Refresh patches

diff --git a/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch b/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch
index 185dfbdc404c22ff406443301b1232c932cb47a5..fe9bbe4d58a8a0ccad282fcfdf3764c4a7f1ee28 100644 (file)
--- a/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch
+++ b/debian/patches/execute-linking-tests-only-when-explicitely-reque.patch
@@ -12,55 +12,12 @@ Subject: execute linking tests only when explicitely
 
 --- a/.travis.yml
 +++ b/.travis.yml
-@@ -11,6 +11,8 @@ env:
+@@ -11,8 +11,6 @@ env:
      - CONDA_PY=3.4
      - CONDA_PY=3.5
      - CONDA_PY=3.6
-+  global:
-+    - PYSAM_LINKING_TEST=1
+-  global:
+-    - PYSAM_LINKING_TEST=1
  
  addons:
    apt:
---- a/tests/TestUtils.py
-+++ b/tests/TestUtils.py
-@@ -23,6 +23,7 @@ LINKDIR = os.path.abspath(os.path.join(o
- 
- IS_PYTHON3 = sys.version_info[0] >= 3
- 
-+
- if IS_PYTHON3:
-     from itertools import zip_longest
-     from urllib.request import urlopen
---- a/tests/linking_test.py
-+++ b/tests/linking_test.py
-@@ -31,6 +31,9 @@ def check_tests_pass(statement):
-     return True
- 
- 
-+@unittest.skipUnless(
-+    os.environ.get("PYSAM_LINKING_TESTS", None),
-+    "enable linking tests by setting PYSAM_LINKING_TESTS environment variable")
- class TestLinking(unittest.TestCase):
- 
-     package_name = "link_with_rpath"
-@@ -43,6 +46,10 @@ class TestLinking(unittest.TestCase):
-             "cd {} && rm -rf build && python setup.py install".format(self.workdir),
-                 shell=True)
- 
-+
-+@unittest.skipUnless(
-+    os.environ.get("PYSAM_LINKING_TESTS", None),
-+    "enable linking tests by setting PYSAM_LINKING_TESTS environment variable")
- class TestLinkWithRpath(TestLinking):
- 
-     package_name = "link_with_rpath"
-@@ -52,6 +59,9 @@ class TestLinkWithRpath(TestLinking):
-             "cd {} && python test_module.py".format(os.path.join(self.workdir, "tests"))))
- 
- 
-+@unittest.skipUnless(
-+    os.environ.get("PYSAM_LINKING_TESTS", None),
-+    "enable linking tests by setting PYSAM_LINKING_TESTS environment variable")
- class TestLinkWithoutRpath(TestLinking):
- 
-     package_name = "link_without_rpath"

diff --git a/debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch b/debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch
deleted file mode 100644 (file)
index d96b801..0000000
--- a/debian/patches/rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-From: Andreas Heger <andreas.heger@gmail.com>
-Date: Mon, 18 Sep 2017 16:48:21 +0100
-Bug-Debian: https://bugs.debian.org/871083
-Subject: rename helper function to prevent it from being picked
- up by nose, fixes #541
-
----
- tests/linking_test.py | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
---- a/tests/linking_test.py
-+++ b/tests/linking_test.py
-@@ -20,7 +20,7 @@ def check_import(statement):
-             raise
- 
- 
--def check_tests_pass(statement):
-+def check_pass(statement):
-     try:
-         output = subprocess.check_output(
-             statement, stderr=subprocess.STDOUT, shell=True)
-@@ -55,7 +55,7 @@ class TestLinkWithRpath(TestLinking):
-     package_name = "link_with_rpath"
-     
-     def test_package_tests_pass(self):
--        self.assertTrue(check_tests_pass(
-+        self.assertTrue(check_pass(
-             "cd {} && python test_module.py".format(os.path.join(self.workdir, "tests"))))
- 
- 
-@@ -79,7 +79,7 @@ class TestLinkWithoutRpath(TestLinking):
-         pysam_libdirs, pysam_libs = zip(*[os.path.split(x) for x in pysam_libraries])
-         pysam_libdir = pysam_libdirs[0]
- 
--        self.assertTrue(check_tests_pass(
-+        self.assertTrue(check_pass(
-             "export LD_LIBRARY_PATH={}:$PATH && cd {} && python test_module.py".format(
-                 pysam_libdir,
-                 os.path.join(self.workdir, "tests"))))

diff --git a/debian/patches/series b/debian/patches/series
index 5014bfafe77745a527d300b5f0d0a6b2e244aa73..c2c2f2838824e2a4f9bf72af35c6c1db7e3cad01 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
 execute-linking-tests-only-when-explicitely-reque.patch
-rename-helper-function-to-prevent-it-from-being-picked-up-by-nose.patch
 xfail.patch

diff --git a/debian/patches/xfail.patch b/debian/patches/xfail.patch
index 8a214a2e0d100865a44728ff15ea7f9a24967b14..15c77fe43279e4adfecf39f2307295fba56e09f1 100644 (file)
--- a/debian/patches/xfail.patch
+++ b/debian/patches/xfail.patch
@@ -3,9 +3,9 @@ Description: temporarily skip failing test
 Author: Afif Elghraoui <afif@debian.org>
 Forwarded: not-needed
 Last-Update: 2017-10-01
---- python-pysam.orig/tests/AlignmentFile_test.py
-+++ python-pysam/tests/AlignmentFile_test.py
-@@ -521,6 +521,7 @@
+--- a/tests/AlignmentFile_test.py
++++ b/tests/AlignmentFile_test.py
+@@ -521,6 +521,7 @@ class TestIO(unittest.TestCase):
                         "tmp_ex2.bam",
                         "rb", "wb")