#!/usr/bin/make -f


%:
	dh $@ --with python3


override_dh_auto_configure:
	CFLAGS="-I/usr/include/json-c/ -I/usr/include/libsvm/"  CXXFLAGS="-I/usr/include/json-c/ -I/usr/include/libsvm/" dh_auto_configure -- --with-cluster --without-python --with-python3 --without-forester --without-doc --without-tutorial
	if [ -r man/help2manWrapper.sh ]; then chmod +x man/help2manWrapper.sh; fi

override_dh_auto_build:
	if [ ! -d src/cthreadpool ]; then \
	  mkdir -p src/cthreadpool && \
	  cd src/cthreadpool && \
	  ln -s /usr/include/cthreadpool/thpool.h . && \
	  ln -s /usr/share/cthreadpool/thpool.c . ; \
	fi

	dh_auto_build
	if [ -r doc/RNAlib-*pdf; then cd doc && ln -f RNAlib-*.pdf RNAlib.pdf; fi

override_dh_auto_install:
	# rename perl scripts to remove the *.pl extension and create manpage via perldoc
	mkdir -p $(CURDIR)/debian/tmp/usr/bin
	mkdir -p $(CURDIR)/debian/tmp/usr/share/man/man1
	#for script in `ls Utils/*.pl` ; do \
	#  newscript=`basename $${script} .pl` ; \
	#  cp -a $${script} $(CURDIR)/debian/tmp/usr/bin/$${newscript} ; \
	#  perldoc -onroff -F $${script} | \
	#  sed -e "s/$${newscript}\.pl/$${newscript}/g" \
	#  > $(CURDIR)/debian/tmp/usr/share/man/man1/$${newscript}.1 ; \
	#  if [ ! -s $(CURDIR)/debian/tmp/usr/share/man/man1/$${newscript}.1 ] ; then \
	#    rm -f $(CURDIR)/debian/tmp/usr/share/man/man1/$${newscript}.1 ; \
	#  fi ; \
	#done
	dh_auto_install
	find debian/ -name .gitignore -delete

SHELL=/bin/bash
override_dh_auto_clean:
	dh_auto_clean
	rm -f doc/RNAlib*
	rm -f doc/*.db
	rm -f interfaces/Perl/Makefile.perl.old
	rm -f interfaces/Python/install.record
	rm -rf doc/html
	rm -rf doc/latex
	rm -rf src/cthreadpool
	#find . \( -type f -a \( -name config.status -o -name config.sub -o -name config.guess \) \) -delete
	find src/ViennaRNA -name "*.hex" -delete
	find . -name "*eps-converted-to.pdf" -delete
	rm -f src/bin/RNAfold_cmdl.[ch]
	rm -f aclocal.m4 src/Kinfold/aclocal.m4
	grep -rl "DO NOT MODIFY THIS FILE!  It was generated by help2man" man | xargs -r rm -f
	grep -lri "DO NOT EDIT THIS FILE." src | grep -v debian | xargs -r rm
	grep -lri "File autogenerated by gengetopt" src | grep -v debian | xargs -r rm
	grep -lri "Generated from configure.ac" . | grep -v debian | xargs -r rm
	grep -lri "generated by GNU Gengetopt" . | grep -v debian | xargs -r rm
	grep -lri "DO NOT MODIFY THIS FILE" man | grep -v debian | xargs -r rm
	grep -lri "made by GNU Bison" src | grep -v debian | xargs -r rm
	grep -lri "produced by makeinfo version" man | grep -v debian | xargs -r rm
	#rm -f src/Kinfold/INSTALL src/RNAforester/INSTALL src/RNAlocmin/RNAlocmin
	# removal of self-added symbolic links
	rm -rf src/cthreadpool/
	find . -name Makefile.in -delete
	#rm -f  config/ar-lib config/compile config/depcomp config/install-sh config/ltmain.sh config/missing config/test-driver config/texinfo.tex
	rm -f configure
	rm -f m4/libtool.m4
	rm -f src/{RNAforester,RNAlocmin,Kinfold,Kinwalker}/{compile,depcomp,install-sh,missing,aclocal.m4,ylwrap}
	rm -f src/{Kinwalker,RNAforester}/{aclocal.m4,ylwrap,install-sh
	rm  -f src/Kinfold/config.guess src/Kinfold/config.sub src/Kinfold/configure
	rm  -f src/Kinwalker/configure
	rm  -f src/RNAforester/configure src/RNAforester/g2-0.72/configure
	rm  -f src/RNAlocmin/config.guess src/RNAlocmin/config.sub src/RNAlocmin/configure
	rm -f config/ltmain.sh src/Kinfold/INSTALL src/RNAforester/INSTALL

	# removing self-created man pages
	find man/ -name "*.1" -delete


override_dh_compress:
	dh_compress --exclude=.pdf

override_dh_missing: