#!/usr/bin/make -f
# -*- makefile -*-
# debian/rules file for beast2-mcmc
# Andreas Tille <tille@debian.org>
# GPL

#export DH_VERBOSE=1
export LC_ALL=C.UTF-8

JAVA_HOME  := /usr/lib/jvm/default-java

DEBJAR    := /usr/share/java
# This does not seem to have any effect at all.  The only way to add
# CLASSPATH relieably is editing build.xml
# CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(DEBJAR)/antlr4-runtime.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:$(DEBJAR)/colt.jar:$(DEBJAR)/fest-util.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar

# to run the test suite
JAVA       := $(JAVA_HOME)/bin/java
ANT_HOME   := /usr/share/ant
ANT_BIN    := $(ANT_HOME)/bin/ant
ANT_ARGS   := -Dcompile.debug=true -Dcompile.optimize=true

%:
	dh $@ --with javahelper

CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
PDFLATEX:=pdflatex -interaction=batchmode

override_dh_compress:
	dh_compress --exclude=.pdf

override_dh_clean:
	# Removing our files generated manually with antlr4.
	if [ -e debian/treeparser ]; then \
	    rm src/beast/base/evolution/tree/treeparser/*.java; \
	    mv debian/treeparser/*.java src/beast/base/evolution/tree/treeparser; \
	    rm -rf debian/treeparser; \
	fi
	# Removing the build dirs, with build .class, .jar and .zip inside
	rm -rf build beastfx/build release/package
	# Saving three files ro restore the orig source tree after dh_clean
	for F in examples/nexus/primate-mtDNA.nex~ examples/nexus/ringe.nex~ examples/testHKY.xml~; do \
	    cp $$F $$F.save; \
	done
	dh_clean
	for F in examples/nexus/primate-mtDNA.nex~ examples/nexus/ringe.nex~ examples/testHKY.xml~; do \
	    mv $$F.save $$F; \
	done

execute_before_dh_auto_configure:
	# Replacing upstream .java files generated by a recent antlr4 with ones
	# generated on-the-fly with Debian-packaged antlr4.
	mkdir debian/treeparser
	mv src/beast/base/evolution/tree/treeparser/*.java debian/treeparser
	antlr4 -visitor -listener -package beast.base.evolution.tree.treeparser src/beast/base/evolution/tree/treeparser/*.g4

override_dh_auto_build:
	ant -Duser.name debian -f beastfx/build.xml dist_all_BEAST dist_all_BeastFX

override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
	ant -Duser.name debian -f beastfx/build.xml junit
endif