debian/changelog

+grabix (0.1.7-2) UNRELEASED; urgency=medium
+
+  * Use 2to3 to port to Python3
+    Closes: #936648
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Tue, 10 Sep 2019 16:50:14 +0200
+
 grabix (0.1.7-1) unstable; urgency=medium
 
   * Team upload.

debian/compat

-11

debian/control

@@ -3,13 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Steffen Moeller <moeller@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                zlib1g-dev,
-               python,
+               python3,
                tabix,
                time,
                less
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/grabix
 Vcs-Git: https://salsa.debian.org/med-team/grabix.git
 Homepage: https://github.com/arq5x/grabix

debian/patches/2to3.patch

+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/936648
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 10 Sep 2019 16:50:14 +0200
+
+--- a/test.sh
++++ b/test.sh
+@@ -4,11 +4,11 @@ FQ=test.cnt.gz
+ rm -f ${FQ}{,.gbi}
+ 
+ lines=500000
+-python tests/make-test-fastq.py $lines | bgzip -c > $FQ
++python3 tests/make-test-fastq.py $lines | bgzip -c > $FQ
+ echo "indexing"
+ time ./grabix index $FQ
+ echo "indexed"
+-python tests/test-fastq.py $FQ
++python3 tests/test-fastq.py $FQ
+ a=$(grabix grab test.cnt.gz $(($lines * 4)))
+ b=$(zless $FQ | tail -1)
+ if [[ "$a" != "$b" ]]; then
+--- a/tests/make-test-fastq.py
++++ b/tests/make-test-fastq.py
+@@ -2,8 +2,8 @@ import sys
+ n = int(sys.argv[1]) + 1
+ for i in range(1, n):
+     s = str(i) + "ACTG"
+-    print "@read_%i" % i
++    print("@read_%i" % i)
+     seq = "".join([s] * 20)[:100]
+-    print seq
+-    print "+"
+-    print seq
++    print(seq)
++    print("+")
++    print(seq)
+--- a/tests/test-fastq.py
++++ b/tests/test-fastq.py
+@@ -5,21 +5,21 @@ import gzip
+ f = sys.argv[1]
+ lines = ["EMPTY"] + [x.strip() for x in gzip.open(f).readlines()]
+ 
+-print "checking indexing at bounds:"
++print("checking indexing at bounds:")
+ 
+ def check(gzname, start, end=None):
+     run = subprocess.check_output
+     exp = lines[start:start+1] if end is None else lines[start:end + 1]
+     obs = run("grabix grab %s %d" % (gzname, start), shell=True) if end is None \
+             else run("grabix grab %s %d %d" % (gzname, start, end), shell=True)
+-    obs = [x.strip() for x in obs.strip().split("\n")]
++    obs = [x.strip() for x in obs.strip().split(b"\n")]
+     sys.stdout.write(".")
+     sys.stdout.flush()
+     assert exp == obs, (exp, obs)
+     if start % 4 == 1:
+-        assert obs[0][0] == "@"
++        assert obs[0][0] == "@".encode()[0]
+     else:
+-        assert obs[0][0] != "@"
++        assert obs[0][0] != "@".encode()[0]
+ 
+ for i in range(9990, 10010):
+     check(f, i)

debian/patches/series

@@ -3,3 +3,4 @@ Hardening.patch
 warnings.patch
 introduceLTO.patch
 fix_test.patch
+2to3.patch

debian/testdata/test.sh

@@ -4,11 +4,11 @@ FQ=test.cnt.gz
 rm -f ${FQ}{,.gbi}
 
 lines=500000
-python tests/make-test-fastq.py $lines | bgzip -c > $FQ
+python3 tests/make-test-fastq.py $lines | bgzip -c > $FQ
 echo "indexing"
 time grabix index $FQ
 echo "indexed"
-python tests/test-fastq.py $FQ
+python3 tests/test-fastq.py $FQ
 a=$(grabix grab test.cnt.gz $(($lines * 4)))
 b=$(zless $FQ | tail -1)
 if [ "$a" != "$b" ] ; then