Skip to content
Commits on Source (10)
Show whitespace changes
Inline Side-by-side
debian/changelog
View file @ 21663e8e
ray (2.3.1-7) unstable; urgency=medium
* Use 2to3 to port to Python3
Closes: #945704
* debhelper-compat 12
* Standards-Version: 4.4.1
* Remove trailing whitespace in debian/copyright
* autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
* Use secure URI in debian/watch.
* Remove obsolete fields Name from debian/upstream/metadata.
* Fix day-of-week for changelog entries 2.1.0-1.
-- Andreas Tille <tille@debian.org> Mon, 02 Dec 2019 12:51:58 +0100
ray (2.3.1-6) unstable; urgency=medium
* Team upload
......@@ -99,4 +113,4 @@ ray (2.1.0-1) unstable; urgency=low
* Initial Debian release, Closes: #692238
-- Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca> Fri, 14 Nov 2012 13:32:00 +0000
-- Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca> Wed, 14 Nov 2012 13:32:00 +0000
debian/control
View file @ 21663e8e
......@@ -4,11 +4,11 @@ Uploaders: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11),
Build-Depends: debhelper-compat (= 12),
zlib1g-dev,
libbz2-dev,
mpi-default-dev
Standards-Version: 4.1.4
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/ray
Vcs-Git: https://salsa.debian.org/med-team/ray.git
Homepage: http://denovoassembler.sourceforge.net/
......@@ -45,7 +45,7 @@ Package: ray-extra
Architecture: all
Depends: ${misc:Depends},
r-base-core,
python
python3
Description: Scripts and XSL sheets for post-processing for ray
Ray is a parallel software that computes de novo genome assemblies with
next-generation sequencing data.
......
debian/patches/2to3.patch 0 → 100644
View file @ 21663e8e
Description: Use 2to3 to port to Python3
Bug-Debian: https://bugs.debian.org/945704
Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 02 Dec 2019 12:40:56 +0100
--- a/scripts/NCBI-Taxonomy/Create-Taxon-Names.py
+++ b/scripts/NCBI-Taxonomy/Create-Taxon-Names.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
# encoding: UTF-8
# author: Sébastien Boisvert
# date: 2012-09-19
@@ -74,7 +74,7 @@ stream.close()
print("Done.")
-identifiers=storage.keys()
+identifiers=list(storage.keys())
identifiers.sort()
rankIndex=0
--- a/scripts/NCBI-Taxonomy/GenerateTaxonNames.py
+++ b/scripts/NCBI-Taxonomy/GenerateTaxonNames.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
#encoding: UTF-8
# author: Sébastien Boisvert
@@ -17,7 +17,7 @@ GenerateTaxonNames.py Taxon-Names.tsv Ta
import sys
if len(sys.argv)!=3:
- print __doc__
+ print(__doc__)
sys.exit(1)
namesFile=sys.argv[1]
@@ -45,4 +45,4 @@ for line in open(namesFile):
if type in types:
rank=types[type]
- print taxonNumber+" "+taxonName+" "+rank
+ print(taxonNumber+" "+taxonName+" "+rank)
--- a/scripts/NCBI-Taxonomy/getName.py
+++ b/scripts/NCBI-Taxonomy/getName.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
#>gi|148243635|ref|NC_009467.1| Acidiphilium cryptum JF-5 plasmid pACRY01, complete sequence
@@ -11,4 +11,4 @@ tokens=file.split('/')
tokens2=tokens[1].split("_uid")
name=tokens2[0].strip()
-print name
+print(name)
--- a/scripts/NCBI-Taxonomy/getNameInFile.py
+++ b/scripts/NCBI-Taxonomy/getNameInFile.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
#>gi|148243635|ref|NC_009467.1| Acidiphilium cryptum JF-5 plasmid pACRY01, complete sequence
@@ -15,4 +15,4 @@ name=name.replace(', complete genome',''
name=name.replace(" ","_").replace('/','_').strip()
-print name
+print(name)
--- a/scripts/getSeq.py
+++ b/scripts/getSeq.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
"""Get a sequence from a fasta file by specifying the sequence name
Usage:
@@ -9,7 +9,7 @@ Usage:
import sys
if len(sys.argv)!=3:
- print __doc__
+ print(__doc__)
sys.exit(1)
file=sys.argv[1]
@@ -24,4 +24,4 @@ for line in open(file):
elif dump:
break
if dump:
- print line.strip()
+ print(line.strip())
--- a/scripts/illumina-split-linked-sequences-fastq.py
+++ b/scripts/illumina-split-linked-sequences-fastq.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
import sys
--- a/scripts/interleave-fasta.py
+++ b/scripts/interleave-fasta.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
# encoding:utf8
# author: Sébastien Boisvert
# part of Ray distribution
@@ -17,7 +17,7 @@ if __name__ == '__main__':
file1 = sys.argv[1]
file2 = sys.argv[2]
except:
- print __doc__
+ print(__doc__)
sys.exit(1)
with open(file1) as f1:
@@ -27,8 +27,8 @@ if __name__ == '__main__':
if line.strip() == "":
break
- print line.strip()
- print f1.readline().strip()
- print f2.readline().strip()
- print f2.readline().strip()
+ print(line.strip())
+ print(f1.readline().strip())
+ print(f2.readline().strip())
+ print(f2.readline().strip())
--- a/scripts/interleave-fastq.py
+++ b/scripts/interleave-fastq.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
# encoding:utf8
# author: Sébastien Boisvert
# part of Ray distribution
@@ -17,7 +17,7 @@ if __name__ == '__main__':
file1 = sys.argv[1]
file2 = sys.argv[2]
except:
- print __doc__
+ print(__doc__)
sys.exit(1)
with open(file1) as f1:
@@ -26,11 +26,11 @@ if __name__ == '__main__':
line = f1.readline()
if line.strip() == "":
break
- print line.strip()
+ print(line.strip())
- for i in xrange(3):
- print f1.readline().strip()
+ for i in range(3):
+ print(f1.readline().strip())
- for i in xrange(4):
- print f2.readline().strip()
+ for i in range(4):
+ print(f2.readline().strip())
debian/patches/series
View file @ 21663e8e
......@@ -2,3 +2,4 @@ hardening.patch
mips.patch
gcc-6.patch
stable-link-order.patch
2to3.patch
debian/tests/run-unit-test
View file @ 21663e8e
......@@ -4,12 +4,12 @@ export OMPI_MCA_rmaps_base_oversubscribe=1
pkg=ray
if [ "$ADTTMP" = "" ] ; then
ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $ADTTMP
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/test_data/* .
gunzip -r *
......
debian/upstream/metadata
View file @ 21663e8e
Name: ray
Reference:
- Author: Sébastien Boisvert and François Laviolette and Jacques Corbeil
Title: >
......
debian/watch
View file @ 21663e8e
version=3
http://sf.net/denovoassembler/Ray-v?(\d[\d\.]+)\.tar\.bz2
https://sf.net/denovoassembler/Ray-v?(\d[\d\.]+)\.tar\.bz2