Datasets:

introvoyz045
/

COPASI

License:

Dataset card Files Files and versions

xet

Community

COPASI / data /userdocs /userguide /Makefile

introvoyz045

Migrated from GitHub

7e59e4c verified 14 days ago

Raw History Blame Contribute Delete

7.73 kB

# 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

	# 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