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

[David Seifert]

commit:     3b93bba18c14598747eda127476f093040e6b3b6
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 11 14:55:08 2021 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Oct 11 14:55:08 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3b93bba1

sci-biology/pysam: drop 0.16.0.1-r1

Closes: https://bugs.gentoo.org/812242
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/Manifest                         |  1 -
 .../pysam/files/pysam-0.16.0.1-fix-tests.patch     | 37 -------------
 sci-biology/pysam/pysam-0.16.0.1-r1.ebuild         | 60 ----------------------
 3 files changed, 98 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 1e305c998da..91ca2cac79c 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece SHA512 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28
 DIST pysam-0.17.0.tar.gz 3579324 BLAKE2B 6b88fe771350f20fa7c90a4c02c60fefd6a34d979c687fce1e34a17e1ff203c7d2d07e36b64f7a73f99676b805334df7f049932ce15e26362a5214da03435d64 SHA512 16740f08fb68a1f24656454b834dd9ac52ad9f864f307564566fc244bbd2efb7cb17107b2e85ca5c56af817918a138d1c071533de1b80e5bba42b01bbad7f552

diff --git a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
deleted file mode 100644
index 9d269878e65..00000000000
--- a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- a/tests/pysam_data/Makefile
-+++ b/tests/pysam_data/Makefile
-@@ -3,7 +3,7 @@
- BAI=$(BAM:%.bam=%.bam.bai)
- CRAM=ex1.cram ex2.cram ex3.cram
- CRAI=$(CRAM:%.cram=%.cram.crai)
--NO_PG:=$(findstring --no-PG,$(shell samtools view))
-+NO_PG:=--no-PG
- 
- # ex2.bam - bam file without index
- 
---- a/tests/tabix_test.py
-+++ b/tests/tabix_test.py
-@@ -14,6 +14,7 @@
- import subprocess
- import glob
- import re
-+import pytest
- from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \
-     load_and_convert, TABIX_DATADIR, get_temp_filename
- 
-@@ -1014,6 +1015,7 @@
-     globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
- 
- 
-+@×××××××××××.skip(reason="requires internet connectivity")
- class TestRemoteFileHTTP(unittest.TestCase):
- 
-     url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
-@@ -1053,6 +1055,7 @@
-         self.assertEqual(list(self.local_file.header), [])
- 
- 
-+@×××××××××××.skip(reason="requires internet connectivity")
- class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
- 
-     url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"

diff --git a/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild b/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild
deleted file mode 100644
index e27c998bb91..00000000000
--- a/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="
-	https://github.com/pysam-developers/pysam
-	https://pypi.org/project/pysam/"
-SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.10*:="
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-python/cython[${PYTHON_USEDEP}]
-	<dev-python/setuptools-58[${PYTHON_USEDEP}]
-	test? (
-		=sci-biology/bcftools-1.10*
-		=sci-biology/samtools-1.10*
-	)"
-
-distutils_enable_tests pytest
-
-DISTUTILS_IN_SOURCE_BUILD=1
-
-python_prepare_all() {
-	# unbundle htslib
-	export HTSLIB_MODE="external"
-	export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
-	export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
-	rm -r htslib || die
-
-	# prevent setup.py from adding RPATHs (except $ORIGIN)
-	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
-		-i setup.py || die
-
-	eapply "${FILESDIR}"/${PN}-0.16.0.1-fix-tests.patch
-
-	if use test; then
-		einfo "Building test data"
-		emake -C tests/pysam_data
-		emake -C tests/cbcf_data
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	# breaks with parallel build
-	local MAKEOPTS=-j1
-	distutils-r1_python_compile
-}