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introvoyz045
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COPASI

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COPASI
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# The following variables need to be adjusted to suit your installation
# of dblatex:

# The dblatex installation directory
# DBLATEX_PATH=/home/usr
#DBLATEX_PATH=/sw
DBLATEX_PATH=/usr/

# directory where the profiling/profile.xsl file is located
PROFILE_DIR=/usr/share/xml/docbook/stylesheet/nwalsh/
#PROFILE_XSL=/sw/share/xml/xsl/docbook-xsl/profiling/profile.xsl
PROFILE_XSL=/usr/share/xml/docbook/stylesheet/docbook-xsl/profiling/profile.xsl 

# These should be correct after DBLATEX_PATH
DBLATEX=$(DBLATEX_PATH)/bin/dblatex
DBLATEX_TEXINPUTS=$(DBLATEX_PATH)/share/dblatex/latex//:$(TEXINPUTS)
DBLATEX_SGML_CATALOG_FILES=$(SGML_CATALOG_FILES):/etc/xml/catalog

#PDFLATEX = /sw/bin/pdflatex
PDFLATEX = pdflatex

SOURCES = copasi.xml \
	copasi_GUI.xml \
	copasi_commandLine.xml \
	copasi_fileFormats.xml \
	copasi_methods.xml \
	copasi_errorMessages.xml \
	copasi_bibliography.xml \
	copasi_model.xml \
	copasi_bindings.xml

IMAGES = images/Compartments_01.png \
         images/Compartments_02.png \
         images/Compartments_03.png \
         images/Compartments_04.png \
         images/Compartments_05.png \
         images/Compartments_06.png \
         images/Compartments_07.png \
         images/ElementaryModesTask_01.png \
         images/Functions_01.png \
         images/Functions_02.png \
         images/General_01.png \
         images/Layout_01.png \
         images/MCATask_01.png \
         images/MCATask_02.png \
         images/MCATask_03.png \
         images/MassConservationTask_01.png \
         images/MassConservationTask_02.png \
         images/Species_01.png \
         images/Species_02.png \
         images/Species_03.png \
         images/Species_04.png \
         images/Species_05.png \
         images/GlobalQuantities_01.png \
         images/GlobalQuantities_02.png \
         images/GlobalQuantities_03.png \
         images/ParameterEstimation_01.png \
         images/ParameterEstimation_02.png \
         images/ParameterEstimation_05.png \
         images/Platforms_01.png \
         images/PlotWindow_01.png \
         images/Plots_01.png \
         images/Plots_02.png \
         images/Plots_03.png \
         images/Plots_04.png \
         images/Plots_05.png \
         images/Plots_06.png \
         images/Reactions_01.png \
         images/Reactions_02.png \
         images/Reports_01.png \
         images/Reports_02.png \
         images/Reports_03.png \
         images/Reports_04.png \
         images/Reports_05.png \
         images/Sliders_01.png \
         images/Sliders_02.png \
         images/Sliders_03.png \
         images/SteadyStateTask_01.png \
         images/SteadyStateTask_02.png \
         images/TimeCourseTask_01.png \
         images/TimeCourseTask_02.png \
         images/TimeCourseTask_03.png \
         images/Wizard_01.png \
	 figures/caution.eps \
	 figures/caution.pdf \
	 figures/important.eps \
	 figures/important.pdf \
	 figures/note.eps \
	 figures/note.pdf \
	 figures/tip.eps \
	 figures/tip.pdf \
	 figures/warning.eps \
	 figures/warning.pdf

PYTHON_EXAMPLES = ../../copasi/bindings/python/examples/example1.py \
	          ../../copasi/bindings/python/examples/example2.py \
	          ../../copasi/bindings/python/examples/example3.py \
	          ../../copasi/bindings/python/examples/example4.py 

JAVA_EXAMPLES =   ../../copasi/bindings/java/examples/example1.java \
	          ../../copasi/bindings/java/examples/example2.java \
	          ../../copasi/bindings/java/examples/example3.java \
	          ../../copasi/bindings/java/examples/example4.java 

CPP_EXAMPLES =    ../../copasi/bindings/cpp_examples/example1/example1.cpp \
	          ../../copasi/bindings/cpp_examples/example2/example2.cpp \
	          ../../copasi/bindings/cpp_examples/example3/example3.cpp \
	          ../../copasi/bindings/cpp_examples/example4/example4.cpp 


COPASI_DBLATEX=../../admin/documentation/dblatex
COPASI_TEXINPUTS=.:$(COPASI_DBLATEX):$(DBLATEX_TEXINPUTS):$(TEXINPUTS)

.PHONY: clean all

all: copasi.pdf copasi_bindings_java.pdf copasi_bindings_python.pdf copasi_bindings_cpp.pdf 

copasi.tex: $(SOURCES) copasi_bindings_cpp.xml copasi_bindings_java.xml copasi_bindings_python.xml
	SGML_CATALOG_FILES=$(DBLATEX_SGML_CATALOG_FILES) $(DBLATEX) -p $(COPASI_DBLATEX)/copasi.xsl -t tex copasi.xml

copasi.pdf: copasi.tex $(IMAGES) 
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $< 
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $<
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $<

copasi.xhtml: $(SOURCES) $(IMAGES) copasi_xhtml.xsl copasi_bindings_cpp.xml copasi_bindings_java.xml copasi_bindings_python.xml
	@[ -d $@ ] || mkdir $@
	@[ -d $@/images ] || mkdir $@/images
	@cp images/*.png $@/images
	(cd $@; \
	  xsltproc ../copasi_xhtml.xsl ../copasi.xml; \
	  echo Preparing for mml to png conversion.; \
	  for f in *.html; do \
	    sed -e 's?<mml:math?\n<mml:math?g' \
	        -e 's?</mml:math>?</mml:math>\n?g' $$f > $$f.tmp \
            && mv $$f.tmp $$f; \
          done; \
	  ../../../admin/mml2png.php *.html; \
	  rm *.mml;\
	cd ..)

copasi.html: copasi.tex $(IMAGES) copasi_bindings_cpp.xml copasi_bindings_java.xml copasi_bindings_python.xml 
	@[ -d $@ ] || rm -rf copasi.html
	TEXINPUTS=$(COPASI_TEXINPUTS) \
	latex2html -white -split +0 -show_section_numbers -image_type gif \
		   -no_navigation -local_icons -discard \
		   -mkdir -dir $@ $<

copasi_bindings_cpp.xml: copasi_bindings.xml $(CPP_EXAMPLES)
	xsltproc --stringparam profile.condition "CPP" $(PROFILE_XSL) $< | sed -e '1d' > $@

copasi_bindings_cpp.tex: $(SOURCES) copasi_bindings_cpp.xml 
	SGML_CATALOG_FILES=$(DBLATEX_SGML_CATALOG_FILES) $(DBLATEX) -p $(COPASI_DBLATEX)/copasi.xsl -t tex copasi_bindings_cpp.xml

copasi_bindings_cpp.pdf: copasi_bindings_cpp.tex $(IMAGES) 
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $< 
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $<
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $<


copasi_bindings_java.xml: copasi_bindings.xml $(JAVA_EXAMPLES)
	xsltproc --stringparam profile.condition "JAVA" $(PROFILE_XSL) $< | sed -e '1d' > $@

copasi_bindings_java.tex: $(SOURCES) copasi_bindings_java.xml 
	SGML_CATALOG_FILES=$(DBLATEX_SGML_CATALOG_FILES) $(DBLATEX) -p $(COPASI_DBLATEX)/copasi.xsl -t tex copasi_bindings_java.xml

copasi_bindings_java.pdf: copasi_bindings_java.tex $(IMAGES) 
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $< 
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $<
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $<

copasi_bindings_python.xml: copasi_bindings.xml $(PYTHON_EXAMPLES)
	xsltproc --stringparam profile.condition "PYTHON" $(PROFILE_XSL) $< | sed -e '1d' > $@

copasi_bindings_python.tex: $(SOURCES) copasi_bindings_python.xml 
	SGML_CATALOG_FILES=$(DBLATEX_SGML_CATALOG_FILES) $(DBLATEX) -p $(COPASI_DBLATEX)/copasi.xsl -t tex copasi_bindings_python.xml

copasi_bindings_python.pdf: copasi_bindings_python.tex $(IMAGES) 
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $< 
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $<
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $<


UserManual.xhtml: UserManual.html
	./html2xhtml $<

UserManual.tex: UserManual.xhtml
	xsltproc --novalid $(HLPARAMS) \
		-o $@ xh2latex.xsl $< 

UserManual.bib: UserManual.xhtml
	xsltproc --novalid -o $@ xh2bib.xsl $<

UserManual.pdf: UserManual.tex
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $< 
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $<
	TEXINPUTS=$(COPASI_TEXINPUTS) $(PDFLATEX) $<

clean:
	-rm -f copasi.tex UserManual.tex
	-rm -f copasi.pdf UserManual.pdf
	-rm -f copasi.out UserManual.out
	-rm -f copasi.idx UserManual.idx
	-rm -f copasi.log UserManual.log
	-rm -f copasi.aux UserManual.aux
	-rm -f copasi.glo UserManual.glo
	-rm -f fotex.log
	-rm -rf copasi.html
	-rm -rf copasi.xhtml UserManual.xhtml
	-rm -f copasi_bindings_*.xml