Andreas Tille pushed to branch master at Debian Med / grabix
Commits: 959d167e by Andreas Tille at 2019-09-10T14:51:56Z Use 2to3 to port to Python3 - - - - - 31bb7457 by Andreas Tille at 2019-09-10T14:52:18Z Build-Depends: s/python/python3/ - - - - - 16e27577 by Andreas Tille at 2019-09-10T14:52:45Z debhelper-compat 12 - - - - - 348f11af by Andreas Tille at 2019-09-10T14:52:48Z Standards-Version: 4.4.0 - - - - - f5709f87 by Andreas Tille at 2019-09-10T14:57:36Z Do not use quilt to fix files in debian/ dir - - - - - 887d0cdc by Andreas Tille at 2019-09-11T07:08:42Z Fix patch - - - - - 6 changed files: - debian/changelog - − debian/compat - debian/control - + debian/patches/2to3.patch - debian/patches/series - debian/testdata/test.sh Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +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 <[email protected]> Tue, 10 Sep 2019 16:50:14 +0200 + grabix (0.1.7-1) unstable; urgency=medium * Team upload. ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -11 ===================================== debian/control ===================================== @@ -3,13 +3,13 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Steffen Moeller <[email protected]> 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 ===================================== @@ -0,0 +1,64 @@ +Description: Use 2to3 to port to Python3 +Bug-Debian: https://bugs.debian.org/936648 +Author: Andreas Tille <[email protected]> +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 View it on GitLab: https://salsa.debian.org/med-team/grabix/compare/d8aeefaa6b81ddc92047caa1782dcf385a5a4d37...887d0cdcb48582068e32b032ccb941a578c0cf2a -- View it on GitLab: https://salsa.debian.org/med-team/grabix/compare/d8aeefaa6b81ddc92047caa1782dcf385a5a4d37...887d0cdcb48582068e32b032ccb941a578c0cf2a You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
