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

[David Seifert]

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-biology@g.o</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
-}