From 5ba04e28410af0197d473c6b429a1919a67dc00e Mon Sep 17 00:00:00 2001
From: Andreas Tille <tille@debian.org>
Date: Sat, 17 Feb 2018 14:50:47 +0100
Subject: [PATCH] Update patches and exclude tests using http access

---
 debian/changelog                              |  7 ++
 .../exclude_tests_accessing_remote_http.patch | 71 +------------------
 debian/patches/xfail.patch                    |  6 +-
 debian/rules                                  |  3 +
 4 files changed, 14 insertions(+), 73 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index ccfc64a..b285109 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+python-pysam (0.14+ds-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * d/rules: Exclude tests using http access
+
+ -- Andreas Tille <tille@debian.org>  Sat, 17 Feb 2018 14:44:29 +0100
+
 python-pysam (0.13.0+ds-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/patches/exclude_tests_accessing_remote_http.patch b/debian/patches/exclude_tests_accessing_remote_http.patch
index 1377946..09c25ec 100644
--- a/debian/patches/exclude_tests_accessing_remote_http.patch
+++ b/debian/patches/exclude_tests_accessing_remote_http.patch
@@ -72,7 +72,7 @@ Description: Exclude tests trying to access remote http sites and thus need
      ints = ( 65536, 214748, 2147484, 2147483647 )
 --- a/tests/AlignmentFile_test.py
 +++ b/tests/AlignmentFile_test.py
-@@ -1893,81 +1893,6 @@ class TestDoubleFetchCRAMWithReference(T
+@@ -1559,81 +1559,6 @@ class TestDoubleFetchCRAMWithReference(T
      reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
  
  
@@ -154,72 +154,3 @@ Description: Exclude tests trying to access remote http sites and thus need
  class TestLargeOptValues(unittest.TestCase):
  
      ints = (65536, 214748, 2147484, 2147483647)
---- a/tests/tabix_test.py
-+++ b/tests/tabix_test.py
-@@ -1033,66 +1033,6 @@ for vcf_file in vcf_files:
-     globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
- 
- 
--class TestRemoteFileHTTP(unittest.TestCase):
--
--    url = "http://www.cgat.org/downloads/public/pysam/test/example.gtf.gz"
--    region = "chr1:1-1000"
--    local = os.path.join(TABIX_DATADIR, "example.gtf.gz")
--
--    def setUp(self):
--        if not pysam.config.HAVE_LIBCURL or not checkURL(self.url):
--            self.remote_file = None
--        else:
--            self.remote_file = pysam.TabixFile(self.url, "r")
--            
--        self.local_file = pysam.TabixFile(self.local, "r")
--
--    def tearDown(self):
--        if self.remote_file is None:
--            return
--
--        self.remote_file.close()
--        self.local_file.close()
--
--    def testFetchAll(self):
--        if self.remote_file is None:
--            return
--
--        remote_result = list(self.remote_file.fetch())
--        local_result = list(self.local_file.fetch())
--
--        self.assertEqual(len(remote_result), len(local_result))
--        for x, y in zip(remote_result, local_result):
--            self.assertEqual(x, y)
--
--    def testHeader(self):
--        if self.remote_file is None:
--            return
--
--        self.assertEqual(list(self.local_file.header), [])
--
--
--class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
--
--    url = "http://www.cgat.org/downloads/public/pysam/test/example_comments.gtf.gz"
--    region = "chr1:1-1000"
--    local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
--
--    def setUp(self):
--        if not pysam.config.HAVE_LIBCURL or not checkURL(self.url):
--            self.remote_file = None
--        else:
--            self.remote_file = pysam.TabixFile(self.url, "r")
--        self.local_file = pysam.TabixFile(self.local, "r")
--
--    def testHeader(self):
--        if self.remote_file is None:
--            return
--
--        self.assertEqual(list(self.local_file.header), ["# comment at start"])
--        self.assertEqual(list(self.local_file.header), self.remote_file.header)
--        
--
- class TestIndexArgument(unittest.TestCase):
- 
-     filename_src = os.path.join(TABIX_DATADIR, "example.vcf.gz")
diff --git a/debian/patches/xfail.patch b/debian/patches/xfail.patch
index 15c77fe..40fb7b9 100644
--- a/debian/patches/xfail.patch
+++ b/debian/patches/xfail.patch
@@ -5,11 +5,11 @@ Forwarded: not-needed
 Last-Update: 2017-10-01
 --- a/tests/AlignmentFile_test.py
 +++ b/tests/AlignmentFile_test.py
-@@ -521,6 +521,7 @@ class TestIO(unittest.TestCase):
+@@ -474,6 +474,7 @@ class TestIO(unittest.TestCase):
                         "tmp_ex2.bam",
                         "rb", "wb")
  
 +    @unittest.skip
      def testCRAM2CRAM(self):
-         self.checkEcho("ex2.cram",
-                        "ex2.cram",
+         # in some systems different reference sequence paths might be
+         # embedded in the CRAM files which will result in different headers
diff --git a/debian/rules b/debian/rules
index cb44816..d5ebb44 100755
--- a/debian/rules
+++ b/debian/rules
@@ -15,6 +15,9 @@ HTSLIBDIR  := /usr/lib/$(DEB_HOST_MULTIARCH)
 export HTSLIB_LIBRARY_DIR=$(HTSLIBDIR)
 export HTSLIB_INCLUDE_DIR=/usr/include
 
+export PYBUILD_TEST_ARGS_python2=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
+export PYBUILD_TEST_ARGS_python3=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
+
 clean: clean-tests
 %:
 	dh $@ --with python2,python3 --buildsystem=pybuild
-- 
2.30.2