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-rw-r--r--reproduce/analysis/make/initialize.mk21
-rw-r--r--reproduce/analysis/make/paper.mk74
-rw-r--r--reproduce/analysis/make/top-make.mk7
3 files changed, 55 insertions, 47 deletions
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 75f87ee..0cc04ee 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -77,21 +77,11 @@ endif
# (independent parts of the paper can be added to it independently). To fix
# this problem, when we are in a group setting, we'll use the user's ID to
# create a separate LaTeX build directory for each user.
-#
-# The same logic applies to the final paper PDF: each user will create a
-# separte final PDF (for example `paper-user1.pdf' and `paper-user2.pdf')
-# and no `paper.pdf' will be built. This isn't a problem because
-# `initialize.tex' is a .PHONY prerequisite, so the rule to build the final
-# paper is always executed (even if it is present and nothing has
-# changed). So in terms of over-all efficiency and processing steps, this
-# doesn't change anything.
ifeq (x$(GROUP-NAME),x)
texbtopdir = build
-final-paper = paper.pdf
else
user = $(shell whoami)
texbtopdir = build-$(user)
-final-paper = paper-$(user).pdf
endif
texbdir = $(texdir)/$(texbtopdir)
tikzdir = $(texbdir)/tikz
@@ -220,14 +210,15 @@ project-package-contents = $(texdir)/$(project-package-name)
# we want to ensure that the file is always built in every run: it contains
# the project version which may change between two separate runs, even when
# no file actually differs.
-.PHONY: all clean dist dist-zip dist-lzip distclean clean-mmap \
+.PHONY: all clean dist dist-zip dist-lzip texclean distclean \
$(project-package-contents) $(mtexdir)/initialize.tex
-# --------- Delete for no Gnuastro ---------
-clean-mmap:; rm -f reproduce/config/gnuastro/mmap*
-# ------------------------------------------
+texclean:
+ rm *.pdf
+ rm -rf $(BDIR)/tex/build/*
+ mkdir $(BDIR)/tex/build/tikz # 'tikz' is assumed to already exist.
-clean: clean-mmap
+clean:
# Delete the top-level PDF file.
rm -f *.pdf
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index d8f18b3..1776363 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -18,6 +18,7 @@
+
# LaTeX macros for paper
# ----------------------
#
@@ -55,8 +56,8 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
done
# Possibly print the appendix in the final PDF.
- if [ x"$(noappendix)" = x1 ]; then
- echo "\newcommand{\noappendix}{}" >> $$projecttex
+ if [ x"$(separatesupplement)" = x1 ]; then
+ echo "\newcommand{\separatesupplement}{}" >> $$projecttex
fi
# Possibly highlight the '\new' parts of the text.
@@ -99,17 +100,18 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
# The bibliography
# ----------------
#
-# We need to run the `biber' program on the output of LaTeX to generate the
-# necessary bibliography before making the final paper. So we'll first have
-# one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
+# We need to run the `bibtex' program on the output of LaTeX to generate
+# the necessary bibliography before making the final paper. So we'll first
+# have one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
#
# NOTE: `$(mtexdir)/project.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/src/references.bib' hasn't
# been modified, we don't want to re-build the bibliography, only the final
# PDF.
-$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
- | $(mtexdir)/project.tex
+bbls = $(foreach t,$(subst .pdf,,$(top-pdfs)),$(texbdir)/$(t).bbl)
+$(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
+ $(mtexdir)/dependencies-bib.tex | $(mtexdir)/project.tex
# If `$(mtexdir)/project.tex' is empty, don't build PDF.
@macros=$$(cat $(mtexdir)/project.tex)
@@ -120,14 +122,14 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
# building directory.
p=$$(pwd)
if ! [ -L $(texbdir)/references.bib ]; then
- ln -s $$p/tex/src/references.tex $(texbdir)/references.bib
+ ln -sf $$p/tex/src/references.tex $(texbdir)/references.bib
fi
# Copy the improved IEEE bst file into the build directory.
# The improved bst file provides ArXiv clickable URLs and
# if available, open-access URLs based on the DOIs, with
# closed-access URLs as a fallback, via https://oadoi.org .
- cp -pv $$p/tex/src/IEEEtran_openaccess.bst $(texbdir)
+ ln -sf $$p/tex/src/IEEEtran_openaccess.bst $(texbdir)/
# We'll run LaTeX first to generate the `.bcf' file (necessary
# for `biber') and then run `biber' to generate the `.bbl' file.
@@ -140,19 +142,27 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
# it. It will be built anyway once this rule is done.
rm -f $@
+ # Put a link to the main LaTeX source that we want to build.
+ if [ $* = paper ]; then sdir="$$p"
+ else sdir="$$p"/tex/src
+ fi
+ ln -sf "$$sdir"/$*.tex ./
+
# The pdflatex option '-shell-escape' is "normally disallowed for
# security reasons" according to the `info pdflatex' manual, but
# is enabled here in order to allow the use of PGFPlots. If you
- # do not use PGFPlots, then you should remove the `-shell-escape'
+ # do not use PGFPlots, then you can remove the `-shell-escape'
# option for better security. See
# https://savannah.nongnu.org/task/?15694 for details.
- latex -shell-escape -halt-on-error "$$p"/paper.tex
-
- # Since we have multiple bibliographies (one for the main body,
- # and one for the appendix), we use 'multibib'. Multibib creates
- # a separate '.aux' file for each bibliography.
- bibtex paper
- if [ x"$(noappendix)" != x1 ]; then
+ latex -shell-escape -halt-on-error $*.tex
+
+ # When we are building the main paper and the appendices are to
+ # be built within the main paper's PDF, we need two
+ # bibliographies: one for the main body, and one for the
+ # appendix. For this, we use 'multibib'. Multibib creates a
+ # separate '.aux' file for each bibliography.
+ bibtex $*
+ if [ x"$(separatesupplement)" != x1 ]; then
bibtex appendix
fi
@@ -160,14 +170,14 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
# TODO (better): read Part 4 of
# http://mirrors.ctan.org/info/bibtex/tamethebeast/ttb_en.pdf
# and fix the .bst style properly.
- cp -pv paper.bbl paper-tmp.bbl \
- && sed -e "s/\'/EOLINE/g" paper-tmp.bbl \
+ cp -pv $*.bbl $*-tmp.bbl \
+ && sed -e "s/\'/EOLINE/g" $*-tmp.bbl \
| tr -d '\n' \
| sed -e 's/\([0-9]\)\( \|EOLINE\)}/\1}/g' \
| sed -e 's/\([^,]\) *\( \|EOLINE\) *\\eprint/\1, \\eprint/g' \
| sed -e 's/\([^,]\) *\( \|EOLINE\) *\\doi/\1, \\doi/g' \
- | sed -e 's/EOLINE/\n/g' > paper.bbl
- if [ x"$(noappendix)" != x1 ]; then
+ | sed -e 's/EOLINE/\n/g' > $*.bbl
+ if [ x"$(separatesupplement)" != x1 ]; then
cp -pv appendix.bbl appendix-tmp.bbl \
&& sed -e "s/\'/EOLINE/g" appendix-tmp.bbl \
| tr -d '\n' \
@@ -178,18 +188,19 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
fi
# Paper-specific hacks for reducing very-long author lists.
- cp -pv paper.bbl paper-tmp.bbl \
- && sed -e "s/\'/EOLINE/g" paper-tmp.bbl \
+ cp -pv $*.bbl $*-tmp.bbl \
+ && sed -e "s/\'/EOLINE/g" $*-tmp.bbl \
| tr -d '\n' \
| sed -e 's;, D\..Chong[^{]*Forstag; et al.\\/;' \
| sed -e 's;, V\..Khodiyar[^{]*Whyte; et al.\\/;' \
- | sed -e 's/EOLINE/\n/g' > paper.bbl
+ | sed -e 's/EOLINE/\n/g' > $*.bbl
+
# The pre-final run of LaTeX after 'paper.bbl' was created.
- latex -shell-escape -halt-on-error "$$p"/paper.tex
+ latex -shell-escape -halt-on-error $*.tex
fi
-# | sed -e 's;Chong;HELLO MUM;' \
+
# The final paper
@@ -200,7 +211,8 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
# to run everything cleanly from there, it is necessary to add the current
# directory (top project directory) to the `TEXINPUTS' environment
# variable.
-paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
+$(top-pdfs): %.pdf: $(mtexdir)/project.tex paper.tex \
+ tex/src/appendix-*.tex $(texbdir)/%.bbl
# If `$(mtexdir)/project.tex' is empty, don't build the PDF.
@macros=$$(cat $(mtexdir)/project.tex)
@@ -213,17 +225,17 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
# See above for a warning and brief discussion on the the
# pdflatex option `-shell-escape'.
- latex -shell-escape -halt-on-error "$$p"/paper.tex
+ latex -shell-escape -halt-on-error $*.tex
# Convert the DVI to PostScript, and the PostScript to PDF. The
# `-dNOSAFER' option to GhostScript allows transparencies in the
# conversion from PostScript to PDF, see
# https://www.ghostscript.com/doc/current/Language.htm#Transparency
- dvips paper.dvi
- ps2pdf paper.ps
+ dvips $*.dvi
+ ps2pdf $*.ps
# Come back to the top project directory and copy the built PDF
# file here.
cd "$$p"
- cp $(texbdir)/$@ $(final-paper)
+ cp $(texbdir)/$*.pdf $@
fi
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 18d54b1..d552dc1 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -64,8 +64,13 @@ include reproduce/software/config/LOCAL.conf
# If you are just interested in the processing and don't want to build the
# PDF, you can skip the creation of the final PDF by giving a value of
# `yes' to `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+ifeq ($(separatesupplement),0)
+top-pdfs = paper.pdf
+else
+top-pdfs = paper.pdf supplement.pdf
+endif
ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
-all: paper.pdf
+all: $(top-pdfs)
else
all:
@if [ "x$(GROUP-NAME)" = x ]; then \