[med-svn] [python-pysam] 09/21: Refresh patches

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository python-pysam.

commit dfd66a5bb114b84609d3c869ab7170731d000233
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sat Mar 5 14:21:20 2016 -0800

    Refresh patches
---
 .../patches/disable-tests-requiring-network.patch  | 22 +++++++---------------
 debian/patches/ignore-htslib-dir.patch             | 10 +++++-----
 2 files changed, 12 insertions(+), 20 deletions(-)

diff --git a/debian/patches/disable-tests-requiring-network.patch b/debian/patches/disable-tests-requiring-network.patch
index 07af1b6..b6cf1a1 100644
--- a/debian/patches/disable-tests-requiring-network.patch
+++ b/debian/patches/disable-tests-requiring-network.patch
@@ -4,16 +4,7 @@ Forwarded: no
 Last-Update: 2015-11-13
 --- python-pysam.orig/tests/tabix_test.py
 +++ python-pysam/tests/tabix_test.py
-@@ -504,7 +504,7 @@
-         b = copy.copy(a)
-         self.assertEqual(a, b)
- 
--        
-+
- 
- class TestIterators(unittest.TestCase):
- 
-@@ -944,7 +944,8 @@
+@@ -1124,7 +1124,8 @@
      local = os.path.join(DATADIR, "example.gtf.gz")
  
      def setUp(self):
@@ -23,20 +14,21 @@ Last-Update: 2015-11-13
          self.local_file = pysam.TabixFile(self.local, "r")
  
      def testFetchAll(self):
-@@ -960,11 +961,12 @@
+@@ -1139,11 +1140,12 @@
+             self.assertEqual(x, y)
  
      def testHeader(self):
-         self.assertEqual(list(self.local_file.header), [])
+-        self.assertEqual(list(self.local_file.header), [])
 -        self.assertRaises(AttributeError,
 -                          getattr,
 -                          self.remote_file,
 -                          "header")
- 
 +        if checkURL(self.url):
++            self.assertEqual(list(self.local_file.header), [])
 +            self.assertRaises(AttributeError,
 +                              getattr,
 +                              self.remote_file,
 +                              "header")
  
- class TestIndexArgument(unittest.TestCase):
- 
+     def tearDown(self):
+         self.remote_file.close()
diff --git a/debian/patches/ignore-htslib-dir.patch b/debian/patches/ignore-htslib-dir.patch
index 2ca4cd7..395ff4f 100644
--- a/debian/patches/ignore-htslib-dir.patch
+++ b/debian/patches/ignore-htslib-dir.patch
@@ -8,20 +8,20 @@ Last-Update: 2015-06-24
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- python-pysam.orig/setup.py
 +++ python-pysam/setup.py
-@@ -490,8 +490,6 @@
+@@ -494,8 +494,6 @@
      'url': "https://github.com/pysam-developers/pysam",
      'packages': ['pysam',
                   'pysam.include',
 -                 'pysam.include.htslib',
 -                 'pysam.include.htslib.htslib',
                   'pysam.include.samtools',
-                  # 'pysam.include.samtools.bcftools',
+                  'pysam.include.bcftools',
                   'pysam.include.samtools.win32'],
-@@ -509,7 +507,6 @@
+@@ -512,7 +510,6 @@
                      cutils],
      'cmdclass': cmdclass,
      'package_dir': {'pysam': 'pysam',
 -                    'pysam.include.htslib': 'htslib',
-                     'pysam.include.samtools': 'samtools'},
+                     'pysam.include.samtools': 'samtools',
+                     'pysam.include.bcftools': 'bcftools'},
      'package_data': {'': ['*.pxd', '*.h'], },
-     # do not pack in order to permit linking to csamtools.so

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