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@sanger.ac.uk
+   =================================
 
  -- Andreas Tille <tille@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