From 3a8f314f15775a69d38aa9e59ecaff8cf7e7664e Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Sun, 2 Jul 2017 04:08:59 -0400 Subject: [PATCH] Update patches --- ...st_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(-) delete mode 100644 debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch 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 -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 -- 2.30.2