[med-svn] [Git][med-team/aegean][master] 11 commits: Use 2to3 to convert from Python2 to Python3
Andreas Tille
gitlab at salsa.debian.org
Sat Aug 31 23:31:01 BST 2019
Andreas Tille pushed to branch master at Debian Med / aegean
Commits:
2a930678 by Andreas Tille at 2019-08-31T22:03:28Z
Use 2to3 to convert from Python2 to Python3
- - - - -
40414941 by Andreas Tille at 2019-08-31T22:04:29Z
Standards-Version: 4.4.0
- - - - -
792fdcb6 by Andreas Tille at 2019-08-31T22:04:59Z
Drop git from Build-Depends
- - - - -
b84596db by Andreas Tille at 2019-08-31T22:07:04Z
s/python/python3/ in Build-Depends and Test-Depends
- - - - -
31b2294f by Andreas Tille at 2019-08-31T22:07:55Z
Drop redundant debian/README.source
- - - - -
c70c1e2f by Andreas Tille at 2019-08-31T22:08:12Z
debhelper-compat 12
- - - - -
348bc044 by Andreas Tille at 2019-08-31T22:08:26Z
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.
- - - - -
51cf0a2b by Andreas Tille at 2019-08-31T22:08:26Z
Remove patches missing from debian/patches/series.
Fixes lintian: patch-file-present-but-not-mentioned-in-series
See https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html for more details.
- - - - -
310f521a by Andreas Tille at 2019-08-31T22:08:27Z
Set fields Upstream-Contact in debian/copyright.
- - - - -
7a7ab2ce by Andreas Tille at 2019-08-31T22:08:27Z
Remove obsolete fields Name, Contact from debian/upstream/metadata.
- - - - -
3f268e21 by Andreas Tille at 2019-08-31T22:16:24Z
Really apply 2to3 patch
- - - - -
11 changed files:
- − debian/README.source
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/2to3.patch
- debian/patches/includepaths
- debian/patches/series
- debian/tests/control
- debian/tests/functional-tests
- debian/upstream/metadata
Changes:
=====================================
debian/README.source deleted
=====================================
@@ -1 +0,0 @@
-Please use the 'get-orig-source' rules target to get the source. It needs to be repacked for dfsg reasons.
=====================================
debian/changelog
=====================================
@@ -1,16 +1,22 @@
aegean (0.16.0+dfsg-2) UNRELEASED; urgency=medium
- * Team upload
-
[ Jelmer Vernooij ]
* Move source package lintian overrides to debian/source.
[ Andreas Tille ]
- * Standards-Version: 4.2.1
+ * Standards-Version: 4.4.0
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
* Do not parse d/changelog
-
- -- Andreas Tille <tille at debian.org> Fri, 26 Oct 2018 20:11:46 +0200
+ * Use 2to3 to convert from Python2 to Python3
+ Closes: #936109
+ * Drop git from Build-Depends
+ * Drop redundant debian/README.source
+ * debhelper-compat 12
+ * Use secure URI in Homepage field.
+ * Set fields Upstream-Contact in debian/copyright.
+ * Remove obsolete fields Name, Contact from debian/upstream/metadata.
+
+ -- Andreas Tille <tille at debian.org> Sun, 01 Sep 2019 00:02:16 +0200
aegean (0.16.0+dfsg-1) unstable; urgency=medium
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,15 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Sascha Steinbiss <satta at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11),
+Build-Depends: debhelper-compat (= 12),
libcairo2-dev,
libgenometools0-dev,
- python,
- git
-Standards-Version: 4.2.1
+ python3
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/aegean
Vcs-Git: https://salsa.debian.org/med-team/aegean.git
-Homepage: http://standage.github.io/AEGeAn
+Homepage: https://standage.github.io/AEGeAn
Package: aegean
Architecture: amd64 arm64 armel armhf i386 mipsel powerpc ppc64el s390x hurd-i386 kfreebsd-amd64 kfreebsd-i386 ppc64 x32
=====================================
debian/copyright
=====================================
@@ -2,6 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: aegean
Source: http://aegean.readthedocs.org/en/v0.10.2/license.html
Files-Excluded: data/share/vendor/jquery.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/jquery.js data/share/vendor/jquery.dataTables.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/jquery.dataTables.js data/share/vendor/mootools-core-1.3.2-full-nocompat-yc.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/mootools-core-1.3.2-full-nocompat-yc.js data/share/vendor/mootools-more-1.3.2.1.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/mootools-more-1.3.2.1.js
+Upstream-Contact: Daniel Standage <daniel.standage at gmail.com>
Files:
*
@@ -18,4 +19,4 @@ License: ISC
ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
- OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
\ No newline at end of file
+ OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,159 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 01 Sep 2019 00:01:00 +0200
+Bug-Debian: https://bugs.debian.org/936109
+Description: Use 2to3 to convert from Python2 to Python3
+
+--- a/data/scripts/align-convert.py
++++ b/data/scripts/align-convert.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ # Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+
+-from __future__ import print_function
++
+ import re
+ import sys
+
+@@ -24,14 +24,14 @@ class Peeker:
+ def __iter__(self):
+ return self
+
+- def next(self):
++ def __next__(self):
+ if self.buffer:
+ return self.buffer.pop(0)
+ else:
+ return next(self.iter)
+
+ def __next__(self):
+- return self.next()
++ return next(self)
+
+ def peek(self, n=0):
+ """Return an item n entries ahead in the iteration."""
+--- a/data/scripts/check-gff3.py
++++ b/data/scripts/check-gff3.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ # Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -8,7 +8,7 @@
+ #
+ # Usage: check-gff3.py < annot.gff3
+
+-from __future__ import print_function
++
+ import re
+ import sys
+
+@@ -50,7 +50,7 @@ for line in sys.stdin:
+ topleveltypes[values[2]] += 1
+
+ print('\n===== Types =====')
+-featuretypes = counts.keys()
++featuretypes = list(counts.keys())
+ featuretypes.sort()
+ for featuretype in featuretypes:
+ count = counts[featuretype]
+@@ -60,7 +60,7 @@ for featuretype in featuretypes:
+ print('%s (%lu total, %lu top-level)' % (featuretype, count, topcount))
+
+ print('\n===== Relationships (child --> parent) =====')
+-childtypes = relationships.keys()
++childtypes = list(relationships.keys())
+ childtypes.sort()
+ for childtype in childtypes:
+ parenttypes = list(relationships[childtype].keys())
+--- a/data/scripts/lpdriver.py
++++ b/data/scripts/lpdriver.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ # Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+
+-from __future__ import print_function
++
+ import argparse
+ import os
+ import re
+--- a/data/scripts/miloci.py
++++ b/data/scripts/miloci.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ # Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+
+-from __future__ import print_function
++
+ import re
+ import sys
+
+--- a/data/scripts/seq-reg.py
++++ b/data/scripts/seq-reg.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ # Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+
+-from __future__ import print_function
++
+ import argparse
+ import os
+ import re
+--- a/data/scripts/uloci.py
++++ b/data/scripts/uloci.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ # Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+
+-from __future__ import print_function
++
+ import argparse
+ import re
+ import sys
+--- a/data/scripts/version.py
++++ b/data/scripts/version.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ # Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+
+-from __future__ import print_function
++
+ import re
+ import subprocess
+ import sys
=====================================
debian/patches/includepaths
=====================================
@@ -3,7 +3,7 @@ Description: Adjust include paths
Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/Makefile
+++ b/Makefile
-@@ -62,6 +62,7 @@
+@@ -62,6 +62,7 @@ endif
INCS=$(shell pkg-config --silence-errors --cflags-only-I cairo) \
-I inc/core \
-I /usr/local/include/genometools \
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ remove_license
adjust_datapath
follow_links
includepaths
+2to3.patch
=====================================
debian/tests/control
=====================================
@@ -1,2 +1,2 @@
Tests: functional-tests
-Depends: @, python
+Depends: @, python3
=====================================
debian/tests/functional-tests
=====================================
@@ -24,4 +24,3 @@ for f in *.sh; do
done
echo "run: OK"
-
=====================================
debian/upstream/metadata
=====================================
@@ -1,25 +1,23 @@
-Name: AEGeAn
-Bug-Database: https://github.com/standage/AEGeAn/issues
+Bug-Database: https://github.com/standage/AEGeAn/issues
Bug-Submit: https://github.com/standage/AEGeAn/issues/new
-Contact: Daniel Standage <daniel.standage at gmail.com>
Reference:
Author: Standage, Daniel S and Brendel, Volker P
Title: >
- ParsEval: parallel comparison and analysis of gene structure annotations.
+ ParsEval: parallel comparison and analysis of gene structure annotations.
Journal: BMC Bioinformatics
Year: 2012
Volume: 13
Number: 1
Pages: 187
DOI: 10.1186/1471-2105-13-187
- PMID: 22852583
- URL: http://www.biomedcentral.com/1471-2105/13/187
- eprint: http://www.biomedcentral.com/content/pdf/1471-2105-13-187.pdf
+ PMID: 22852583
+ URL: http://www.biomedcentral.com/1471-2105/13/187
+ eprint: http://www.biomedcentral.com/content/pdf/1471-2105-13-187.pdf
Repository: http://github.com/standage/AEGeAn
Registry:
- - Name: OMICtools
- Entry: OMICS_19721
- - Name: SciCrunch
- Entry: NA
- - Name: bio.tools
- Entry: NA
+- Name: OMICtools
+ Entry: OMICS_19721
+- Name: SciCrunch
+ Entry: NA
+- Name: bio.tools
+ Entry: NA
View it on GitLab: https://salsa.debian.org/med-team/aegean/compare/66b2d9ff5ddf71f4b37e3da788dd14a64e7fecf5...3f268e21b9ef0ac75c85ccf48d97b20fcbd69598
--
View it on GitLab: https://salsa.debian.org/med-team/aegean/compare/66b2d9ff5ddf71f4b37e3da788dd14a64e7fecf5...3f268e21b9ef0ac75c85ccf48d97b20fcbd69598
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190831/d3967f2c/attachment-0001.html>
More information about the debian-med-commit
mailing list