[med-svn] [Git][med-team/harvest-tools][master] 5 commits: Python migration using 2to3 tool
Andreas Tille
gitlab at salsa.debian.org
Fri Apr 10 10:33:26 BST 2020
Andreas Tille pushed to branch master at Debian Med / harvest-tools
Commits:
8797c85c by Antoni Villalonga at 2020-04-10T10:09:45+02:00
Python migration using 2to3 tool
- - - - -
2b649ab9 by Antoni Villalonga at 2020-04-10T10:09:45+02:00
Build-Depends python3-setuptools
- - - - -
0aae0955 by Antoni Villalonga at 2020-04-10T10:22:02+02:00
Standards-Version: 4.5.0
- - - - -
605bed40 by Antoni Villalonga at 2020-04-10T10:26:16+02:00
d/upstream/metadata: Repository and Bug
- - - - -
337cc969 by Antoni Villalonga at 2020-04-10T10:26:16+02:00
Update changelog
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/python-2to3.patch
- debian/patches/series
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+harvest-tools (1.3-4.1) UNRELEASED; urgency=medium
+
+ [ Steffen Möller ]
+ * Non-maintainer upload.
+ * Added ref to conda.
+
+ [ Antoni Villalonga ]
+ * Python migration using 2to3 tool.
+ * Build-Depends python3-setuptools. (Closes: #943055)
+ * Standards-Version: 4.5.0
+ * d/upstream/metadata: Repository and Bug
+
+ -- Antoni Villalonga <antoni at friki.cat> Fri, 10 Apr 2020 10:09:57 +0200
+
harvest-tools (1.3-4) unstable; urgency=medium
[ Adrian Bunk ]
=====================================
debian/control
=====================================
@@ -5,13 +5,13 @@ Section: science
Priority: optional
Build-Depends: debhelper (>= 12~),
cython,
- python-setuptools,
+ python3-setuptools,
protobuf-compiler,
capnproto,
libprotobuf-dev,
libcapnp-dev,
zlib1g-dev
-Standards-Version: 4.3.0
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/harvest-tools
Vcs-Git: https://salsa.debian.org/med-team/harvest-tools.git
Homepage: http://harvest.readthedocs.org/en/latest/content/harvest-tools.html
=====================================
debian/patches/python-2to3.patch
=====================================
@@ -0,0 +1,128 @@
+Author: Antoni Villalonga <antoni at friki.cat>
+Last-Update: Fri, 10 Apr 2020 10:08:15 +0200
+Description: Python migration using 2to3 tool
+
+--- a/INSTALL.py
++++ b/INSTALL.py
+@@ -1,12 +1,12 @@
+ import os,sys,string
+ #harvest utilities INSTALL script
+ user_home = os.environ["HOME"]
+-print "<<Welcome to harVest utility script install>>"
++print("<<Welcome to harVest utility script install>>")
+
+ #check for python version
+ if (sys.version_info[0] < 2) or (sys.version_info[0] == 2 and sys.version_info[1] < 6):
+
+- print "Python version is %s. harvest-tools requires at least 2.6"%(sys.version)
++ print(("Python version is %s. harvest-tools requires at least 2.6"%(sys.version)))
+ sys.exit(1)
+
+ #complete shebang
+--- a/harvest-snps.py
++++ b/harvest-snps.py
+@@ -11,7 +11,7 @@
+
+ #print help/usage
+ if len(sys.argv) == 1 or sys.argv[1] in helpme:
+- print "usage: harvest-snps.py <parsnp.hvt> [outfile]"
++ print("usage: harvest-snps.py <parsnp.hvt> [outfile]")
+ sys.exit(1)
+
+ #check in path for harvest
+--- a/harvest-variants.py
++++ b/harvest-variants.py
+@@ -9,7 +9,7 @@
+
+ #usage/help
+ if len(sys.argv) == 1 or sys.argv[1] in helpme:
+- print "usage: harvest-variants.py <parsnp.hvt> [outfile]"
++ print("usage: harvest-variants.py <parsnp.hvt> [outfile]")
+ sys.exit(1)
+
+ #check in path for harvest
+--- a/src/harvest-alignments.py
++++ b/src/harvest-alignments.py
+@@ -1,4 +1,4 @@
+-#!python
++#!python3
+ import os,sys,string,subprocess
+
+ ##harvest utility file for XMFA file(s) of core genome alignments
+@@ -13,7 +13,7 @@
+
+ #print help/usage
+ if len(sys.argv) == 1 or sys.argv[1] in helpme:
+- print "usage: harvest-alignments.py <parsnp.hvt> [outfile]"
++ print("usage: harvest-alignments.py <parsnp.hvt> [outfile]")
+ sys.exit(1)
+
+ #check in path for harvest
+--- a/src/harvest-backbone.py
++++ b/src/harvest-backbone.py
+@@ -1,4 +1,4 @@
+-#!python
++#!python3
+ import os,sys,string,subprocess
+
+ ##harvest utility file for tab-delimited backbone file
+@@ -12,7 +12,7 @@
+
+ #print help/usage
+ if len(sys.argv) == 1 or sys.argv[1] in helpme:
+- print "usage: harvest-backbone.py <parsnp.hvt> [outfile]"
++ print("usage: harvest-backbone.py <parsnp.hvt> [outfile]")
+ sys.exit(1)
+
+ #check in path for harvest
+--- a/src/harvest-phylogeny.py
++++ b/src/harvest-phylogeny.py
+@@ -1,4 +1,4 @@
+-#!python
++#!python3
+ import os,sys,string,subprocess
+
+ ##harvest utility file for newick file of core genome phylogeny
+@@ -12,7 +12,7 @@
+
+ #print help/usage
+ if len(sys.argv) == 1 or sys.argv[1] in helpme:
+- print "usage: harvest-phylogeny.py <parsnp.hvt> [outfile]"
++ print("usage: harvest-phylogeny.py <parsnp.hvt> [outfile]")
+ sys.exit(1)
+
+ #check in path for harvest
+--- a/src/harvest-snps.py
++++ b/src/harvest-snps.py
+@@ -1,4 +1,4 @@
+-#!python
++#!python3
+ import os,sys,string,subprocess
+
+ ##harvest utility file for multi-fasta file of SNP loci
+@@ -12,7 +12,7 @@
+
+ #print help/usage
+ if len(sys.argv) == 1 or sys.argv[1] in helpme:
+- print "usage: harvest-snps.py <parsnp.hvt> [outfile]"
++ print("usage: harvest-snps.py <parsnp.hvt> [outfile]")
+ sys.exit(1)
+
+ #check in path for harvest
+--- a/src/harvest-variants.py
++++ b/src/harvest-variants.py
+@@ -1,4 +1,4 @@
+-#!python
++#!python3
+ import os,sys,string,subprocess
+ ##harvest utility file for writing VCF file
+ #ROADMAP
+@@ -10,7 +10,7 @@
+
+ #usage/help
+ if len(sys.argv) == 1 or sys.argv[1] in helpme:
+- print "usage: harvest-variants.py <parsnp.hvt> [outfile]"
++ print("usage: harvest-variants.py <parsnp.hvt> [outfile]")
+ sys.exit(1)
+
+ #check in path for harvest
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ hardening.patch
remove_memwrap.patch
parallel.patch
use-c++-14.patch
+python-2to3.patch
=====================================
debian/upstream/metadata
=====================================
@@ -22,3 +22,7 @@ Registry:
Entry: NA
- Name: conda:bioconda
Entry: harvesttools
+Repository: https://github.com/marbl/harvest-tools.git
+Repository-Browse: https://github.com/marbl/harvest-tools
+Bug-Database: https://github.com/marbl/harvest-tools/issues
+Bug-Submit: https://github.com/marbl/harvest-tools/issues/new
View it on GitLab: https://salsa.debian.org/med-team/harvest-tools/-/compare/590bec31132db3400397e8ce4937183df1311cd6...337cc969d05e07fc117dc82bb4794eb6d591f22b
--
View it on GitLab: https://salsa.debian.org/med-team/harvest-tools/-/compare/590bec31132db3400397e8ce4937183df1311cd6...337cc969d05e07fc117dc82bb4794eb6d591f22b
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