debian/changelog

+cnvkit (0.9.3-2) unstable; urgency=medium
+
+  * Add missing build-dep on python3-future. (Closes: #901877)
+  * debian/rules: fix override_dh_auto_test-does-not-check-DEB_BUILD_OPTIONS
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 19 Jun 2018 15:05:43 -0700
+
 cnvkit (0.9.3-1) unstable; urgency=medium
 
   * New upstream version.

debian/control

@@ -17,6 +17,7 @@ Build-Depends: debhelper (>= 11~),
                python3-scipy,
                python3-matplotlib,
                python3-pyvcf,
+               python3-future,
                r-cran-pscbs
 #              python-subprocess32	# required only for python2
 Standards-Version: 4.1.4

debian/patches/python3compat.patch

+Description: enable building with Python3
 Index: cnvkit/test/Makefile
 ===================================================================
 --- cnvkit.orig/test/Makefile

debian/rules

@@ -3,14 +3,7 @@
 export LC_ALL=C.UTF-8
 export PYBUILD_NAME=cnvkit
 
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
-#DEBFLAVOR      := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
-#DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH  := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
-#GIT_TAG        := $(subst ~,_,$(VERSION))
+include /usr/share/dpkg/pkg-info.mk
 
 %:
 	dh $@ --with python3 --buildsystem=pybuild
@@ -42,14 +35,14 @@ override_dh_auto_install:
 	help2man --no-info --version-option=version \
 		--name="a command-line toolkit for copy number analysis." \
 		./cnvkit > debian/cnvkit.1
-	PYTHONPATH=$$PYTHONPATH:. debian/genmanpages.py ${VERSION}
+	PYTHONPATH=$$PYTHONPATH:. debian/genmanpages.py ${DEB_VERSION_UPSTREAM}
 	# no longer distributed
 	#cd scripts && PYTHONPATH=../ help2man --no-info \
-	#	--version-string=${VERSION} --help-option='-h' \
+	#	--version-string=${DEB_VERSION_UPSTREAM} --help-option='-h' \
 	#	./cnvkit-refFlat2bed --name='Generate a BED file of the genes or exons in the reference genome given in UCSC refFlat.txt format.' \
 	#	> ../debian/cnvkit-refFlat2bed.1; 
 	cd scripts && PYTHONPATH=../ help2man --no-info \
-		--version-string=${VERSION} --help-option='-h' \
+		--version-string=${DEB_VERSION_UPSTREAM} --help-option='-h' \
 		./cnvkit-reference2targets --name='Extract target and antitarget BED files from a CNVkit reference file.' \
 		> ../debian/cnvkit-reference2targets.1;
 	cd scripts && for script in *; do \
@@ -59,7 +52,9 @@ override_dh_auto_install:
 	#mv genome2access.py scripts/	# no longer distributed
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	cd test && ${MAKE}
+endif
 
 override_dh_auto_clean:
 	cd test && ${MAKE} clean || /bin/true