[med-svn] r16527 - in trunk/packages/python-biom-format/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Thu Mar 27 13:17:00 UTC 2014
Author: tille
Date: 2014-03-27 13:17:00 +0000 (Thu, 27 Mar 2014)
New Revision: 16527
Added:
trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch
trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch
Removed:
trunk/packages/python-biom-format/trunk/debian/patches/deal_with_none_array_metadata
trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages
trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix
Modified:
trunk/packages/python-biom-format/trunk/debian/changelog
trunk/packages/python-biom-format/trunk/debian/patches/series
Log:
Adapted patches to new upstream version (hope this is correct)
Modified: trunk/packages/python-biom-format/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/changelog 2014-03-27 13:15:57 UTC (rev 16526)
+++ trunk/packages/python-biom-format/trunk/debian/changelog 2014-03-27 13:17:00 UTC (rev 16527)
@@ -1,3 +1,13 @@
+python-biom-format (1.3.1+dfsg-1) UNRELEASED; urgency=medium
+
+ [ Andreas Tille ]
+ * New upstream version (updated patches). New version also does not
+ use Cython
+ Closes: #742691
+ * Incorporate changes by BioLinux
+
+ -- Andreas Tille <tille at debian.org> Thu, 27 Mar 2014 11:52:15 +0100
+
python-biom-format (1.2.0-1biolinux1) precise; urgency=low
* Add runtime dep on PyQi
Deleted: trunk/packages/python-biom-format/trunk/debian/patches/deal_with_none_array_metadata
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/deal_with_none_array_metadata 2014-03-27 13:15:57 UTC (rev 16526)
+++ trunk/packages/python-biom-format/trunk/debian/patches/deal_with_none_array_metadata 2014-03-27 13:17:00 UTC (rev 16527)
@@ -1,17 +0,0 @@
-Allow the conversion of BIOM to a table when the metadata is not held in an array.
-This is probably not the best fix as the BIOM is still corrupt. Maybe should throw
-an error?
---- a/python-code/biom/table.py
-+++ b/python-code/biom/table.py
-@@ -352,8 +352,9 @@
- str_obs_vals = delim.join(map(str, self._conv_to_np(obs_values)))
-
- if header_key and self.ObservationMetadata is not None:
-- md = self.ObservationMetadata[self._obs_index[obs_id]]
-- md_out = metadata_formatter(md.get(header_key,None))
-+ md = self.ObservationMetadata[self._obs_index[obs_id]].get(header_key,None)
-+ if isinstance(md, basestring) : md = md,
-+ md_out = metadata_formatter(md)
- output.append('%s%s%s\t%s' % (obs_id, delim, str_obs_vals, md_out))
- else:
- output.append('%s%s%s' % (obs_id, delim, str_obs_vals))
Deleted: trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages 2014-03-27 13:15:57 UTC (rev 16526)
+++ trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages 2014-03-27 13:17:00 UTC (rev 16527)
@@ -1,24 +0,0 @@
-This patch allows biom to work even if there is an older installation of the biom
-libs in /usr/local/...
-Not sure if this is the neatest fix, but absolute_imports doesn't seem to be 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.
---- a/scripts/biom
-+++ b/scripts/biom
-@@ -11,4 +11,6 @@
- # __maintainer__ = "Greg Caporaso"
- # __email__ = "gregcaporaso at gmail.com"
-
-+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 -- "$@"
---- a/python-code/biom/__init__.py
-+++ b/python-code/biom/__init__.py
-@@ -1,5 +1,7 @@
- #!/usr/bin/env python
-
-+from __future__ import absolute_import
-+
- __author__ = "Daniel McDonald"
- __copyright__ = "Copyright 2012, BIOM-Format Project"
- __credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso",
Added: trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch (rev 0)
+++ trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch 2014-03-27 13:17:00 UTC (rev 16527)
@@ -0,0 +1,28 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Fri, 28 Feb 2014 16:25:41 +0000
+Description: This patch allows biom to work even if there is an older
+ installation of the biom libs in /usr/local/...
+ Not sure if this is the neatest fix, but absolute_imports doesn't seem to be
+ the full answer here as we have one module hooking in another, and probably
+ looking for the default installed version is normally what you'd want.
+
+--- a/scripts/biom
++++ b/scripts/biom
+@@ -19,4 +19,6 @@
+ # __maintainer__ = "Greg Caporaso"
+ # __email__ = "gregcaporaso at gmail.com"
+
++export PYTHONPATH=/usr/lib/python`python --version 2>&1 | grep -o '[1-9]\.[0-9]\+'`/dist-packages
++
+ exec pyqi --driver-name biom --command-config-module biom.interfaces.optparse.config -- "$@"
+--- a/biom/__init__.py
++++ b/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"
+ __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/series
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/series 2014-03-27 13:15:57 UTC (rev 16526)
+++ trunk/packages/python-biom-format/trunk/debian/patches/series 2014-03-27 13:17:00 UTC (rev 16527)
@@ -1,3 +1,2 @@
-#deal_with_none_array_metadata
-smart_arse_fix
-ignore_local_dist-packages
+smart_arse_fix.patch
+ignore_local_dist-packages.patch
Deleted: trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix 2014-03-27 13:15:57 UTC (rev 16526)
+++ trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix 2014-03-27 13:17:00 UTC (rev 16527)
@@ -1,17 +0,0 @@
---- a/python-code/biom/table.py
-+++ b/python-code/biom/table.py
-@@ -332,12 +332,8 @@
-
- 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:
Added: trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch (rev 0)
+++ trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch 2014-03-27 13:17:00 UTC (rev 16527)
@@ -0,0 +1,21 @@
+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:
More information about the debian-med-commit
mailing list