debian/changelog

 pdb2pqr (2.1.1+dfsg-5) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Build-Depends: dh-python
 
- -- Andreas Tille <tille@debian.org>  Wed, 18 Jul 2018 09:59:58 +0200
+  [ Andrius Merkys ]
+  * Fixing autopkgtest 'installation-test' by substituting non-existent PDB
+    file with an existing one. Removing autopkgtest 'ligands-test' as it
+    depended on files that are not shipped by the upstream anymore.
+    (Closes: #903759)
+
+ -- Andrius Merkys <andrius.merkys@gmail.com>  Sat, 09 Mar 2019 06:16:19 -0500
 
 pdb2pqr (2.1.1+dfsg-4) unstable; urgency=medium
 

debian/tests/control

@@ -2,10 +2,6 @@ Tests: installation-test
 Depends: pdb2pqr
 Restrictions: allow-stderr
 
-Tests: ligands-test
-Depends: @
-Restrictions: allow-stderr
-
 Tests: pdb2pka-test
 Depends: @, python-networkx
 Restrictions: allow-stderr

debian/tests/installation-test

@@ -4,15 +4,6 @@
 
 set -e
 
-pkg=pdb2pqr
-
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cd $ADTTMP
-
 echo "Run pdb2pqr..."
-pdb2pqr --ff=amber "1FAS" output.txt
-[ -s output.txt ]
+pdb2pqr --ff=amber examples/1a1p/1a1p.pdb ${AUTOPKGTEST_TMP}/output.txt
+[ -s ${AUTOPKGTEST_TMP}/output.txt ]

debian/tests/ligands-test

-#!/bin/sh
-# autopkgtest check: build and run with default test data
-# Author: Tatiana Malygina <merlettaia@gmail.com>
-
-set -e
-
-pkg=pdb2pqr
-example_pkg=pdb2pqr
-
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cd $ADTTMP
-
-cp -a /usr/share/doc/${example_pkg}/examples/* .
-find . -type f -name "*.gz" -exec gunzip \{\} \;
-for lnk in `find . -type l -name "*.gz"` ; do
-    ln -s `basename $(readlink $lnk) .gz` `echo $lnk | sed 's/\.gz$//'`
-    rm $lnk
-done
-
-echo "Run pdb2pqr..."
-
-# following sample call was adopted from fabfile.py, 
-#     method "linux_bin_cross_platform_test":
-for pdb in 1ABF 1HPV 1HPX 1QBS 1XL5; do
-  echo "******** ${pdb} starting"
-  pdb2pqr --ff=parse --verbose --ligand="ligands/LIG_${pdb}.mol2" ${pdb} "${pdb}.pqr"
-  [ -s "${pdb}.pqr" ]
-  echo "******** ${pdb} done"
-done