Imported recent work in master, minor conflict fixed in paper.mk

Only two conflicts came up in the newly added comments of 'paper.mk' in the
Maneage branch. It happened because in this project we don't use
'pdflatex', but 'latex' alone.

2 files changed, 14 insertions, 6 deletions

diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 489f9e3..d01cda0 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -243,6 +243,7 @@ clean: clean-mmap
 	rm -rf $(BDIR)/tex/macros/!(dependencies.tex|dependencies-bib.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
 
 distclean: clean
         #  Without cleaning the Git hooks, we won't be able to easily
@@ -385,19 +386,15 @@ dist-zip: $(project-package-contents)
 # Package the software tarballs.
 dist-software:
 	curdir=$$(pwd)
+	dirname=software-$(project-commit-hash)
 	cd $(BDIR)
-	if [ -d .git ]; then
-	  dirname="software-$$(git describe --dirty --always --long)"
-	else
-	  dirname="software-NOGIT";
-	fi
 	mkdir $$dirname
 	cp -L software/tarballs/* $$dirname/
 	tar -cf $$dirname.tar $$dirname
 	gzip -f --best $$dirname.tar
 	rm -rf $$dirname
 	cd $$curdir
-	mv $(BDIR)/$$dir.tar.gz ./
+	mv $(BDIR)/$$dirname.tar.gz ./
 
 
 
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index cc43117..6d69d49 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -112,8 +112,16 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
           # for `biber') and then run `biber' to generate the `.bbl' file.
 	  export TEXINPUTS=$$p:
 	  cd $(texbdir);
+
+          # Note: the option '-shell-escape' is "normally disallowed for
+          # security reasons" according to the `info pdflatex' manual, but
+          # is enabled here in order to allow the use of PGFPlots. If you
+          # do not use PGFPlots, then you should remove the `-shell-escape'
+          # option for better security. See
+          # https://savannah.nongnu.org/task/?15694 for details.
 	  latex -shell-escape -halt-on-error $$p/paper.tex
 	  bibtex paper
+
           # Hack: tidy up eprint+doi style that didn't work in .bst file.
           # TODO (better): read Part 4 of
           # http://mirrors.ctan.org/info/bibtex/tamethebeast/ttb_en.pdf
@@ -150,6 +158,9 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
 	  p=$$(pwd)
 	  export TEXINPUTS=$$p:
 	  cd $(texbdir)
+
+          # See above for a warning and brief discussion on the the
+          # pdflatex option `-shell-escape'.
 	  latex -shell-escape -halt-on-error $$p/paper.tex
 
           # Convert the DVI to PostScript, and the PostScript to PDF. The