sci-biology/pysam: Remove old

Closes: https://bugs.gentoo.org/645060
Closes: https://bugs.gentoo.org/646986
Closes: https://bugs.gentoo.org/718472
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert <soap@gentoo.org>

sci-biology/pysam/Manifest

@@ -1,2 +1 @@
-DIST pysam-0.12.0.1.tar.gz 2672020 BLAKE2B 4bc6330405724f7b1126da91ba3338687f4dd17f015895f42b971f22ffbb6c32eda65e2667035a4cc830c0370b34d95d3aa6ae0f026b2b3276af1fd6841eed28 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d
 DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece SHA512 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28

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

@@ -1,63 +0,0 @@
-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-0.12.0.1.ebuild

@@ -1,47 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_6 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="
-	https://github.com/pysam-developers/pysam
-	https://pypi.org/project/pysam/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.5*:="
-DEPEND="${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)
-	rm -r htslib || die
-
-	# prevent setup.py from adding RPATHs
-	sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
-		-i cy_build.py || die
-	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-src_compile() {
-	# TODO
-	# empty compile, as the build system runs the whole build again in install
-	:
-}