Imported recent work in Maneage, minor conflicts fixed

Some minor conflicts (all expected from the commit messages in the Maneage
branch) occurred but were easily fixed.

7 files changed, 104 insertions, 43 deletions

diff --git a/reproduce/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf
index 470e429..b1f657b 100644
--- a/reproduce/analysis/config/metadata.conf
+++ b/reproduce/analysis/config/metadata.conf
@@ -1,6 +1,19 @@
-# Project meta-data that can be used in a project's output datasets and
+# Project meta-data that will be used in a project's output datasets and
 # final paper. Please set the values here and use them in your analysis or
-# paper, don't repeat them
+# paper, don't repeat them.
+#
+# These variables are used in 'reproduce/analysis/make/initialize.mk': 1)
+# to create a Make variable called 'print-general-metadata'. You can simply
+# print this variable's value in any plain-text output.
+#
+# Why add a Copyright for the data? people need to know if they can "use"
+# the dataset (i.e., modify it), or possibly re-distribute it and their
+# derived products. They also need to know how they can contact the creator
+# of the datset (who is usually also the copyright owner). So take this
+# seriously and add your name and email-address (or the name of the person
+# and email of the person who was in charge of that part of the project),
+# and the copyright license name and standard link to the fully copyright
+# license.
 #
 # Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
@@ -12,7 +25,9 @@
 # Project information
 metadata-title = Towards Long-term and Archivable Reproducibility
 
-# DOIs and identifiers.
+# DOIs and identifiers (don't include fixed URL prefixes like
+# 'https://doi.org/' or 'https://arxiv.org/abs'), they will be added
+# automatically where necessary.
 metadata-arxiv          = 2006.03018
 metadata-doi-zenodo     = 10.5281/zenodo.4291207
 metadata-doi-journal    = 10.1109/MCSE.2021.3072860
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 8af3199..bc73df8 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -224,7 +224,7 @@ project-package-contents = $(texdir)/$(project-package-name)
         $(project-package-contents) $(mtexdir)/initialize.tex
 
 texclean:
-	rm *.pdf
+	rm -f *.pdf
 	rm -rf $(texdir)/build/*
 	mkdir $(texdir)/build/tikz # 'tikz' is assumed to already exist.
 
@@ -253,8 +253,7 @@ 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 .local .build $(pconfdir)/LOCAL.conf
 
 
 
@@ -367,18 +366,18 @@ $(project-package-contents): paper.pdf | $(texdir)
 	sed -e's|{tikz/}|{tex/tikz/}|' $$pgfsettings > $$pgfsettings.new
 	mv $$pgfsettings.new $$pgfsettings
 
-        # Clean temporary (currently those ending in `~') files.
-	cd $(texdir)
-	find $(project-package-name) -name \*~ -delete
-	find $(project-package-name) -name \*.swp -delete
-
         # PROJECT SPECIFIC
         # ----------------
-        # Put any project specific distribution steps here.
+        # Put any project-specific distribution steps here.
 	cd $$curdir
 	cp tex/build/build/appendix.bbl $$dir/
         # ----------------
 
+        # Clean temporary files that may have been created by text editors.
+	cd $(texdir)
+	find $(project-package-name) -name \*~ -delete
+	find $(project-package-name) -name \*.swp -delete
+
 # Package into `.tar.gz' or '.tar.lz'.
 dist dist-lzip: $(project-package-contents)
 	curdir=$$(pwd)
@@ -460,15 +459,21 @@ $(data-publish-dir):; mkdir $@
 # Print Copyright statement
 # -------------------------
 #
-# This statement can be used in published datasets that are in plain-text
-# format. It assumes you have already put the data-specific statements in
-# its first argument, it will supplement them with general project links.
-doi-prefix-url = https://doi.org
+# The 'print-general-metadata' can be used to print the general metadata in
+# published datasets that are in plain-text format. It should be called
+# with make's 'call' function like this (where 'FILENAME' is the name of
+# the file it will append this content to):
+#
+#    $(call print-general-metadata, FILENAME)
+#
+# See 'reproduce/analysis/make/delete-me.mk' (in the Maneage branch) for a
+# real-world usage of this variable.
+doi-prefix-url   = https://doi.org
 arxiv-prefix-url = https://arxiv.org/abs
 print-general-metadata = \
 	echo "\# Project title: $(metadata-title)" >> $(1); \
 	echo "\# Git commit (that produced this dataset): $(project-commit-hash)" >> $(1); \
-	echo "\# Project's Git repository: $(metadata-git-repository)" >> $(1); \
+	echo "\# Git repository: $(metadata-git-repository)" >> $(1); \
 	if [ x$(metadata-arxiv) != x ]; then \
 	  echo "\# Pre-print: $(arxiv-prefix-url)/abs/$(metadata-arxiv)" >> $(1); fi; \
 	if [ x$(metadata-doi-journal) != x ]; then \
@@ -501,6 +506,8 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	echo "\newcommand{\projectdate}{$$d}" > $@
 	echo "\newcommand{\projecttitle}{$(metadata-title)}" >> $@
 	echo "\newcommand{\projectversion}{$(project-commit-hash)}" >> $@
+	echo "\newcommand{\projectgitrepo}{$(metadata-git-repository)}" >> $@
+	echo "\newcommand{\projectcopyrightowner}{$(metadata-copyright-owner)}" >> $@
 
         # arXiv/Zenodo identifier (necessary for download link):
 	echo "\newcommand{\projectarxivid}{$(metadata-arxiv)}" >> $@
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 6b055f7..27c1b5b 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -51,7 +51,7 @@ include reproduce/software/config/LOCAL.conf
 # Controlling this requires two variables that are available at this stage:
 #
 #   - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure').
-#   - `reproducible_paper_group_name': value to the `--group' option.
+#   - `maneage_group_name': value to the `--group' option.
 #
 # The analysis is only done when both have the same group name. Note that
 # when the project isn't being built for a group, both variables will be an
@@ -69,7 +69,7 @@ top-pdfs = paper.pdf
 else
 top-pdfs = paper.pdf supplement.pdf
 endif
-ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
+ifeq (x$(maneage_group_name),x$(GROUP-NAME))
 all: $(top-pdfs)
 else
 all:
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index f81ac07..fb5700e 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -35,7 +35,7 @@ include reproduce/software/config/LOCAL.conf
 # -------------------------------
 #
 # See `top-make.mk' for complete explanation.
-ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
+ifeq (x$(maneage_group_name),x$(GROUP-NAME))
 all: $(BDIR)/software/preparation-done.mk
 	@echo "Project preparation is complete.";
 else
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 9217ee9..fb378b8 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -86,7 +86,8 @@ export SHELL := $(ibdir)/dash
 export PATH := $(ibdir):$(PATH)
 export PKG_CONFIG_PATH := $(ildir)/pkgconfig
 export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
-export CPPFLAGS := -I$(idir)/include $(CPPFLAGS)
+export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) \
+                   -Wno-nullability-completeness
 export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS)
 
 # This is the "basic" tools where we are relying on the host operating
@@ -210,7 +211,10 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
         #   POSIX Threads library for multi-threaded programs.
 	for l in dl pthread; do
 	  if [ -f /usr/lib/lib$$l.a ]; then
-	    ln -sf /usr/lib/lib$$l.* $(ildir)/
+	    for f in /usr/lib/lib$$l.*; do
+	      ln -sf $$(realpath $$f) \
+	         $$(echo $$f | sed -e's|/usr/lib|$(ildir)|')
+	    done
 	  fi
 	done
 
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index d69722e..6ea782c 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -125,10 +125,10 @@ all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) \
 export PATH := $(ibdir)
 export CCACHE_DISABLE := 1
 export SHELL := $(ibdir)/bash
-export CPPFLAGS := -I$(idir)/include
 .SHELLFLAGS := --noprofile --norc -ec
 export LDFLAGS := $(rpath_command) -L$(ildir)
 export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
+export CPPFLAGS := -I$(idir)/include -Wno-nullability-completeness
 export PKG_CONFIG_PATH := $(ildir)/pkgconfig:$(idir)/share/pkgconfig
 
 # Settings specific to this Makefile.
@@ -428,7 +428,8 @@ $(ibidir)/cfitsio-$(cfitsio-version):
 	export gbuild_tar=$(ddir)/$$customtar
 	$(call gbuild, cfitsio-$(cfitsio-version), , \
 	               --enable-sse2 --enable-reentrant \
-	               --with-bzip2=$(idir), , make shared fpack funpack)
+	               --with-bzip2=$(idir), , \
+	               make shared fpack funpack)
 	rm $$customtar
 	echo "CFITSIO $(cfitsio-version)" > $@
 
@@ -1316,7 +1317,8 @@ $(ibidir)/swig-$(swig-version):
         # pcr is a dependency of swig
 	tarball=swig-$(swig-version).tar.gz
 	$(call import-source, $(swig-url), $(swig-checksum))
-	$(call gbuild, swig-$(swig-version), static, --without-pcre)
+	$(call gbuild, swig-$(swig-version), static, \
+	               --without-pcre --without-tcl)
 	echo "Swig $(swig-version)" > $@
 
 # The disables:
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 812f3d3..e15a8e9 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -3,6 +3,7 @@
 # Necessary preparations/configurations for the reproducible project.
 #
 # Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021      Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # This script is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -423,8 +424,17 @@ if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi
 
 # Check C compiler
 # ----------------
+#
+# Here we check if the C compiler works properly. About the "no warning"
+# variable ('nowarnings'):
+#
+#   -Wno-nullability-completeness: on macOS Big Sur 11.2.3 and Xcode 12.4,
+#    hundreds of 'nullability-completeness' warnings are printed which can
+#    be very annoying and even hide important errors or warnings. It is
+#    also harmless for our test here, so it is generally added.
 testprog=$compilertestdir/test
 testsource=$compilertestdir/test.c
+noccwarnings="-Wno-nullability-completeness"
 echo; echo; echo "Checking host C compiler ('$CC')...";
 cat > $testsource <<EOF
 #include <stdio.h>
@@ -432,7 +442,7 @@ cat > $testsource <<EOF
 int main(void){printf("...C compiler works.\n");
                return EXIT_SUCCESS;}
 EOF
-if $CC $testsource -o$testprog && $testprog; then
+if $CC $noccwarnings $testsource -o$testprog && $testprog; then
     rm $testsource $testprog
 else
     rm $testsource
@@ -761,7 +771,7 @@ fi
 # exists and we don't want to re-write it).
 if [ $rewritepconfig = no ]; then
     oldgroupname=$(awk '/GROUP-NAME/ {print $3; exit 0}' $pconf)
-    if [ "x$oldgroupname" = "x$reproducible_paper_group_name" ]; then
+    if [ "x$oldgroupname" = "x$maneage_group_name" ]; then
         just_a_place_holder_to_avoid_not_equal_test=1;
     else
         echo "-----------------------------"
@@ -1079,7 +1089,7 @@ if [ $rewritepconfig = yes ]; then
         -e's|@ddir[@]|'"$ddir"'|' \
         -e's|@sys_cpath[@]|'"$sys_cpath"'|' \
         -e's|@downloader[@]|'"$downloader"'|' \
-        -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \
+        -e's|@groupname[@]|'"$maneage_group_name"'|' \
         $pconf.in >> $pconf
 else
     # Read the values from existing configuration file. Note that the build
@@ -1238,7 +1248,7 @@ if ! [ -d "$mtexdir" ]; then mkdir "$mtexdir"; fi
 # TeX build directory. If built in a group scenario, the TeX build
 # directory must be separate for each member (so they can work on their
 # relevant parts of the paper without conflicting with each other).
-if [ "x$reproducible_paper_group_name" = x ]; then
+if [ "x$maneage_group_name" = x ]; then
     texbdir="$texdir"/build
 else
     user=$(whoami)
@@ -1458,18 +1468,19 @@ fi
 # which will download the DOI-resolved webpage, and extract the Zenodo-URL
 # of the most recent version from there (using the 'coreutils' tarball as
 # an example, the directory part of the URL for all the other software are
-# the same).
+# the same). This is not done if the option `--debug' is used.
+zenodourl=""
 user_backup_urls=""
 zenodocheck=.build/software/zenodo-check.html
-if $downloader $zenodocheck https://doi.org/10.5281/zenodo.3883409; then
-    zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \
-                    | sed -n -e'/http/p' \
-                    | tr ' ' '\n' \
-                    | grep http \
-                    | sed -e 's/href="//' -e 's|/coreutils| |' \
-                    | awk 'NR==1{print $1}')
-else
-    zenodourl=""
+if [ x$debug = x ]; then
+  if $downloader $zenodocheck https://doi.org/10.5281/zenodo.3883409; then
+      zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \
+                      | sed -n -e'/http/p' \
+                      | tr ' ' '\n' \
+                      | grep http \
+                      | sed -e 's/href="//' -e 's|/coreutils| |' \
+                      | awk 'NR==1{print $1}')
+  fi
 fi
 rm -f $zenodocheck
 
@@ -1497,6 +1508,28 @@ user_backup_urls="$user_backup_urls $zenodourl"
 
 
 
+# Corrections for debugging mode
+# ------------------------------
+#
+# If the user wants to debug the software configuration, they are usually
+# focused on the building of the single problematic software. Therefore,
+# the default multi-threaded execution of Make with the '--keep-going'
+# option are very annoying and can even hide important warnings. Recall
+# that with '--keep-going', Make will continue building other targets, even
+# if one target fails. When the user runs './project configure --debug',
+# the 'debug' variable will not be empty and this mode will be activated.
+if [ x$debug = x ]; then
+  keepgoing="--keep-going"
+else
+  jobs=1
+  numthreads=1
+  keepgoing=""
+fi
+
+
+
+
+
 # Build other basic tools our own GNU Make
 # ----------------------------------------
 #
@@ -1504,7 +1537,7 @@ user_backup_urls="$user_backup_urls $zenodourl"
 # Bash, Make, or AWK. In this step, we'll install such low-level basic
 # tools, but we have to be very portable (and use minimal features in all).
 echo; echo "Building necessary software (if necessary)..."
-.local/bin/make -k -f reproduce/software/make/basic.mk \
+.local/bin/make $keepgoing -f reproduce/software/make/basic.mk \
      user_backup_urls="$user_backup_urls" \
      sys_library_path=$sys_library_path \
      rpath_command=$rpath_command \
@@ -1532,7 +1565,7 @@ else
     numthreads=$jobs
 fi
 .local/bin/env -i HOME=$bdir \
-     .local/bin/make -k -f reproduce/software/make/high-level.mk \
+     .local/bin/make $keepgoing -f reproduce/software/make/high-level.mk \
           user_backup_urls="$user_backup_urls" \
           sys_library_path=$sys_library_path \
           rpath_command=$rpath_command \
@@ -1725,10 +1758,10 @@ echo `.local/bin/date` > $finaltarget
 #
 # The configuration is now complete, we can inform the user on the next
 # step(s) to take.
-if [ x$reproducible_paper_group_name = x ]; then
+if [ x$maneage_group_name = x ]; then
     buildcommand="./project make -j8"
 else
-    buildcommand="./project make --group=$reproducible_paper_group_name -j8"
+    buildcommand="./project make --group=$maneage_group_name -j8"
 fi
 cat <<EOF