[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

[Justin Lecher]

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
+}