Gentoo Archives: gentoo-commits

From: Andrew Ammerlaan <andrewammerlaan@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-libs/rdkit/files/, sci-libs/rdkit/
Date: Mon, 24 Jan 2022 19:51:18
Message-Id: 1643049748.ebaf7f2da08feb9b7e0460f6ef8fadec55d91c12.andrewammerlaan@gentoo
1 commit: ebaf7f2da08feb9b7e0460f6ef8fadec55d91c12
2 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
3 AuthorDate: Mon Jan 24 18:42:28 2022 +0000
4 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
5 CommitDate: Mon Jan 24 18:42:28 2022 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ebaf7f2d
7
8 sci-libs/rdkit: bump to 2021.09.4
9
10 Package-Manager: Portage-3.0.30, Repoman-3.0.3
11 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
12
13 .../rdkit-2020.03.6-no_dynamic_checking.patch | 59 ----------------------
14 .../files/rdkit-2021.09.4-find-rapidjson.patch | 22 ++++++++
15 sci-libs/rdkit/rdkit-2020.03.6.ebuild | 57 ---------------------
16 sci-libs/rdkit/rdkit-2021.09.4.ebuild | 58 +++++++++++++++++++++
17 4 files changed, 80 insertions(+), 116 deletions(-)
18
19 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
20 deleted file mode 100644
21 index 2f7656245..000000000
22 --- a/sci-libs/rdkit/files/rdkit-2020.03.6-no_dynamic_checking.patch
23 +++ /dev/null
24 @@ -1,59 +0,0 @@
25 ---- a/External/catch/CMakeLists.txt 2020-09-28 05:09:11.307595711 -0400
26 -+++ b/External/catch/CMakeLists.txt 2020-09-28 05:10:35.188570785 -0400
27 -@@ -13,9 +13,6 @@
28 - message("-- Catch not found in ${CATCH_DIR}")
29 - include(RDKitUtils)
30 - set(RELEASE_NO "2.1.2")
31 -- downloadAndCheckMD5("https://github.com/catchorg/Catch2/archive/v${RELEASE_NO}.tar.gz"
32 -- "${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz"
33 -- "4c5740d7446d9b4e3735dcff0951aaca")
34 - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
35 - ${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz
36 - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
37 ---- a/External/CoordGen/CMakeLists.txt 2020-09-28 05:13:38.351584109 -0400
38 -+++ b/External/CoordGen/CMakeLists.txt 2020-09-28 05:15:49.396007762 -0400
39 -@@ -38,9 +38,6 @@
40 -
41 - if(NOT EXISTS "${MAEPARSER_DIR}/MaeParser.hpp")
42 - set(RELEASE_NO "1.2.3")
43 -- set(MD5 "4ead02a0bf87110d1caae79ab42a5747")
44 -- downloadAndCheckMD5("https://github.com/schrodinger/maeparser/archive/v${RELEASE_NO}.tar.gz"
45 -- "${CMAKE_CURRENT_SOURCE_DIR}/maeparser-v${RELEASE_NO}.tar.gz" ${MD5})
46 - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
47 - ${CMAKE_CURRENT_SOURCE_DIR}/maeparser-v${RELEASE_NO}.tar.gz
48 - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
49 ---- a/External/CoordGen/CMakeLists.txt 2020-09-28 05:31:21.353305949 -0400
50 -+++ b/External/CoordGen/CMakeLists.txt 2020-09-28 05:32:04.187783628 -0400
51 -@@ -67,9 +67,6 @@
52 -
53 - if(NOT EXISTS "${COORDGEN_DIR}/sketcherMinimizer.h")
54 - set(RELEASE_NO "1.4.0")
55 -- set(MD5 "5f663c8809b494f0548dd504c011c739")
56 -- downloadAndCheckMD5("https://github.com/schrodinger/coordgenlibs/archive/v${RELEASE_NO}.tar.gz"
57 -- "${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz" ${MD5})
58 - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
59 - ${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz
60 - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
61 ---- a/External/RingFamilies/CMakeLists.txt 2020-09-18 11:18:37.000000000 -0400
62 -+++ b/External/RingFamilies/CMakeLists.txt 2020-09-28 05:35:04.427800305 -0400
63 -@@ -8,9 +8,6 @@
64 -
65 - if(NOT EXISTS "${URFLIB_DIR}/RingDecomposerLib.h")
66 - set(RELEASE_NO "1.1.3_rdkit")
67 -- set(MD5 "e9a0bcdda8b921a35e812b9888a9a874")
68 -- downloadAndCheckMD5("https://github.com/rareylab/RingDecomposerLib/archive/v${RELEASE_NO}.tar.gz"
69 -- "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz" ${MD5})
70 - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
71 - ${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz
72 - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
73 ---- a/Code/GraphMol/MolInterchange/CMakeLists.txt 2020-09-18 11:18:37.000000000 -0400
74 -+++ b/Code/GraphMol/MolInterchange/CMakeLists.txt 2020-09-28 05:36:47.759960868 -0400
75 -@@ -1,8 +1,5 @@
76 -
77 - if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0")
78 -- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"
79 -- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz"
80 -- "badd12c511e081fec6c89c43a7027bce")
81 - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
82 - ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz
83 - WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External)
84
85 diff --git a/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch
86 new file mode 100644
87 index 000000000..94a209e0f
88 --- /dev/null
89 +++ b/sci-libs/rdkit/files/rdkit-2021.09.4-find-rapidjson.patch
90 @@ -0,0 +1,22 @@
91 +diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt
92 +index 8027444..6a8c715 100644
93 +--- a/Code/GraphMol/MolInterchange/CMakeLists.txt
94 ++++ b/Code/GraphMol/MolInterchange/CMakeLists.txt
95 +@@ -1,16 +1,5 @@
96 +
97 +-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0")
98 +- downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"
99 +- "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz"
100 +- "badd12c511e081fec6c89c43a7027bce")
101 +- execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
102 +- ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz
103 +- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External)
104 +-else()
105 +- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External")
106 +-endif()
107 +-
108 +-include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include)
109 ++include_directories(/usr/include/rapidjson)
110 +
111 +
112 + rdkit_library(MolInterchange
113
114 diff --git a/sci-libs/rdkit/rdkit-2020.03.6.ebuild b/sci-libs/rdkit/rdkit-2020.03.6.ebuild
115 deleted file mode 100644
116 index b73817270..000000000
117 --- a/sci-libs/rdkit/rdkit-2020.03.6.ebuild
118 +++ /dev/null
119 @@ -1,57 +0,0 @@
120 -# Copyright 1999-2021 Gentoo Authors
121 -# Distributed under the terms of the GNU General Public License v2
122 -
123 -EAPI=7
124 -
125 -PYTHON_COMPAT=( python3_{7..9} )
126 -
127 -inherit cmake python-r1
128 -
129 -DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python"
130 -HOMEPAGE="http://www.rdkit.org/"
131 -SRC_URI="
132 - https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz
133 - https://github.com/schrodinger/maeparser/archive/v1.2.3.tar.gz -> maeparser-1.2.3.tar.gz
134 - https://github.com/schrodinger/coordgenlibs/archive/v1.4.0.tar.gz -> coordgenlibs-1.4.0.tar.gz
135 - https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz -> rapidjson-1.1.0.tar.gz
136 - "
137 -# issues with bundled packages; dev-libs/rapidjson, at least, should be unbundled:
138 -# https://github.com/rdkit/rdkit/issues/3443
139 -
140 -LICENSE="BSD"
141 -SLOT="0"
142 -KEYWORDS=""
143 -# build configuration issues https://github.com/rdkit/rdkit/issues/3444
144 -IUSE="+python static-libs"
145 -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
146 -
147 -RDEPEND="dev-libs/boost
148 - python? (
149 - dev-libs/boost[python,${PYTHON_USEDEP}]
150 - dev-python/numpy[${PYTHON_USEDEP}]
151 - ${PYTHON_DEPS}
152 - )
153 - >=dev-db/sqlite-3"
154 -DEPEND="${RDEPEND}"
155 -
156 -S="${WORKDIR}"/rdkit-Release_${PV//./_}
157 -
158 -PATCHES=( "${FILESDIR}"/${P}-no_dynamic_checking.patch )
159 -
160 -src_prepare() {
161 - cp ../maeparser-* -rf External/CoordGen/ || die
162 - cp ../coordgenlibs-* -rf External/CoordGen/ || die
163 - cp ../rapidjson-* -rf External/ || die
164 - cmake_src_prepare
165 -}
166 -
167 -src_configure() {
168 - local mycmakeargs=(
169 - -DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}"/usr
170 - -DRDK_INSTALL_INTREE=0
171 - -DRDK_BUILD_CPP_TESTS=OFF
172 - -DRDK_INSTALL_STATIC_LIBS="$(usex static-libs)"
173 - -DRDK_BUILD_PYTHON_WRAPPERS="$(usex python)"
174 - )
175 - cmake_src_configure
176 -}
177
178 diff --git a/sci-libs/rdkit/rdkit-2021.09.4.ebuild b/sci-libs/rdkit/rdkit-2021.09.4.ebuild
179 new file mode 100644
180 index 000000000..a9b1258c9
181 --- /dev/null
182 +++ b/sci-libs/rdkit/rdkit-2021.09.4.ebuild
183 @@ -0,0 +1,58 @@
184 +# Copyright 1999-2022 Gentoo Authors
185 +# Distributed under the terms of the GNU General Public License v2
186 +
187 +EAPI=8
188 +
189 +PYTHON_COMPAT=( python3_{8..10} )
190 +
191 +inherit cmake python-single-r1
192 +
193 +DESCRIPTION="Cheminformatics and machine-learning software written in C++ and Python"
194 +HOMEPAGE="http://www.rdkit.org/"
195 +SRC_URI="https://github.com/rdkit/rdkit/archive/Release_${PV//./_}.tar.gz -> ${P}.tar.gz"
196 +S="${WORKDIR}/rdkit-Release_${PV//./_}"
197 +
198 +LICENSE="BSD"
199 +SLOT="0"
200 +KEYWORDS="~amd64"
201 +IUSE="+python static-libs test"
202 +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
203 +RESTRICT="!test? ( test )"
204 +
205 +RDEPEND="dev-libs/boost
206 + python? (
207 + $(python_gen_cond_dep '
208 + dev-libs/boost:=[numpy,python,${PYTHON_USEDEP}]
209 + dev-python/numpy[${PYTHON_USEDEP}]
210 + ')
211 + ${PYTHON_DEPS}
212 + )
213 + dev-cpp/catch:0
214 + dev-libs/rapidjson
215 + >=dev-db/sqlite-3"
216 +DEPEND="${RDEPEND}"
217 +
218 +PATCHES=(
219 + "${FILESDIR}/${PN}-2021.09.4-find-rapidjson.patch"
220 +)
221 +
222 +src_configure() {
223 + local mycmakeargs=(
224 + -DCATCH_DIR="${EPREFIX}/usr/include/catch2"
225 + -DCMAKE_INSTALL_PREFIX:PATH="${EPREFIX}/usr"
226 + -DRDK_INSTALL_INTREE=0
227 + -DRDK_BUILD_CPP_TESTS="$(usex test)"
228 + -DRDK_INSTALL_STATIC_LIBS="$(usex static-libs)"
229 + -DRDK_BUILD_PYTHON_WRAPPERS="$(usex python)"
230 + # Disable things that trigger fetching and are not packaged
231 + -DRDK_INSTALL_COMIC_FONTS=OFF
232 + -DRDK_BUILD_COORDGEN_SUPPORT=OFF
233 + -DRDK_BUILD_MAEPARSER_SUPPORT=OFF
234 + -DRDK_USE_URF=OFF
235 + )
236 + cmake_src_configure
237 +}
238 +
239 +src_test() {
240 + RDBASE="${WORKDIR}/${PN}-Release_2021_09_4_build" cmake_src_test
241 +}