debian/changelog

+python-biopython (1.75+dfsg-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Skip PDB_ResidueDepth test, as http://mgltools.scripps.edu/packages/MSMS
+    is not yet packaged for Debian
+  * Skip test_mmtf{,_online} as https://github.com/rcsb/mmtf-python is not yet
+    packaged for Debian
+  * Added missing test dependencies: python-unittest2, python{,3}-networkx,
+    samtools
+  * i386: build-dep on raxml for testing purposes
+  * Fix the ignoring of the test errors so that the python3 tests are still
+    run.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 10 Dec 2019 10:12:10 +0100
+
 python-biopython (1.75+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -31,6 +31,8 @@ Build-Depends: debhelper-compat (= 12),
                phyml [any-amd64 any-i386 arm64 armhf sparc64],
                prank,
                probcons,
+               python-networkx,
+               python3-networkx,
                python-mysqldb,
                python3-mysqldb,
                python-matplotlib,
@@ -47,7 +49,9 @@ Build-Depends: debhelper-compat (= 12),
                python3-scipy,
                python-setuptools,
                python3-setuptools,
-               raxml [any-amd64],
+               python-unittest2,
+               raxml [any-amd64 any-i386],
+               samtools [alpha arm64 armel armhf hppa ia64 m68k mips mips64el mipsel powerpc powerpcspe ppc64 ppc64el s390x sh4 sparc64],
                t-coffee,
                wise,
                python3-pygments

debian/rules

@@ -26,7 +26,7 @@ EXCLUDENONFREE=PAML_tools EmbossPhylipNew
 
 # avoid testing tools that are not packaged for Debian yet (or will never be packaged since they might be outdated)
 # This would not trigger a failure but bloats the build log with irrelevant noise
-EXCLUDENOTPACKAGED=MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool
+EXCLUDENOTPACKAGED=MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool PDB_ResidueDepth mmtf mmtf_online
 
 # avoid amd64 only tools on other architectures
 ifeq ($(BUILDARCH),amd64)
@@ -109,7 +109,7 @@ else
                              cp -a Doc/examples {build_dir}/Doc; \
                              cp -a Tests {build_dir}; \
                              cd {build_dir}/Tests; \
-                             env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline' || true
+                             env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline || true'
 	mv Tests_avoid/* Tests
 	rmdir Tests_avoid
 endif