Imported recent work in Maneage, minor conflicts fixed

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

4 files changed, 27 insertions, 25 deletions

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