Update patches

diff --git a/debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch b/debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch
deleted file mode 100644 (file)
index 33f4a22..0000000
--- a/debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Description: Exclude test tyring to access remote ftpserver
-Bug-Debian: https://bugs.debian.org/861496
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Thu, 04 May 2017 12:50:22 +0200
-
---- a/tests/faidx_test.py
-+++ b/tests/faidx_test.py
-@@ -216,21 +216,5 @@ class TestFastxFileWithEmptySequence(uni
-         self.assertEqual(ref_num, l)
- 
- 
--class TestRemoteFileFTP(unittest.TestCase):
--    '''test remote access.
--    '''
--
--    url = "ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa"
--
--
--    def testFTPView(self):
--        if not checkURL(self.url):
--            return
--        with pysam.Fastafile(self.url) as f:
--            self.assertEqual(
--                len(f.fetch("chr1", 0, 1000)),
--                1000)
--
--
- if __name__ == "__main__":
-     unittest.main()

diff --git a/debian/patches/htslib-external-config.patch b/debian/patches/htslib-external-config.patch
index ab7a1443f30b40431fef0e719695acc1c8bd474b..cf4915f9f263bce16ca2007dfa0bba2918c9074e 100644 (file)
--- a/debian/patches/htslib-external-config.patch
+++ b/debian/patches/htslib-external-config.patch
@@ -4,12 +4,12 @@ Forwarded: not-needed
 Last-Update: 2017-01-26
 --- python-pysam.orig/setup.py
 +++ python-pysam/setup.py
-@@ -255,7 +255,7 @@
- else:
-     raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE)
- 
--internal_htslib_libraries = [os.path.splitext("chtslib{}".format(sysconfig.get_config_var('SO')))[0]]
+@@ -263,7 +263,7 @@
+ suffix = sysconfig.get_config_var('EXT_SUFFIX')
+ if not suffix:
+     suffix = sysconfig.get_config_var('SO')
+-internal_htslib_libraries = [os.path.splitext("chtslib{}".format(suffix))[0]]
 +internal_htslib_libraries = []
  
- # build config.py
- with open(os.path.join("pysam", "config.py"), "w") as outf:
+ internal_tools_libraries = [
+     os.path.splitext("csamtools{}".format(suffix))[0],

diff --git a/debian/patches/rpath.patch b/debian/patches/rpath.patch
index 44a34aa23ae315857714aac04a679f0dd19ecf66..9d68920e071e48bbb1081d03cf263b09ce1c28d9 100644 (file)
--- a/debian/patches/rpath.patch
+++ b/debian/patches/rpath.patch
@@ -20,13 +20,3 @@ Last-Update: 2016-03-05
 -            ext.extra_link_args += ['-Wl,-rpath,$ORIGIN']
                                      
          build_ext.build_extension(self, ext)
---- python-pysam.orig/setup.py
-+++ python-pysam/setup.py
-@@ -353,7 +353,6 @@
-     shared_htslib_sources +
-     os_c_files,
-     library_dirs=htslib_library_dirs,
--    runtime_library_dirs=htslib_library_dirs,
-     include_dirs=["pysam", "."] + include_os + htslib_include_dirs,
-     libraries=external_htslib_libraries,
-     language="c",

diff --git a/debian/patches/series b/debian/patches/series
index 8730a1cf304d41e1e80ce24e8b186b3985114540..af88631bc1c353ed3a4d1b207a2dd00e11f4cb61 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
 rpath.patch
 htslib-external-config.patch
-exclude_test_tyring_to_access_remote_ftpserver.patch