Gentoo Archives: gentoo-commits

From: Andreas Sturmlechner <asturm@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/apbs/files/, sci-chemistry/apbs/
Date: Mon, 31 Dec 2018 21:14:57
Message-Id: 1546290826.23df63ca4ab84f0deee052ac6365c07e4eeff234.asturm@gentoo
1 commit: 23df63ca4ab84f0deee052ac6365c07e4eeff234
2 Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
3 AuthorDate: Mon Dec 31 20:26:22 2018 +0000
4 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
5 CommitDate: Mon Dec 31 21:13:46 2018 +0000
6 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=23df63ca
7
8 sci-chemistry/apbs: EAPI-6 bump
9
10 Package-Manager: Portage-2.3.52, Repoman-2.3.12
11 Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
12
13 sci-chemistry/apbs/apbs-1.4.1-r2.ebuild | 32 ++++++++++----------
14 sci-chemistry/apbs/files/apbs-1.4.1-manip.patch | 18 +++++------
15 sci-chemistry/apbs/files/apbs-1.4.1-python.patch | 38 ++++++++++++------------
16 3 files changed, 43 insertions(+), 45 deletions(-)
17
18 diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
19 index 108e43bf904..b3c4f192894 100644
20 --- a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
21 +++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
22 @@ -1,19 +1,17 @@
23 # Copyright 1999-2018 Gentoo Authors
24 # Distributed under the terms of the GNU General Public License v2
25
26 -EAPI=5
27 +EAPI=6
28
29 PYTHON_COMPAT=( python2_7 )
30 DISTUTILS_SINGLE_IMPL=true
31 -
32 -inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs
33 -
34 -GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
35 +COMMIT="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
36 +inherit cmake-utils distutils-r1 flag-o-matic toolchain-funcs
37
38 DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
39 HOMEPAGE="https://www.poissonboltzmann.org/apbs/"
40 #SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
41 -SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip"
42 +SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${COMMIT}.zip -> ${P}.zip"
43
44 SLOT="0"
45 LICENSE="BSD"
46 @@ -44,7 +42,7 @@ DEPEND="${RDEPEND}
47 doc? ( app-doc/doxygen )
48 "
49
50 -S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN}
51 +S="${WORKDIR}"/${PN}-pdb2pqr-${COMMIT}/${PN}
52
53 PATCHES=(
54 "${FILESDIR}"/${P}-multilib.patch
55 @@ -71,24 +69,24 @@ src_prepare() {
56 src_configure() {
57 local mycmakeargs=(
58 -DCMAKE_SKIP_RPATH=ON
59 - -DTOOLS_PATH="${ED}"/usr
60 + -DTOOLS_PATH="${ED%/}"/usr
61 -DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir)
62 -DLIBRARY_INSTALL_PATH=$(get_libdir)
63 -DFETK_PATH="${EPREFIX}"/usr/
64 -DBUILD_SHARED_LIBS=ON
65 -DENABLE_QUIT=OFF
66 - $(cmake-utils_use_build doc DOC)
67 - $(cmake-utils_use_build tools TOOLS)
68 + -DBUILD_DOC=$(usex doc)
69 + -DBUILD_TOOLS=$(usex tools)
70 -DENABLE_BEM=OFF
71 # ENABLE_BEM: Boundary element method using TABIPB
72 - $(cmake-utils_use_enable debug DEBUG)
73 - $(cmake-utils_use_enable debug VERBOSE_DEBUG)
74 - $(cmake-utils_use_enable fast FAST)
75 - $(cmake-utils_use_enable fetk FETK)
76 - $(cmake-utils_use_enable mpi MPI)
77 - $(cmake-utils_use_enable python PYTHON)
78 + -DENABLE_DEBUG=$(usex debug)
79 + -DENABLE_VERBOSE_DEBUG=$(usex debug)
80 + -DENABLE_FAST=$(usex fast)
81 + -DENABLE_FETK=$(usex fetk)
82 + -DENABLE_MPI=$(usex mpi)
83 + -DENABLE_PYTHON=$(usex python)
84 # ENABLE_TINKER: Enable TINKER support
85 - $(cmake-utils_use_enable iapbs iAPBS)
86 + -DENABLE_iAPBS=$(usex iapbs)
87 # MAX_MEMORY: Set the maximum memory (in MB) to be used for a job
88 )
89 cmake-utils_src_configure
90
91 diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
92 index 37822339759..090a27d8a5a 100644
93 --- a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
94 +++ b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
95 @@ -3,10 +3,10 @@
96 apbs/tools/mesh/CMakeLists.txt | 4 ++--
97 4 files changed, 5 insertions(+), 9 deletions(-)
98
99 -diff --git a/apbs/CMakeLists.txt b/apbs/CMakeLists.txt
100 +diff --git a/CMakeLists.txt b/CMakeLists.txt
101 index 8917fc4..5152008 100644
102 ---- a/apbs/CMakeLists.txt
103 -+++ b/apbs/CMakeLists.txt
104 +--- a/CMakeLists.txt
105 ++++ b/CMakeLists.txt
106 @@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF)
107
108 if(ENABLE_FETK)
109 @@ -16,10 +16,10 @@ index 8917fc4..5152008 100644
110
111 list(APPEND APBS_LIBS "-lstdc++")
112 list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
113 -diff --git a/apbs/tools/manip/CMakeLists.txt b/apbs/tools/manip/CMakeLists.txt
114 +diff --git a/tools/manip/CMakeLists.txt b/tools/manip/CMakeLists.txt
115 index 937dac7..5768cc5 100644
116 ---- a/apbs/tools/manip/CMakeLists.txt
117 -+++ b/apbs/tools/manip/CMakeLists.txt
118 +--- a/tools/manip/CMakeLists.txt
119 ++++ b/tools/manip/CMakeLists.txt
120 @@ -4,9 +4,9 @@ set(LIBS "")
121 list(APPEND LIBS "apbs_generic")
122 list(APPEND LIBS "apbs_mg")
123 @@ -32,10 +32,10 @@ index 937dac7..5768cc5 100644
124
125 message(STATUS "libraries: ${LIBS}")
126
127 -diff --git a/apbs/tools/mesh/CMakeLists.txt b/apbs/tools/mesh/CMakeLists.txt
128 +diff --git a/tools/mesh/CMakeLists.txt b/tools/mesh/CMakeLists.txt
129 index 1406377..6e6dfb9 100644
130 ---- a/apbs/tools/mesh/CMakeLists.txt
131 -+++ b/apbs/tools/mesh/CMakeLists.txt
132 +--- a/tools/mesh/CMakeLists.txt
133 ++++ b/tools/mesh/CMakeLists.txt
134 @@ -4,9 +4,9 @@ set(LIBS "")
135 list(APPEND LIBS "apbs_generic")
136 list(APPEND LIBS "apbs_mg")
137
138 diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
139 index db9f86ba120..5ad6613615f 100644
140 --- a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
141 +++ b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
142 @@ -7,10 +7,10 @@
143 apbs/tools/python/setup.py | 16 ++++++++++++++++
144 7 files changed, 26 insertions(+), 8 deletions(-)
145
146 -diff --git a/apbs/contrib/iapbs/src/apbs_driver.c b/apbs/contrib/iapbs/src/apbs_driver.c
147 +diff --git a/contrib/iapbs/src/apbs_driver.c b/contrib/iapbs/src/apbs_driver.c
148 index c9e443b..e1ad67f 100644
149 ---- a/apbs/contrib/iapbs/src/apbs_driver.c
150 -+++ b/apbs/contrib/iapbs/src/apbs_driver.c
151 +--- a/contrib/iapbs/src/apbs_driver.c
152 ++++ b/contrib/iapbs/src/apbs_driver.c
153 @@ -595,7 +595,7 @@ int apbsdrv_(
154 printPBEPARM(pbeparm);
155
156 @@ -38,10 +38,10 @@ index c9e443b..e1ad67f 100644
157 }
158 bytesTotal = Vmem_bytesTotal();
159 highWater = Vmem_highWaterTotal();
160 -diff --git a/apbs/src/CMakeLists.txt b/apbs/src/CMakeLists.txt
161 +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
162 index 44d20fa..2577343 100644
163 ---- a/apbs/src/CMakeLists.txt
164 -+++ b/apbs/src/CMakeLists.txt
165 +--- a/src/CMakeLists.txt
166 ++++ b/src/CMakeLists.txt
167 @@ -68,6 +68,7 @@ configure_file(
168
169 if(ENABLE_iAPBS)
170 @@ -50,10 +50,10 @@ index 44d20fa..2577343 100644
171 INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH})
172 INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH})
173 endif()
174 -diff --git a/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt
175 +diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
176 index 1982a3c..4acbe68 100644
177 ---- a/apbs/tools/CMakeLists.txt
178 -+++ b/apbs/tools/CMakeLists.txt
179 +--- a/tools/CMakeLists.txt
180 ++++ b/tools/CMakeLists.txt
181 @@ -4,5 +4,5 @@ add_subdirectory(mesh)
182 add_subdirectory(manip)
183
184 @@ -61,17 +61,17 @@ index 1982a3c..4acbe68 100644
185 - add_subdirectory(manip)
186 + add_subdirectory(python)
187 endif(ENABLE_PYTHON)
188 -diff --git a/apbs/tools/python/CMakeLists.txt b/apbs/tools/python/CMakeLists.txt
189 +diff --git a/tools/python/CMakeLists.txt b/tools/python/CMakeLists.txt
190 new file mode 100644
191 index 0000000..8b13789
192 --- /dev/null
193 -+++ b/apbs/tools/python/CMakeLists.txt
194 ++++ b/tools/python/CMakeLists.txt
195 @@ -0,0 +1 @@
196 +
197 -diff --git a/apbs/tools/python/apbslib.c b/apbs/tools/python/apbslib.c
198 +diff --git a/tools/python/apbslib.c b/tools/python/apbslib.c
199 index fef5cc8..feaaa2c 100644
200 ---- a/apbs/tools/python/apbslib.c
201 -+++ b/apbs/tools/python/apbslib.c
202 +--- a/tools/python/apbslib.c
203 ++++ b/tools/python/apbslib.c
204 @@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0};
205 #include "maloc/maloc.h"
206 #include "apbscfg.h"
207 @@ -83,10 +83,10 @@ index fef5cc8..feaaa2c 100644
208
209
210 #include <limits.h>
211 -diff --git a/apbs/tools/python/apbslib.i b/apbs/tools/python/apbslib.i
212 +diff --git a/tools/python/apbslib.i b/tools/python/apbslib.i
213 index 17fe521..44d05ea 100644
214 ---- a/apbs/tools/python/apbslib.i
215 -+++ b/apbs/tools/python/apbslib.i
216 +--- a/tools/python/apbslib.i
217 ++++ b/tools/python/apbslib.i
218 @@ -15,8 +15,8 @@ Header files:
219 #include "maloc/maloc.h"
220 #include "apbscfg.h"
221 @@ -98,11 +98,11 @@ index 17fe521..44d05ea 100644
222 %}
223
224 /*
225 -diff --git a/apbs/tools/python/setup.py b/apbs/tools/python/setup.py
226 +diff --git a/tools/python/setup.py b/tools/python/setup.py
227 new file mode 100644
228 index 0000000..4a20198
229 --- /dev/null
230 -+++ b/apbs/tools/python/setup.py
231 ++++ b/tools/python/setup.py
232 @@ -0,0 +1,16 @@
233 +from distutils.core import setup, Extension
234 +setup(name='apbs',