[med-svn] [Git][med-team/tvc][master] 5 commits: Use Python 3 in package

[Stuart Prescott]

Stuart Prescott pushed to branch master at Debian Med / tvc


Commits:
bc168444 by Stuart Prescott at 2020-03-01T16:07:31+11:00
Use Python 3 in package

- - - - -
d9b250b7 by Stuart Prescott at 2020-03-01T16:07:31+11:00
Update S-V to 4.5.0

- - - - -
e0c907d9 by Stuart Prescott at 2020-03-01T16:07:31+11:00
Switch to debhelper-compat (= 12)

- - - - -
634b53df by Stuart Prescott at 2020-03-01T16:07:31+11:00
Add R3: no

- - - - -
67c05a77 by Stuart Prescott at 2020-03-01T16:07:51+11:00
Add changelog for upload

- - - - -


5 changed files:

- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/python3.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+tvc (5.0.3+git20151221.80e144e+dfsg-3) unstable; urgency=medium
+
+  * Team upload.
+  * Use Python 3 in scripts (Closes: #945720).
+  * Add Rules-Requires-Root: no.
+  * Update Standards-Version to 4.5.0 (no changes required).
+  * Switch to debhelper-compat (= 12).
+
+ -- Stuart Prescott <stuart at debian.org>  Sun, 01 Mar 2020 15:57:45 +1100
+
 tvc (5.0.3+git20151221.80e144e+dfsg-2) unstable; urgency=medium
 
   [ Logan Rosen ]


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -4,23 +4,24 @@ Uploaders: Dominique Belhachemi <domibel at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                cmake,
                libbamtools-dev,
                libjsoncpp-dev,
                libarmadillo-dev,
                libboost-math-dev,
                libsmithwaterman-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/tvc
 Vcs-Git: https://salsa.debian.org/med-team/tvc.git
 Homepage: http://ioncommunity.thermofisher.com
+Rules-Requires-Root: no
 
 Package: tvc
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         python
+         python3
 Description: genetic variant caller for Ion Torrent sequencing platforms
  Torrent Variant Caller (TVC) is a genetic variant caller for
  Ion Torrent sequencing platforms, and is specially optimized to exploit the


=====================================
debian/patches/python3.patch
=====================================
@@ -0,0 +1,45 @@
+--- a/bin/variant_caller_pipeline.py
++++ b/bin/variant_caller_pipeline.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+ # Copyright (C) 2011 Ion Torrent Systems, Inc. All Rights Reserved
+ 
+ import sys
+@@ -12,7 +12,7 @@
+ def printtime(message, *args):
+     if args:
+         message = message % args
+-    print "[ " + time.strftime('%a %Y-%m-%d %X %Z') + " ] " + message
++    print("[ " + time.strftime('%a %Y-%m-%d %X %Z') + " ] " + message)
+     sys.stdout.flush()
+     sys.stderr.flush()
+ 
+@@ -133,7 +133,7 @@
+             json_file = open(options.paramfile, 'r')
+             parameters = json.load(json_file)
+             json_file.close()
+-            if parameters.has_key('pluginconfig'):
++            if 'pluginconfig' in parameters:
+                 parameters = parameters['pluginconfig']
+         except:
+             printtime('ERROR: No parameter file found at: ' + options.paramfile)
+--- a/external/vcflib/multichoose/multipermute.py
++++ b/external/vcflib/multichoose/multipermute.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ # multipermute.py - permutations of a multiset
+ # Erik Garrison <erik.garrison at bc.edu> 2010
+@@ -92,7 +92,7 @@
+     if multiset != []:
+         for permutation in permutations(multiset):
+             for item in permutation:
+-                print item,
+-            print
++                print(item, end=" ")
++            print()
+     else:
+-        print "usage", sys.argv[0], "<multiset>"
++        print("usage", sys.argv[0], "<multiset>")


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ hurd.patch
 sse.patch
 use_debian_packaged_smithwaterman.patch
 # use_debian_packaged_vcflib.patch
+python3.patch



View it on GitLab: https://salsa.debian.org/med-team/tvc/-/compare/5dcfc9d6151a421a74112f9f103e52d19aa5bb74...67c05a770495833ab9cc7dbaecc6e6f25e08df35

-- 
View it on GitLab: https://salsa.debian.org/med-team/tvc/-/compare/5dcfc9d6151a421a74112f9f103e52d19aa5bb74...67c05a770495833ab9cc7dbaecc6e6f25e08df35
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