commit: ebcdc8895b15d89af6600d8241e5cda417a4f7e3 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Aug 3 21:11:13 2020 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Aug 3 21:11:13 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ebcdc889
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 <AT> gentoo.org> sci-biology/pysam/Manifest | 1 - .../pysam/files/pysam-0.12-fix-buildsystem.patch | 63 ---------------------- sci-biology/pysam/pysam-0.12.0.1.ebuild | 47 ---------------- 3 files changed, 111 deletions(-) diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 661592294a2..f349d8ddc8a 100644 --- a/sci-biology/pysam/Manifest +++ b/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 diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch deleted file mode 100644 index 8b323a63fba..00000000000 --- a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch +++ /dev/null @@ -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", diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.12.0.1.ebuild deleted file mode 100644 index e7567f3501b..00000000000 --- a/sci-biology/pysam/pysam-0.12.0.1.ebuild +++ /dev/null @@ -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 - : -}
