debian/changelog

@@ -7,7 +7,7 @@ clearcut (1.0.9-4) UNRELEASED; urgency=medium
   * Add autopkgtest
     Closes: #909711
 
- -- Joyce Zhou <jyzhou15@uw.edu>  Thu, 28 Mar 2019 09:01:31 +0100
+ -- Joyce Zhou <jyzhou15@uw.edu>  Thu, 28 Mar 2019 22:16:52 -0700
 
 clearcut (1.0.9-3) unstable; urgency=medium
 

debian/tests/check-malformed

+#!/bin/sh
+# do not use set -e because we expect an error code
+
+kg="clearcut"
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  # Double quote below to expand the temporary directory variable now versus
+  # later is on purpose.
+  # shellcheck disable=SC2064
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+# run clearcut with no args, passing in empty content.
+# This should return nonzero (malformed input)
+echo "" | clearcut
+
+exit [ "$?" -neq 0 ]
+

debian/tests/control

 Tests: run-unit-test
 Depends: @
 Restrictions: allow-stderr
+
+Tests: check-malformed
+Depends: @
+Restrictions: allow-stderr

debian/tests/run-unit-test

@@ -19,5 +19,7 @@ cd "${AUTOPKGTEST_TMP}"
 clearcut --alignment --DNA --in=alignment1.dist --out=treefile.tre
 # Compute tree from matrix
 clearcut --distance --in=symmetric.dist --out=symmtree.tre
+# Run clearcut with properly formatted stdin input
+cat lower_diag.dist | clearcut
 
 echo "test pass"