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 <[email protected]> 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__ = "[email protected]" - -+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 -- "$@" ---- a/python-code/biom/__init__.py -+++ b/python-code/biom/__init__.py -@@ -1,5 +1,7 @@ - #!/usr/bin/env python - -+from __future__ import absolute_import -+ - __author__ = "Daniel McDonald" - __copyright__ = "Copyright 2012, BIOM-Format Project" - __credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso", Added: trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch =================================================================== --- trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch (rev 0) +++ trunk/packages/python-biom-format/trunk/debian/patches/ignore_local_dist-packages.patch 2014-03-27 13:17:00 UTC (rev 16527) @@ -0,0 +1,28 @@ +Author: Tim Booth <[email protected]> +Last-Update: Fri, 28 Feb 2014 16:25:41 +0000 +Description: This patch allows biom to work even if there is an older + installation of the biom libs in /usr/local/... + Not sure if this is the neatest fix, but absolute_imports doesn't seem to be + the full answer here as we have one module hooking in another, and probably + looking for the default installed version is normally what you'd want. + +--- a/scripts/biom ++++ b/scripts/biom +@@ -19,4 +19,6 @@ + # __maintainer__ = "Greg Caporaso" + # __email__ = "[email protected]" + ++export PYTHONPATH=/usr/lib/python`python --version 2>&1 | grep -o '[1-9]\.[0-9]\+'`/dist-packages ++ + exec pyqi --driver-name biom --command-config-module biom.interfaces.optparse.config -- "$@" +--- 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 <[email protected]> +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: _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
