Imported recent updates in Maneage, conflicts fixed

Until now, Maneage had undergone some updates.

With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.

In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).

1 files changed, 198 insertions, 109 deletions

diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 102ebbd..34d074c 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -1,7 +1,8 @@
 # Versions of the various dependencies
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C)      2022 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
@@ -15,47 +16,47 @@
 # Basic/low-level programs and libraires (installed in any case)
 # --------------------------------------------------------------
 #
-# CLASS:BASIC (important identifier, don't modify this line)
-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 = 5.39
-findutils-version = 4.7.0
-flock-version = 0.2.3
+# CLASS:BASIC (important identifier for 'awk'; don't modify this line)
+bash-version = 5.1.8
+binutils-version = 2.37
+coreutils-version = 9.1
+curl-version = 7.79.1
+dash-version = 0.5.11.5
+diffutils-version = 3.8
+file-version = 5.41
+findutils-version = 4.8.0
+flock-version = 0.4.0
 gawk-version = 5.1.0
-gcc-version = 10.2.0
+gcc-version = 11.2.0
 gettext-version = 0.21
-git-version = 2.28.0
-gmp-version = 6.2.0
-grep-version = 3.4
-gzip-version = 1.10
+git-version = 2.36.0
+gmp-version = 6.2.1
+grep-version = 3.7
+gzip-version = 1.11
 isl-version = 0.18
-less-version = 563
-libbsd-version = 0.10.0
+less-version = 590
 libiconv-version = 1.16
 libtool-version = 2.4.6
-libunistring-version = 0.9.10
-libxml2-version = 2.9.9
-lzip-version = 1.22-rc2
-m4-version = 1.4.18-patched
+libunistring-version = 1.0
+libxml2-version = 2.9.12
+lzip-version = 1.22
+m4-version = 1.4.19
 make-version = 4.3
-metastore-version = 1.1.2-23-fa9170b
-mpc-version = 1.1.0
-mpfr-version = 4.0.2
-nano-version = 5.2
-ncurses-version = 6.2
-patchelf-version = 0.10
-perl-version = 5.32.0
+mpc-version = 1.2.1
+mpfr-version = 4.1.0
+nano-version = 6.0
+ncurses-version = 6.3
+openssl-version = 3.0.0
+patchelf-version = 0.13
+perl-version = 5.34.0
 pkgconfig-version = 0.29.2
-readline-version = 8.0
+podlators-version = 4.14
+readline-version = 8.1.1
 sed-version = 4.8
-tar-version = 1.32
-texinfo-version = 6.7
+tar-version = 1.34
+texinfo-version = 6.8
 unzip-version = 6.0
-wget-version = 1.20.3
+wget-version = 1.21.2
 which-version = 2.21
 xz-version = 5.2.5
 zip-version = 3.0
@@ -67,7 +68,16 @@ zlib-version = 1.2.11
 # 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
+bzip2-version = 1.0.8
+
+# PEM Certificate File
+# --------------------
+#
+# This file should be shipped with operating systems and can be found in
+# '/etc/ssl/cert.pem' (which may be a symbolic link to its actual
+# location). The current version was taken from an up-to-date ArchLinux at
+# the date that is also equal to the version.
+certpem-version = 2021-10-15
 
 
 
@@ -77,108 +87,104 @@ bzip2-version = 1.0.6
 # ------------------------------------------
 #
 # These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/TARGETS.conf' will be built as
+# '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.
+# '-version' suffix from the list below.
 #
-# CLASS:HIGHLEVEL (important identifier, don't modify this line.)
-apachelog4cxx-version = 0.10.0-603-014954db
+# CLASS:HIGHLEVEL (important identifier for 'awk'; don't modify this line)
+apachelog4cxx-version = 0.12.1
 apr-version = 1.7.0
 apr-util-version = 1.6.1
-astrometrynet-version = 0.80
+astrometrynet-version = 0.85
 atlas-version = 3.10.3
-autoconf-version = 2.69.200-babc
-automake-version = 1.16.2
-bison-version = 3.7
-boost-version = 1.73.0
+autoconf-version = 2.71
+automake-version = 1.16.5
+bison-version = 3.8.2
+boost-version = 1.77.0
 cairo-version = 1.16.0
 cdsclient-version = 3.84
-cfitsio-version = 3.48
-cmake-version = 3.18.1
-eigen-version = 3.3.7
-emacs-version = 27.1
-expat-version = 2.2.9
-fftw-version = 3.3.8
-flex-version = 2.6.4-91-ga631f5d
-freetype-version = 2.10.2
-gdb-version = 9.2
-ghostscript-version = 9.52
+cfitsio-version = 4.0.0
+cmake-version = 3.21.4
+eigen-version = 3.4.0
+emacs-version = 28.1
+expat-version = 2.4.1
+fftw-version = 3.3.10
+flex-version = 2.6.4
+freetype-version = 2.11.0
+gdb-version = 11.1
+ghostscript-version = 9.55.0
 ghostscript-fonts-gnu-version = 6.0
 ghostscript-fonts-std-version = 8.11
-gnuastro-version = 0.12
+gnuastro-version = 0.16.1-e0f1
 gperf-version = 3.1
-gsl-version = 2.6
-healpix-version = 3.50
-help2man-version = 1.47.11
-imagemagick-version = 7.0.8-67
+gsl-version = 2.7
+help2man-version = 1.48.5
+icu-version = 70.1
+imagemagick-version = 7.1.0-13
 imfit-version = 1.6.1
-libffi-version = 3.2.1
-libidn-version = 1.36
-libjpeg-version = v9b
+libbsd-version = 0.11.3
+libffi-version = 3.4.2
+libidn-version = 1.38
+libjpeg-version = 9d
+libmd-version = 1.0.4
 libnsl-version = 1.2.0-4a062cf
 libpaper-version = 1.1.28
 libpng-version = 1.6.37
-libtiff-version = 4.0.10
+libtiff-version = 4.3.0
 libtirpc-version = 1.2.6
+metastore-version = 1.1.2-23-fa9170b
 missfits-version = 2.8.0
-openblas-version = 0.3.10
-openmpi-version = 4.0.4
+openblas-version = 0.3.18
+openmpi-version = 4.1.1
 openssh-version = 8.0p1
 patch-version = 2.7.6
 pcre-version = 8.44
-pixman-version = 0.38.0
-python-version = 3.8.5
-R-version = 4.0.2
+pixman-version = 0.40.0
+python-version = 3.10.0
+r-cran-version = 4.1.2
 rpcsvc-proto-version = 1.4
 scamp-version = 2.6.7
 scons-version = 3.0.5
 sextractor-version = 2.25.0
 swarp-version = 2.38.0
-swig-version = 3.0.12
+swig-version = 4.0.2
 tides-version = 2.0
-util-linux-version = 2.35
+util-linux-version = 2.37.2
+valgrind-version = 3.18.1
 vim-version = 8.2
 xlsxio-version = 0.2.21
 yaml-version = 0.2.5
 
 # Xorg packages
-util-macros-version = 1.19.2
-xorgproto-version = 2020.1
+util-macros-version = 1.19.3
+xorgproto-version = 2021.5
 libxau-version = 1.0.9
 libxdmcp-version = 1.1.3
-xcb-proto-version = 1.14
+xcb-proto-version = 1.14.1
 libxcb-version = 1.14
-fontconfig-version = 2.13.1
+fontconfig-version = 2.13.94
 xtrans-version = 1.4.0
-libx11-version = 1.6.9
+libx11-version = 1.7.2
 libxext-version = 1.3.4
 libice-version = 1.0.10
 libsm-version = 1.2.3
-libxt-version = 1.2.0
+libxt-version = 1.2.1
 libpthread-stubs-version = 0.4
 
 # Version-dependent build
 # -----------------------
 lapack-version = 3.8.0
-libgit2-version = 1.0.1
-wcslib-version = 7.3
+libgit2-version = 1.3.0
+wcslib-version = 7.7
 
 # Netpbm's questions in the configure steps maybe change with different or
 # new versions.
-netpbm-version = 10.86.99
+netpbm-version = 10.73.38
 
-# Minizip is installed with the same `zlib' tarball, and they have the same
+# 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
 
 # Be careful with updateing hdf5 because h5py 2.10.0 doesn't work with
 # version 1.12.0.
@@ -187,6 +193,7 @@ hdf5-version = 1.10.5
 
 
 
+
 # Python packages
 # ---------------
 #
@@ -194,65 +201,147 @@ hdf5-version = 1.10.5
 #
 # 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'.
+# URL in 'reproduce/software/make/python.mk'.
 #
-# CLASS:PYTHON (important identifier, don't modify this line.)
+# CLASS:PYTHON-START (important identifier for 'awk'; don't modify this line)
 asn1crypto-version = 0.24.0
 asteval-version = 0.9.16
-astropy-version = 4.0
-astroquery-version = 0.4
-beautifulsoup4-version = 4.7.1
+astropy-version = 5.0
+beautifulsoup4-version = 4.10.0
+beniget-version = 0.4.1
 certifi-version = 2018.11.29
-cffi-version = 1.12.2
+cffi-version = 1.15.0
 chardet-version = 3.0.4
 corner-version = 2.0.1
-cryptography-version = 2.6.1
-cycler-version = 0.10.0
-cython-version = 0.29.21
+cycler-version = 0.11.0
+cython-version = 0.29.24
 eigency-version = 1.77
 emcee-version = 3.0.1
 entrypoints-version = 0.3
-esutil-version = 0.6.4
+esutil-version = 0.6.9
+extension-helpers-version = 0.1
 flake8-version = 3.7.8
 future-version = 0.18.1
-galsim-version = 2.2.1
+galsim-version = 2.3.3
+gast-version = 0.5.3
 h5py-version = 2.10.0
 html5lib-version = 1.0.1
 idna-version = 2.8
 jeepney-version = 0.4
-keyring-version = 18.0.0
+jinja2-version = 3.0.3
 kiwisolver-version = 1.0.1
 lmfit-version = 0.9.14
 lsstdesccoord-version = 1.2.0
+markupsafe-version = 2.0.1
 matplotlib-version = 3.3.0
-mpi4py-version = 3.0.3
+mpi4py-version = 3.1.3
 mpmath-version = 1.1.0
-numpy-version = 1.19.1
+numpy-version = 1.21.3
+packaging-version = 21.3
 pexpect-version = 4.7.0
+pillow-version = 8.4.0
 pip-version = 19.0.2
+ply-version = 3.11
 pycodestyle-version = 2.5.0
 pycparser-version = 2.19
+pyerfa-version = 2.0.0.1
 pyflakes-version = 2.1.1
 pybind11-version = 2.5.0
-pyparsing-version = 2.3.1
+pyparsing-version = 3.0.4
 pypkgconfig-version = 1.5.1
 python-dateutil-version = 2.8.0
+pythran-version = 0.11.0
 pyyaml-version = 5.1
 requests-version = 2.21.0
-scipy-version = 1.5.2
-secretstorage-version = 3.1.1
-setuptools-version = 41.6.0
+scipy-version = 1.7.3
+setuptools-version = 58.3.0
 setuptools_scm-version = 3.3.3
 sip_tpv-version = 1.1
-six-version = 1.12.0
+six-version = 1.16.0
 soupsieve-version = 1.8
 sympy-version = 1.4
-uncertainties-version = 3.1.2
+uncertainties-version = 3.1.6
 urllib3-version = 1.24.1
 webencodings-version = 0.5.1
+wheel-version = 0.37.0
+# CLASS:PYTHON-END (important identifier for 'awk'; don't modify this line)
 
 # Special Python modules:
 #
 # Healpy: When any Python module is requested, healpix will also build its
 #         Python module Healpy.
-healpy-version = xxxxx
+#
+# Bug: Healpix 3.50 doesn't yet support Python 3.10, so we are commenting
+# it here. When future versions fix the problem, we'll un-comment it again.
+#healpy-version = xxxxx
+
+
+
+
+
+# Problematic software that are currently ignored:
+
+# Healpix 3.80 has different installation scheme that is not yet
+# implemented here, and unfortunately healpix 3.50 has conflicts with
+# CFITSIO's new version macro and Python 3.10. So for now, we are ignoring
+# it.
+#healpix-version = 3.50
+
+# Setuptools-rust crash (https://savannah.nongnu.org/bugs/index.php?61731),
+# so it and its dependencies are being ignored: 'cryptography', and thus
+# 'secretstorage' and thus 'keyring' and thus 'astroquery'.
+#setuptools-rust-version = 1.1.2
+#cryptography-version = 36.0.1
+#secretstorage-version = 3.1.1
+#keyring-version = 18.0.0
+#astroquery-version = 0.4
+
+
+
+
+
+# R-CRAN (i.e. 'R') packages
+# ------------------
+#
+# Similar to optional programs and libraries above.
+#
+# Notation: The R package and variables associated with it are by default
+# called 'R-CRAN' (or 'r-cran') in Maneage, because searching on a single
+# letter string 'R' is extremely inefficient.
+#
+# IMPORTANT: If you intend to change the version of any of the R-CRAN
+# modules/libraries below, please fix the hash strings of the respective
+# packages in 'reproduce/software/conf/checksums.conf'.
+#
+# CLASS:R-CRAN-START (important identifier for 'awk'; don't modify this line)
+r-cran-cli-version = 2.5.0
+r-cran-colorspace-version = 2.0-1
+r-cran-cowplot-version = 1.1.1
+r-cran-crayon-version = 1.4.1
+r-cran-digest-version = 0.6.27
+r-cran-ellipsis-version = 0.3.2
+r-cran-fansi-version = 0.5.0
+r-cran-farver-version = 2.1.0
+r-cran-ggplot2-version = 3.3.4
+r-cran-glue-version = 1.4.2
+r-cran-gridExtra-version = 2.3
+r-cran-gtable-version = 0.3.0
+r-cran-isoband-version = 0.2.4
+r-cran-labeling-version = 0.4.2
+r-cran-lifecycle-version = 1.0.0
+r-cran-magrittr-version = 2.0.1
+r-cran-MASS-version = 7.3-54
+r-cran-mgcv-version = 1.8-36
+r-cran-munsell-version = 0.5.0
+r-cran-pillar-version = 1.6.1
+r-cran-pkgconfig-version = 2.0.3
+r-cran-R6-version = 2.5.0
+r-cran-RColorBrewer-version = 1.1-2
+r-cran-rlang-version = 0.4.11
+r-cran-scales-version = 1.1.1
+r-cran-tibble-version = 3.1.2
+r-cran-utf8-version = 1.2.1
+r-cran-vctrs-version = 0.3.8
+r-cran-viridisLite-version = 0.4.0
+r-cran-withr-version = 2.4.2
+# CLASS:R-CRAN-END (important identifier for 'awk'; don't modify this line)