Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/debian/changelog
+++ b/debian/changelog
-idba (1.1.3-4) UNRELEASED; urgency=medium
+idba (1.1.3-5) unstable; urgency=medium

+  [ Jelmer Vernooĳ ]
  * Use secure copyright file specification URI.
  * Trim trailing whitespace.

- -- Jelmer Vernooĳ <jelmer@debian.org>  Sun, 14 Oct 2018 19:43:45 +0000
+  [ Andreas Tille ]
+  * Run build time test
+  * Use 2to3 to port Python2 to Python3 scripts
+    Closes: #945684
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Set upstream metadata fields: Bug-Submit, Repository, Repository-
+    Browse.
+
+ -- Andreas Tille <tille@debian.org>  Thu, 28 Nov 2019 12:08:11 +0100

 idba (1.1.3-3) unstable; urgency=medium


--- a/debian/compat
+++ b/debian/compat
-11
--- a/debian/control
+++ b/debian/control
@@ -3,8 +3,10 @@ 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~)
-Standards-Version: 4.2.1
+Build-Depends: debhelper-compat (= 12),
+               libgtest-dev <!nocheck>,
+               python3 <!nocheck>
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/idba
 Vcs-Git: https://salsa.debian.org/med-team/idba.git
 Homepage: https://github.com/loneknightpy/idba
@@ -13,7 +15,7 @@ Package: idba
 Architecture: any
 Depends: ${shlibs:Depends},
         ${misc:Depends},
-         python
+         python3
 Description: iterative De Bruijn Graph short read assemblers
 IDBA stands for iterative de Bruijn graph assembler. In computational
 sequence biology, an assembler solves the puzzle coming from large

--- a/debian/patches/2to3.patch
+++ b/debian/patches/2to3.patch
+Description: Use 2to3 to port Python2 to Python3 scripts
+Bug-Debian: https://bugs.debian.org/945684
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 28 Nov 2019 10:05:54 +0100
+
+--- a/script/run-unittest.py
+++ b/script/run-unittest.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/python
+#!/usr/bin/python3
+ ##
+ # @file run-unittest.py
+ # @brief Scan test directory and run all unit tests.
+--- a/script/scan.py
+++ b/script/scan.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/python
+#!/usr/bin/python3
+ ##
+ # @file scan.py
+ # @brief Scan src directory recursively to build Makefile.am automatically.
+@@ -15,11 +15,11 @@ install = []
+ noninstall = []
+ 
+ def Usage():
+-    print "Usage: scan.py {bin, lib, test}\n"
+    print("Usage: scan.py {bin, lib, test}\n")
+ 
+ 
+ def ParamsToString(params):
+-    return "".join(["%s = %s\n" % (k, v) for k, v in params.items()])
+    return "".join(["%s = %s\n" % (k, v) for k, v in list(params.items())])
+ 
+ def Scan(paths, pattern):
+     files = []
+@@ -62,11 +62,11 @@ if __name__ == "__main__":
+             + "-I$(top_srcdir)/gtest_src "
+     
+     if (sys.argv[1] == "lib"):
+-        print ParamsToString(params)
+        print(ParamsToString(params))
+         #print "noinst_LIBRARIES = libcommon.a libassembly.a\n"
+ 
+         #print ScanLibrary("libcommon.a", ["include/common", "src/common"], "\.cpp$|\.h$"), "\n"
+-        print ScanLibrary("libassembly.a", 
+        print(ScanLibrary("libassembly.a", 
+                 [#"src/common", "src/common", 
+                     "src/basic", 
+                     "src/container", 
+@@ -74,16 +74,16 @@ if __name__ == "__main__":
+                     "src/sequence", 
+                     "src/graph", 
+                     "src/assembly", ], 
+-                "\.cpp$|\.h$"), "\n"
+                "\.cpp$|\.h$"), "\n")
+ 
+-        print "noinst_LIBRARIES = \\\n\t" + " \\\n\t".join(noninstall), "\n"
+        print("noinst_LIBRARIES = \\\n\t" + " \\\n\t".join(noninstall), "\n")
+ 
+     elif (sys.argv[1] == "lib-test"):
+-        print ParamsToString(params)
+        print(ParamsToString(params))
+         #print "noinst_LIBRARIES = libcommon.a libassembly.a\n"
+ 
+         #print ScanLibrary("libcommon.a", ["include/common", "src/common"], "\.cpp$|\.h$"), "\n"
+-        print ScanLibrary("libassembly.a", 
+        print(ScanLibrary("libassembly.a", 
+                 [#"src/common", "src/common", 
+                     "src/basic", 
+                     "src/container", 
+@@ -91,39 +91,39 @@ if __name__ == "__main__":
+                     "src/sequence", 
+                     "src/graph", 
+                     "src/assembly", ], 
+-                "\.cpp$|\.h$"), "\n"
+                "\.cpp$|\.h$"), "\n")
+ 
+-        print ScanLibrary("libgtest.a", 
+        print(ScanLibrary("libgtest.a", 
+                 [ "gtest_src/gtest" ],
+-                "\.cpp$|\.h$|.cc$"), "\n"
+                "\.cpp$|\.h$|.cc$"), "\n")
+ 
+-        print "noinst_LIBRARIES = \\\n\t" + " \\\n\t".join(noninstall), "\n"
+        print("noinst_LIBRARIES = \\\n\t" + " \\\n\t".join(noninstall), "\n")
+ 
+     elif (sys.argv[1] == "bin"):
+         params["LIBS"] = "$(top_srcdir)/lib/libassembly.a @LIBS@";
+-        print ParamsToString(params)
+-        print ScanBinary(["src/tools"], "\.cpp$"), "\n"
+-        print ScanBinary(["src/release"], "\.cpp$"), "\n"
+        print(ParamsToString(params))
+        print(ScanBinary(["src/tools"], "\.cpp$"), "\n")
+        print(ScanBinary(["src/release"], "\.cpp$"), "\n")
+ 
+         SetInstall("idba_hybrid")
+-        print "bin_PROGRAMS = \\\n\t" + " \\\n\t".join(install), "\n"
+-        print "noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n"
+        print("bin_PROGRAMS = \\\n\t" + " \\\n\t".join(install), "\n")
+        print("noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n")
+ 
+     elif (sys.argv[1] == "release"):
+         params["LIBS"] = "$(top_srcdir)/lib/libassembly.a @LIBS@";
+-        print ParamsToString(params)
+-        print ScanBinary(["src/release"], "\.cpp$"), "\n"
+        print(ParamsToString(params))
+        print(ScanBinary(["src/release"], "\.cpp$"), "\n")
+ 
+         SetInstall("idba_hybrid")
+-        print "bin_PROGRAMS = \\\n\t" + " \\\n\t".join(install), "\n"
+-        print "noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n"
+        print("bin_PROGRAMS = \\\n\t" + " \\\n\t".join(install), "\n")
+        print("noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n")
+ 
+     elif (sys.argv[1] == "test"):
+         params["LIBS"] = "$(top_srcdir)/lib/libassembly.a $(top_srcdir)/lib/libgtest.a @LIBS@";
+-        print ParamsToString(params)
+-        print ScanBinary(["src/test"], "\.cpp$"), "\n"
+        print(ParamsToString(params))
+        print(ScanBinary(["src/test"], "\.cpp$"), "\n")
+ 
+-        print "noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n"
+        print("noinst_PROGRAMS = \\\n\t" + " \\\n\t".join(noninstall), "\n")
+ 
+ 
+ 
--- a/debian/patches/series
+++ b/debian/patches/series
 install_all_idba_flavours.patch
 use-atomic-for-mips.patch
 spelling.patch
+2to3.patch
+use_debian_packaged_googletest.patch
--- a/debian/patches/use_debian_packaged_googletest.patch
+++ b/debian/patches/use_debian_packaged_googletest.patch
+Description: Use Debian packaged googletest library
+Bug-Debian: https://bugs.debian.org/945684
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 28 Nov 2019 10:05:54 +0100
+
+--- a/test/Makefile.am
+++ b/test/Makefile.am
+@@ -1,20 +1,20 @@
+ AM_LDFLAGS = -fopenmp -pthread
+-LIBS = $(top_srcdir)/lib/libassembly.a $(top_srcdir)/lib/libgtest.a @LIBS@
+LIBS = $(top_srcdir)/lib/libassembly.a -lgtest @LIBS@
+ AM_CXXFLAGS = -Wall -O3 -fopenmp -pthread
+-INCLUDES =  -I$(top_srcdir)/src -I$(top_srcdir)/gtest_src 
+INCLUDES =  -I$(top_srcdir)/src
+ 
+-compact_sequence_unittest_SOURCES = $(top_srcdir)/src/test/compact_sequence_unittest.cpp
+-hash_table_unittest_SOURCES = $(top_srcdir)/src/test/hash_table_unittest.cpp
+-bit_edges_unittest_SOURCES = $(top_srcdir)/src/test/bit_edges_unittest.cpp
+-kmer_unittest_SOURCES = $(top_srcdir)/src/test/kmer_unittest.cpp
+-hash_set_unittest_SOURCES = $(top_srcdir)/src/test/hash_set_unittest.cpp
+-atomic_integer_unittest_SOURCES = $(top_srcdir)/src/test/atomic_integer_unittest.cpp
+-vertex_status_unittest_SOURCES = $(top_srcdir)/src/test/vertex_status_unittest.cpp
+-histgram_unittest_SOURCES = $(top_srcdir)/src/test/histgram_unittest.cpp
+-managed_list_unittest_SOURCES = $(top_srcdir)/src/test/managed_list_unittest.cpp
+-sequence_unittest_SOURCES = $(top_srcdir)/src/test/sequence_unittest.cpp
+-short_sequence_unittest_SOURCES = $(top_srcdir)/src/test/short_sequence_unittest.cpp
+-hash_map_unittest_SOURCES = $(top_srcdir)/src/test/hash_map_unittest.cpp 
+compact_sequence_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/compact_sequence_unittest.cpp
+hash_table_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/hash_table_unittest.cpp
+bit_edges_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/bit_edges_unittest.cpp
+kmer_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/kmer_unittest.cpp
+hash_set_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/hash_set_unittest.cpp
+atomic_integer_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/atomic_integer_unittest.cpp
+vertex_status_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/vertex_status_unittest.cpp
+histgram_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/histgram_unittest.cpp
+managed_list_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/managed_list_unittest.cpp
+sequence_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/sequence_unittest.cpp
+short_sequence_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/short_sequence_unittest.cpp
+hash_map_unittest_SOURCES = $(top_srcdir)/gtest_src/gtest/gtest_main.cc $(top_srcdir)/src/test/hash_map_unittest.cpp 
+ 
+ check_PROGRAMS = \
+ 	compact_sequence_unittest \
--- a/debian/rules
+++ b/debian/rules
@@ -17,3 +17,9 @@ override_dh_install:
 	# for the moment the role of these scripts is totally unknown but they do not seem to be necessary
 	mv debian/$(DEB_SOURCE)/usr/bin/*.py debian/$(DEB_SOURCE)/usr/lib/idba/
 	mv debian/$(DEB_SOURCE)/usr/bin/validate_blat* debian/$(DEB_SOURCE)/usr/lib/idba/
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	# $(MAKE) unittest
+	cd test && $(MAKE) check
+endif
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -12,8 +12,7 @@ Reference:
  DOI: 10.1093/bioinformatics/bts174
  PMID: 22495754
  URL: http://bioinformatics.oxfordjournals.org/content/28/11/1420.full
-   eprint: "http://bioinformatics.oxfordjournals.org/content/\
-    28/11/1420.full.pdf+html"
+  eprint: "http://bioinformatics.oxfordjournals.org/content/28/11/1420.full.pdf+html"
 - Author: >
    Yu Peng and Henry C. M. Leung and Siu-Ming Yiu and Ming-Ju Lv and
    Xin-Guang Zhu and Francis Y. L. Chin
@@ -29,10 +28,8 @@ Reference:
  Pages: i326-i334
  DOI: 10.1093/bioinformatics/btt219
  PMID: 23813001
-   URL: "https://academic.oup.com/bioinformatics/article-lookup/doi/\
-    10.1093/bioinformatics/btt219"
-   eprint: "https://academic.oup.com/bioinformatics/article-pdf/\
-    29/13/i326/18534891/btt219.pdf"
+  URL: "https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btt219"
+  eprint: "https://academic.oup.com/bioinformatics/article-pdf/29/13/i326/18534891/btt219.pdf"
 Registry:
 - Name: bio.tools
  Entry: IDBA
@@ -44,3 +41,6 @@ Registry:
  Entry: SCR_011912
 - Name: conda:bioconda
  Entry: idba
+Repository: https://github.com/loneknightpy/idba
+Bug-Submit: loneknightpy@gmail.com
+Repository-Browse: https://github.com/loneknightpy/idba