IMPORTANT: Updates to almost all software

This commit primarily affects the configuration step of Maneage'd projects,
and in particular, updated versions of the many of the software (see
P.S.). So it shouldn't affect your high-level analysis other than the
version bumps of the software you use (and the software's possibly
improve/changed behavior).

The following software (and thus their dependencies) couldn't be updated as
described below:
  - Cryptography: isn't building because it depends on a new
    setuptools-rust package that has problems
    (https://savannah.nongnu.org/bugs/index.php?61731), so it has been
    commented in 'versions.conf'.
  - SecretStorage: because it depends on Cryptography.
  - Keyring: because it depends on SecretStorage.
  - Astroquery: because it depends on Keyring.

This is a "squashed" commit after rebasing a development branch of 60
commits corresponding to a roughly two-month time interval. The following
people contributed to this branch.
  - Boudewijn Roukema added all the R software infrastructure and the R
    packages, as well as greatly helping in fixing many bugs during the
    update.
  - Raul Infante-Sainz helped in testing and debugging the build.
  - Pedram Ashofteh Ardakani found and fixed a bug.
  - Zahra Sharbaf helped in testing and found several bugs.

Below a description of the most noteworthy points is given.

  - Software tarballs: all updated software now have a unified format
    tarball (ustar; if not possible, pax) and unified compression (Lzip) in
    Maneage's software repository in Zenodo
    (https://doi.org/10.5281/zenodo.3883409). For more on this See
    https://savannah.nongnu.org/task/?15699 . This won't affect any extra
    software you would like to add; you can use any format recognized by
    GNU Tar, and all common compression algorithms. This new requirement is
    only for software that get merged to the core Maneage branch.

  - Metastore (and thus libbsd and libmd) moved to highlevel: Metastore
    (and the packages it depends on) is a high-level product that is only
    relevant during the project development (like Emacs!): when the user
    wants the file meta data (like dates) to be unchanged after checking
    out branches. So it should be considered a high-level software, not
    basic. Metastore also usually causes many more headaches and error
    messages, so personally, I have stopped using it! Instead I simply
    merge my branches in a separate clone, then pull the merge commit: in
    this way, the files of my project aren't re-written during the checkout
    phase and therefore their dates are untouched (which can conflict with
    Make's dates on configuration files).

  - The un-official cloned version of Flex (2.6.4-91 until this commit) was
    causing problems in the building of Netpbm, so with this commit, it has
    been moved back to version 2.6.4.

  - Netpbm's official page had version 10.73.38 as the latest stable
    tarball that was just released in late 2021. But I couldn't find our
    previously-used version 10.86.99 anywhere (to see when it was released
    and why we used it! Its at last more than one year old!). So the
    official stable version is being used now.

  - Improved instructions in 'README.md' for building software environment
    in a Docker container (while having project source and output data
    products on the local system; including the usage of the host's
    '/dev/shm' to speed up temporary operations).

  - Until now, the convention in Maneage was to put eight SPACE characters
    before the comment lines within recipes. This was done because by
    default GNU Emacs (also many other editors) show a TAB as eight
    characters. However, in other text editors, online browsers, or even
    the Git diff, a TAB can correspond to a different number of
    characters. In such cases, the Maneage recipes wouldn't look too
    interesting (the comments and the recipe commands would show a
    different indentation!).

    With this commit, all the comment lines in the Makefiles within the
    core Maneage branch have a hash ('#') as their first character and a
    TAB as the second. This allows the comment lines in recipes to have the
    same indentation as code; making the code much more easier to read in a
    general scenario including a 'git diff' (editor agnostic!).

P.S. List of updated software with their old and new versions
 - Software with no version update are not mentioned.
 - The old version of newly added software are shown with '--'.

Name (Basic)              Old version    New version
------------              -----------    -----------
Bzip2                     1.0.6          1.0.8
CURL                      7.71.1         7.79.1
Dash                      0.5.10.2       0.5.11.5
File                      5.39           5.41
Flock                     0.2.3          0.4.0
GNU Bash                  5.0.18         5.1.8
GNU Binutils              2.35           2.37
GNU Coreutils             8.32           9.0
GNU GCC                   10.2.0         11.2.0
GNU M4                    1.4.18         1.4.19
GNU Readline              8.0            8.1.1
GNU Tar                   1.32           1.34
GNU Texinfo               6.7            6.8
GNU diffutils             3.7            3.8
GNU findutils             4.7.0          4.8.0
GNU gmp                   6.2.0          6.2.1
GNU grep                  3.4            3.7
GNU gzip                  1.10           1.11
GNU libunistring          0.9.10         1.0
GNU mpc                   1.1.0          1.2.1
GNU mpfr                  4.0.2          4.1.0
GNU nano                  5.2            6.0
GNU ncurses               6.2            6.3
GNU wget                  1.20.3         1.21.2
Git                       2.28.0         2.34.0
Less                      563            590
Libxml2                   2.9.9          2.9.12
Lzip                      1.22-rc2       1.22
OpenSLL                   1.1.1a         3.0.0
Patchelf                  0.10           0.13
Perl                      5.32.0         5.34.0
Podlators                 --             4.14

Name (Highlevel)          Old version    New version
----------------          -----------    -----------
Apachelog4cxx             0.10.0-603     0.12.1
Astrometry.net            0.80           0.85
Boost                     1.73.0         1.77.0
CFITSIO                   3.48           4.0.0
Cmake                     3.18.1         3.21.4
Eigen                     3.3.7          3.4.0
Expat                     2.2.9          2.4.1
FFTW                      3.3.8          3.3.10
Flex                      2.6.4-91       2.6.4
Fontconfig                2.13.1         2.13.94
Freetype                  2.10.2         2.11.0
GNU Astronomy Utilities   0.12           0.16.1-e0f1
GNU Autoconf              2.69.200-babc  2.71
GNU Automake              1.16.2         1.16.5
GNU Bison                 3.7            3.8.2
GNU Emacs                 27.1           27.2
GNU GDB                   9.2            11.1
GNU GSL                   2.6            2.7
GNU Help2man              1.47.11        1.48.5
Ghostscript               9.52           9.55.0
ICU                       --             70.1
ImageMagick               7.0.8-67       7.1.0-13
Libbsd                    0.10.0         0.11.3
Libffi                    3.2.1          3.4.2
Libgit2                   1.0.1          1.3.0
Libidn                    1.36           1.38
Libjpeg                   9b             9d
Libmd                     --             1.0.4
Libtiff                   4.0.10         4.3.0
Libx11                    1.6.9          1.7.2
Libxt                     1.2.0          1.2.1
Netpbm                    10.86.99       10.73.38
OpenBLAS                  0.3.10         0.3.18
OpenMPI                   4.0.4          4.1.1
Pixman                    0.38.0         0.40.0
Python                    3.8.5          3.10.0
R                         4.0.2          4.1.2
SWIG                      3.0.12         4.0.2
Util-linux                2.35           2.37.2
Util-macros               1.19.2         1.19.3
Valgrind                  3.15.0         3.18.1
WCSLIB                    7.3            7.7
Xcb-proto                 1.14           1.14.1
Xorgproto                 2020.1         2021.5

Name (Python)             Old version    New version
-------------             -----------    -----------
Astropy                   4.0            5.0
Beautifulsoup4            4.7.1          4.10.0
Beniget                   --             0.4.1
Cffi                      1.12.2         1.15.0
Cryptography              2.6.1          36.0.1
Cycler                    0.10.0         0.11.0+}
Cython                    0.29.21        0.29.24
Esutil                    0.6.4          0.6.9
Extension-helpers         --             0.1
Galsim                    2.2.1          2.3.3
Gast                      --             0.5.3
Jinja2                    --             3.0.3
MPI4py                    3.0.3          3.1.3
Markupsafe                --             2.0.1
Numpy                     1.19.1         1.21.3
Packaging                 --             21.3
Pillow                    --             8.4.0
Ply                       --             3.11
Pyerfa                    --             2.0.0.1
Pyparsing                 2.3.1          3.0.4
Pythran                   --             0.11.0
Scipy                     1.5.2          1.7.3
Setuptools                41.6.0         58.3.0
Six                       1.12.0         1.16.0
Uncertainties             3.1.2          3.1.6
Wheel                     --             0.37.0

Name (R)                  Old version    New version
--------                  -----------    -----------
Cli                       --             2.5.0
Colorspace                --             2.0-1
Cowplot                   --             1.1.1
Crayon                    --             1.4.1
Digest                    --             0.6.27
Ellipsis                  --             0.3.2
Fansi                     --             0.5.0
Farver                    --             2.1.0
Ggplot2                   --             3.3.4
Glue                      --             1.4.2
GridExtra                 --             2.3
Gtable                    --             0.3.0
Isoband                   --             0.2.4
Labeling                  --             0.4.2
Lifecycle                 --             1.0.0
Magrittr                  --             2.0.1
MASS                      --             7.3-54
Mgcv                      --             1.8-36
Munsell                   --             0.5.0
Pillar                    --             1.6.1
R-Pkgconfig               --             2.0.3
R6                        --             2.5.0
RColorBrewer              --             1.1-2
Rlang                     --             0.4.11
Scales                    --             1.1.1
Tibble                    --             3.1.2
Utf8                      --             1.2.1
Vctrs                     --             0.3.8
ViridisLite               --             0.4.0
Withr                     --             2.4.2

1 files changed, 42 insertions, 41 deletions

diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index b5b5b29..740dc7d 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -1,6 +1,6 @@
 # Build the final PDF paper/report.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -23,14 +23,14 @@
 #
 # To report the input settings and results, the final report's PDF (final
 # target of this project) uses macros generated from various steps of the
-# project. All these macros are defined through `$(mtexdir)/project.tex'.
+# project. All these macros are defined through '$(mtexdir)/project.tex'.
 #
-# `$(mtexdir)/project.tex' is actually just a combination of separate files
+# '$(mtexdir)/project.tex' is actually just a combination of separate files
 # that keep the LaTeX macros related to each workhorse Makefile (in
-# `reproduce/src/make/*.mk'). Those individual macros are pre-requisites to
-# `$(mtexdir)/verify.tex' which will check them before starting to build
+# 'reproduce/src/make/*.mk'). Those individual macros are pre-requisites to
+# '$(mtexdir)/verify.tex' which will check them before starting to build
 # the paper. The only workhorse Makefile that doesn't need to produce LaTeX
-# macros is this Makefile (`reproduce/src/make/paper.mk').
+# macros is this Makefile ('reproduce/src/make/paper.mk').
 #
 # This file is thus the interface between the analysis/processing steps and
 # the final PDF: when we get to this point, all the processing has been
@@ -38,33 +38,33 @@
 #
 # Note that if you don't want the final PDF and just want the processing
 # and file outputs, you can give any value other than 'yes' to
-# 'pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+# 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'.
 $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 
-        # If no PDF is requested, or if LaTeX isn't available, don't
-        # continue to building the final PDF. Otherwise, merge all the TeX
-        # macros into one for building the PDF.
+#	If no PDF is requested, or if LaTeX isn't available, don't continue
+#	to building the final PDF. Otherwise, merge all the TeX macros into
+#	one for building the PDF.
 	@if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ]; then
 
-          # Put a LaTeX input command for all the necessary macro files.
-          # 'hardware-parameters.tex' is created in 'configure.sh'.
+#	  Put a LaTeX input command for all the necessary macro files.
+#	  'hardware-parameters.tex' is created in 'configure.sh'.
 	  projecttex=$(mtexdir)/project.tex
 	  rm -f $$projecttex
 	  for t in $(subst paper,,$(makesrc)) hardware-parameters; do
 	    echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex
 	  done
 
-          # Possibly highlight the '\new' parts of the text.
+#	  Possibly highlight the '\new' parts of the text.
 	  if [ x"$(highlightnew)" = x1 ]; then
 	    echo "\newcommand{\highlightnew}{}" >> $$projecttex
 	  fi
 
-          # Possibly show the text within '\tonote'.
+#	  Possibly show the text within '\tonote'.
 	  if [ x"$(highlightnotes)" = x1 ]; then
 	    echo "\newcommand{\highlightnotes}{}" >> $$projecttex
 	  fi
 
-        # The paper shouldn't be built.
+#	The paper shouldn't be built.
 	else
 	  echo
 	  echo "-----"
@@ -95,39 +95,39 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 # The bibliography
 # ----------------
 #
-# We need to run the `biber' program on the output of LaTeX to generate the
+# We need to run the 'biber' program on the output of LaTeX to generate the
 # necessary bibliography before making the final paper. So we'll first have
-# one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
+# one run of LaTeX (similar to the 'paper.pdf' recipe), then 'biber'.
 #
-# NOTE: `$(mtexdir)/project.tex' is an order-only-prerequisite for
-# `paper.bbl'. This is because we need to run LaTeX in both the `paper.bbl'
-# recipe and the `paper.pdf' recipe. But if `tex/src/references.tex' hasn't
+# NOTE: '$(mtexdir)/project.tex' is an order-only-prerequisite for
+# 'paper.bbl'. This is because we need to run LaTeX in both the 'paper.bbl'
+# recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't
 # been modified, we don't want to re-build the bibliography, only the final
 # PDF.
 $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
                       | $(mtexdir)/project.tex
-        # If `$(mtexdir)/project.tex' is empty, don't build PDF.
+#	If '$(mtexdir)/project.tex' is empty, don't build PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
 	if [ x"$$macros" != x ]; then
 
-          # We'll run LaTeX first to generate the `.bcf' file (necessary
-          # for `biber') and then run `biber' to generate the `.bbl' file.
+#	  We'll run LaTeX first to generate the '.bcf' file (necessary for
+#	  'biber') and then run 'biber' to generate the '.bbl' file.
 	  p=$$(pwd)
 	  export TEXINPUTS=$$p:
 	  cd $(texbdir);
 
-          # Delete any possibly existing target (a '.bbl' file) to avoid
-          # complications with LaTeX being run before the command that
-          # generates it. Otherwise users will have to manually delete
-          # it. It will be built anyway once this rule is done.
+#	  Delete any possibly existing target (a '.bbl' file) to avoid
+#	  complications with LaTeX being run before the command that
+#	  generates it. Otherwise users will have to manually delete it. It
+#	  will be built anyway once this rule is done.
 	  rm -f $@
 
-          # The pdflatex option '-shell-escape' is "normally disallowed for
-          # security reasons" according to the `info pdflatex' manual, but
-          # is enabled here in order to allow the use of PGFPlots. If you
-          # do not use PGFPlots, then you should remove the `-shell-escape'
-          # option for better security. See
-          # https://savannah.nongnu.org/task/?15694 for details.
+#	  The pdflatex option '-shell-escape' is "normally disallowed for
+#	  security reasons" according to the 'info pdflatex' manual, but is
+#	  enabled here in order to allow the use of PGFPlots. If you do not
+#	  use PGFPlots, then you should remove the '-shell-escape' option
+#	  for better security. See https://savannah.nongnu.org/task/?15694
+#	  for details.
 	  pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
 	  biber paper
 
@@ -140,27 +140,28 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
 # The final paper
 # ---------------
 #
-# Run LaTeX in the `$(texbdir)' directory so all the intermediate and
+# Run LaTeX in the '$(texbdir)' directory so all the intermediate and
 # auxiliary files stay there and keep the top directory clean. To be able
 # to run everything cleanly from there, it is necessary to add the current
-# directory (top project directory) to the `TEXINPUTS' environment
+# directory (top project directory) to the 'TEXINPUTS' environment
 # variable.
 paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
 
-        # If `$(mtexdir)/project.tex' is empty, don't build the PDF.
+#	If '$(mtexdir)/project.tex' is empty, don't build the PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
 	if [ x"$$macros" != x ]; then
 
-          # Go into the top TeX build directory and make the paper.
+#	  Go into the top TeX build directory and make the paper.
 	  p=$$(pwd)
 	  export TEXINPUTS=$$p:
 	  cd $(texbdir)
-          # See above for a warning and brief discussion on the the
-          # pdflatex option `-shell-escape'.
+
+#	  See above for a warning and brief discussion on the the pdflatex
+#	  option '-shell-escape'.
 	  pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
 
-          # Come back to the top project directory and copy the built PDF
-          # file here.
+#	  Come back to the top project directory and copy the built PDF
+#	  file here.
 	  cd "$$p"
 	  cp $(texbdir)/$@ $(final-paper)