[med-svn] [python-pysam] 03/04: Update patches

[Afif Elghraoui]

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

commit 3a8f314f15775a69d38aa9e59ecaff8cf7e7664e
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Jul 2 04:08:59 2017 -0400

    Update patches
---
 ...de_test_tyring_to_access_remote_ftpserver.patch | 29 ----------------------
 debian/patches/htslib-external-config.patch        | 14 +++++------
 debian/patches/rpath.patch                         | 10 --------
 debian/patches/series                              |  1 -
 4 files changed, 7 insertions(+), 47 deletions(-)

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
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 at 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 ab7a144..cf4915f 100644
--- 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 44a34aa..9d68920 100644
--- 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 8730a1c..af88631 100644
--- 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

-- 
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