sci-biology/pysam: Fix broken relative -I

Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670
Package-Manager: Portage-2.3.8, Repoman-2.3.3

sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch

@@ -0,0 +1,63 @@
+The build system is not designed with partial out-of-source
+builds in mind. This is evident by using relative includes
+such as '-Isamtools' instead of proper relative or absolute
+paths.
+
+Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670
+
+--- a/setup.py
++++ b/setup.py
+@@ -359,6 +359,8 @@
+
+ define_macros = []
+
++samtools_include_dirs = [os.path.abspath("samtools")]
++
+ chtslib = Extension(
+     "pysam.libchtslib",
+     [source_pattern % "htslib",
+@@ -385,7 +387,7 @@
+     htslib_sources +
+     os_c_files,
+     library_dirs=htslib_library_dirs,
+-    include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs,
++    include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries + internal_htslib_libraries,
+     language="c",
+     extra_compile_args=extra_compile_args,
+@@ -404,7 +406,7 @@
+     htslib_sources +
+     os_c_files,
+     library_dirs=htslib_library_dirs,
+-    include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs,
++    include_dirs=["pysam"] + samtools_include_dirs + include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries + internal_htslib_libraries,
+     language="c",
+     extra_compile_args=extra_compile_args,
+@@ -423,7 +425,7 @@
+     htslib_sources +
+     os_c_files,
+     library_dirs=htslib_library_dirs,
+-    include_dirs=["pysam", "samtools", "."] + include_os + htslib_include_dirs,
++    include_dirs=["pysam", "."] + samtools_include_dirs + include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries + internal_htslib_libraries,
+     language="c",
+     extra_compile_args=extra_compile_args,
+@@ -467,7 +469,7 @@
+     htslib_sources +
+     os_c_files,
+     library_dirs=["pysam"] + htslib_library_dirs,
+-    include_dirs=["samtools", "pysam", "."] +
++    include_dirs=["pysam", "."] + samtools_include_dirs +
+     include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries + internal_htslib_libraries,
+     language="c",
+@@ -482,7 +484,7 @@
+     htslib_sources +
+     os_c_files,
+     library_dirs=["pysam"] + htslib_library_dirs,
+-    include_dirs=["bcftools", "pysam", "."] +
++    include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs +
+     include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries + internal_htslib_libraries,
+     language="c",

sci-biology/pysam/pysam-0.12.ebuild

@@ -22,10 +22,14 @@ DEPEND="${RDEPEND}
 	dev-python/cython[${PYTHON_USEDEP}]
 	dev-python/setuptools[${PYTHON_USEDEP}]"
 
+PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch )
+
 python_prepare_all() {
+	# unbundle htslib
+	export HTSLIB_MODE="external"
 	export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
 	export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
-	export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+	rm -r htslib || die
 
 	# prevent setup.py from adding RPATHs
 	sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \