debian/changelog

+srst2 (0.2.0-7) UNRELEASED; urgency=medium
+
+  * Use 2to3 to port from Python2 to Python3
+    Closes: #938560
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Remove trailing whitespace in debian/rules
+  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
+  * Set upstream metadata fields: Repository, Repository-Browse.
+  * Use markdown instead of python-markdown
+  
+  TODO:
+cd tests && python3 test_slurm_srst2.py && python3 test_srst2.py
+...........
+----------------------------------------------------------------------
+Ran 11 tests in 0.024s
+
+OK
+...........EE....
+======================================================================
+ERROR: test_get_pileup_with_defaults (__main__.TestMPileup)
+----------------------------------------------------------------------
+Traceback (most recent call last):
+  File "/usr/lib/python3/dist-packages/mock/mock.py", line 1330, in patched
+    return func(*args, **keywargs)
+  File "test_srst2.py", line 294, in test_get_pileup_with_defaults
+    'bowtie_sam_mod', 'fasta', 'pileup')
+  File "/build/srst2-0.2.0/scripts/srst2.py", line 735, in get_pileup
+    if args.threads > 1 and samtools_v1:
+TypeError: '>' not supported between instances of 'MagicMock' and 'int'
+
+======================================================================
+ERROR: test_get_pileup_with_overides (__main__.TestMPileup)
+----------------------------------------------------------------------
+Traceback (most recent call last):
+  File "/usr/lib/python3/dist-packages/mock/mock.py", line 1330, in patched
+    return func(*args, **keywargs)
+  File "test_srst2.py", line 242, in test_get_pileup_with_overides
+    'bowtie_sam_mod', 'fasta', 'pileup')
+  File "/build/srst2-0.2.0/scripts/srst2.py", line 735, in get_pileup
+    if args.threads > 1 and samtools_v1:
+TypeError: '>' not supported between instances of 'MagicMock' and 'int'
+
+----------------------------------------------------------------------
+Ran 17 tests in 0.042s
+
+FAILED (errors=2)
+make[1]: *** [debian/rules:34: override_dh_auto_test] Error 1
+
+
+ -- Andreas Tille <tille@debian.org>  Wed, 11 Dec 2019 15:20:13 +0100
+
 srst2 (0.2.0-6) unstable; urgency=medium
 
   * Respect DEB_BUILD_OPTIONS in override_dh_auto_test

debian/compat

-11

debian/control

@@ -3,31 +3,31 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python-all,
-               python-setuptools,
-               python-markdown,
+               python3-all,
+               python3-setuptools,
+               markdown,
                dos2unix,
-               python-mock,
-               python-scipy,
-               bowtie2,
-               samtools
-Standards-Version: 4.2.1
+               python3-mock <!nocheck>,
+               python3-scipy <!nocheck>,
+               bowtie2 <!nocheck>,
+               samtools <!nocheck>
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/srst2
 Vcs-Git: https://salsa.debian.org/med-team/srst2.git
 Homepage: https://katholt.github.io/srst2/
 
 Package: srst2
 Architecture: any
-Depends: ${python:Depends},
+Depends: ${python3:Depends},
          ${misc:Depends},
          bowtie2,
          cd-hit,
          samtools,
-         python-scipy,
-         python-biopython
-Recommends: python-rpy2
+         python3-scipy,
+         python3-biopython
+Recommends: python3-rpy2
 Description: Short Read Sequence Typing for Bacterial Pathogens
  This program is designed to take Illumina sequence data, a MLST database
  and/or a database of gene sequences (e.g. resistance genes, virulence

debian/patches/series

@@ -2,3 +2,4 @@ check_command_line_arguments.patch
 add_usr_bin_python_to_scripts.patch
 fix_test.patch
 fix_grep_call.patch
+2to3.patch

debian/rules

@@ -5,20 +5,20 @@
 include /usr/share/dpkg/default.mk
 
 %:
-	dh $@ --with python2
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_build:
 	dh_auto_build
-	markdown_py -f README.html README.md
-	markdown_py -f README_database_clustering.html database_clustering/README.md
+	markdown README.md > README.html
+	markdown database_clustering/README.md > database_clustering_README.html
 
 override_dh_install:
 	dh_install
 	mv debian/$(DEB_SOURCE)/usr/lib/*/dist-packages/$(DEB_SOURCE)/* debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)
 	rm -rf debian/*/usr/bin/*.py debian/$(DEB_SOURCE)/usr/lib/*/dist-packages/
-	# fix line endings to make sure Python interpreter will be found
+	# fix line endings to make sure Python3 interpreter will be found
 	find debian/*/usr/share -name "VFDB*" -exec dos2unix \{\} \;
-	sed -i '1s:^#!/usr/local.*python[.0-9]*$$:#!/usr/bin/python:' debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)/qsub_srst2.py
+	sed -i '1s:^#!/usr/local.*python[.0-9]*$$:#!/usr/bin/python3:' debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)/qsub_srst2.py
 
 override_dh_fixperms:
 	dh_fixperms
@@ -31,13 +31,9 @@ override_dh_fixperms:
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	cd tests && python test_slurm_srst2.py && python test_srst2.py 
+	cd tests && python3 test_slurm_srst2.py && python3 test_srst2.py
 endif
 
 override_dh_installdocs:
 	dh_installdocs
 	sed -i "s?sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__).*scripts.*?sys.path.append(os.path.abspath('/usr/share/$(DEB_SOURCE)'))?" debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/tests/*.py
-
-# README.html contains a really maintained changelog
-#override_dh_installchangelogs:
-#	dh_installchangelogs CHANGES.txt

debian/tests/control

 Tests: run-unit-test
-Depends: @, python-mock
+Depends: @, python3-mock
 Restrictions: allow-stderr

debian/tests/run-unit-test

@@ -2,13 +2,13 @@
 
 pkg=srst2
 
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
 fi
-cd $ADTTMP
-cp /usr/share/doc/$pkg/tests/* $ADTTMP
+cd $AUTOPKGTEST_TMP
+cp /usr/share/doc/$pkg/tests/* $AUTOPKGTEST_TMP
 find . -name "*.gz" -exec gunzip \{\} \;
 for runtest in *.py ; do
-    python $runtest
+    python3 $runtest
 done
 # rm -rf *

debian/upstream/metadata

@@ -24,3 +24,5 @@ Registry:
   Entry: NA
 - Name: SciCrunch
   Entry: NA
+Repository: https://github.com/katholt/srst2.git
+Repository-Browse: https://github.com/katholt/srst2