commit: de55574a2c871cd8baaf5fdc33960f90401d3e44 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Sep 2 11:07:41 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Sep 2 12:36:59 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=de55574a
sci-biology/pysam: Remove old Package-Manager: Portage-2.3.8, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5593 sci-biology/pysam/Manifest | 1 - .../pysam/files/pysam-0.9.0-missing-config.h.patch | 40 ------------------- sci-biology/pysam/pysam-0.9.0.ebuild | 45 ---------------------- 3 files changed, 86 deletions(-) diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index b2e7af85717..c95db9a1dcd 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1,2 +1 @@ DIST pysam-0.12.tar.gz 2537142 SHA256 33922cb3277ed9a63457c1b6a9dcad2774a217ababcc97a854435be87ba80488 SHA512 095a47cd7258ef093a172445c425f382996da886e44e1beb81ecdec2325024e099d14bee6fcd928c4449099f51ad92b6d7ceb464815c463ab4478f162a40f21e WHIRLPOOL 2331e24d817cd3e7372df8e115498456e685ac426796b29c6d5a28edbaab2321f7efc9db0f14a000750fcd9e30391c02b81e439a07596813bdf7fc6c6e1a3ae3 -DIST pysam-0.9.0.tar.gz 2701721 SHA256 dd4946c8efa6786a754e2b50c6027dd03aa82c8ee6c2be3b4e51384da80b4c7c SHA512 9189ef2b56df0f5e2c84586c0c2b2cd46a77dbedd3aa6fd25ddcc4a93320038bead073206fff528ae9775f153c875838726dd0af8e4c7bf4e0c6063145e2bc06 WHIRLPOOL 6c7d459057fed3961e983b3e8563e10a47cb87f5da2fb99ca893eff9e19a8b9e4c27b5d82a978a611d615eba8052fbe3e36498ea461e03521a075d9aee8da463 diff --git a/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch b/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch deleted file mode 100644 index 617786a5a58..00000000000 --- a/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch +++ /dev/null @@ -1,40 +0,0 @@ -From 55f5d8ce51ad999123a779f31fcf0fecd60de9e6 Mon Sep 17 00:00:00 2001 -From: Andreas Heger <andreas.he...@gmail.com> -Date: Mon, 21 Mar 2016 21:10:04 +0000 -Subject: [PATCH] {AH} create empty config.h for samtools if it does not exist, - fixes #245 - ---- - setup.py | 12 +++++++++++- - 1 file changed, 11 insertions(+), 1 deletion(-) - -diff --git a/setup.py b/setup.py -index 7b59b69..2f00c37 100644 ---- a/setup.py -+++ b/setup.py -@@ -155,7 +155,7 @@ def run_configure(option): - outf.write( - "/* empty config.h created by pysam */\n") - outf.write( -- "/* conservative compilation options */") -+ "/* conservative compilation options */\n") - - if HTSLIB_LIBRARY_DIR: - # linking against a shared, externally installed htslib version, no -@@ -259,6 +259,16 @@ def run_configure(option): - "adding shared libcurl and libcrypto") - external_htslib_libraries.extend(["curl", "crypto"]) - -+# 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": -+ if not os.path.exists(fn): -+ with open(fn, "w") as outf: -+ outf.write( -+ "/* empty config.h created by pysam */\n") -+ outf.write( -+ "/* conservative compilation options */\n") -+ - parts = ["samtools", - "bcftools", - "htslib", diff --git a/sci-biology/pysam/pysam-0.9.0.ebuild b/sci-biology/pysam/pysam-0.9.0.ebuild deleted file mode 100644 index ba886f80899..00000000000 --- a/sci-biology/pysam/pysam-0.9.0.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 python3_{4,5} ) - -inherit distutils-r1 python-r1 - -DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" -HOMEPAGE="https://github.com/pysam-developers/pysam http://pypi.python.org/pypi/pysam"; -SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="=sci-libs/htslib-1.3*" -DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}]" - -PATCHES=( - "${FILESDIR}/${P}-missing-config.h.patch" -) - -src_prepare() { - default - - export HTSLIB_INCLUDE_DIR=${EPREFIX}/usr/include - export HTSLIB_LIBRARY_DIR=${EPREFIX}/usr/$(get_libdir) - export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl" - - 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 -} - -src_compile() { - # TODO - # empty compile, as the build system runs the whole build again in install - : -}
