 4.0.10
 libtirpc-version = 1.2.6
 missfits-version = 2.8.0
 openblas-version = 0.3.10
-openmpi-version = 4.0.1
+openmpi-version = 4.0.4
 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
+python-version = 3.8.5
+R-version = 4.0.2
 rpcsvc-proto-version = 1.4
 scamp-version = 2.6.7
 scons-version = 3.0.5
@@ -136,7 +135,7 @@ swig-version = 3.0.12
 tides-version = 2.0
 util-linux-version = 2.35
 xlsxio-version = 0.2.21
-yaml-version = 0.2.2
+yaml-version = 0.2.5
 
 # Xorg packages
 util-macros-version = 1.19.2
@@ -157,8 +156,8 @@ libpthread-stubs-version = 0.4
 # Version-dependent build
 # -----------------------
 lapack-version = 3.8.0
-libgit2-version = 0.28.2
-wcslib-version = 6.4
+libgit2-version = 1.0.1
+wcslib-version = 7.3
 
 # Netpbm's questions in the configure steps maybe change with different or
 # new versions.
@@ -177,6 +176,9 @@ openssl-version = 1.1.1a
 # any future release.
 valgrind-version = 3.15.0
 
+# Be careful with updateing hdf5 because h5py 2.10.0 doesn't work with
+# version 1.12.0.
+hdf5-version = 1.10.5
 
 
 
@@ -202,7 +204,7 @@ chardet-version = 3.0.4
 corner-version = 2.0.1
 cryptography-version = 2.6.1
 cycler-version = 0.10.0
-cython-version = 0.29.6
+cython-version = 0.29.21
 eigency-version = 1.77
 emcee-version = 3.0.1
 entrypoints-version = 0.3
@@ -210,7 +212,7 @@ esutil-version = 0.6.4
 flake8-version = 3.7.8
 future-version = 0.18.1
 galsim-version = 2.2.1
-h5py-version = 2.9.0
+h5py-version = 2.10.0
 html5lib-version = 1.0.1
 idna-version = 2.8
 jeepney-version = 0.4
@@ -218,22 +220,22 @@ keyring-version = 18.0.0
 kiwisolver-version = 1.0.1
 lmfit-version = 0.9.14
 lsstdesccoord-version = 1.2.0
-matplotlib-version = 3.1.1
-mpi4py-version = 3.0.2
+matplotlib-version = 3.3.0
+mpi4py-version = 3.0.3
 mpmath-version = 1.1.0
-numpy-version = 1.17.2
+numpy-version = 1.19.1
 pexpect-version = 4.7.0
 pip-version = 19.0.2
 pycodestyle-version = 2.5.0
 pycparser-version = 2.19
 pyflakes-version = 2.1.1
-pybind11-version = 2.4.3
+pybind11-version = 2.5.0
 pyparsing-version = 2.3.1
 pypkgconfig-version = 1.5.1
 python-dateutil-version = 2.8.0
 pyyaml-version = 5.1
 requests-version = 2.21.0
-scipy-version = 1.3.1
+scipy-version = 1.5.2
 secretstorage-version = 3.1.1
 setuptools-version = 41.6.0
 setuptools_scm-version = 3.3.3
@@ -249,3 +251,4 @@ webencodings-version = 0.5.1
 #
 # Healpy: When any Python module is requested, healpix will also build its
 #         Python module Healpy.
+healpy-version = xxxxx