Drop patch applied upstream

diff --git a/debian/patches/external-htslib.patch b/debian/patches/external-htslib.patch
deleted file mode 100644 (file)
index c7c37ad..0000000
--- a/debian/patches/external-htslib.patch
+++ /dev/null
@@ -1,102 +0,0 @@
-Description: Fix external htslib support
-Author: Afif Elghraoui <afif@debian.org>
-Forwarded: no
-Last-Update: 2016-03-05
---- python-pysam.orig/setup.py
-+++ python-pysam/setup.py
-@@ -87,10 +87,21 @@
- #         pysam.
- # external: use shared libhts.so compiled outside of
- #           pysam
--HTSLIB_MODE = "shared"
-+HTSLIB_MODE = os.environ.get("HTSLIB_MODE","shared")
- HTSLIB_LIBRARY_DIR = os.environ.get("HTSLIB_LIBRARY_DIR", None)
- HTSLIB_INCLUDE_DIR = os.environ.get("HTSLIB_INCLUDE_DIR", None)
- HTSLIB_CONFIGURE_OPTIONS = os.environ.get("HTSLIB_CONFIGURE_OPTIONS", None)
-+HTSLIB_SOURCE = None
-+
-+package_list = ['pysam',
-+                'pysam.include',
-+                'pysam.include.samtools',
-+                'pysam.include.bcftools',
-+                'pysam.include.samtools.win32']
-+package_dirs = {'pysam': 'pysam',
-+                'pysam.include.samtools': 'samtools',
-+                'pysam.include.bcftools': 'bcftools'}
-+config_headers = ["samtools/config.h"]
- 
- # Check if cython is available
- #
-@@ -101,13 +112,15 @@
-     from cy_build import CyExtension as Extension, cy_build_ext as build_ext
-     source_pattern = "pysam/c%s.pyx"
-     cmdclass = {'build_ext': build_ext}
--    HTSLIB_MODE = "shared"
-+    if HTSLIB_MODE != "external":
-+        HTSLIB_MODE = "shared"
- except ImportError:
-     # no Cython available - use existing C code
-     cmdclass = {}
-     source_pattern = "pysam/c%s.c"
-     # Set mode to separate, as "shared" not fully tested yet.
--    HTSLIB_MODE = "separate"
-+    if HTSLIB_MODE != "external":
-+        HTSLIB_MODE = "separate"
- 
- # collect pysam version
- sys.path.insert(0, "pysam")
-@@ -140,6 +153,10 @@
- htslib_configure_options = None
- 
- if HTSLIB_MODE in ['shared', 'separate']:
-+    package_list += ['pysam.include.htslib',
-+                     'pysam.include.htslib.htslib']
-+    package_dirs.update({'pysam.include.htslib':'htslib'})
-+
-     htslib_configure_options = configure_library(
-         "htslib",
-         HTSLIB_CONFIGURE_OPTIONS,
-@@ -149,6 +166,7 @@
-     print ("# pysam: htslib configure options: {}".format(
-         str(htslib_configure_options)))
- 
-+    config_headers += ["htslib/config.h"]
-     if htslib_configure_options is None:
-         # create empty config.h file
-         with open("htslib/config.h", "w") as outf:
-@@ -261,7 +279,7 @@
- 
- # create empty config.h files if they have not been created automatically
- # or created by the user:
--for fn in "samtools/config.h", "htslib/config.h":
-+for fn in config_headers:
-     if not os.path.exists(fn):
-         with open(fn, "w") as outf:
-             outf.write(
-@@ -493,13 +511,7 @@
-     'license': "MIT",
-     'platforms': "ALL",
-     'url': "https://github.com/pysam-developers/pysam",
--    'packages': ['pysam',
--                 'pysam.include',
--                 'pysam.include.htslib',
--                 'pysam.include.htslib.htslib',
--                 'pysam.include.samtools',
--                 'pysam.include.bcftools',
--                 'pysam.include.samtools.win32'],
-+    'packages': package_list,
-     'requires': ['cython (>=0.21)'],
-     'ext_modules': [chtslib,
-                     csamfile,
-@@ -512,10 +524,7 @@
-                     cfaidx,
-                     cutils],
-     'cmdclass': cmdclass,
--    'package_dir': {'pysam': 'pysam',
--                    'pysam.include.htslib': 'htslib',
--                    'pysam.include.samtools': 'samtools',
--                    'pysam.include.bcftools': 'bcftools'},
-+    'package_dir': package_dirs,
-     'package_data': {'': ['*.pxd', '*.h'], },
-     # do not pack in order to permit linking to csamtools.so
-     'zip_safe': False,

diff --git a/debian/patches/series b/debian/patches/series
index 2f83d471329f81b454421aa8fe762fca42f1011f..da8b79080b4d9bdb52ef264ac43f936283f0956a 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
-external-htslib.patch
 rpath.patch