commit: 02fbd9cb160ec37e7a85eb4349717237e120aeeb Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Sep 2 12:45:42 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Sep 2 12:45:42 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=02fbd9cb
sci-biology/pysam: Remove old .../pysam/files/pysam-0.8.3-cython-0.23.patch | 32 ---------------------- sci-biology/pysam/metadata.xml | 8 ------ sci-biology/pysam/pysam-0.7.5.ebuild | 25 ----------------- 3 files changed, 65 deletions(-) diff --git a/sci-biology/pysam/files/pysam-0.8.3-cython-0.23.patch b/sci-biology/pysam/files/pysam-0.8.3-cython-0.23.patch deleted file mode 100644 index d14fec5a8..000000000 --- a/sci-biology/pysam/files/pysam-0.8.3-cython-0.23.patch +++ /dev/null @@ -1,32 +0,0 @@ -Patch for building with Cython 0.23 -See also -https://github.com/pysam-developers/pysam/issues/164 - ---- pysam-0.8.3/pysam/chtslib.pxd -+++ pysam-0.8.3/pysam/chtslib.pxd -@@ -363,7 +363,7 @@ - hFILE *hfile - void *voidp - -- ctypedef enum htsFormatCategory: -+ cdef enum htsFormatCategory: - unknown_category - sequence_data # Sequence data -- SAM, BAM, CRAM, etc - variant_data # Variant calling data -- VCF, BCF, etc -@@ -371,14 +371,14 @@ - region_list # Coordinate intervals or regions -- BED, etc - category_maximum - -- ctypedef enum htsExactFormat: -+ cdef enum htsExactFormat: - unknown_format - binary_format - text_format - sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed - format_maximum - -- ctypedef enum htsCompression: -+ cdef enum htsCompression: - no_compression, gzip, bgzf, custom - compression_maximum - diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml deleted file mode 100644 index 3ff9cd0b0..000000000 --- a/sci-biology/pysam/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/pysam/pysam-0.7.5.ebuild b/sci-biology/pysam/pysam-0.7.5.ebuild deleted file mode 100644 index ef596c29d..000000000 --- a/sci-biology/pysam/pysam-0.7.5.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 - -DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" -HOMEPAGE="http://code.google.com/p/pysam http://pypi.python.org/pypi/pysam"; -SRC_URI="http://${PN}.googlecode.com/files/${P}.tar.gz"; - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="dev-python/setuptools[${PYTHON_USEDEP}] - <=sci-biology/samtools-0.1.19-r2[${PYTHON_USEDEP}]" - -python_compile() { - python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing" - distutils-r1_python_compile -}
