gentoo resync : 16.09.2020

8 files changed, 18 insertions, 284 deletions

diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 12365d2c556e..5ce9c67f4212 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,13 +1,6 @@
-AUX seqan-1.4.2-buildsystem.patch 870 BLAKE2B 2b3e32e4bea47caf6165e1c0ab89cdadf1e4d4756bb3ddd77b943b89a9366fb28d49dfdc22d69d5c431f78a83fc73b20c486085804a153c987020b3e28120b20 SHA512 d769eb4137c8c0ddb7137ecfdb0673ba8648ae720673848cbb473a0c80d479b6e5c564c12f1a9dd01953d955605eb2f273e04808ae50058c565e997381c3f748
-AUX seqan-1.4.2-include.patch 552 BLAKE2B f8d67014e59751616227471995254684b3edfacacfb455099f99c719f5602c88f0d106df01354921557d3324f77e03934606f698801516bc8432837c6211b67e SHA512 b02ab4fe49a511494134e44855d865f0ff210392810970834deb304499b5017764ed1c04d8f8dbfb513c333ac302946e5c72c9160cd38a5ef5ad095a865cb6d0
-AUX seqan-1.4.2-shared.patch 974 BLAKE2B e46b6b61c4927ca36c53e68e39c77eb5d983221dd074040a8911a7d7dfb04d2fb4c4ded0f3c9b6d90082a26f704654daa1d2b70e547b9ad657cc48bb96fc435b SHA512 a509c243244b6b40b26700a73be267558ceb17c4e0079f3eca606835ecfe8d1417b88fd37719ca9cf226e6d2d33ee3e22790b20e39a86a300f722eb186cabaad
 AUX seqan-2.4.0-fix-pthread.patch 541 BLAKE2B 16d42c72d6ea0654ba6727ce1007b89d3fc76141320f5a71cfd0fe102b8e511ccb36d48e021baf0928ac8857e97f6addde3f15f4f0577c531285027f23f5eea8 SHA512 f8a3df0892a81a65562dbd85f0945e5722df524e07b9949f860df4e0f07c285df3a48a112c8e1e5dca28a97c219dc9feed677e803ec5d3964216f7052b6f431b
 AUX seqan.pc.in 263 BLAKE2B ffd2a2c1ac74af7bc6b33c5959792551447ee61fe87fbb8bc6966ad44c33ae5bd512e836bc67175a3bf1895554364e48fcfea207f94f18ef72b7eae74fbe82d5 SHA512 bde1c89624284a37dac1a8717049a3b14340a2543003d9cf8406bddf4033541b65b617b802b18c80b2c7733d55ad9d7484bd85fdc927582363885da6d0210af7
-DIST seqan-src-1.4.2.tar.gz 120601994 BLAKE2B 62de2f961ba3c7c564090d746877d2b0b94ec7967c56f28786a286160770e66f0a8f08aacbe76d828cf429f92f0aa640ab29f5220297686979df9b7e9f9a0408 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a
-DIST seqan-src-2.2.0.tar.gz 110936119 BLAKE2B be41f266e140ec5992f7e9e507659dc7902aad0e0dd17e6a8c6c9ef0b11f690454a771ba10a5998ccf70e2e50ef9b24904ebf537d982b2cbc68963c004097614 SHA512 1097372976ec9c86baa3787ac38aa4fde3a3e153d81c22435e6a12df87d8063165f27406de33851bffadd904b0ac4ea579a28625cff6257fe8c14d906f408421
 DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b
-EBUILD seqan-1.4.2-r1.ebuild 1997 BLAKE2B 7e7934e70e17b65cc3557dc2f9e7c7d16db4f57bee1b0238d211ed57039e47cc03f495dc068e94d5d4502983c0d0e3b4cca21c0e88ff6c63a9e4d1496ba2850d SHA512 b1ba7611fe3de91484b05e06e4313eb7422bf38d5987c164e9ae7b788b4e7c3cdc0cd5702c215bd6747d2dd94f305f9ae8ea359699e5c32114e8a03514007bfd
-EBUILD seqan-2.2.0-r1.ebuild 2703 BLAKE2B e56cdb3ad4cf674e2349a8d380b49c58b68b528ae28e7b52066a24cf09efbc262855d51f8f3a6ae8111e46b3f95bcec8eaa117a43a895c5bca59963769300307 SHA512 e9524b59db85d13554f99b01c681e2d9137d8971a7df628c2a0b7f5774f8ea324191b3ed6bf0c51b8023b7b1947586adad22709c959656cf1fda58c92c3d89a6
-EBUILD seqan-2.4.0.ebuild 1917 BLAKE2B c53b1c51fd7b8a1c1498f5b2072f26a7829545f626fef177e0e64bc488784f7b9273c2f101db4c045203b3198aa6f37fa6f3226c633575815fbb95174ed5d30a SHA512 6f17b5d2d3be7a19fadcad798f0328fe467bc811d0a931c7b43df87fe23d17ebf2fb48aa197b838c9756bf9f3af7eaa04d346b0b5a05b03b28d03e4e80400c71
-EBUILD seqan-9999.ebuild 1860 BLAKE2B 745e69b7a80868f3faf45a6dfc9727835c8482737b3902a9e0f809a456ce5b3335d821d1106579da01fa495bc3df1caf222f425e41e172479b7de4e4a6e6a2b4 SHA512 3da317388c84933b817705825385c20c3673208c9a3fa1867078f7aea6a9959c6db3b8463cc3713d728180e30093cb1e30220072866305ac58f7b3de6b412f83
+EBUILD seqan-2.4.0.ebuild 1624 BLAKE2B e2b8d8c2e7f87abc063255e0c6c826a57e4da29b063eb3fc82d143593e06d8cbbf5744cd6e39e9cc1b2623c010d181e4361665946a8489ad454f3e1fb9a33c88 SHA512 1d39216baa3877df91b19f36519103114a6858b4600d5bfe3ba01e5619bcfb2543d208e7d5af2806a5c964ebcb8399a8244ca65f4e7ecf169e02827e055545d3
+EBUILD seqan-9999.ebuild 1567 BLAKE2B b171570acf62243121541b771c26fd7ef86e4be86878c060050af2cd665973182e2498f9ba9c336e8a382768b71aa3547edde927682dcdd844c6fd0ed9e2cd99 SHA512 b91b532d3655de47c0cfb9f243e46c120d5259f9166be4e41d7b0dd02a6f681e714fd5941aadb54b6ee89a0f5a4aa10628157c9b25bfd8074178dc36b70e5944
 MISC metadata.xml 372 BLAKE2B d620401f1aab9be80ddb6dc7abe737fd3e6322c560136e2c3b33d9246beca2986b4d91225b506e8c3035550994c3f714a11c0d8b17efd30c29278002d4eb7a12 SHA512 ae6c49e7e45c0ce4dd4fe27d21c5376c6fb8d7bfd2f98b7775f4689811680fa92c0b71ac0db70f6969660c4aee344f710ef752a467d6d46dd83aa47386d2ec17
diff --git a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
deleted file mode 100644
index 4c7893e90c05..000000000000
--- a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-Add default disabled flag to enable generation of documentation.
-For SeqAn 1.4.2 we generally do not want docs, as 1.4.2 is only a
-support library for legacy tools.
-
---- seqan-1.4.2/CMakeLists.txt
-+++ seqan-1.4.2/CMakeLists.txt
-@@ -123,10 +123,12 @@
- add_subdirectory (core)
- message (STATUS "Configuring extras")
- add_subdirectory (extras)
-+if (NOT SEQAN_NO_DOX)
- message (STATUS "Configuring docs")
- add_subdirectory (docs)
- message (STATUS "Configuring manual")
- add_subdirectory (manual)
-+endif ()
- message (STATUS "Configuring sandbox")
- add_subdirectory (sandbox)
- message (STATUS "Configuring util/py_lib")
---- seqan-1.4.2/docs/main.py
-+++ seqan-1.4.2/docs/main.py
-@@ -123,7 +123,7 @@
- 
-         # Done, print end message.
-         print 'Documentation created/updated.'
--        return dddoc_html.WARNING_COUNT > 0
-+        return 0
-     
-     
- def main(argv):
diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch
deleted file mode 100644
index 5baee4d8ebc0..000000000000
--- a/sci-biology/seqan/files/seqan-1.4.2-include.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- core/include/seqan/index/index_qgram_openaddressing.h | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h
-index 4a6c2e6..8cc9a42 100644
---- a/core/include/seqan/index/index_qgram_openaddressing.h
-+++ b/core/include/seqan/index/index_qgram_openaddressing.h
-@@ -35,6 +35,8 @@
- #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
- #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
- 
-+#include <smmintrin.h>
-+
- namespace SEQAN_NAMESPACE_MAIN
- {
- 
diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
deleted file mode 100644
index 0f438ff07bce..000000000000
--- a/sci-biology/seqan/files/seqan-1.4.2-shared.patch
+++ /dev/null
@@ -1,22 +0,0 @@
- util/cmake/SeqAnBuildSystem.cmake | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
-index bcba2c0..d53cd01 100644
---- a/util/cmake/SeqAnBuildSystem.cmake
-+++ b/util/cmake/SeqAnBuildSystem.cmake
-@@ -144,10 +144,10 @@ macro (seqan_register_apps)
-     set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
- 
-     # enable static linkage for seqan apps
--    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
--      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
--      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
--    endif ()
-+#    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
-+#      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
-+#      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
-+#    endif ()
- 
-     # Get all direct entries of the current source directory into ENTRIES.
-     file (GLOB ENTRIES
diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild b/sci-biology/seqan/seqan-1.4.2-r1.ebuild
deleted file mode 100644
index 3a7f55c710c3..000000000000
--- a/sci-biology/seqan/seqan-1.4.2-r1.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-any-r1 versionator
-
-DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/"
-SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
-
-SLOT="$(get_version_component_range 1-2)"
-LICENSE="BSD GPL-3"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="cpu_flags_x86_sse4_1 test"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="cpu_flags_x86_sse4_1"
-
-RDEPEND="
-	app-arch/bzip2
-	sys-libs/zlib"
-DEPEND="
-	${RDEPEND}
-	test? (
-		$(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)"
-
-PATCHES=(
-	"${FILESDIR}/${P}-shared.patch"
-	"${FILESDIR}/${P}-include.patch"
-	"${FILESDIR}/${P}-buildsystem.patch"
-)
-
-pkg_setup() {
-	use test && python-any-r1_pkg_setup
-}
-
-src_prepare() {
-	# pkg-config file, taken from seqan 2.1
-	cp "${FILESDIR}"/${PN}.pc.in ${PN}-${SLOT}.pc || die
-	sed -e "s#@CMAKE_INSTALL_PREFIX@#${EPREFIX}/usr#" \
-		-e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${SLOT}#" \
-		-e "s#@CMAKE_PROJECT_NAME@#${PN}#" \
-		-e "s#@SEQAN_VERSION_STRING@#${PV}#" \
-		-i ${PN}-${SLOT}.pc || die
-
-	rm -f util/cmake/FindZLIB.cmake || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBoost_NO_BOOST_CMAKE=ON
-		-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-		-DSEQAN_NO_DOX=ON
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# SLOT header such that different seqan versions can be used in parallel
-	mkdir "${ED}"/usr/include/${PN}-${SLOT} || die
-	mv "${ED}"/usr/include/{${PN},${PN}-${SLOT}/} || die
-
-	# pkg-config file
-	insinto /usr/share/pkgconfig/
-	doins ${PN}-${SLOT}.pc
-}
-
-pkg_postinst() {
-	einfo "${CATEGORY}/${PF} is only intended as support library for older"
-	einfo "bioinformatics tools relying on the SeqAn 1.* API. Please develop"
-	einfo "any new software against the latest SeqAn release and not this one."
-}
diff --git a/sci-biology/seqan/seqan-2.2.0-r1.ebuild b/sci-biology/seqan/seqan-2.2.0-r1.ebuild
deleted file mode 100644
index 5e139cd7e601..000000000000
--- a/sci-biology/seqan/seqan-2.2.0-r1.ebuild
+++ /dev/null
@@ -1,94 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-any-r1 versionator
-
-DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/"
-SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cpu_flags_x86_sse4_1 doc test"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="cpu_flags_x86_sse4_1"
-
-RDEPEND="
-	app-arch/bzip2
-	sys-libs/zlib
-	!!sci-biology/seqan:2.0
-	!!sci-biology/seqan:2.1
-	!!sci-biology/seqan:2.2"
-DEPEND="
-	${RDEPEND}
-	doc? (
-		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)
-	test? (
-		$(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)"
-
-S="${WORKDIR}"/${PN}-${PN}-v${PV}
-
-pkg_setup() {
-	if use test || use doc; then
-		python-any-r1_pkg_setup
-	fi
-}
-
-src_prepare() {
-	seqan_major_ver=$(get_version_component_range 1)
-	seqan_majorminor_ver=$(get_version_component_range 1-2)
-
-	# install docs in proper Gentoo structure
-	sed -e "s#share/doc/seqan#share/doc/${PF}#" \
-		-e "s#\"share/doc/\${APP_NAME}\"#\"share/doc/${PF}/\${APP_NAME}\"#" \
-		-i util/cmake/SeqAnBuildSystem.cmake dox/CMakeLists.txt || die
-
-	# cmake module
-	sed -e "s#find_path(_SEQAN_BASEDIR \"seqan\"#find_path(_SEQAN_BASEDIR \"seqan-${seqan_majorminor_ver}\"#" \
-		-e 's#NO_DEFAULT_PATH)#PATHS /usr)#' \
-		-e "s#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR})#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR}/seqan-${seqan_majorminor_ver})#" \
-		-i util/cmake/FindSeqAn.cmake || die
-
-	# pkg-config file
-	sed -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${seqan_majorminor_ver}#" \
-		-i util/pkgconfig/${PN}.pc.in || die
-
-	rm -f util/cmake/FindZLIB.cmake || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-		-DSEQAN_NO_DOX=$(usex !doc)
-	)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	use doc && cmake-utils_src_compile -C "${BUILD_DIR}" dox
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# multi-version header such that different seqan versions can be installed in parallel
-	mkdir "${ED%/}"/usr/include/${PN}-${seqan_majorminor_ver} || die
-	mv "${ED%/}"/usr/include/${PN}{,-${seqan_majorminor_ver}/} || die
-
-	# pkg-config file
-	mv "${ED%/}"/usr/share/pkgconfig/${PN}-{${seqan_major_ver},${seqan_majorminor_ver}}.pc || die
-
-	# create pkg-config symlink to restore default behaviour
-	dosym ${PN}-${seqan_majorminor_ver}.pc /usr/share/pkgconfig/${PN}-${seqan_major_ver}.pc
-}
diff --git a/sci-biology/seqan/seqan-2.4.0.ebuild b/sci-biology/seqan/seqan-2.4.0.ebuild
index 8b337e77e6be..5653a1ec94e4 100644
--- a/sci-biology/seqan/seqan-2.4.0.ebuild
+++ b/sci-biology/seqan/seqan-2.4.0.ebuild
@@ -1,12 +1,11 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
 : ${CMAKE_MAKEFILE_GENERATOR:=ninja}
-PYTHON_COMPAT=( python2_7 )
 
-inherit cmake-utils multibuild python-any-r1 toolchain-funcs
+inherit cmake-utils multibuild toolchain-funcs
 
 DESCRIPTION="C++ Sequence Analysis Library"
 HOMEPAGE="http://www.seqan.de/"
@@ -24,7 +23,7 @@ fi
 
 LICENSE="BSD GPL-3"
 SLOT="0"
-IUSE="cpu_flags_x86_sse4_1 doc tools"
+IUSE="cpu_flags_x86_sse4_1 tools"
 REQUIRED_USE="cpu_flags_x86_sse4_1"
 
 RDEPEND="
@@ -34,21 +33,12 @@ RDEPEND="
 	!!sci-biology/seqan:2.1
 	!!sci-biology/seqan:2.2"
 DEPEND="
-	${RDEPEND}
-	doc? (
-		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)"
+	${RDEPEND}"
 
 PATCHES=( "${FILESDIR}"/${PN}-2.4.0-fix-pthread.patch )
 
-python_check_deps() {
-	use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]"
-}
-
 pkg_setup() {
 	if [[ ${MERGE_TYPE} != binary ]]; then
-		use doc && python-any-r1_pkg_setup
 		use tools && tc-check-openmp
 
 		MULTIBUILD_VARIANTS=(
@@ -60,18 +50,19 @@ pkg_setup() {
 
 src_configure() {
 	my_configure() {
-		local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" )
+		local mycmakeargs=(
+			-DCMAKE_INSTALL_DOCDIR="share/doc/${PF}"
+			-DSEQAN_NO_DOX=ON
+		)
 		case "${MULTIBUILD_ID}" in
 			tools)
 				mycmakeargs+=(
 					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS
-					-DSEQAN_NO_DOX=ON
 				)
 				;;
 			library)
 				mycmakeargs+=(
 					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-					-DSEQAN_NO_DOX=$(usex !doc)
 				)
 				;;
 			*)
diff --git a/sci-biology/seqan/seqan-9999.ebuild b/sci-biology/seqan/seqan-9999.ebuild
index 0005819ff4d3..b344b39cbc46 100644
--- a/sci-biology/seqan/seqan-9999.ebuild
+++ b/sci-biology/seqan/seqan-9999.ebuild
@@ -1,12 +1,11 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
 : ${CMAKE_MAKEFILE_GENERATOR:=ninja}
-PYTHON_COMPAT=( python2_7 )
 
-inherit cmake-utils multibuild python-any-r1 toolchain-funcs
+inherit cmake-utils multibuild toolchain-funcs
 
 DESCRIPTION="C++ Sequence Analysis Library"
 HOMEPAGE="http://www.seqan.de/"
@@ -24,7 +23,7 @@ fi
 
 LICENSE="BSD GPL-3"
 SLOT="0"
-IUSE="cpu_flags_x86_sse4_1 doc tools"
+IUSE="cpu_flags_x86_sse4_1 tools"
 REQUIRED_USE="cpu_flags_x86_sse4_1"
 
 RDEPEND="
@@ -34,19 +33,10 @@ RDEPEND="
 	!!sci-biology/seqan:2.1
 	!!sci-biology/seqan:2.2"
 DEPEND="
-	${RDEPEND}
-	doc? (
-		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)"
-
-python_check_deps() {
-	use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]"
-}
+	${RDEPEND}"
 
 pkg_setup() {
 	if [[ ${MERGE_TYPE} != binary ]]; then
-		use doc && python-any-r1_pkg_setup
 		use tools && tc-check-openmp
 
 		MULTIBUILD_VARIANTS=(
@@ -58,18 +48,19 @@ pkg_setup() {
 
 src_configure() {
 	my_configure() {
-		local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" )
+		local mycmakeargs=(
+			-DCMAKE_INSTALL_DOCDIR="share/doc/${PF}"
+			-DSEQAN_NO_DOX=ON
+		)
 		case "${MULTIBUILD_ID}" in
 			tools)
 				mycmakeargs+=(
 					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS
-					-DSEQAN_NO_DOX=ON
 				)
 				;;
 			library)
 				mycmakeargs+=(
 					-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-					-DSEQAN_NO_DOX=$(usex !doc)
 				)
 				;;
 			*)