[med-svn] [Git][med-team/ray][master] 10 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Mon Dec 2 12:28:16 GMT 2019
Andreas Tille pushed to branch master at Debian Med / ray
Commits:
da7c50b9 by Andreas Tille at 2019-12-02T11:42:37Z
Use 2to3 to port to Python3
- - - - -
c88c13cb by Andreas Tille at 2019-12-02T11:43:10Z
debhelper-compat 12
- - - - -
03dfb661 by Andreas Tille at 2019-12-02T11:43:14Z
Standards-Version: 4.4.1
- - - - -
dca13f9d by Andreas Tille at 2019-12-02T11:43:15Z
Remove trailing whitespace in debian/copyright
- - - - -
34895e11 by Andreas Tille at 2019-12-02T11:43:15Z
autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
- - - - -
db9a808e by Andreas Tille at 2019-12-02T11:43:20Z
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.
- - - - -
0d46e88b by Andreas Tille at 2019-12-02T11:43:26Z
Remove obsolete fields Name from debian/upstream/metadata.
- - - - -
02a952d2 by Andreas Tille at 2019-12-02T11:43:26Z
Fix day-of-week for changelog entries 2.1.0-1.
Fixes lintian: debian-changelog-has-wrong-day-of-week
See https://lintian.debian.org/tags/debian-changelog-has-wrong-day-of-week.html for more details.
- - - - -
c58c2e4e by Andreas Tille at 2019-12-02T11:52:12Z
Depends Python3 once the scripts were ported
- - - - -
21663e8e by Andreas Tille at 2019-12-02T11:57:05Z
Upload to unstable
- - - - -
9 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/2to3.patch
- debian/patches/series
- debian/tests/run-unit-test
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+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 at 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 at ulaval.ca> Fri, 14 Nov 2012 13:32:00 +0000
+ -- Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> Wed, 14 Nov 2012 13:32:00 +0000
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -4,11 +4,11 @@ Uploaders: Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca>,
Andreas Tille <tille at 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/copyright
=====================================
@@ -25,7 +25,7 @@ License: LGPL-3
GNU Lesser General Public License for more details.
.
You have received a copy of the GNU Lesser General Public License
- along with this program (lgpl-3.0.txt).
+ along with this program (lgpl-3.0.txt).
see <http://www.gnu.org/licenses/>
Comment: On Debian systems, the complete text of the GNU Lesser General Public
License version 3 can be found in /usr/share/common-licenses/LGPL-3
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,168 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/945704
+Author: Andreas Tille <tille at 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
=====================================
@@ -2,3 +2,4 @@ hardening.patch
mips.patch
gcc-6.patch
stable-link-order.patch
+2to3.patch
=====================================
debian/tests/run-unit-test
=====================================
@@ -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
=====================================
@@ -1,38 +1,37 @@
-Name: ray
Reference:
- - Author: Sébastien Boisvert and François Laviolette and Jacques Corbeil
- Title: >
+- Author: Sébastien Boisvert and François Laviolette and Jacques Corbeil
+ Title: >
Ray: Simultaneous Assembly of Reads from a Mix of
High-Throughput Sequencing Technologies
- Journal: Journal of Computational Biology
- Year: 2010
- Volume: 17
- Number: 11
- Pages: 1519-1533
- DOI: 10.1089/cmb.2009.0238
- PMID: 20958248
- URL: http://online.liebertpub.com/doi/abs/10.1089/cmb.2009.0238
- eprint: http://online.liebertpub.com/doi/pdfplus/10.1089/cmb.2009.0238
- - Comment: for Ray Meta and Ray Communities
- Author: >
+ Journal: Journal of Computational Biology
+ Year: 2010
+ Volume: 17
+ Number: 11
+ Pages: 1519-1533
+ DOI: 10.1089/cmb.2009.0238
+ PMID: 20958248
+ URL: http://online.liebertpub.com/doi/abs/10.1089/cmb.2009.0238
+ eprint: http://online.liebertpub.com/doi/pdfplus/10.1089/cmb.2009.0238
+- Comment: for Ray Meta and Ray Communities
+ Author: >
Sébastien Boisvert and Frédéric Raymond and Élénie Godzaridis and
François Laviolette and Jacques Corbeil
- Title: "Ray Meta: scalable de novo metagenome assembly and profiling"
- Journal: Genome Biology
- Year: 2012
- Volume: 13
- Number: 12
- Pages: R112
- DOI: 10.1186/gb-2012-13-12-r122
- PMID: 23259615
- URL: http://genomebiology.com/2012/13/12/R122/abstract
- eprint: http://genomebiology.com/content/pdf/gb-2012-13-12-r122.pdf
+ Title: "Ray Meta: scalable de novo metagenome assembly and profiling"
+ Journal: Genome Biology
+ Year: 2012
+ Volume: 13
+ Number: 12
+ Pages: R112
+ DOI: 10.1186/gb-2012-13-12-r122
+ PMID: 23259615
+ URL: http://genomebiology.com/2012/13/12/R122/abstract
+ eprint: http://genomebiology.com/content/pdf/gb-2012-13-12-r122.pdf
Registry:
- - Name: OMICtools
- Entry: OMICS_00027
- - Name: bio.tools
- Entry: ray
- - Name: SciCrunch
- Entry: SCR_001916
- - Name: conda:bioconda
- Entry: ray
+- Name: OMICtools
+ Entry: OMICS_00027
+- Name: bio.tools
+ Entry: ray
+- Name: SciCrunch
+ Entry: SCR_001916
+- Name: conda:bioconda
+ Entry: ray
=====================================
debian/watch
=====================================
@@ -1,2 +1,2 @@
version=3
-http://sf.net/denovoassembler/Ray-v?(\d[\d\.]+)\.tar\.bz2
+https://sf.net/denovoassembler/Ray-v?(\d[\d\.]+)\.tar\.bz2
View it on GitLab: https://salsa.debian.org/med-team/ray/compare/29c74fa00482b33faa65006bf7464fc3e1fac60e...21663e8e448a6c407526c4d99b7a858704442612
--
View it on GitLab: https://salsa.debian.org/med-team/ray/compare/29c74fa00482b33faa65006bf7464fc3e1fac60e...21663e8e448a6c407526c4d99b7a858704442612
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