gentoo auto-resync : 23:03:2025 - 00:31:41

3 files changed, 0 insertions, 70 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 90cc60347dff..9f68854701fd 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index ffaea98560f6..094134f6269d 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,6 +1,4 @@
-DIST pysam-0.22.1.gh.tar.gz 3885851 BLAKE2B 6f83c445c7e63e28823f443b0f106726303b0609f4040e9dca930c820d48c2adfe13d33ecffb514ce75c3b03968af050652689a0be39aaabca1af546e9188480 SHA512 fb8dc7c4a6ae908d8d409789f2706cce589d4b6a1057bcc4043f8a26a5b390f79d30d1a1cbe69cbf370caabf261ed8367685393240765080e94f1782ed7f0350
 DIST pysam-0.23.0.gh.tar.gz 4076476 BLAKE2B 74f5fd99aff357c59aa4cd13214fbb87577d213461feff2afd59679c6b442ccee1fe23a7b7d6ddc723f57f4e00516fb7b67207e8f8619b707d1f909c62663006 SHA512 7c7b3806dbf316f7d9283dbabcd86e55d5dd18a01a127af5f26279e2266fb9b6e44546de0d22c82de963eca19c9e9b3ed1cc00c465acc2ddd810824902c87add
-EBUILD pysam-0.22.1.ebuild 1648 BLAKE2B 9d0c666e39b48dea088445a0959d364892f9b2a3e90664788f214ac66df709c70eaaf8c90240488a4c948409f0548641f4d511af983037b3afc481444621f7fb SHA512 e35adedadd3c3726eb817c85f225fc2715eccdcd0c2bed5c11f749d07a7e99b2f28fee0244bd64f1383329d20edb7a2364112483af8a814b447b29fc3d1b762b
 EBUILD pysam-0.23.0.ebuild 1502 BLAKE2B 2c9d24996e912dfa7b89b71fe03471f7e121edd897e55dd5510e75225935ba6e14502e254cbbcab3fbf0fb54964fc72949b1668ae73817641b460ca45ee9c934 SHA512 cd033f4b81ac6330af3558ec9048cac33982afc45e076354c3fa43cae36d39204f632582a02b99da7efe70a747d4b6c702b1ffab6d3a986564bffea8f26232e9
 EBUILD pysam-9999.ebuild 1619 BLAKE2B b27488491b0c85ec53dbb48cef114b7ef27b730f1faa40d4ebe070b38010e2b835140dedece889f3c0c48454c0e5c44e6a5633122e7059c403e9c6ba53f989ab SHA512 a898f0665b50ae5342964e127ea684ebc20a33d9d7ebf9b7e7712f9bc6d434500da29af800451055d3f065cf3446813d7ddb75ce02a7baf3bce004ff1d223c42
 MISC metadata.xml 442 BLAKE2B e3d339868a09d8930ff6d83f414f8166ed283a66d83d5b0fed0031024db151b17b1347f5e015f2b9c2152a041e2beb70696362be9b4e3fc225078bc5c520ad58 SHA512 4b1d08c5524e1bb04129e0d38f0584654b34979024afd2cf15bd482654ca8fac9c82e6db0661f7370f9fefa6949f1291ba3c18a9dca5d5041bd6f76554fa33c7
diff --git a/sci-biology/pysam/pysam-0.22.1.ebuild b/sci-biology/pysam/pysam-0.22.1.ebuild
deleted file mode 100644
index 9070476873e1..000000000000
--- a/sci-biology/pysam/pysam-0.22.1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..12} )
-
-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 -> ${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.20*:="
-DEPEND="${RDEPEND}
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-BDEPEND="
-	dev-python/cython[${PYTHON_USEDEP}]
-	test? (
-		=sci-biology/bcftools-1.20*
-		=sci-biology/samtools-1.20*
-	)"
-
-distutils_enable_tests pytest
-
-DISTUTILS_IN_SOURCE_BUILD=1
-
-EPYTEST_DESELECT=(
-	# only work with bundled htslib
-	'tests/tabix_test.py::TestRemoteFileHTTP'
-	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
-
-	'tests/AlignedSegment_test.py::TestBaseModifications'
-)
-
-python_prepare_all() {
-	# unbundle htslib
-	export HTSLIB_MODE="external"
-	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
-	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/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
-
-	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
-	# need to avoid dropping .so plugins into
-	# build-lib, which breaks tests
-	esetup.py build_ext --inplace -j1
-	distutils-r1_python_compile -j1
-}