[med-svn] [snakemake] 03/04: Refresh patches

[Kevin Murray]

This is an automated email from the git hooks/post-receive script.

daube-guest pushed a commit to branch master
in repository snakemake.

commit 0b56de4a992cf689e5561336872d9fd9c4321c07
Author: Kevin Murray <kdmfoss at gmail.com>
Date:   Thu Jan 19 11:29:12 2017 +1100

    Refresh patches
---
 .../0004-drop_test_symlink_time_handling.patch     |  2 +-
 debian/patches/0005-drop_test_symlink_temp.patch   |  2 +-
 .../0007-Backport-bugfix-for-dynamic-rules.patch   | 22 ----------------------
 debian/patches/series                              |  1 -
 4 files changed, 2 insertions(+), 25 deletions(-)

diff --git a/debian/patches/0004-drop_test_symlink_time_handling.patch b/debian/patches/0004-drop_test_symlink_time_handling.patch
index 6711e28..8ef1559 100644
--- a/debian/patches/0004-drop_test_symlink_time_handling.patch
+++ b/debian/patches/0004-drop_test_symlink_time_handling.patch
@@ -5,7 +5,7 @@ Description: Ignore failures of test that might happpen in pbuilder
 
 --- a/tests/tests.py
 +++ b/tests/tests.py
-@@ -345,7 +345,11 @@ def test_input_generator():
+@@ -353,7 +353,11 @@
  def test_symlink_time_handling():
      #See Snakefile for notes on why this fails on some systems
      if os.utime in os.supports_follow_symlinks:
diff --git a/debian/patches/0005-drop_test_symlink_temp.patch b/debian/patches/0005-drop_test_symlink_temp.patch
index 09faa34..58bc6f8 100644
--- a/debian/patches/0005-drop_test_symlink_temp.patch
+++ b/debian/patches/0005-drop_test_symlink_temp.patch
@@ -5,7 +5,7 @@ Description: Ignore failures of test that might happpen in pbuilder
 
 --- a/tests/tests.py
 +++ b/tests/tests.py
-@@ -300,10 +300,6 @@ def test_cluster_sync():
+@@ -308,10 +308,6 @@
          cluster_sync="./qsub")
  
  
diff --git a/debian/patches/0007-Backport-bugfix-for-dynamic-rules.patch b/debian/patches/0007-Backport-bugfix-for-dynamic-rules.patch
deleted file mode 100644
index d729216..0000000
--- a/debian/patches/0007-Backport-bugfix-for-dynamic-rules.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From: Kevin Murray <kdmfoss at gmail.com>
-Date: Wed, 18 Jan 2017 11:17:46 +1100
-Subject: Backport bugfix for dynamic rules
-
->From https://bitbucket.org/snakemake/snakemake/pull-requests/168
----
- snakemake/io.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/snakemake/io.py b/snakemake/io.py
-index d60a055..ae38f14 100644
---- a/snakemake/io.py
-+++ b/snakemake/io.py
-@@ -758,7 +758,7 @@ class Namedlist(list):
-         add = len(items) - 1
-         for name, (i, j) in self._names.items():
-             if i > index:
--                self._names[name] = (i + add, j + add)
-+                self._names[name] = (i + add, None if j is None else j + add)
-             elif i == index:
-                 self.set_name(name, i, end=i + len(items))
- 
diff --git a/debian/patches/series b/debian/patches/series
index f6364e5..1bf9663 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,4 +4,3 @@
 0004-drop_test_symlink_time_handling.patch
 0005-drop_test_symlink_temp.patch
 0006-restore-bin.patch
-0007-Backport-bugfix-for-dynamic-rules.patch

-- 
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