diff options
Diffstat (limited to 'reproduce/analysis')
| -rw-r--r-- | reproduce/analysis/make/initialize.mk | 21 | ||||
| -rw-r--r-- | reproduce/analysis/make/paper.mk | 74 | ||||
| -rw-r--r-- | reproduce/analysis/make/top-make.mk | 7 |
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 \ |