[med-svn] r20299 - in trunk/packages/python-biom-format/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Sat Oct 24 16:46:09 UTC 2015
Author: tille
Date: 2015-10-24 16:46:08 +0000 (Sat, 24 Oct 2015)
New Revision: 20299
Added:
trunk/packages/python-biom-format/trunk/debian/patches/fix_future_import.patch
Removed:
trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch
Modified:
trunk/packages/python-biom-format/trunk/debian/changelog
trunk/packages/python-biom-format/trunk/debian/control
trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch
trunk/packages/python-biom-format/trunk/debian/patches/no-web-adds.patch
trunk/packages/python-biom-format/trunk/debian/patches/series
Log:
Prepare new upstream version
Modified: trunk/packages/python-biom-format/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/changelog 2015-10-23 22:31:59 UTC (rev 20298)
+++ trunk/packages/python-biom-format/trunk/debian/changelog 2015-10-24 16:46:08 UTC (rev 20299)
@@ -1,3 +1,9 @@
+python-biom-format (2.1.5+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Sat, 24 Oct 2015 18:07:11 +0200
+
python-biom-format (2.1+dfsg-1) unstable; urgency=medium
* New upstream version
Modified: trunk/packages/python-biom-format/trunk/debian/control
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/control 2015-10-23 22:31:59 UTC (rev 20298)
+++ trunk/packages/python-biom-format/trunk/debian/control 2015-10-24 16:46:08 UTC (rev 20299)
@@ -14,6 +14,7 @@
help2man,
python-cogent,
pyqi (>= 0.3.2),
+ python-future,
python-nose,
python-tox,
python-sphinx,
Added: trunk/packages/python-biom-format/trunk/debian/patches/fix_future_import.patch
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/fix_future_import.patch (rev 0)
+++ trunk/packages/python-biom-format/trunk/debian/patches/fix_future_import.patch 2015-10-24 16:46:08 UTC (rev 20299)
@@ -0,0 +1,21 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 24 Oct 2015 18:07:11 +0200
+Description: "from __future__ import" needs to be the first line of code
+
+--- a/biom/__init__.py
++++ b/biom/__init__.py
+@@ -48,12 +48,12 @@ either in TSV, HDF5, JSON, gzip'd JSON o
+ # The full license is in the file COPYING.txt, distributed with this software.
+ # ----------------------------------------------------------------------------
+
++from __future__ import absolute_import
++
+ from .table import Table
+ from .parse import parse_biom_table as parse_table, load_table
+ from .util import __format_version__, __version__
+
+-from __future__ import absolute_import
+-
+ __author__ = "Daniel McDonald"
+ __copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
+ __credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso",
Modified: trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch 2015-10-23 22:31:59 UTC (rev 20298)
+++ trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch 2015-10-24 16:46:08 UTC (rev 20299)
@@ -6,21 +6,12 @@
the full answer here as we have one module hooking in another, and probably
looking for the default installed version is normally what you'd want.
---- biom-format-2.0.0.orig/scripts/biom
-+++ biom-format-2.0.0/scripts/biom
-@@ -19,4 +19,6 @@
- # __maintainer__ = "Greg Caporaso"
- # __email__ = "gregcaporaso at gmail.com"
+--- a/biom/__init__.py
++++ b/biom/__init__.py
+@@ -52,6 +52,8 @@ from .table import Table
+ from .parse import parse_biom_table as parse_table, load_table
+ from .util import __format_version__, __version__
-+export PYTHONPATH=/usr/lib/python`python --version 2>&1 | grep -o '[1-9]\.[0-9]\+'`/dist-packages
-+
- exec pyqi --driver-name biom --command-config-module biom.interfaces.optparse.config -- "$@"
---- biom-format-2.0.0.orig/biom/__init__.py
-+++ biom-format-2.0.0/biom/__init__.py
-@@ -8,6 +8,8 @@
- # The full license is in the file COPYING.txt, distributed with this software.
- # ----------------------------------------------------------------------------
-
+from __future__ import absolute_import
+
__author__ = "Daniel McDonald"
Modified: trunk/packages/python-biom-format/trunk/debian/patches/no-web-adds.patch
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/no-web-adds.patch 2015-10-23 22:31:59 UTC (rev 20298)
+++ trunk/packages/python-biom-format/trunk/debian/patches/no-web-adds.patch 2015-10-24 16:46:08 UTC (rev 20299)
@@ -2,7 +2,7 @@
Last-Update: Tue, 20 May 2014 19:16:23 +0200
Description: Save user privacy by preventing inclusion of web adds
---- biom-format-2.0.0.orig/doc/_templates/layout.html
+--- a/doc/_templates/layout.html
+++ /dev/null
@@ -1,28 +0,0 @@
-{% extends "!layout.html" %}
Modified: trunk/packages/python-biom-format/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/series 2015-10-23 22:31:59 UTC (rev 20298)
+++ trunk/packages/python-biom-format/trunk/debian/patches/series 2015-10-24 16:46:08 UTC (rev 20299)
@@ -1,3 +1,3 @@
-# smart_arse_fix.patch
ignore_local_dist-packages.patch
no-web-adds.patch
+fix_future_import.patch
Deleted: trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch 2015-10-23 22:31:59 UTC (rev 20298)
+++ trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch 2015-10-24 16:46:08 UTC (rev 20299)
@@ -1,21 +0,0 @@
-Author: Tim Booth <tbooth at ceh.ac.uk>
-Last-Update: Fri, 28 Feb 2014 16:25:41 +0000
-Description: Deal with cases when h_key xor h_value is set
-
---- a/biom/table.py
-+++ b/biom/table.py
-@@ -338,12 +338,8 @@ class Table(object):
-
- samp_ids = delim.join(map(str, self.SampleIds))
-
-- # 17 hrs of straight programming later...
-- if header_key is not None:
-- if header_value is None:
-- raise TableException, "You need to specify both header_key and header_value"
-- if header_value is not None:
-- if header_key is None:
-+ # If h_key xor h_value is set we have a problem...
-+ if (header_key is None) != (header_value is None):
- raise TableException, "You need to specify both header_key and header_value"
-
- if header_value:
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