sci-libs/rdkit: version and PYTHON_COMPAT update

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr@chymera.eu>

5 files changed, 119 insertions, 80 deletions

diff --git a/sci-libs/rdkit/Manifest b/sci-libs/rdkit/Manifest
index 986f3e392..94554cc96 100644
--- a/sci-libs/rdkit/Manifest
+++ b/sci-libs/rdkit/Manifest
@@ -1 +1,4 @@
-DIST rdkit-2015.03.1.tar.gz 24859988 BLAKE2B 84e80f370a605fb6edf178720a429f3d3d60f3ea9d535d69550b3035a7a757eacc221c3e0b9c9756367ab117c7c0f6cab3c248929684c7ccbf356d635e49c0f0 SHA512 dd76bfa260e126b2e2ec59ee049ef9f4dfdb2b51c784b750148c39f26447f77f1cfe58ae0694b8286627d622447678935590724b835bab09cdb54dca4a15f386
+DIST coordgenlibs-1.4.0.tar.gz 154413 BLAKE2B f8965135d15c3f0b0c70577907990221df61f480dc5c23df17944ef799044825f82ce5dd774f7e23f5a28394e4da9370a0abc0c2b983555c0eacc1c9b0f74c8b SHA512 8fcf8e959797dcefbac0f713fdb5f1f120c8a0ffd0e7619a675a22882a5dcee79352bad85ba91df9a7a30a6b832e5f59300be08a5e9aa7313edeec8efac1a95a
+DIST maeparser-1.2.3.tar.gz 38435 BLAKE2B 666bad8d53b53702ecba434a77ae23fbc006eaa509d5b709c722416a2a1f551a23ea22c302789da6c1b62d96009d75f510e641d8996624a157a5eb6a62a425dd SHA512 fbe398a65dd3f375e320a44464bce57b37382ac78460e34875180d72f319b5fcf4bdbc0ce3b4787767f2d3d3d84cff752ed02e7b1c4890dc40760d9efe036e1b
+DIST rapidjson-1.1.0.tar.gz 1019402 BLAKE2B e1564b3cfa020f76437b0a35048a42ff2cd98b5ce285e63f228e158885182e5cecda13407cdf30c03fa39b47cbc579ff0065f6c2682d04b806e8f9ea8d36fc4e SHA512 2e82a4bddcd6c4669541f5945c2d240fb1b4fdd6e239200246d3dd50ce98733f0a4f6d3daa56f865d8c88779c036099c52a9ae85d47ad263686b68a88d832dff
+DIST rdkit-2020.03.6.tar.gz 60759026 BLAKE2B 9f7e9ad832bc779bc687d7de6109d58588c8a1151d50483a4c09c16281d1cf97e596e5075d4122e7f97e3ca67c981aa7d1e3bb09bb97ce6b4230e63f3280f4c3 SHA512 bc0a1ca21eaced83332de52f0d8ca81a5efc9585013edbccf277cf791672dac20cef16eff459441c9a699d6486064108311968247122d403e690f3d391b16b68
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
new file mode 100644
index 000000000..2f7656245
--- /dev/null
+++ b/sci-libs/rdkit/files/rdkit-2020.03.6-no_dynamic_checking.patch
@@ -0,0 +1,59 @@
+--- 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 ${CMAKE_SOURCE_DIR}/External)
diff --git a/sci-libs/rdkit/rdkit-2015.03.1.ebuild b/sci-libs/rdkit/rdkit-2015.03.1.ebuild
deleted file mode 100644
index 818630481..000000000
--- a/sci-libs/rdkit/rdkit-2015.03.1.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit cmake-utils python-r1
-
-DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python"
-HOMEPAGE="http://www.rdkit.org/"
-SRC_URI="https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+python -static-libs"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="dev-libs/boost
-	python? (
-		dev-libs/boost[python,${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	>=dev-db/sqlite-3"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"/rdkit-Release_${PV//./_}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}"/usr
-		-DRDK_INSTALL_INTREE=0
-		-DRDK_BUILD_CPP_TESTS=OFF
-		$(cmake-utils_use static-libs RDK_INSTALL_STATIC_LIBS)
-		$(cmake-utils_use python RDK_BUILD_PYTHON_WRAPPERS)
-	)
-
-	cmake-utils_src_configure
-}
diff --git a/sci-libs/rdkit/rdkit-2020.03.6.ebuild b/sci-libs/rdkit/rdkit-2020.03.6.ebuild
new file mode 100644
index 000000000..2c8ef5817
--- /dev/null
+++ b/sci-libs/rdkit/rdkit-2020.03.6.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+
+inherit cmake python-r1
+
+DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python"
+HOMEPAGE="http://www.rdkit.org/"
+SRC_URI="
+	https://github.com/rdkit/rdkit/archive/Release_${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[${PYTHON_USEDEP}]
+	)
+	>=dev-db/sqlite-3"
+DEPEND="${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-9999.ebuild b/sci-libs/rdkit/rdkit-9999.ebuild
deleted file mode 100644
index 1c4a4e45a..000000000
--- a/sci-libs/rdkit/rdkit-9999.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit cmake-utils python-r1 git-r3
-
-DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python"
-HOMEPAGE="http://www.rdkit.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/rdkit/rdkit.git"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+python -static-libs"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="dev-libs/boost
-	python? (
-		dev-libs/boost[python,${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	>=dev-db/sqlite-3"
-DEPEND="${RDEPEND}"
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}"/usr
-		-DRDK_INSTALL_INTREE=0
-		-DRDK_BUILD_CPP_TESTS=OFF
-		$(cmake-utils_use static-libs RDK_INSTALL_STATIC_LIBS)
-		$(cmake-utils_use python RDK_BUILD_PYTHON_WRAPPERS)
-	)
-
-	cmake-utils_src_configure
-}