commit: 0c71d353954ad0e01c6e1595f4e493ad7857f6dc Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com> AuthorDate: Sat Oct 10 15:12:58 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sat Oct 10 15:12:58 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0c71d353
sci-biology/pysam: version bump to 0.8.3 This also includes a fix for building with Cython 0.23. .../pysam/files/pysam-0.8.3-cython-0.23.patch | 32 ++++++++++++++++++++++ sci-biology/pysam/pysam-0.8.3.ebuild | 29 ++++++++++++++++++++ 2 files changed, 61 insertions(+) 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 new file mode 100644 index 0000000..d14fec5 --- /dev/null +++ b/sci-biology/pysam/files/pysam-0.8.3-cython-0.23.patch @@ -0,0 +1,32 @@ +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/pysam-0.8.3.ebuild b/sci-biology/pysam/pysam-0.8.3.ebuild new file mode 100644 index 0000000..a08855f --- /dev/null +++ b/sci-biology/pysam/pysam-0.8.3.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-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"; + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="dev-python/setuptools[${PYTHON_USEDEP}] + >=sci-biology/samtools-1.2[${PYTHON_USEDEP}] + >=sci-libs/htslib-1.2.1" + +PATCHES=( "${FILESDIR}/${P}-cython-0.23.patch" ) + +python_compile() { + python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing" + distutils-r1_python_compile +}
