[med-svn] [python-biopython] 06/06: Adapt patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository python-biopython.

commit 4de2b1d462ffedd7fdf9849c64cc3b875840f34d
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 8 21:27:14 2016 +0200

    Adapt patches
---
 debian/patches/fix_test_NCBI_BLAST_tools.patch | 32 --------------------------
 debian/patches/fix_test_phyml_tool.patch       |  2 +-
 debian/patches/series                          |  1 -
 3 files changed, 1 insertion(+), 34 deletions(-)

diff --git a/debian/patches/fix_test_NCBI_BLAST_tools.patch b/debian/patches/fix_test_NCBI_BLAST_tools.patch
deleted file mode 100644
index 96478c3..0000000
--- a/debian/patches/fix_test_NCBI_BLAST_tools.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-Author: Peter Cock <p.j.a.cock at googlemail.com>
-Bug-Debian: https://bugs.debian.org/824048
-Upstream: https://github.com/biopython/biopython/issues/827
-Last-Update: Thu, 19 May 2016 12:32:17 +0100
-Description: sanity test which failed due to a change in the NCBI output
-
---- a/Tests/test_NCBI_BLAST_tools.py
-+++ b/Tests/test_NCBI_BLAST_tools.py
-@@ -100,12 +100,18 @@ class Pairwise(unittest.TestCase):
-         return_code = child.returncode
-         self.assertEqual(return_code, 0, "Got error code %i back from:\n%s"
-                          % (return_code, cline))
--        self.assertEqual(10, stdoutdata.count("Query= "))
--        if stdoutdata.count("***** No hits found *****") == 7:
--            # This happens with BLAST 2.2.26+ which is potentially a bug
--            pass
-+        # Used to get 10 matches from 10 pairwise searches,
-+        # as of NCBI BLAST+ 2.3.0 only get 1 Query= line:
-+        if stdoutdata.count("Query= ") == 10:
-+            if stdoutdata.count("***** No hits found *****") == 7:
-+                # This happens with BLAST 2.2.26+ which is potentially a bug
-+                pass
-+            else:
-+                self.assertEqual(9, stdoutdata.count("***** No hits found *****"))
-         else:
--            self.assertEqual(9, stdoutdata.count("***** No hits found *****"))
-+            # Assume this is NCBI BLAST+ 2.3.0 or later,
-+            self.assertEqual(1, stdoutdata.count("Query= "))
-+            self.assertEqual(0, stdoutdata.count("***** No hits found *****"))
- 
-         # TODO - Parse it? I think we'd need to update this obsole code :(
-         # records = list(NCBIStandalone.Iterator(StringIO(stdoutdata),
diff --git a/debian/patches/fix_test_phyml_tool.patch b/debian/patches/fix_test_phyml_tool.patch
index f484ce2..75014df 100644
--- a/debian/patches/fix_test_phyml_tool.patch
+++ b/debian/patches/fix_test_phyml_tool.patch
@@ -7,7 +7,7 @@ Description: Fix test_phyml_tool.py
 
 --- a/Tests/test_phyml_tool.py
 +++ b/Tests/test_phyml_tool.py
-@@ -47,7 +47,7 @@ class AppTests(unittest.TestCase):
+@@ -52,7 +52,7 @@ class AppTests(unittest.TestCase):
              self.assertTrue(len(out) > 0)
              self.assertEqual(len(err), 0)
              # Check the output tree
diff --git a/debian/patches/series b/debian/patches/series
index 85da082..60dbfde 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
 remove_mathml-qname.patch
 privacy_breach.patch
 fix_test_phyml_tool.patch
-fix_test_NCBI_BLAST_tools.patch

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