[med-svn] [Git][med-team/smalt][master] 8 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Thu Sep 5 14:36:13 BST 2019
Andreas Tille pushed to branch master at Debian Med / smalt
Commits:
dbd3bcef by Andreas Tille at 2019-09-05T13:09:38Z
Use 2to3 to port to Python3
- - - - -
c893b0ea by Andreas Tille at 2019-09-05T13:09:55Z
debhelper-compat 12
- - - - -
0baa95c8 by Andreas Tille at 2019-09-05T13:10:01Z
Standards-Version: 4.4.0
- - - - -
7f2a2aac by Andreas Tille at 2019-09-05T13:10:01Z
Remove trailing whitespace in debian/changelog
- - - - -
f915116b by Andreas Tille at 2019-09-05T13:10:06Z
Use secure URI in debian/watch.
Fixes lintian: debian-watch-uses-insecure-uri
See https://lintian.debian.org/tags/debian-watch-uses-insecure-uri.html for more details.
- - - - -
0cc9e7b1 by Andreas Tille at 2019-09-05T13:10:09Z
Use secure URI in Homepage field.
Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.
- - - - -
f54efbac by Andreas Tille at 2019-09-05T13:10:09Z
Set upstream metadata fields: Archive, Bug-Submit.
- - - - -
2e03054c by Andreas Tille at 2019-09-05T13:35:43Z
Add TODO
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+smalt (0.7.6-9) UNRELEASED; urgency=medium
+
+ * Use 2to3 to port to Python3
+ Closes: #938501
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * 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.
+ TODO: Fix some Python3 issues in test scripts
+
+ -- Andreas Tille <tille at debian.org> Thu, 05 Sep 2019 15:07:37 +0200
+
smalt (0.7.6-8) unstable; urgency=medium
* debhelper 11
@@ -46,7 +60,7 @@ smalt (0.7.6-5) unstable; urgency=medium
smalt (0.7.6-4) unstable; urgency=medium
* cme fix dpkg-control
- * Use autotools-dev / since dh-autoreconf does not work this hopefully also
+ * Use autotools-dev / since dh-autoreconf does not work this hopefully also
Closes: #765256
-- Andreas Tille <tille at debian.org> Tue, 14 Oct 2014 13:33:15 +0200
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,15 +3,15 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
zlib1g-dev,
- python,
+ python3,
samtools,
libbambamc-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/smalt
Vcs-Git: https://salsa.debian.org/med-team/smalt.git
-Homepage: http://www.sanger.ac.uk/science/tools/smalt-0
+Homepage: https://www.sanger.ac.uk/science/tools/smalt-0
Package: smalt
Architecture: any
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,306 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/938501
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 05 Sep 2019 15:07:37 +0200
+
+--- a/misc/SAM.py
++++ b/misc/SAM.py
+@@ -85,7 +85,7 @@ class Sam:
+ self.tags[tagnam] = (typ, fld)
+ self.ok = True
+ else:
+- if is_verbose: print "NOT PARSED '%s'" % lin
++ if is_verbose: print("NOT PARSED '%s'" % lin)
+ self.blank()
+
+ def clip(self):
+@@ -106,7 +106,7 @@ class Sam:
+ return (typ, isCorrect, s, e)
+
+ def strand(self):
+- print "(%i, %s)" % (self.flag, bool(self.flag & Sam.FLAG_STRAND))
++ print("(%i, %s)" % (self.flag, bool(self.flag & Sam.FLAG_STRAND)))
+ return bool(self.flag & Sam.FLAG_STRAND)
+
+ def calcUnclippedStart(self):
+@@ -207,7 +207,7 @@ class Sam:
+ if bool(self.flag & Sam.FLAG_STRAND):
+ (seq, qual, okflg) = self.reverseComplement()
+ if not okflg:
+- print "ERROR: when reverse complementing sequence!"
++ print("ERROR: when reverse complementing sequence!")
+ exit(1)
+ else:
+ seq = self.nt
+@@ -218,7 +218,7 @@ class Sam:
+ def asFastq(self, clip=0):
+ namstr, seq, qual = self.asFastqStr()
+ if clip >= len(self.nt):
+- print "ERROR: clipped fragment > sequence length\n%s" % (self.qname)
++ print("ERROR: clipped fragment > sequence length\n%s" % (self.qname))
+ return Sam.FASTQ_FORMAT % (namstr, seq[clip:], qual[clip:])
+
+ def reverseComplement(self):
+@@ -245,7 +245,7 @@ class Sam:
+ if not lin: break
+ self.parse(lin, is_verbose)
+ if self.ok: break
+- if is_verbose: print "not parsed: %s" % lin
++ if is_verbose: print("not parsed: %s" % lin)
+ return not lin # True if EOF
+
+
+@@ -259,7 +259,7 @@ def fetchNextRead(infil, read):
+ break
+ read.parse(lin)
+ if not read.ok:
+- print "not parsed: %s" % lin
++ print("not parsed: %s" % lin)
+ continue
+ break
+ #print read.target.varnum()
+@@ -291,8 +291,8 @@ def fetchNextPair(infil, samA, samB):
+ errflg = True
+
+ if errflg:
+- print "ERROR: unexpected pair flags.\n%s\n%s\n%s\n%s" % \
+- (samA.qname, samA.strFlags(), samB.qname, samB.strFlags())
++ print("ERROR: unexpected pair flags.\n%s\n%s\n%s\n%s" % \
++ (samA.qname, samA.strFlags(), samB.qname, samB.strFlags()))
+ exit(1)
+
+ return (isEOF, switch_flag)
+@@ -307,7 +307,7 @@ def openFile(filnam, mode):
+ else:
+ oufil = open(filnam, mode)
+ except:
+- print "ERROR when opening file '%s'" % filnam
++ print("ERROR when opening file '%s'" % filnam)
+ exit(1)
+
+ return oufil
+@@ -316,7 +316,7 @@ if __name__ == '__main__':
+ from sys import argv, exit
+
+ if len(argv) < 3:
+- print "usage: %s <SAM file (input)> <mapping score threshold>" % argv[0]
++ print("usage: %s <SAM file (input)> <mapping score threshold>" % argv[0])
+ exit(1)
+
+ infilnam = argv[1]
+@@ -360,36 +360,36 @@ if __name__ == '__main__':
+ if mnam == old_qnam:
+ if read.rname != old_rnam:
+ chimictr = chimictr + 1
+- print "[%i, %i]%s: rname1: %s, rname2: %s" % \
+- (readctr, chimictr, mnam, old_rnam, read.rname)
++ print("[%i, %i]%s: rname1: %s, rname2: %s" % \
++ (readctr, chimictr, mnam, old_rnam, read.rname))
+
+ else:
+ # a 'proper' pair
+- print "%s %i %i %x" % (read.qname, abs(read.isize), read.mapq, int(read.flag))
++ print("%s %i %i %x" % (read.qname, abs(read.isize), read.mapq, int(read.flag)))
+ propctr = propctr + 1
+ isizarr.append(abs(read.isize))
+ else:
+ lowqctr = lowqctr + 1
+ if readctr % 100000 == 0:
+- print "%i reads ..." % readctr
++ print("%i reads ..." % readctr)
+ pairctr = pairctr/2
+
+ infil.close()
+
+- print "%i out of a total of %i reads (%5.2f%%) were mapped." % \
+- (readctr - nomapctr, readctr, 100*float(readctr - nomapctr)/readctr)
+- print "%i out of a total of %i reads (%5.2f%%) mapped with a mapping score > %i" % \
+- (minqctr, readctr, 100*float(minqctr)/readctr, Sam.MAPQ_NONRANDOM)
++ print("%i out of a total of %i reads (%5.2f%%) were mapped." % \
++ (readctr - nomapctr, readctr, 100*float(readctr - nomapctr)/readctr))
++ print("%i out of a total of %i reads (%5.2f%%) mapped with a mapping score > %i" % \
++ (minqctr, readctr, 100*float(minqctr)/readctr, Sam.MAPQ_NONRANDOM))
+ if Sam.MAPQ_NONRANDOM != mapq_min:
+- print "%i out of a total of %i reads (%5.2f%%) mapped with a mapping score > %i" % \
+- (highqctr, readctr, 100*float(highqctr)/readctr, mapq_min)
++ print("%i out of a total of %i reads (%5.2f%%) mapped with a mapping score > %i" % \
++ (highqctr, readctr, 100*float(highqctr)/readctr, mapq_min))
+
+ if pairctr > 0:
+- print "%i out of a total of %i reads (%5.2f%%) mapped as a proper pair with a mapping score > %i" % \
+- (propctr, readctr, 100*float(propctr)/readctr, mapq_min)
+- print "%i of %i pairs (%6.3f%%) with a mapping score >= %i mapped to different chromosomes" % \
+- (chimictr, pairctr, 200*float(chimictr)/pairctr, mapq_min)
++ print("%i out of a total of %i reads (%5.2f%%) mapped as a proper pair with a mapping score > %i" % \
++ (propctr, readctr, 100*float(propctr)/readctr, mapq_min))
++ print("%i of %i pairs (%6.3f%%) with a mapping score >= %i mapped to different chromosomes" % \
++ (chimictr, pairctr, 200*float(chimictr)/pairctr, mapq_min))
+ else:
+- print "There were no reads mapped as pairs."
++ print("There were no reads mapped as pairs.")
+
+ exit(0)
+--- a/test/bam_cigar_test.py
++++ b/test/bam_cigar_test.py
+@@ -164,19 +164,19 @@ def testSAMfilesAreIdentical(filnamA, fi
+ okflg = len(fldA) == len(fldB)
+
+ if not okflg:
+- print "lines differ in the number of fields:\n%s\n%s\n" % \
+- (linA.strip(), linB.strip())
++ print("lines differ in the number of fields:\n%s\n%s\n" % \
++ (linA.strip(), linB.strip()))
+ break
+
+- for i in SAM_TEST_FIELDS.keys():
++ for i in list(SAM_TEST_FIELDS.keys()):
+ okflg = fldA[i] == fldB[i]
+ if not okflg and i == 0:
+ # samtools-0.1.18 view -h produces non-printing char
+ # directly after header
+ okflg = fldA[i][1:] == fldB[i] or fldA[i] == fldB[i][1:]
+ if not okflg:
+- print "lines differ in %s:\n%s\n%s\n" % \
+- (SAM_TEST_FIELDS[i], linA.strip(), linB.strip())
++ print("lines differ in %s:\n%s\n%s\n" % \
++ (SAM_TEST_FIELDS[i], linA.strip(), linB.strip()))
+ break
+ if not okflg:
+ break
+--- a/test/formats.py
++++ b/test/formats.py
+@@ -45,9 +45,9 @@ class Cigar:
+ self.parse(lin)
+ okflg = self.ok
+ if Cigar.DEBUG:
+- print "DEBUG:Cigar.next %s" % (okflg)
++ print("DEBUG:Cigar.next %s" % (okflg))
+ if Cigar.DEBUG:
+- print "DEBUG:Cigar.next returns %s" % (isEOF)
++ print("DEBUG:Cigar.next returns %s" % (isEOF))
+ return isEOF
+
+ def parse(self, lin):
+@@ -66,11 +66,11 @@ class Cigar:
+ self.cigar.strip()
+ self.ok = True
+ if Cigar.DEBUG:
+- print "DEBUG:Cigar.parse('%s')::'%s'" % (self.lin, self.cigar)
++ print("DEBUG:Cigar.parse('%s')::'%s'" % (self.lin, self.cigar))
+ else:
+ lin.strip()
+ if lin[0] != '#':
+- print "not parsed: %s" % (lin)
++ print("not parsed: %s" % (lin))
+ self._blank()
+
+ def getMateNo(self):
+@@ -118,10 +118,10 @@ def getNextCigarPair(infil, cigA, cigB,
+ isOk = True
+ if not isEOF and mateno_check:
+ if cigA.qnam[-2] != cigB.qnam[-2]:
+- print "ERROR: read names don't match %s, %s" % (cigA.qnam, cigB.qnam)
++ print("ERROR: read names don't match %s, %s" % (cigA.qnam, cigB.qnam))
+ isOk = False
+ elif cigA.getMateNo() != 1 or cigB.getMateNo() != 2:
+- print "ERROR in mate number %s [1] and %s [2]" % (cigA.qnam, cigB.qnam)
++ print("ERROR in mate number %s [1] and %s [2]" % (cigA.qnam, cigB.qnam))
+ isOk = False
+
+ return (isOk, isEOF)
+@@ -151,6 +151,6 @@ if __name__ == "__main__":
+ infil = openFile(argv[1])
+
+ while not cig.next(infil):
+- print cig.qnam
++ print(cig.qnam)
+
+ infil.close()
+--- a/test/mthread_test.py
++++ b/test/mthread_test.py
+@@ -57,12 +57,12 @@ def cmpCigarFiles(cigfilA, cigfilB, is_v
+ break
+ if cigA1 != cigB1:
+ if is_verbose:
+- 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))
+ if cigA2 != cigB2:
+ if is_verbose:
+- print "Not matching:\n%s\n%s" % (cigA2.lin, cigB2.lin)
++ print("Not matching:\n%s\n%s" % (cigA2.lin, cigB2.lin))
+ if cigA2.mapq > MAPQ_THRESH and cigB2.mapq > MAPQ_THRESH:
+ exit("Discrepancy:\n%s\n%s" % (cigA2.lin, cigB2.lin))
+ ctr = ctr + 1
+@@ -93,7 +93,7 @@ if __name__ == '__main__':
+
+ isOK, pairctr = cmpCigarFiles(oufilnam_ref, oufilnam_thread, VERBOSE)
+ if VERBOSE:
+- print "Test ok=%s, number of pairs = %i" % (isOK, pairctr)
++ print("Test ok=%s, number of pairs = %i" % (isOK, pairctr))
+ if not isOK or pairctr != n_pairs_expected:
+ exit("Using smalt in multi-threaded mode gave inconsistent results!")
+
+--- a/test/results_split_test.py
++++ b/test/results_split_test.py
+@@ -35,7 +35,7 @@ READSEQS = ("@SIM_000000000_contig5121_0
+ "AAAAGAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAA\n"\
+ "+\n"\
+ "daBZddeYdBfe`fBf`ecfdfcf`c\eacXdbLe^b``ccadK]e]^_T"\
+- "fccbcd\Tffb^Yfdfdf^efa\[fbfdad`X\Ue_^eBfcfcfNfdf^!\n"
++ "fccbcd\Tffb^Yfdfdf^efa\[fbfdad`X\\Ue_^eBfcfcfNfdf^!\n"
+ )
+
+ # cigar:S:16 SIM_000000000_contig5121_000000001_5120_R_20m/1 20 1 - contig5121 1 20 + 20 M 20
+--- a/test/splitReads_test.py
++++ b/test/splitReads_test.py
+@@ -79,13 +79,13 @@ def checkOutput(cigfilnam, expected_tup)
+ while not cig.next(infil):
+ if linctr > n_tup:
+ allok = False
+- print "ERROR: %i cigar lines, expected %i" % \
+- (linctr, n_tup)
++ print("ERROR: %i cigar lines, expected %i" % \
++ (linctr, n_tup))
+ break
+ mateno = cig.getMateNo()
+ observed_tup = (cig.mapcls, mateno, cig.qseg, cig.snam, cig.sseg)
+ if observed_tup not in expected_tup:
+- print "ERROR: unexpected tuple: ", observed_tup
++ print("ERROR: unexpected tuple: ", observed_tup)
+ allok = False
+ break
+
+@@ -94,7 +94,7 @@ def checkOutput(cigfilnam, expected_tup)
+
+ for i in range(n_tup):
+ if not okflgs[i]:
+- print "ERROR: could not find tuple: ", expected_tup[i]
++ print("ERROR: could not find tuple: ", expected_tup[i])
+ allok = False
+
+ if not allok:
+--- a/test/testdata.py
++++ b/test/testdata.py
+@@ -139,9 +139,9 @@ class DataFiles:
+ for filnam in (self.datafiles + self.tmpfiles):
+ if access(filnam, F_OK):
+ remove(filnam)
+- if is_verbose: print "Removed file '%s'" % filnam
++ if is_verbose: print("Removed file '%s'" % filnam)
+ else:
+- print "Could not access file '%s'" % filnam
++ print("Could not access file '%s'" % filnam)
+ self.datafiles = []
+ self.tmpfiles = []
+ try:
+@@ -159,7 +159,7 @@ def openFile(filnam, mode = 'r'):
+ else:
+ oufil = open(filnam, mode)
+ except:
+- print "ERROR when opening file '%s'" % filnam
++ print("ERROR when opening file '%s'" % filnam)
+ exit(1)
+
+ return oufil
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
#bam_cigar_test_makefile.patch
#try_to_fix_automake.patch
+2to3.patch
=====================================
debian/upstream/metadata
=====================================
@@ -1,7 +1,9 @@
Registry:
- - Name: OMICtools
- Entry: OMICS_00686
- - Name: SciCrunch
- Entry: SCR_000544
- - Name: bio.tools
- Entry: Smalt
+- Name: OMICtools
+ Entry: OMICS_00686
+- Name: SciCrunch
+ Entry: SCR_000544
+- Name: bio.tools
+ Entry: Smalt
+Archive: SourceForge
+Bug-Submit: hp3 at sanger.ac.uk
=====================================
debian/watch
=====================================
@@ -1,2 +1,2 @@
version=3
-http://sf.net/smalt/smalt-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
+https://sf.net/smalt/smalt-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
View it on GitLab: https://salsa.debian.org/med-team/smalt/compare/abc9854746910d3415d1a0fe521b9a9b9e1b3ff7...2e03054c73b3a523e8fcaebcb94c979f63e01e92
--
View it on GitLab: https://salsa.debian.org/med-team/smalt/compare/abc9854746910d3415d1a0fe521b9a9b9e1b3ff7...2e03054c73b3a523e8fcaebcb94c979f63e01e92
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