debian/control

@@ -8,12 +8,13 @@ Testsuite: autopkgtest-pkg-python
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                dh-python,
-               python3-all,
-               python3-all-dev,
+               python3,
+               python3-dev,
                python3-setuptools,
-               python3-six,
-               python3-nose,
-               python3-xopen (>= 0.3.2),
+               python3-setuptools-scm,
+               python3-pytest-timeout,
+               python3-xopen (>= 0.5.0),
+               python3-dnaio (>= 0.3),
                cython3
 Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-cutadapt

debian/patches/series

+skip_cutadapt_executable_test.patch

debian/patches/skip_cutadapt_executable_test.patch

+Author: Liubov Chuprikova <chuprikovalv@gmail.com>
+Last-Update: Sat, 29 Jun 2019 01:12:11 +0200
+Description: Since built-time tests are running before installation,
+ executables are not available yet.
+
+
+--- a/tests/test_commandline.py
++++ b/tests/test_commandline.py
+@@ -541,6 +541,7 @@
+     run('--length -5', 'shortened-negative.fastq', 'small.fastq')
+ 
+ 
++@pytest.mark.skip(reason='We cannot test this during built-time tests')
+ def test_run_cutadapt_process():
+     subprocess.check_call(['cutadapt', '--version'])
+ 

debian/rules

@@ -17,9 +17,6 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 export PYBUILD_NAME=cutadapt
 
-PYTHON3 := $(shell py3versions -r)
-
-# main packaging script based on dh7 syntax
 %:
 	dh $@ --with python3 --buildsystem=pybuild
 
@@ -29,8 +26,5 @@ override_dh_install:
 	mv debian/python3-cutadapt/usr/bin/cutadapt debian/cutadapt/usr/bin/
 
 override_dh_auto_test:
-ifeq ($(filter nocheck,$(DEB_BUILD_OPTIONS)),)
-	for py in $(PYTHON3) ; do\
-	    $$py setup.py nosetests -v ; \
-	done
-endif
+	dh_auto_test -- -s custom --test-args="cd {build_dir}; \
+		py.test-3 --pyargs cutadapt tests"