Imported recent work in Maneage, minor conflicts fixed

Some minor conflicts that came up during the merge were fixed.

14 files changed, 144 insertions, 182 deletions

diff --git a/README-hacking.md b/README-hacking.md
index a598373..d944fb0 100644
--- a/README-hacking.md
+++ b/README-hacking.md
@@ -180,13 +180,22 @@ evolving rapidly, so some details will differ between the different
 versions. The more recent papers will tend to be the most useful as good
 working examples.
 
-  - Roukema ([2020](https://arxiv.org/abs/2007.11779),
+ - Peper & Roukema ([2020](https://arxiv.org/abs/2010.03742),
+   arXiv:2010.03742): The live version of the controlled source is [at
+   Codeberg](https://codeberg.org/boud/elaphrocentre); the main input
+   dataset, a software snapshot, the software tarballs, the project
+   outputs and editing history are available at
+   [zenodo.4062461](https://zenodo.org/record/4062461); and the
+   archived git history is available at
+   [swh:1:dir:c4770e81288f340083dd8aa9fe017103c4eaf476](https://archive.softwareheritage.org/swh:1:dir:c4770e81288f340083dd8aa9fe017103c4eaf476).
+
+ - Roukema ([2020](https://arxiv.org/abs/2007.11779),
    arXiv:2007.11779): The live version of the controlled source is [at
    Codeberg](https://codeberg.org/boud/subpoisson); the main input
    dataset, a software snapshot, the software tarballs, the project
    outputs and editing history are available at
    [zenodo.3951152](https://zenodo.org/record/3951152); and the
-   archived git history is also available at
+   archived git history is available at
    [swh:1:dir:fcc9d6b111e319e51af88502fe6b233dc78d5166](https://archive.softwareheritage.org/swh:1:dir:fcc9d6b111e319e51af88502fe6b233dc78d5166).
 
  - Akhlaghi et al. ([2020](https://arxiv.org/abs/2006.03018),
@@ -240,10 +249,9 @@ working examples.
 Citation
 --------
 
-A paper to fully describe Maneage has been submitted. Until then, if you
-used it in your work, please cite the paper that implemented its first
-version: Akhlaghi & Ichikawa
-([2015](http://adsabs.harvard.edu/abs/2015ApJS..220....1A), ApJS, 220, 1).
+If you use Maneage in your project please cite Akhlaghi et
+al. ([2020](https://arxiv.org/abs/2006.03018), arXiv:2006.03018). It has
+been submitted and is under peer review.
 
 Also, when your paper is published, don't forget to add a notice in your
 own paper (in coordination with the publishing editor) that the paper is
@@ -1254,11 +1262,9 @@ for the benefit of others.
    - *Configuration files*: If your research uses special programs as part
       of the processing, put all their configuration files in a devoted
       directory (with the program's name) within
-      `reproduce/software/config`. Similar to the
-      `reproduce/software/config/gnuastro` directory (which is put in
-      Maneage as a demo in case you use GNU Astronomy Utilities). It is
-      much cleaner and readable (thus less buggy) to avoid mixing the
-      configuration files, even if there is no technical necessity.
+      `reproduce/software/config`. It is much cleaner and readable (thus
+      less buggy) to avoid mixing the configuration files, even if there is
+      no technical necessity.
 
 
  - **Contents**: It is good practice to follow the following
diff --git a/README.md b/README.md
index 24e12d8..c7c76ac 100644
--- a/README.md
+++ b/README.md
@@ -419,6 +419,18 @@ command).
 docker cp CONTAINER:/file/path/within/container /host/path/target
 ```
 
+#### Deleting all Docker images
+
+After doing your tests/work, you may no longer need the multi-gigabyte
+files images, so its best to just delete them. To do this, just run the two
+commands below to first stop all running containers and then to delete all
+the images:
+
+```shell
+docker ps -a -q | xargs docker rm
+docker images -a -q | xargs docker rmi -f
+```
+
 
 
 
diff --git a/paper.tex b/paper.tex
index c3d17a8..e8b7cc9 100644
--- a/paper.tex
+++ b/paper.tex
@@ -14,14 +14,15 @@
 %% assumed to be if you use `\includetikz' when `\makepdf' is not defined.
 \newcommand{\makepdf}{}
 
-%% Import the project's processing macros 'project.tex' and the
-%% Maneage-specific preambles.
+%% VALUES FROM ANALYSIS (NUMBERS AND STRINGS): this file is automatically
+%% generated at the end of the processing and includes LaTeX macros
+%% (defined with '\newcommand') for various processing outputs to be used
+%% within the paper.
 \input{tex/build/macros/project.tex}
 \input{tex/src/preamble-maneage.tex}
 
 %% Import the other necessary TeX files for this particular project.
 \input{tex/src/preamble-project.tex}
-\input{tex/src/preamble-pgfplots.tex}
 
 %% Title and author names.
 \title{\projecttitle}
diff --git a/reproduce/analysis/config/gnuastro/astbuildprog.conf b/reproduce/analysis/config/gnuastro/astbuildprog.conf
deleted file mode 100644
index 7adb4d1..0000000
--- a/reproduce/analysis/config/gnuastro/astbuildprog.conf
+++ /dev/null
@@ -1,16 +0,0 @@
-# BuildProgram's configuration file depends on the build and is installed
-# along with the rest of Gnuastro. So we'll set any specific configuration
-# we want here, then import those.
-#
-# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-#
-# 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.
-
-# To keep the program's compiled excutable file, comment this line.
-deletecompiled 1
-
-# Import the built configuration file
-config .local/etc/astbuildprog.conf
\ No newline at end of file
diff --git a/reproduce/analysis/config/gnuastro/astconvertt.conf b/reproduce/analysis/config/gnuastro/astconvertt.conf
deleted file mode 100644
index 770ac39..0000000
--- a/reproduce/analysis/config/gnuastro/astconvertt.conf
+++ /dev/null
@@ -1,33 +0,0 @@
-# Default parameters (System) for ConvertType.
-# ConvertType is part of GNU Astronomy Utitlies.
-#
-# Use the long option name of each parameter followed by a value. The name
-# and value should be separated by atleast one white-space character (for
-# example ` '[space], or tab). Lines starting with `#' are ignored.
-#
-# For more information, please run these commands:
-#
-#  $ astconvertt --help                  # Full list of options, short doc.
-#  $ astconvertt -P                      # Print all options and used values.
-#  $ info astconvertt                    # All options and input/output.
-#  $ info gnuastro "Configuration files" # How to use configuration files.
-#
-# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-#
-# 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.
-
-# Input:
-
-# Output:
- quality              100
- widthincm            10.0
- borderwidth          1
- output               jpg
-
-# Flux:
- invert               0
-
-# Common options
diff --git a/reproduce/analysis/config/gnuastro/aststatistics.conf b/reproduce/analysis/config/gnuastro/aststatistics.conf
deleted file mode 100644
index 90f985d..0000000
--- a/reproduce/analysis/config/gnuastro/aststatistics.conf
+++ /dev/null
@@ -1,36 +0,0 @@
-# Default parameters (System) for Statistics.
-# Statistics is part of GNU Astronomy Utitlies.
-#
-# Use the long option name of each parameter followed by a value. The name
-# and value should be separated by atleast one white-space character (for
-# example ` '[space], or tab). Lines starting with `#' are ignored.
-#
-# For more information, please run these commands:
-#
-#  $ aststatistics --help                # Full list of options, short doc.
-#  $ aststatistics -P                    # Print all options and used values.
-#  $ info aststatistics                  # All options and input/output.
-#  $ info gnuastro "Configuration files" # How to use configuration files.
-#
-# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-#
-# 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.
-
-# Input image:
-
-# Sky and its STD settings
- khdu                 1
- meanmedqdiff     0.005
- outliersigma        10
- outliersclip     3,0.2
- smoothwidth          3
- sclipparams      3,0.1
-
-# Histogram and CFP settings
- numasciibins        70
- asciiheight         10
- numbins            100
- mirrordist         1.5
diff --git a/reproduce/analysis/config/gnuastro/gnuastro.conf b/reproduce/analysis/config/gnuastro/gnuastro.conf
deleted file mode 100644
index 82cb100..0000000
--- a/reproduce/analysis/config/gnuastro/gnuastro.conf
+++ /dev/null
@@ -1,43 +0,0 @@
-# Default values for the common options to all the programs in GNU
-# Astronomy Utitlies.
-#
-# IMPORTANT NOTE: The `lastconfig' option is very important in a
-# reproducible environment. Because we don't want any of Gnuastro's
-# programs to go into an un-controlled environment (user or system wide
-# configuration files).
-#
-# The rest of this configuration file is taken from the default Gnuastro
-# configuration from its source (`bin/gnuastro.conf').
-#
-# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-#
-# 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.
-
-# Local project settings (`config' has to be before `lastconfig').
- config           .gnuastro/gnuastro-local.conf
- lastconfig       1
-
-# Input:
- hdu              1
- ignorecase       1
- searchin         name
- stdintimeout     100000
-
-# Tessellation
- tilesize         30,30
- numchannels      1,1
- remainderfrac    0.1
- workoverch       0
- interpmetric     radial
- interpnumngb     9
- interponlyblank  0
-
-# Output:
- tableformat      fits-binary
-
-# Operating mode
- quietmmap        0
- minmapsize       2000000000
diff --git a/reproduce/analysis/config/pdf-build.conf b/reproduce/analysis/config/pdf-build.conf
index e2d59cc..48585b4 100644
--- a/reproduce/analysis/config/pdf-build.conf
+++ b/reproduce/analysis/config/pdf-build.conf
@@ -3,13 +3,13 @@
 #
 # During the project's early phases, it is usually not necessary to build
 # the PDF file (which makes a lot of output lines on the command-line and
-# can make it hard to find the commands and possible errors (and their
-# outputs). Also, in some cases, only the produced results may be of
+# can make it hard to find the analysis commands and possible errors (and
+# their outputs). Also, in some cases, only the produced results may be of
 # interest and not the final PDF, so LaTeX (and its necessary packages) may
-# not be installed.
+# not be installed at all.
 #
-# If this variable is given any string, a PDF will be made with
-# LaTeX. Otherwise, a notice will just printed that for now, no PDF will be
+# If 'pdf-build-final' is given the value 'yes', a PDF will be made with
+# LaTeX. Otherwise, a notice will just printed that, no PDF will be
 # created.
 #
 # Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 6431863..75f87ee 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -38,9 +38,6 @@ mtexdir     = $(texdir)/macros
 bashdir     = reproduce/analysis/bash
 pconfdir    = reproduce/analysis/config
 installdir  = $(BDIR)/software/installed
-# --------- Delete for no Gnuastro ---------
-gconfdir    = reproduce/analysis/config/gnuastro
-# ------------------------------------------
 
 
 
@@ -240,7 +237,7 @@ clean: clean-mmap
         # features like ignoring the listing of a file with `!()' that we
         # are using afterwards.
 	shopt -s extglob
-	rm -rf $(BDIR)/tex/macros/!(dependencies.tex|dependencies-bib.tex)
+	rm -rf $(BDIR)/tex/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex)
 	rm -rf $(BDIR)/!(software|tex) $(BDIR)/tex/!(macros|$(texbtopdir))
 	rm -rf $(BDIR)/tex/build/!(tikz) $(BDIR)/tex/build/tikz/*
 	rm -rf $(BDIR)/software/preparation-done.mk
@@ -255,8 +252,8 @@ distclean: clean
         # `rm' program. So for this recipe, we'll use the host system's
         # `rm', not our own.
 	$$sys_rm -rf $(BDIR)
+	$$sys_rm -f $(pconfdir)/LOCAL.conf
 	$$sys_rm -f Makefile .gnuastro .local .build
-	$$sys_rm -f $(pconfdir)/LOCAL.conf $(gconfdir)/gnuastro-local.conf
 
 
 
@@ -487,8 +484,13 @@ print-copyright = \
 # actually exists, it is also aded as a `.PHONY' target above.
 $(mtexdir)/initialize.tex: | $(mtexdir)
 
-        # Version and title of project.
-	@echo "\newcommand{\projecttitle}{$(metadata-title)}" > $@
+        # Version and title of project. About the starting '@': since these
+        # commands are run every time with './project make', it is annoying
+        # to print them on the standard output every time. With the '@',
+        # make will not print the commands that it runs in this recipe.
+	@d=$$(git show -s --format=%aD HEAD | awk '{print $$2, $$3, $$4}')
+	echo "\newcommand{\projectdate}{$$d}" > $@
+	echo "\newcommand{\projecttitle}{$(metadata-title)}" >> $@
 	echo "\newcommand{\projectversion}{$(project-commit-hash)}" >> $@
 
         # arXiv/Zenodo identifier (necessary for download link):
@@ -505,10 +507,6 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
         #    after cloning from a fork that didn't include it!). In this
         #    case, we'll just return the string a clear string.
 	v=$$(git describe --always --long maneage) || v=maneage-ref-missing
+	d=$$(git show -s --format=%aD $$v | awk '{print $$2, $$3, $$4}')
+	echo "\newcommand{\maneagedate}{$$d}" >> $@
 	echo "\newcommand{\maneageversion}{$$v}" >> $@
-
-        # Get the date of the most recent commit from the Maneage
-        # branch. Note that with '%aD', the format looks like this:
-        #    Wed, 9 Sep 2020 10:08:20 +0200
-	v=$$(git show -s --format=%aD $$v | awk '{print $$2, $$3, $$4}')
-	echo "\newcommand{\maneagedate}{$$v}" >> $@
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 6a974d9..d8f18b3 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -37,14 +37,14 @@
 # completed.
 #
 # Note that if you don't want the final PDF and just want the processing
-# and file outputs, you can remove the value of `pdf-build-final' in
-# `reproduce/analysis/config/pdf-build.conf'.
+# and file outputs, you can give any value other than 'yes' to
+# '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 [ -f .local/bin/latex ] && [ x"$(pdf-build-final)" != x ]; then
+	@if [ -f .local/bin/latex ] && [ x"$(pdf-build-final)" = xyes ]; then
 
           # Put a LaTeX input command for all the necessary macro files.
           # 'hardware-parameters.tex' is created in 'configure.sh'.
@@ -77,11 +77,11 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 	  echo "LaTeX-built PDF paper will not be built."
 	  echo
 	  if [ x$(more-on-building-pdf) = x1 ]; then
-	    echo "To do so, make sure you have LaTeX within the project (you"
-	    echo "can check by running './.local/bin/latex --version'), _AND_"
-	    echo "make sure that the 'pdf-build-final' variable has a value."
-	    echo "'pdf-build-final' is defined in: "
-	    echo     "'reproduce/analysis/config/pdf-build.conf'."
+	    echo "To build the PDF, make sure you have LaTeX within the "
+	    echo "project (you can check by running "
+	    echo "'./.local/bin/latex --version'), _AND_ make sure that "
+	    echo "the 'pdf-build-final' variable has a value of 'yes', it "
+	    echo "is defined in: 'reproduce/analysis/config/pdf-build.conf'."
 	    echo
 	    echo "If you don't have LaTeX within the project, please re-run"
 	    echo "'./project configure -e' when you have internet access."
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 55b1f43..18d54b1 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -62,8 +62,8 @@ include reproduce/software/config/LOCAL.conf
 # -----------------------------
 #
 # If you are just interested in the processing and don't want to build the
-# PDF, you can skip the creation of the final PDF by removing the value
-# of `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+# PDF, you can skip the creation of the final PDF by giving a value of
+# `yes' to `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
 ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
 all: paper.pdf
 else
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index fe828dd..35f49db 100644
--- a/reproduce/analysis/make/verify.mk
+++ b/reproduce/analysis/make/verify.mk
@@ -114,8 +114,12 @@ verify-dep = $(subst verify,,$(subst paper,,$(makesrc)))
 verify-check = $(subst initialize,,$(verify-dep))
 $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
 
-        # Make sure that verification is actually requested.
-	if [ x"$(verify-outputs)" = xyes ]; then
+        # Make sure that verification is actually requested, the '@' at the
+        # start of the recipe is added so Make doesn't print the commands
+        # on the standard output because this recipe is run on every call
+        # to the project and can be annoying (get mixed in the middle of
+        # the analysis outputs or the LaTeX outputs).
+	@if [ x"$(verify-outputs)" = xyes ]; then
 
           # Make sure the temporary output doesn't exist (because we want
           # to append to it). We are making a temporary output target so if
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index d9a1b46..0b0daea 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -212,13 +212,31 @@ if [ x$kernelname = xLinux ]; then
     # Don't forget to add the respective C++ compiler below (leave 'cc' in
     # the end).
     c_compiler_list="gcc clang cc"
-else
+elif [ x$kernelname = xDarwin ]; then
     host_cc=1
     on_mac_os=yes
 
     # Don't forget to add the respective C++ compiler below (leave 'cc' in
     # the end).
     c_compiler_list="clang gcc cc"
+else
+    on_mac_os=no
+    cat <<EOF
+______________________________________________________
+!!!!!!!                 WARNING                !!!!!!!
+
+Maneage has been tested on GNU/Linux and Darwin (macOS) systems. But, it
+seems that the current system is not GNU/Linux or Darwin (macOS). If you
+notice any problem during the configure phase, please contact us with this
+web-form:
+
+    https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+The configuration will continue in 10 seconds...
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    sleep 10
 fi
 
 
@@ -281,6 +299,47 @@ fi
 
 
 
+# Check for Xcode in macOS systems
+# --------------------------------
+#
+# When trying to build Maneage on macOS systems, there are some problems
+# related with the Xcode and Command Line Tools. As a consequnce, in order to
+# avoid these error it is highly recommended to install Xcode in the host
+# system.  Here, it is checked that this is the case, and if not, warn the user
+# about not having Xcode already installed.
+if [ x$on_mac_os = xyes ]; then
+  xcode=$(which xcodebuild)
+  if [ x$xcode != x ]; then
+    xcode_version=$(xcodebuild -version | grep Xcode)
+    echo "                                              "
+    echo "$xcode_version already installed in the system"
+    echo "                                              "
+  else
+    cat <<EOF
+______________________________________________________
+!!!!!!!                 WARNING                !!!!!!!
+
+Maneage has been tested Darwin (macOS) systems with host Xcode
+installation.  However, Xcode cannot be found in this system. As a
+consequence, the configure step may fail at some point. If this is the
+case, please install Xcode and try to run again the configure step. If the
+problem still persist after installing Xcode, please contact us with this
+web-form:
+
+    https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+The configuration will continue in 5 seconds ...
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    sleep 5
+  fi
+fi
+
+
+
+
+
 # Check for C/C++ compilers
 # -------------------------
 #
@@ -1211,7 +1270,6 @@ ln -s "$tikzdir" tex/tikz
 
 # --------- Delete for no Gnuastro ---------
 rm -f .gnuastro
-ln -s "$topdir"/reproduce/analysis/config/gnuastro .gnuastro
 # ------------------------------------------
 
 
diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex
index 4382485..11bf9c3 100644
--- a/tex/src/preamble-project.tex
+++ b/tex/src/preamble-project.tex
@@ -1,16 +1,24 @@
-%% Settings specific to this project (beyond the journal's style).
+%% Necessary macros for this project.
+%%
+%% These are a set of packages that have been commonly necessary in most
+%% LaTeX usages. However, if any are not needed in your work, please feel
+%% free to remove them.
 %
-%% Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) YYYY Your Name <your@email.address>
 %
-%% This LaTeX file is part of Maneage. Maneage 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 file 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.
 %
-%% Maneage is distributed in the hope that it will be useful, but WITHOUT
+%% This file 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. See <http://www.gnu.org/licenses/>.
+%% for more details.
+%
+%% You should have received a copy of the GNU General Public License along
+%% with this file.  If not, see <http://www.gnu.org/licenses/>.
 
 
 
@@ -78,3 +86,6 @@
 \newcommand\eprint[1]{\href{https://arXiv.org/abs/#1}{{arXiv:#1}}}
 
 \newcommand\doi[1]{\href{https://oadoi.org/#1}{{DOI:#1}}}
+
+%% Import Maneage template for PGFPlots.
+\input{tex/src/preamble-pgfplots.tex}