commit: ebaf7f2da08feb9b7e0460f6ef8fadec55d91c12
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 24 18:42:28 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon Jan 24 18:42:28 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ebaf7f2d
sci-libs/rdkit: bump to 2021.09.4
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../rdkit-2020.03.6-no_dynamic_checking.patch | 59 ----------------------
.../files/rdkit-2021.09.4-find-rapidjson.patch | 22 ++++++++
sci-libs/rdkit/rdkit-2020.03.6.ebuild | 57 ---------------------
sci-libs/rdkit/rdkit-2021.09.4.ebuild | 58 +++++++++++++++++++++
4 files changed, 80 insertions(+), 116 deletions(-)
diff --git a/sci-libs/rdkit/files/rdkit-2020.03.6-no_dynamic_checking.patch
b/sci-libs/rdkit/files/rdkit-2020.03.6-no_dynamic_checking.patch
deleted file mode 100644
index 2f7656245..000000000
--- a/sci-libs/rdkit/files/rdkit-2020.03.6-no_dynamic_checking.patch
+++ /dev/null
@@ -1,59 +0,0 @@
---- a/External/catch/CMakeLists.txt 2020-09-28 05:09:11.307595711 -0400
-+++ b/External/catch/CMakeLists.txt 2020-09-28 05:10:35.188570785 -0400
-@@ -13,9 +13,6 @@
- message("-- Catch not found in ${CATCH_DIR}")
- include(RDKitUtils)
- set(RELEASE_NO "2.1.2")
--
downloadAndCheckMD5("https://github.com/catchorg/Catch2/archive/v${RELEASE_NO}.tar.gz";
-- "${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz"
-- "4c5740d7446d9b4e3735dcff0951aaca")
- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
- ${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
---- a/External/CoordGen/CMakeLists.txt 2020-09-28 05:13:38.351584109 -0400
-+++ b/External/CoordGen/CMakeLists.txt 2020-09-28 05:15:49.396007762 -0400
-@@ -38,9 +38,6 @@
-
- if(NOT EXISTS "${MAEPARSER_DIR}/MaeParser.hpp")
- set(RELEASE_NO "1.2.3")
-- set(MD5 "4ead02a0bf87110d1caae79ab42a5747")
--
downloadAndCheckMD5("https://github.com/schrodinger/maeparser/archive/v${RELEASE_NO}.tar.gz";
-- "${CMAKE_CURRENT_SOURCE_DIR}/maeparser-v${RELEASE_NO}.tar.gz"
${MD5})
- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
- ${CMAKE_CURRENT_SOURCE_DIR}/maeparser-v${RELEASE_NO}.tar.gz
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
---- a/External/CoordGen/CMakeLists.txt 2020-09-28 05:31:21.353305949 -0400
-+++ b/External/CoordGen/CMakeLists.txt 2020-09-28 05:32:04.187783628
-0400
-@@ -67,9 +67,6 @@
-
- if(NOT EXISTS "${COORDGEN_DIR}/sketcherMinimizer.h")
- set(RELEASE_NO "1.4.0")
-- set(MD5 "5f663c8809b494f0548dd504c011c739")
--
downloadAndCheckMD5("https://github.com/schrodinger/coordgenlibs/archive/v${RELEASE_NO}.tar.gz";
-- "${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz"
${MD5})
- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
- ${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
---- a/External/RingFamilies/CMakeLists.txt 2020-09-18 11:18:37.000000000
-0400
-+++ b/External/RingFamilies/CMakeLists.txt 2020-09-28 05:35:04.427800305
-0400
-@@ -8,9 +8,6 @@
-
- if(NOT EXISTS "${URFLIB_DIR}/RingDecomposerLib.h")
- set(RELEASE_NO "1.1.3_rdkit")
-- set(MD5 "e9a0bcdda8b921a35e812b9888a9a874")
--
downloadAndCheckMD5("https://github.com/rareylab/RingDecomposerLib/archive/v${RELEASE_NO}.tar.gz";
--
"${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz" ${MD5})
- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
- ${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
---- a/Code/GraphMol/MolInterchange/CMakeLists.txt 2020-09-18
11:18:37.000000000 -0400
-+++ b/Code/GraphMol/MolInterchange/CMakeLists.txt 2020-09-28
05:36:47.759960868 -0400
-@@ -1,8 +1,5 @@
-
- if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0")
--
downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz";
-- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz"
-- "badd12c511e081fec6c89c43a7027bce")
- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External)
diff --git a/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch
b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch
new file mode 100644
index 000000000..94a209e0f
--- /dev/null
+++ b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch
@@ -0,0 +1,22 @@
+diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt
b/Code/GraphMol/MolInterchange/CMakeLists.txt
+index 8027444..6a8c715 100644
+--- a/Code/GraphMol/MolInterchange/CMakeLists.txt
++++ b/Code/GraphMol/MolInterchange/CMakeLists.txt
+@@ -1,16 +1,5 @@
+
+-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0")
+-
downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz";
+- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz"
+- "badd12c511e081fec6c89c43a7027bce")
+- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
+- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz
+- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External)
+-else()
+- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External")
+-endif()
+-
+-include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include)
++include_directories(/usr/include/rapidjson)
+
+
+ rdkit_library(MolInterchange
diff --git a/sci-libs/rdkit/rdkit-2020.03.6.ebuild
b/sci-libs/rdkit/rdkit-2020.03.6.ebuild
deleted file mode 100644
index b73817270..000000000
--- a/sci-libs/rdkit/rdkit-2020.03.6.ebuild
+++ /dev/null
@@ -1,57 +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 cmake python-r1
-
-DESCRIPTION="Cheminformatics and machine-learning software written in C++ and
Python"
-HOMEPAGE="http://www.rdkit.org/";
-SRC_URI="
- https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz ->
${P}.tar.gz
- https://github.com/schrodinger/maeparser/archive/v1.2.3.tar.gz ->
maeparser-1.2.3.tar.gz
- https://github.com/schrodinger/coordgenlibs/archive/v1.4.0.tar.gz ->
coordgenlibs-1.4.0.tar.gz
- https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz ->
rapidjson-1.1.0.tar.gz
- "
-# issues with bundled packages; dev-libs/rapidjson, at least, should be
unbundled:
-# https://github.com/rdkit/rdkit/issues/3443
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-# build configuration issues https://github.com/rdkit/rdkit/issues/3444
-IUSE="+python static-libs"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="dev-libs/boost
- python? (
- dev-libs/boost[python,${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- ${PYTHON_DEPS}
- )
- >=dev-db/sqlite-3"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/rdkit-Release_${PV//./_}
-
-PATCHES=( "${FILESDIR}"/${P}-no_dynamic_checking.patch )
-
-src_prepare() {
- cp ../maeparser-* -rf External/CoordGen/ || die
- cp ../coordgenlibs-* -rf External/CoordGen/ || die
- cp ../rapidjson-* -rf External/ || die
- cmake_src_prepare
-}
-
-src_configure() {
- local mycmakeargs=(
- -DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}"/usr
- -DRDK_INSTALL_INTREE=0
- -DRDK_BUILD_CPP_TESTS=OFF
- -DRDK_INSTALL_STATIC_LIBS="$(usex static-libs)"
- -DRDK_BUILD_PYTHON_WRAPPERS="$(usex python)"
- )
- cmake_src_configure
-}
diff --git a/sci-libs/rdkit/rdkit-2021.09.4.ebuild
b/sci-libs/rdkit/rdkit-2021.09.4.ebuild
new file mode 100644
index 000000000..a9b1258c9
--- /dev/null
+++ b/sci-libs/rdkit/rdkit-2021.09.4.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit cmake python-single-r1
+
+DESCRIPTION="Cheminformatics and machine-learning software written in C++ and
Python"
+HOMEPAGE="http://www.rdkit.org/";
+SRC_URI="https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz ->
${P}.tar.gz"
+S="${WORKDIR}/rdkit-Release_${PV//./_}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="+python static-libs test"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+RESTRICT="!test? ( test )"
+
+RDEPEND="dev-libs/boost
+ python? (
+ $(python_gen_cond_dep '
+ dev-libs/boost:=[numpy,python,${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ ')
+ ${PYTHON_DEPS}
+ )
+ dev-cpp/catch:0
+ dev-libs/rapidjson
+ >=dev-db/sqlite-3"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2021.09.4-find-rapidjson.patch"
+)
+
+src_configure() {
+ local mycmakeargs=(
+ -DCATCH_DIR="${EPREFIX}/usr/include/catch2"
+ -DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}/usr"
+ -DRDK_INSTALL_INTREE=0
+ -DRDK_BUILD_CPP_TESTS="$(usex test)"
+ -DRDK_INSTALL_STATIC_LIBS="$(usex static-libs)"
+ -DRDK_BUILD_PYTHON_WRAPPERS="$(usex python)"
+ # Disable things that trigger fetching and are not packaged
+ -DRDK_INSTALL_COMIC_FONTS=OFF
+ -DRDK_BUILD_COORDGEN_SUPPORT=OFF
+ -DRDK_BUILD_MAEPARSER_SUPPORT=OFF
+ -DRDK_USE_URF=OFF
+ )
+ cmake_src_configure
+}
+
+src_test() {
+ RDBASE="${WORKDIR}/${PN}-Release_2021_09_4_build" cmake_src_test
+}
