[med-svn] [Git][med-team/smalt][master] 3 commits: routine-update: Standards-Version: 4.4.1
Andreas Tille
gitlab at salsa.debian.org
Tue Dec 17 17:57:42 GMT 2019
Andreas Tille pushed to branch master at Debian Med / smalt
Commits:
7c08f253 by Andreas Tille at 2019-12-17T17:02:58Z
routine-update: Standards-Version: 4.4.1
- - - - -
1f0ab665 by Andreas Tille at 2019-12-17T17:03:01Z
R-U: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
- - - - -
6e66f8eb by Andreas Tille at 2019-12-17T17:52:09Z
Try to fix some tests or at least make these more verbose but failed.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/2to3.patch
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -3,12 +3,41 @@ smalt (0.7.6-9) UNRELEASED; urgency=medium
* Use 2to3 to port to Python3
Closes: #938501
* debhelper-compat 12
- * Standards-Version: 4.4.0
+ * Standards-Version: 4.4.1
* Remove trailing whitespace in debian/changelog
* Use secure URI in debian/watch.
* Use secure URI in Homepage field.
* Set upstream metadata fields: Archive, Bug-Submit.
+ * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
TODO: Fix some Python3 issues in test scripts
+ make check-TESTS
+ make[4]: Entering directory '/build/smalt-0.7.6/test'
+ PASS: splitReads_test.py
+ PASS: results_split_test.py
+ PASS: ouform_cigar_test.py
+ mappings don't match for read 'SIM_000000000_MAL11_001337747_10_F_75m/1'
+ FAIL: sample_test.py
+ PASS: cigar_test.py
+ Discrepancy:
+ cigar:A:60 SIM_000000000_MAL11_001337747_10_F_75m/1 1 75 + MAL11 1337747 1337821 + 75 M 75
+ cigar:A:60 SIM_000000000_MAL11_001337747_10_F_75m/1 1 75 + MAL11 1337747 1337821 + 75 M 75
+ cigA1.mapq=60 > MAPQ_THRESH=6 and cigB1.mapq=60 > MAPQ_THRESH=6
+ FAIL: mthread_test.py
+ PASS: ioform_test.py
+ PASS: xali_test.py
+ Traceback (most recent call last):
+ File "./bam_cigar_test.py", line 254, in <module>
+ isOK = testSAMfilesAreIdentical(sambamnam, samoufilnam)
+ File "./bam_cigar_test.py", line 149, in testSAMfilesAreIdentical
+ linA = infilA.readline()
+ File "/usr/lib/python3.7/codecs.py", line 322, in decode
+ (result, consumed) = self._buffer_decode(data, self.errors, final)
+ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 366: invalid start byte
+ FAIL: bam_cigar_test.py
+ =================================
+ 3 of 9 tests failed
+ Please report to hp3 at sanger.ac.uk
+ =================================
-- Andreas Tille <tille at debian.org> Thu, 05 Sep 2019 15:07:37 +0200
=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 12),
python3,
samtools,
libbambamc-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/smalt
Vcs-Git: https://salsa.debian.org/med-team/smalt.git
Homepage: https://www.sanger.ac.uk/science/tools/smalt-0
=====================================
debian/patches/2to3.patch
=====================================
@@ -225,7 +225,8 @@ Last-Update: Thu, 05 Sep 2019 15:07:37 +0200
- print "Not matching:\n%s\n%s" % (cigA1.lin, cigB1.lin)
+ print("Not matching:\n%s\n%s" % (cigA1.lin, cigB1.lin))
if cigA1.mapq > MAPQ_THRESH and cigB1.mapq > MAPQ_THRESH:
- exit("Discrepancy:\n%s\n%s" % (cigA1.lin, cigB1.lin))
+- exit("Discrepancy:\n%s\n%s" % (cigA1.lin, cigB1.lin))
++ exit("Discrepancy:\n%s\n%s\ncigA1.mapq=%i > MAPQ_THRESH=%i and cigB1.mapq=%i > MAPQ_THRESH=%i" % (cigA1.lin, cigB1.lin, cigA1.mapq, MAPQ_THRESH, cigB1.mapq, MAPQ_THRESH))
if cigA2 != cigB2:
if is_verbose:
- print "Not matching:\n%s\n%s" % (cigA2.lin, cigB2.lin)
@@ -283,6 +284,15 @@ Last-Update: Thu, 05 Sep 2019 15:07:37 +0200
if not allok:
--- a/test/testdata.py
+++ b/test/testdata.py
+@@ -62,7 +62,7 @@ class DataFiles:
+ if len(filnam) < 4 or filnam[-3:] != '.gz': fn_from = fn_from + '.gz'
+ fn_to = path.join(DataFiles.WORKDIR, filnam)
+ infil = openFile(fn_from, 'r')
+- oufil = openFile(fn_to, 'w')
++ oufil = openFile(fn_to, 'wb')
+ self.logfil_out.write("unpacking '%s' -> '%s'\n" % (fn_from, fn_to))
+ while 1:
+ lin = infil.readline()
@@ -139,9 +139,9 @@ class DataFiles:
for filnam in (self.datafiles + self.tmpfiles):
if access(filnam, F_OK):
@@ -304,3 +314,26 @@ Last-Update: Thu, 05 Sep 2019 15:07:37 +0200
exit(1)
return oufil
+--- a/test/sample_test.py
++++ b/test/sample_test.py
+@@ -1,5 +1,7 @@
+ # test sampling of insert lengths
+
++from operator import ne
++
+ PROGNAM = "../src/smalt"
+ REF_FASTA_NAME = "genome_1.fa.gz"
+ READ_PREFIX = "gen1l75i300e0"
+@@ -105,10 +107,10 @@ def compare_mapping(oufilnam1, oufilnam2
+ break
+ ctr2 = ctr2 + 1
+
+- if cmp(cig1.qnam, cig2.qnam):
++ if ne(cig1.qnam, cig2.qnam):
+ exit("readnames don't match: '%s' vs '%s'" % \
+ (cig1.qnam, cig2.qnam))
+- if cmp(cig1,cig2) and cig1.mapq > 5 and cig2.mapq > 5:
++ if ne(cig1,cig2) and cig1.mapq > 5 and cig2.mapq > 5:
+ exit("mappings don't match for read '%s'" % \
+ cig1.qnam)
+ infil2.close()
=====================================
debian/tests/run-unit-test
=====================================
@@ -2,11 +2,11 @@
#debug=1
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=`mktemp -d /tmp/smalt-test.XXXXXX`
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/smalt-test.XXXXXX`
fi
-cd $ADTTMP
-cp -a /usr/share/doc/smalt/test/* $ADTTMP
+cd $AUTOPKGTEST_TMP
+cp -a /usr/share/doc/smalt/test/* $AUTOPKGTEST_TMP
gunzip *.py.gz data/*.bam.gz
TESTS="splitReads_test.py
View it on GitLab: https://salsa.debian.org/med-team/smalt/compare/13e417919ba28b0a287b4dc3d962f7196c6cc2fe...6e66f8ebd8689f24558644a187e06a1e7327d59d
--
View it on GitLab: https://salsa.debian.org/med-team/smalt/compare/13e417919ba28b0a287b4dc3d962f7196c6cc2fe...6e66f8ebd8689f24558644a187e06a1e7327d59d
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