Better management for .tex directories to build from tarball

In order to collaborate effectively in the project, even project members
that don't necessarily want (or have the capacity) to do the whole analysis
must be able to contribute to the project. Until now, the users of the
distributed tarball could only modify the text and not the figures (built
with PGFPlots) of the paper.

With this commit, the management of TeX source files in the pipeline was
slightly modified to allow this as cleanly as I could think of now! In
short, the hand-written TeX files are now kept in `tex/src' and for the
pipeline's generated TeX files (in particular the old `tex/pipeline.tex'),
we now have a `tex/pipeline' symbolic-link/directory that points to the
`tex' directory under the build directory.

When packaging the project, `tex/pipeline' will be a full directory with a
copy of all the necessary files. Therefore as far as LaTeX is concerned,
having a build-directory is no longer relevant. Many other small changes
were made to do this job cleanly which will just make this commit message
too long!

Also, the old `tarball' and `zip' targets are now `dist' and `dist-zip' (as
in the standard GNU Build system).

2 files changed, 79 insertions, 44 deletions

diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk
index b3180e3..ff06dcb 100644
--- a/reproduce/src/make/initialize.mk
+++ b/reproduce/src/make/initialize.mk
@@ -140,9 +140,9 @@ export CPPFLAGS        := -I$(installdir)/include
 # option: they add too many extra checks that make it hard to find what you
 # are looking for in this pipeline.
 .SUFFIXES:
-$(tikzdir): | $(texbdir); mkdir $@
 $(texdir) $(lockdir): | $(BDIR); mkdir $@
 $(mtexdir) $(texbdir): | $(texdir); mkdir $@
+$(tikzdir): | $(texbdir); mkdir $@ && ln -s $(tikzdir) tex/tikz
 
 
 
@@ -160,7 +160,7 @@ $(mtexdir) $(texbdir): | $(texdir); mkdir $@
 # when no file actually differs.
 packagebasename := $(shell echo paper-$$(git describe --dirty --always))
 packagecontents = $(texdir)/$(packagebasename)
-.PHONY: all clean distclean clean-mmap tarball zip $(packagecontents) \
+.PHONY: all clean dist dist-zip distclean clean-mmap $(packagecontents) \
         $(mtexdir)/initialize.tex
 
 # --------- Delete for no Gnuastro ---------
@@ -206,32 +206,67 @@ $(packagecontents): | $(texdir)
 	rm -rf $$dir
 	mkdir $$dir
 
+        # Build a small Makefile to help in automatizing the paper building
+        # (including the bibliography).
+	m=$$dir/Makefile
+	echo   "paper.pdf: paper.tex paper.bbl"                   > $$m
+	printf "\tpdflatex -shell-escape -halt-on-error paper\n" >> $$m
+	echo   "paper.bbl: tex/src/references.tex"               >> $$m
+	printf "\tpdflatex -shell-escape -halt-on-error paper\n" >> $$m
+	printf "\tbiber paper\n"                                 >> $$m
+	echo   ".PHONY: clean"                                   >> $$m
+	echo   "clean:"                                          >> $$m
+	printf "\trm -f *.aux *.auxlock *.bbl *.bcf\n"           >> $$m
+	printf "\trm -f *.blg *.log *.out *.run.xml\n"           >> $$m
+
         # Copy the top-level contents into it.
 	cp configure COPYING for-group README.md README-hacking.md $$dir/
 
-        # Since the tarball is mainly intended for high-level building of
-        # the PDF with LaTeX, we'll comment the `makepdf' LaTeX macro in
-        # the paper.
-	sed -e's|\\newcommand{\\makepdf}{}|%\\newcommand{\\makepdf}{}|' \
-	    paper.tex > $$dir/paper.tex
+        # Build the top-level directories.
+	mkdir $$dir/reproduce $$dir/tex $$dir/tex/tikz $$dir/tex/pipeline
 
         # Copy all the `reproduce' contents except for the `build' symbolic
         # link.
 	shopt -s extglob
-	mkdir $$dir/reproduce $$dir/tex $$dir/tex/tikz
-	cp tex/*.tex             $$dir/tex
-	cp -r reproduce/!(build) $$dir/reproduce
-	cp tex/tikz/*.pdf        $$dir/tex/tikz
+	cp -r tex/src                            $$dir/tex/src
+	cp tex/tikz/*.pdf                        $$dir/tex/tikz
+	cp -r reproduce/!(build)                 $$dir/reproduce
+	cp -r tex/pipeline/!($(packagebasename)) $$dir/tex/pipeline
+
+        # Clean up un-necessary/local files: 1) the $(texdir)/build*
+        # directories (when building in a group structure, there will be
+        # `build-user1', `build-user2' and etc), are just temporary LaTeX
+        # build files and don't have any relevant/hand-written files in
+        # them. 2) The `LOCAL.mk' and `gnuastro-local.conf' files just have
+        # this machine's local settings and are irrelevant for anyone else.
+	rm -rf $$dir/tex/pipeline/build*
+	rm $$dir/reproduce/config/pipeline/LOCAL.mk
+	rm $$dir/reproduce/config/gnuastro/gnuastro-local.conf
+
+        # PIPELINE SPECIFIC: under this comment, copy any other file for
+        # packaging, or remove any of the copied files above to suite your
+        # project.
+
+        # Since the packaging is mainly intended for high-level building of
+        # the PDF with LaTeX, we'll comment the `makepdf' LaTeX macro in
+        # the paper.
+	sed -e's|\\newcommand{\\makepdf}{}|%\\newcommand{\\makepdf}{}|' \
+	    paper.tex > $$dir/paper.tex
 
-        # PIPELINE SPECIFIC: add or remove any of the copied files above,
-        # specific to your pipeline here.
+        # Just in case the package users want to rebuild some of the
+        # figures (manually un-comments the `makepdf' command we commented
+        # above), correct the TikZ external directory, so the figures can
+        # be rebuilt.
+	pgfsettings="$$dir/tex/src/preamble-pgfplots.tex"
+	sed -e's|{tikz/}|{tex/tikz/}|' $$pgfsettings > $$pgfsettings.new
+	mv $$pgfsettings.new $$pgfsettings
 
-        # Clean all temporary files.
+        # Clean temporary (currently those ending in `~') files.
 	cd $(texdir)
 	find $(packagebasename) -name \*~ -delete
 
 # Package into `.tar.gz'.
-tarball: $(packagecontents)
+dist: $(packagecontents)
 	curdir=$$(pwd)
 	cd $(texdir)
 	tar -cf $(packagebasename).tar $(packagebasename)
@@ -240,7 +275,7 @@ tarball: $(packagecontents)
 	mv $(texdir)/$(packagebasename).tar.gz ./
 
 # Package into `.zip'.
-zip: $(packagecontents)
+dist-zip: $(packagecontents)
 	curdir=$$(pwd)
 	cd $(texdir)
 	zip -q -r $(packagebasename).zip $(packagebasename)
@@ -294,7 +329,6 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
         # Version of the pipeline and build directory (for LaTeX inputs).
 	@v=$$(git describe --dirty --always);
 	echo "\newcommand{\pipelineversion}{$$v}"  > $@
-	@echo "\newcommand{\bdir}{$(BDIR)}"       >> $@
 
         # Versions of programs (same order as 'dependency-versions.mk'),
         # ordered alphabetically (by their executable name).
diff --git a/reproduce/src/make/paper.mk b/reproduce/src/make/paper.mk
index aea6c60..d148c08 100644
--- a/reproduce/src/make/paper.mk
+++ b/reproduce/src/make/paper.mk
@@ -25,17 +25,16 @@
 # LaTeX macros for paper
 # ----------------------
 #
-# To report the input settings and results, the final report's PDF
-# (final target of this reproduction pipeline) uses macros generated
-# from various steps of the pipeline. All these macros are defined in
-# `tex/pipeline.tex'.
+# To report the input settings and results, the final report's PDF (final
+# target of this reproduction pipeline) uses macros generated from various
+# steps of the pipeline. All these macros are defined in
+# `$(mtexdir)/pipeline.tex'.
 #
-# `tex/pipeline.tex' is actually just a combination of separate files
-# that keep the LaTeX macros related to each workhorse Makefile (in
-# `reproduce/src/make/*.mk'). Those individual macros are
-# pre-requisites to `tex/pipeline.tex'. The only workhorse Makefile
-# that doesn't need to produce LaTeX macros is this Makefile
-# (`reproduce/src/make/paper.mk').
+# `$(mtexdir)/pipeline.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)/pipeline.tex'. The only workhorse Makefile that doesn't need
+# to produce LaTeX macros is this Makefile (`reproduce/src/make/paper.mk').
 #
 # This file is thus the interface between the pipeline scripts and the
 # final PDF: when we get to this point, all the processing has been
@@ -44,13 +43,21 @@
 # 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/config/pipeline/pdf-build.mk'.
-tex/pipeline.tex: $(foreach s, $(subst paper,,$(makesrc)), $(mtexdir)/$(s).tex)
+$(mtexdir)/pipeline.tex: $(foreach s, $(subst paper,,$(makesrc)), $(mtexdir)/$(s).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/pdflatex ] && [ x"$(pdf-build-final)" != x ]; then
-	  cat $(mtexdir)/*.tex > $@
+
+          # First make sure the `tex/pipeline' symbolic link exists.
+	  if [ ! -e tex/pipeline ]; then ln -s $(texdir) tex/pipeline; fi
+
+          # Put a LaTeX input command for all the necessary macro files.
+	  rm -f $(mtexdir)/pipeline.tex
+	  for t in $(subst paper,,$(makesrc)); do
+	    echo "\input{tex/pipeline/macros/$$t.tex}" >> $(mtexdir)/pipeline.tex
+	  done
 	else
 	  echo
 	  echo "-----"
@@ -86,15 +93,15 @@ tex/pipeline.tex: $(foreach s, $(subst paper,,$(makesrc)), $(mtexdir)/$(s).tex)
 # necessary bibliography before making the final paper. So we'll first have
 # one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
 #
-# NOTE: `tex/pipeline.tex' is an order-only-prerequisite for
+# NOTE: `$(mtexdir)/pipeline.tex' is an order-only-prerequisite for
 # `paper.bbl'. This is because we need to run LaTeX in both the `paper.bbl'
-# recipe and the `paper.pdf' recipe. But if `tex/references.tex' hasn't
+# recipe and the `paper.pdf' recipe. But if `tex/src/references.tex' hasn't
 # been modified, we don't want to re-build the bibliography, only the final
 # PDF.
-$(texbdir)/paper.bbl: tex/references.tex                         \
-                      | $(tikzdir) $(texbdir) tex/pipeline.tex
-        # If `tex/pipeline.tex' is empty, then the PDF must not be built.
-	@macros=$$(cat tex/pipeline.tex)
+$(texbdir)/paper.bbl: tex/src/references.tex                         \
+                      | $(tikzdir) $(texbdir) $(mtexdir)/pipeline.tex
+        # If `$(mtexdir)/pipeline.tex' is empty, don't build PDF.
+	@macros=$$(cat $(mtexdir)/pipeline.tex)
 	if [ x"$$macros" != x ]; then
 
           # We'll run LaTeX first to generate the `.bcf' file (necessary
@@ -119,19 +126,13 @@ $(texbdir)/paper.bbl: tex/references.tex                         \
 # to run everything cleanly from there, it is necessary to add the current
 # directory (top reproduction pipeline directory) to the `TEXINPUTS'
 # environment variable.
-paper.pdf: tex/pipeline.tex paper.tex $(texbdir)/paper.bbl       \
+paper.pdf: $(mtexdir)/pipeline.tex paper.tex $(texbdir)/paper.bbl       \
 	   | $(tikzdir) $(texbdir)
 
-        # If `tex/pipeline.tex' is empty, then the PDF must not be built.
-	@macros=$$(cat tex/pipeline.tex)
+        # If `$(mtexdir)/pipeline.tex' is empty, don't build the PDF.
+	@macros=$$(cat $(mtexdir)/pipeline.tex)
 	if [ x"$$macros" != x ]; then
 
-          # If it doesn't exist, make the `tex/tikz' symbolic link
-          # directory. This is necessary for situations when we just want
-          # TeX to use built figures instead of actually building the
-          # figures.
-	  if [ ! -e tex/tikz ]; then ln -s $(tikzdir) tex/tikz; fi
-
           # Go into the top TeX build directory and make the paper.
 	  p=$$(pwd)
 	  export TEXINPUTS=$$p:$$TEXINPUTS