[med-svn] r15585 - in trunk/packages/qiime/trunk/debian: . patches

Andreas Tille tille at moszumanska.debian.org
Sat Dec 21 08:14:25 UTC 2013 

Author: tille
Date: 2013-12-21 08:14:25 +0000 (Sat, 21 Dec 2013)
New Revision: 15585

Removed:
   trunk/packages/qiime/trunk/debian/patches/fix_typo_in_error_message
   trunk/packages/qiime/trunk/debian/patches/remove_matplotlib_warning
Modified:
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch
   trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
   trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files
   trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier
   trunk/packages/qiime/trunk/debian/patches/series
Log:
Adapted patches to new upstream version


Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	2013-12-21 08:08:52 UTC (rev 15584)
+++ trunk/packages/qiime/trunk/debian/changelog	2013-12-21 08:14:25 UTC (rev 15585)
@@ -1,6 +1,6 @@
 qiime (1.8.0+dfsg-1) UNRELEASED; urgency=low
 
-  * New upstream version
+  * New upstream version (adapted patches)
   * Fixed debian/watch
   * Suggests: torque-client
     Closes: #721902

Modified: trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch	2013-12-21 08:08:52 UTC (rev 15584)
+++ trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch	2013-12-21 08:14:25 UTC (rev 15585)
@@ -3,7 +3,7 @@
 
 --- a/scripts/print_qiime_config.py
 +++ b/scripts/print_qiime_config.py
-@@ -252,8 +252,7 @@
+@@ -210,8 +210,7 @@ class QIIMEConfig(TestCase):
          """local qiime_config has no extra params"""
          
          qiime_project_dir = get_qiime_project_dir()

Modified: trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch	2013-12-21 08:08:52 UTC (rev 15584)
+++ trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch	2013-12-21 08:14:25 UTC (rev 15585)
@@ -1,6 +1,6 @@
 --- a/qiime/denoiser/utils.py
 +++ b/qiime/denoiser/utils.py
-@@ -42,8 +42,9 @@
+@@ -60,8 +60,9 @@ def get_denoiser_data_dir():
  def get_flowgram_ali_exe():
      """Return the path to the flowgram alignment prog
      """

Modified: trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files	2013-12-21 08:08:52 UTC (rev 15584)
+++ trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files	2013-12-21 08:14:25 UTC (rev 15585)
@@ -4,7 +4,7 @@
 
 --- a/qiime/util.py
 +++ b/qiime/util.py
-@@ -301,8 +301,9 @@
+@@ -302,8 +302,9 @@ def get_qiime_project_dir():
      # Get the directory containing util.py
      current_dir_path = dirname(current_file_path)
      # Return the directory containing the directory containing util.py

Deleted: trunk/packages/qiime/trunk/debian/patches/fix_typo_in_error_message
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_typo_in_error_message	2013-12-21 08:08:52 UTC (rev 15584)
+++ trunk/packages/qiime/trunk/debian/patches/fix_typo_in_error_message	2013-12-21 08:14:25 UTC (rev 15585)
@@ -1,9 +0,0 @@
---- a/scripts/pick_otus_through_otu_table.py
-+++ b/scripts/pick_otus_through_otu_table.py
-@@ -10,4 +10,4 @@
- __email__ = "gregcaporaso at gmail.com"
- __status__ = "Release"
- 
--print "\nThis script has been renamed pick_de_novo_otus.py for clarity. For help, call pick_denovo_otus.py -h\n"
-\ No newline at end of file
-+print "\nThis script has been renamed pick_de_novo_otus.py for clarity. For help, call pick_de_novo_otus.py -h\n"

Modified: trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier	2013-12-21 08:08:52 UTC (rev 15584)
+++ trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier	2013-12-21 08:14:25 UTC (rev 15585)
@@ -4,7 +4,7 @@
 This is a nasty hack and hopefully the patch can be dropped for QIIME 1.6
 --- a/qiime/assign_taxonomy.py
 +++ b/qiime/assign_taxonomy.py
-@@ -60,14 +60,20 @@
+@@ -65,14 +65,20 @@ def validate_rdp_version(rdp_jarpath=Non
              "http://qiime.org/install/install.html#rdp-install"
              )
  
@@ -34,7 +34,7 @@
              "RDP Classifier does not look like version 2.2 or greater."
 --- a/scripts/assign_taxonomy.py
 +++ b/scripts/assign_taxonomy.py
-@@ -260,6 +260,11 @@
+@@ -301,6 +301,11 @@ def main():
          params['training_data_properties_fp'] = opts.training_data_properties_fp
          params['max_memory'] = "%sM" % opts.rdp_max_memory
  

Deleted: trunk/packages/qiime/trunk/debian/patches/remove_matplotlib_warning
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/remove_matplotlib_warning	2013-12-21 08:08:52 UTC (rev 15584)
+++ trunk/packages/qiime/trunk/debian/patches/remove_matplotlib_warning	2013-12-21 08:14:25 UTC (rev 15585)
@@ -1,28 +0,0 @@
-We get a warning about having Matplotlib 1.1.1 instead of 1.1.0, but
-I don't believe this monor version has introduced any incompatibilities.
---- a/scripts/make_2d_plots.py
-+++ b/scripts/make_2d_plots.py
-@@ -157,8 +157,8 @@
-     matplotlib_version_info = tuple([int(i) for i in matplotlib_version if \
-                             i.isdigit()])
- 
--    if matplotlib_version_info != (1,1,0):
--        print "This code was only tested with Matplotlib-1.1.0"
-+    if matplotlib_version_info[0:2] != (1,1):
-+        print "This code was only tested with Matplotlib-1.1.x"
-         
-     data = {}
- 
---- a/scripts/plot_taxa_summary.py
-+++ b/scripts/plot_taxa_summary.py
-@@ -180,8 +180,8 @@
-     matplotlib_version_info = tuple([int(i) for i in matplotlib_version if \
-                             i.isdigit()])
- 
--    if matplotlib_version_info != (1,1,0):
--        print "This code was only tested with Matplotlib-1.1.0"
-+    if matplotlib_version_info[0:2] != (1,1):
-+        print "This code was only tested with Matplotlib-1.1.x"
- 
-     #get QIIME directory
-     qiime_dir=get_qiime_project_dir()

Modified: trunk/packages/qiime/trunk/debian/patches/series
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/series	2013-12-21 08:08:52 UTC (rev 15584)
+++ trunk/packages/qiime/trunk/debian/patches/series	2013-12-21 08:14:25 UTC (rev 15585)
@@ -2,5 +2,3 @@
 fix_binary_helper_location.patch
 make_qiime_accept_new_rdp_classifier
 fix_path_for_support_files
-fix_typo_in_error_message
-remove_matplotlib_warning

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