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commit: ebaf7f2da08feb9b7e0460f6ef8fadec55d91c12 |
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Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
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AuthorDate: Mon Jan 24 18:42:28 2022 +0000 |
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Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
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CommitDate: Mon Jan 24 18:42:28 2022 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ebaf7f2d |
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|
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sci-libs/rdkit: bump to 2021.09.4 |
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|
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Package-Manager: Portage-3.0.30, Repoman-3.0.3 |
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Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> |
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|
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.../rdkit-2020.03.6-no_dynamic_checking.patch | 59 ---------------------- |
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.../files/rdkit-2021.09.4-find-rapidjson.patch | 22 ++++++++ |
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sci-libs/rdkit/rdkit-2020.03.6.ebuild | 57 --------------------- |
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sci-libs/rdkit/rdkit-2021.09.4.ebuild | 58 +++++++++++++++++++++ |
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4 files changed, 80 insertions(+), 116 deletions(-) |
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|
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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 |
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deleted file mode 100644 |
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index 2f7656245..000000000 |
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--- a/sci-libs/rdkit/files/rdkit-2020.03.6-no_dynamic_checking.patch |
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+++ /dev/null |
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@@ -1,59 +0,0 @@ |
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---- a/External/catch/CMakeLists.txt 2020-09-28 05:09:11.307595711 -0400 |
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-+++ b/External/catch/CMakeLists.txt 2020-09-28 05:10:35.188570785 -0400 |
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-@@ -13,9 +13,6 @@ |
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- message("-- Catch not found in ${CATCH_DIR}") |
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- include(RDKitUtils) |
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- set(RELEASE_NO "2.1.2") |
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-- downloadAndCheckMD5("https://github.com/catchorg/Catch2/archive/v${RELEASE_NO}.tar.gz" |
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-- "${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz" |
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-- "4c5740d7446d9b4e3735dcff0951aaca") |
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- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf |
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- ${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz |
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- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) |
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---- a/External/CoordGen/CMakeLists.txt 2020-09-28 05:13:38.351584109 -0400 |
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-+++ b/External/CoordGen/CMakeLists.txt 2020-09-28 05:15:49.396007762 -0400 |
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-@@ -38,9 +38,6 @@ |
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- |
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- if(NOT EXISTS "${MAEPARSER_DIR}/MaeParser.hpp") |
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- set(RELEASE_NO "1.2.3") |
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-- set(MD5 "4ead02a0bf87110d1caae79ab42a5747") |
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-- downloadAndCheckMD5("https://github.com/schrodinger/maeparser/archive/v${RELEASE_NO}.tar.gz" |
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-- "${CMAKE_CURRENT_SOURCE_DIR}/maeparser-v${RELEASE_NO}.tar.gz" ${MD5}) |
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- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf |
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- ${CMAKE_CURRENT_SOURCE_DIR}/maeparser-v${RELEASE_NO}.tar.gz |
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- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) |
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---- a/External/CoordGen/CMakeLists.txt 2020-09-28 05:31:21.353305949 -0400 |
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-+++ b/External/CoordGen/CMakeLists.txt 2020-09-28 05:32:04.187783628 -0400 |
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-@@ -67,9 +67,6 @@ |
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- |
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- if(NOT EXISTS "${COORDGEN_DIR}/sketcherMinimizer.h") |
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- set(RELEASE_NO "1.4.0") |
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-- set(MD5 "5f663c8809b494f0548dd504c011c739") |
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-- downloadAndCheckMD5("https://github.com/schrodinger/coordgenlibs/archive/v${RELEASE_NO}.tar.gz" |
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-- "${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz" ${MD5}) |
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- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf |
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- ${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz |
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- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) |
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---- a/External/RingFamilies/CMakeLists.txt 2020-09-18 11:18:37.000000000 -0400 |
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-+++ b/External/RingFamilies/CMakeLists.txt 2020-09-28 05:35:04.427800305 -0400 |
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-@@ -8,9 +8,6 @@ |
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- |
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- if(NOT EXISTS "${URFLIB_DIR}/RingDecomposerLib.h") |
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- set(RELEASE_NO "1.1.3_rdkit") |
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-- set(MD5 "e9a0bcdda8b921a35e812b9888a9a874") |
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-- downloadAndCheckMD5("https://github.com/rareylab/RingDecomposerLib/archive/v${RELEASE_NO}.tar.gz" |
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-- "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz" ${MD5}) |
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- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf |
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- ${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz |
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- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) |
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---- a/Code/GraphMol/MolInterchange/CMakeLists.txt 2020-09-18 11:18:37.000000000 -0400 |
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-+++ b/Code/GraphMol/MolInterchange/CMakeLists.txt 2020-09-28 05:36:47.759960868 -0400 |
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-@@ -1,8 +1,5 @@ |
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- |
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- if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0") |
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-- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz" |
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-- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz" |
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-- "badd12c511e081fec6c89c43a7027bce") |
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- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf |
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- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz |
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- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External) |
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|
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diff --git a/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch |
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new file mode 100644 |
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index 000000000..94a209e0f |
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--- /dev/null |
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+++ b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch |
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@@ -0,0 +1,22 @@ |
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+diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt |
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+index 8027444..6a8c715 100644 |
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+--- a/Code/GraphMol/MolInterchange/CMakeLists.txt |
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++++ b/Code/GraphMol/MolInterchange/CMakeLists.txt |
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+@@ -1,16 +1,5 @@ |
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+ |
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+-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0") |
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+- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz" |
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+- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz" |
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+- "badd12c511e081fec6c89c43a7027bce") |
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+- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf |
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+- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz |
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+- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External) |
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+-else() |
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+- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External") |
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+-endif() |
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+- |
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+-include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include) |
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++include_directories(/usr/include/rapidjson) |
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+ |
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+ |
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+ rdkit_library(MolInterchange |
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|
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diff --git a/sci-libs/rdkit/rdkit-2020.03.6.ebuild b/sci-libs/rdkit/rdkit-2020.03.6.ebuild |
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deleted file mode 100644 |
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index b73817270..000000000 |
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--- a/sci-libs/rdkit/rdkit-2020.03.6.ebuild |
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+++ /dev/null |
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@@ -1,57 +0,0 @@ |
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-# Copyright 1999-2021 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=7 |
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- |
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-PYTHON_COMPAT=( python3_{7..9} ) |
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- |
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-inherit cmake python-r1 |
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- |
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-DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python" |
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-HOMEPAGE="http://www.rdkit.org/" |
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-SRC_URI=" |
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- https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz |
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- https://github.com/schrodinger/maeparser/archive/v1.2.3.tar.gz -> maeparser-1.2.3.tar.gz |
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- https://github.com/schrodinger/coordgenlibs/archive/v1.4.0.tar.gz -> coordgenlibs-1.4.0.tar.gz |
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- https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz -> rapidjson-1.1.0.tar.gz |
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- " |
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-# issues with bundled packages; dev-libs/rapidjson, at least, should be unbundled: |
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-# https://github.com/rdkit/rdkit/issues/3443 |
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- |
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-LICENSE="BSD" |
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-SLOT="0" |
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-KEYWORDS="" |
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-# build configuration issues https://github.com/rdkit/rdkit/issues/3444 |
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-IUSE="+python static-libs" |
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-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" |
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- |
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-RDEPEND="dev-libs/boost |
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- python? ( |
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- dev-libs/boost[python,${PYTHON_USEDEP}] |
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- dev-python/numpy[${PYTHON_USEDEP}] |
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- ${PYTHON_DEPS} |
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- ) |
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- >=dev-db/sqlite-3" |
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-DEPEND="${RDEPEND}" |
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- |
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-S="${WORKDIR}"/rdkit-Release_${PV//./_} |
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- |
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-PATCHES=( "${FILESDIR}"/${P}-no_dynamic_checking.patch ) |
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- |
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-src_prepare() { |
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- cp ../maeparser-* -rf External/CoordGen/ || die |
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- cp ../coordgenlibs-* -rf External/CoordGen/ || die |
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- cp ../rapidjson-* -rf External/ || die |
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- cmake_src_prepare |
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-} |
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- |
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-src_configure() { |
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- local mycmakeargs=( |
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- -DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}"/usr |
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- -DRDK_INSTALL_INTREE=0 |
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- -DRDK_BUILD_CPP_TESTS=OFF |
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- -DRDK_INSTALL_STATIC_LIBS="$(usex static-libs)" |
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- -DRDK_BUILD_PYTHON_WRAPPERS="$(usex python)" |
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- ) |
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- cmake_src_configure |
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-} |
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|
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diff --git a/sci-libs/rdkit/rdkit-2021.09.4.ebuild b/sci-libs/rdkit/rdkit-2021.09.4.ebuild |
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new file mode 100644 |
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index 000000000..a9b1258c9 |
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--- /dev/null |
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+++ b/sci-libs/rdkit/rdkit-2021.09.4.ebuild |
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@@ -0,0 +1,58 @@ |
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+# Copyright 1999-2022 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=8 |
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+ |
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+PYTHON_COMPAT=( python3_{8..10} ) |
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+ |
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+inherit cmake python-single-r1 |
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+ |
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+DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python" |
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+HOMEPAGE="http://www.rdkit.org/" |
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+SRC_URI="https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz" |
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+S="${WORKDIR}/rdkit-Release_${PV//./_}" |
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+ |
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+LICENSE="BSD" |
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+SLOT="0" |
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+KEYWORDS="~amd64" |
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+IUSE="+python static-libs test" |
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+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" |
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+RESTRICT="!test? ( test )" |
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+ |
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+RDEPEND="dev-libs/boost |
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+ python? ( |
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+ $(python_gen_cond_dep ' |
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+ dev-libs/boost:=[numpy,python,${PYTHON_USEDEP}] |
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+ dev-python/numpy[${PYTHON_USEDEP}] |
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+ ') |
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+ ${PYTHON_DEPS} |
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+ ) |
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+ dev-cpp/catch:0 |
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+ dev-libs/rapidjson |
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+ >=dev-db/sqlite-3" |
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+DEPEND="${RDEPEND}" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}/${PN}-2021.09.4-find-rapidjson.patch" |
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+) |
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+ |
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+src_configure() { |
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+ local mycmakeargs=( |
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+ -DCATCH_DIR="${EPREFIX}/usr/include/catch2" |
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+ -DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}/usr" |
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+ -DRDK_INSTALL_INTREE=0 |
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+ -DRDK_BUILD_CPP_TESTS="$(usex test)" |
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+ -DRDK_INSTALL_STATIC_LIBS="$(usex static-libs)" |
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+ -DRDK_BUILD_PYTHON_WRAPPERS="$(usex python)" |
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+ # Disable things that trigger fetching and are not packaged |
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+ -DRDK_INSTALL_COMIC_FONTS=OFF |
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+ -DRDK_BUILD_COORDGEN_SUPPORT=OFF |
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+ -DRDK_BUILD_MAEPARSER_SUPPORT=OFF |
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+ -DRDK_USE_URF=OFF |
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+ ) |
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+ cmake_src_configure |
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+} |
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+ |
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+src_test() { |
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+ RDBASE="${WORKDIR}/${PN}-Release_2021_09_4_build" cmake_src_test |
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+} |