[med-svn] [Git][med-team/pdb2pqr][master] 4 commits: Fixing autopkgtest 'installation-test' by substituting non-existent PDB file with an existing one.

[Andrius Merkys]

Andrius Merkys pushed to branch master at Debian Med / pdb2pqr


Commits:
b05b5ddc by Andrius Merkys at 2019-03-09T10:54:36Z
Fixing autopkgtest 'installation-test' by substituting non-existent PDB file with an existing one.

- - - - -
a7d90a7e by Andrius Merkys at 2019-03-09T11:09:06Z
Removing autopkgtest 'ligands-test' as it depended on files that are not shipped by the upstream anymore.

- - - - -
2c267912 by Andrius Merkys at 2019-03-09T11:13:23Z
Removing 'ligands-test' from debian/tests/control.

- - - - -
3b3c1168 by Andrius Merkys at 2019-03-09T11:17:33Z
Updating debian/changelog.

- - - - -


4 changed files:

- debian/changelog
- debian/tests/control
- debian/tests/installation-test
- − debian/tests/ligands-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,8 +1,15 @@
 pdb2pqr (2.1.1+dfsg-5) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Build-Depends: dh-python
 
- -- Andreas Tille <tille at 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 at 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 deleted
=====================================
@@ -1,33 +0,0 @@
-#!/bin/sh
-# autopkgtest check: build and run with default test data
-# Author: Tatiana Malygina <merlettaia at 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



View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/compare/c417245a2589ef09845c5f4ebbe6f485f8764555...3b3c1168828880de2a5ab73b7422d0f5b3707c13

-- 
View it on GitLab: https://salsa.debian.org/med-team/pdb2pqr/compare/c417245a2589ef09845c5f4ebbe6f485f8764555...3b3c1168828880de2a5ab73b7422d0f5b3707c13
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