1 |
commit: e90988ae0224a9a72e24e10e62b6df297a4b8fc4 |
2 |
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> |
3 |
AuthorDate: Sun Oct 14 19:35:13 2018 +0000 |
4 |
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> |
5 |
CommitDate: Sun Oct 14 19:35:13 2018 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e90988ae |
7 |
|
8 |
sci-chemistry/openbabel-python: Drop 2.3.2 |
9 |
|
10 |
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> |
11 |
Package-Manager: Portage-2.3.51, Repoman-2.3.11 |
12 |
|
13 |
sci-chemistry/openbabel-python/Manifest | 1 - |
14 |
.../openbabel-python-2.3.2-bindings_only.patch | 209 --------------------- |
15 |
.../files/openbabel-python-2.3.2-swig-3.0.3.patch | 97 ---------- |
16 |
.../files/openbabel-python-2.3.2-testpybel.patch | 28 --- |
17 |
.../openbabel-python/openbabel-python-2.3.2.ebuild | 93 --------- |
18 |
5 files changed, 428 deletions(-) |
19 |
|
20 |
diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest |
21 |
index b44e078a63a..ac268758e8c 100644 |
22 |
--- a/sci-chemistry/openbabel-python/Manifest |
23 |
+++ b/sci-chemistry/openbabel-python/Manifest |
24 |
@@ -1,2 +1 @@ |
25 |
-DIST openbabel-2.3.2.tar.gz 20509105 BLAKE2B d475c2da0d7171650eeb4b78a948421b783bdbb9342c81114d3dbc19d5cbb273f7303438920ffaeef5b6332e4b72606a86ded5cbd3d7e541f62b59b46483bb69 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 |
26 |
DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 |
27 |
|
28 |
diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch |
29 |
deleted file mode 100644 |
30 |
index 2e776b4029e..00000000000 |
31 |
--- a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch |
32 |
+++ /dev/null |
33 |
@@ -1,209 +0,0 @@ |
34 |
-diff --git a/CMakeLists.txt b/CMakeLists.txt |
35 |
-index 449f4b4..1c9ad00 100644 |
36 |
---- a/CMakeLists.txt |
37 |
-+++ b/CMakeLists.txt |
38 |
-@@ -252,7 +252,8 @@ if(NOT MSVC) |
39 |
- } |
40 |
- " SCANDIR_NEEDS_CONST) |
41 |
- |
42 |
-- set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}") |
43 |
-+ set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}" |
44 |
-+ CACHE PATH "Set to system install for bindings only build") |
45 |
- add_definitions(-DOB_MODULE_PATH="\\"${OB_MODULE_PATH}\\"") |
46 |
- |
47 |
- # Add some visibility support when using GCC |
48 |
-@@ -380,7 +381,8 @@ if(UNIX AND BUILD_SHARED) |
49 |
- if(APPLE) |
50 |
- set(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}) |
51 |
- else() |
52 |
-- set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}") |
53 |
-+ set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}" |
54 |
-+ CACHE PATH "Set sane rpath") |
55 |
- set(CMAKE_SKIP_BUILD_RPATH FALSE) |
56 |
- set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) |
57 |
- set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) |
58 |
-@@ -477,6 +479,13 @@ endif() |
59 |
- # Should the language bindings be regenereted? |
60 |
- option(RUN_SWIG "Generate language bindings with SWIG" OFF) |
61 |
- |
62 |
-+# Build bindings only |
63 |
-+option(BINDINGS_ONLY "Build bindings only" OFF) |
64 |
-+ |
65 |
-+# Point to library if building bindings only |
66 |
-+set(BABEL_SYSTEM_LIBRARY ${BABEL_LIBRARY} |
67 |
-+ CACHE PATH "Point to openbabel library if building bindings only") |
68 |
-+ |
69 |
- # Should all bindings be built? |
70 |
- option(ALL_BINDINGS "Build all languages bindings" OFF) |
71 |
- |
72 |
-diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt |
73 |
-index 16e9000..ecd2295 100644 |
74 |
---- a/scripts/CMakeLists.txt |
75 |
-+++ b/scripts/CMakeLists.txt |
76 |
-@@ -92,16 +92,30 @@ if (DO_PYTHON_BINDINGS) |
77 |
- endif(RUN_SWIG) |
78 |
- |
79 |
- add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel-python.cpp) |
80 |
-- target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY}) |
81 |
-+ if(BINDINGS_ONLY) |
82 |
-+ target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_SYSTEM_LIBRARY}) |
83 |
-+ else() |
84 |
-+ target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY}) |
85 |
-+ endif() |
86 |
-+ |
87 |
- if(NOT WIN32) |
88 |
- set_target_properties(bindings_python PROPERTIES |
89 |
- OUTPUT_NAME _openbabel |
90 |
- PREFIX "" |
91 |
- SUFFIX .so ) |
92 |
-- add_dependencies(bindings_python openbabel) |
93 |
-- install(TARGETS bindings_python LIBRARY DESTINATION ${LIB_INSTALL_DIR}) |
94 |
-- install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py DESTINATION ${LIB_INSTALL_DIR}) |
95 |
-- install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py DESTINATION ${LIB_INSTALL_DIR}) |
96 |
-+ if(NOT BINDINGS_ONLY) |
97 |
-+ add_dependencies(bindings_python openbabel) |
98 |
-+ endif() |
99 |
-+ |
100 |
-+ install(TARGETS bindings_python |
101 |
-+ LIBRARY DESTINATION ${LIB_INSTALL_DIR} |
102 |
-+ COMPONENT bindings_python) |
103 |
-+ install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py |
104 |
-+ DESTINATION ${LIB_INSTALL_DIR} |
105 |
-+ COMPONENT bindings_python) |
106 |
-+ install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py |
107 |
-+ DESTINATION ${LIB_INSTALL_DIR} |
108 |
-+ COMPONENT bindings_python) |
109 |
- else(NOT WIN32) |
110 |
- set_target_properties(bindings_python PROPERTIES |
111 |
- OUTPUT_NAME _openbabel |
112 |
-diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt |
113 |
-index 7841782..6f3495f 100644 |
114 |
---- a/test/CMakeLists.txt |
115 |
-+++ b/test/CMakeLists.txt |
116 |
-@@ -2,7 +2,12 @@ |
117 |
- add_definitions(-DTESTDATADIR="\\"${CMAKE_SOURCE_DIR}/test/files/\\"") |
118 |
- |
119 |
- # define FORMATDIR for location of format plugin binaries |
120 |
--add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib/\\"") |
121 |
-+if(BINDINGS_ONLY) |
122 |
-+ set(FORMATDIR "${OB_MODULE_PATH}/") |
123 |
-+else() |
124 |
-+ set(FORMATDIR "${openbabel_BINARY_DIR}/lib${LIB_SUFFIX}/") |
125 |
-+endif() |
126 |
-+add_definitions(-DFORMATDIR="\\"${FORMATDIR}/\\"") |
127 |
- |
128 |
- ########################################################### |
129 |
- # new tests using obtest.h |
130 |
-@@ -89,7 +94,7 @@ foreach(test ${tests}) |
131 |
- add_test(${test}_Test ${TEST_PATH}/test_${test}) |
132 |
- set_tests_properties(${test}_Test PROPERTIES |
133 |
- FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed" |
134 |
-- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib") |
135 |
-+ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}") |
136 |
- endforeach(test ${tests}) |
137 |
- |
138 |
- ############################################################ |
139 |
-@@ -152,7 +157,7 @@ if(WITH_INCHI) |
140 |
- ${TEST_PATH}/test_inchiwrite ${inchidata}/${test} ${inchidata}/${test}.txt) |
141 |
- set_tests_properties(inchi${test}_Test PROPERTIES |
142 |
- FAIL_REGULAR_EXPRESSION "Not ok" |
143 |
-- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib" |
144 |
-+ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" |
145 |
- ) |
146 |
- endforeach(test ${inchitests}) |
147 |
- endif(WITH_INCHI) |
148 |
-@@ -166,7 +171,7 @@ foreach(test ${old_tests}) |
149 |
- add_test(${test}_Test ${TEST_PATH}/test_${test}) |
150 |
- set_tests_properties(${test}_Test PROPERTIES |
151 |
- FAIL_REGULAR_EXPRESSION "not ok" |
152 |
-- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib" |
153 |
-+ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" |
154 |
- ) |
155 |
- endforeach(test ${old_tests}) |
156 |
- |
157 |
-@@ -181,8 +186,8 @@ if(NOT BUILD_SHARED AND NOT BUILD_MIXED) |
158 |
- endif() |
159 |
- install(TARGETS roundtrip |
160 |
- RUNTIME DESTINATION bin |
161 |
-- LIBRARY DESTINATION lib |
162 |
-- ARCHIVE DESTINATION lib |
163 |
-+ LIBRARY DESTINATION lib${LIB_SUFFIX} |
164 |
-+ ARCHIVE DESTINATION lib${LIB_SUFFIX} |
165 |
- ) |
166 |
- |
167 |
- ########################### |
168 |
-@@ -199,10 +204,10 @@ if(NOT MINGW AND NOT CYGWIN) |
169 |
- babel sym smartssym fastsearch unique kekule) |
170 |
- foreach(pytest ${pytests}) |
171 |
- SET_SOURCE_FILES_PROPERTIES(test${pytest}.py PROPERTIES |
172 |
-- PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib" |
173 |
-- BABEL_LIBDIR "${CMAKE_BINARY_DIR}/lib" |
174 |
-+ PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" |
175 |
-+ BABEL_LIBDIR "${FORMATDIR}" |
176 |
- BABEL_DATADIR "${CMAKE_SOURCE_DIR}/data" |
177 |
-- LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib" |
178 |
-+ LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" |
179 |
- ) |
180 |
- ADD_PYTHON_TEST(pytest_${pytest} test${pytest}.py) |
181 |
- set_tests_properties(pytest_${pytest} PROPERTIES |
182 |
-@@ -221,10 +226,10 @@ if (PYTHON_BINDINGS) |
183 |
- bindings _pybel example) |
184 |
- foreach(pybindtest ${pybindtests}) |
185 |
- SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES |
186 |
-- PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib" |
187 |
-- BABEL_LIBDIR "${CMAKE_BINARY_DIR}/lib" |
188 |
-+ PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" |
189 |
-+ BABEL_LIBDIR "${FORMATDIR}" |
190 |
- BABEL_DATADIR "${CMAKE_SOURCE_DIR}/data" |
191 |
-- LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib" |
192 |
-+ LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" |
193 |
- ) |
194 |
- if(MSVC) |
195 |
- SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES |
196 |
-diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt |
197 |
-index 1f547bf..fb98441 100644 |
198 |
---- a/tools/CMakeLists.txt |
199 |
-+++ b/tools/CMakeLists.txt |
200 |
-@@ -38,8 +38,8 @@ if(BUILD_SHARED) |
201 |
- target_link_libraries(${tool} ${BABEL_LIBRARY}) |
202 |
- install(TARGETS ${tool} |
203 |
- RUNTIME DESTINATION bin |
204 |
-- LIBRARY DESTINATION lib |
205 |
-- ARCHIVE DESTINATION lib |
206 |
-+ LIBRARY DESTINATION lib${LIB_SUFFIX} |
207 |
-+ ARCHIVE DESTINATION lib${LIB_SUFFIX} |
208 |
- ) |
209 |
- endforeach(tool) |
210 |
- |
211 |
-@@ -53,8 +53,8 @@ if(BUILD_SHARED) |
212 |
- target_link_libraries(obspectrophore ${BABEL_LIBRARY}) |
213 |
- install(TARGETS obspectrophore |
214 |
- RUNTIME DESTINATION bin |
215 |
-- LIBRARY DESTINATION lib |
216 |
-- ARCHIVE DESTINATION lib |
217 |
-+ LIBRARY DESTINATION lib${LIB_SUFFIX} |
218 |
-+ ARCHIVE DESTINATION lib${LIB_SUFFIX} |
219 |
- ) |
220 |
- |
221 |
- # obgrep -- requires getopt |
222 |
-@@ -66,8 +66,8 @@ if(BUILD_SHARED) |
223 |
- target_link_libraries(obgrep ${BABEL_LIBRARY}) |
224 |
- install(TARGETS obgrep |
225 |
- RUNTIME DESTINATION bin |
226 |
-- LIBRARY DESTINATION lib |
227 |
-- ARCHIVE DESTINATION lib |
228 |
-+ LIBRARY DESTINATION lib${LIB_SUFFIX} |
229 |
-+ ARCHIVE DESTINATION lib${LIB_SUFFIX} |
230 |
- ) |
231 |
- endif(NOT MINIMAL_BUILD) |
232 |
- |
233 |
-@@ -146,7 +146,7 @@ else(BUILD_SHARED) |
234 |
- |
235 |
- install(TARGETS babel |
236 |
- RUNTIME DESTINATION bin |
237 |
-- LIBRARY DESTINATION lib |
238 |
-- ARCHIVE DESTINATION lib) |
239 |
-+ LIBRARY DESTINATION lib${LIB_SUFFIX} |
240 |
-+ ARCHIVE DESTINATION lib${LIB_SUFFIX}) |
241 |
- |
242 |
- endif(BUILD_SHARED) |
243 |
|
244 |
diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch |
245 |
deleted file mode 100644 |
246 |
index d30efd55bd9..00000000000 |
247 |
--- a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch |
248 |
+++ /dev/null |
249 |
@@ -1,97 +0,0 @@ |
250 |
- scripts/openbabel-python.i | 34 +++++++++++++++++----------------- |
251 |
- 1 file changed, 17 insertions(+), 17 deletions(-) |
252 |
- |
253 |
-diff --git a/scripts/openbabel-python.i b/scripts/openbabel-python.i |
254 |
-index 7cb8f24..d893129 100644 |
255 |
---- a/scripts/openbabel-python.i |
256 |
-+++ b/scripts/openbabel-python.i |
257 |
-@@ -227,7 +227,7 @@ CAST_GENERICDATA_TO(SquarePlanarStereo) |
258 |
- %include <openbabel/math/transform3d.h> |
259 |
- %include <openbabel/math/spacegroup.h> |
260 |
- |
261 |
--# CloneData should be used instead of the following method |
262 |
-+// CloneData should be used instead of the following method |
263 |
- %ignore OpenBabel::OBBase::SetData; |
264 |
- %include <openbabel/base.h> |
265 |
- |
266 |
-@@ -289,7 +289,7 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue |
267 |
- %ignore OpenBabel::OBDescriptor::LessThan; |
268 |
- %include <openbabel/descriptor.h> |
269 |
- |
270 |
--# Ignore shadowed methods |
271 |
-+// Ignore shadowed methods |
272 |
- %ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const double *const, double *); |
273 |
- %ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const double, double *); |
274 |
- %include <openbabel/forcefield.h> |
275 |
-@@ -310,7 +310,7 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue |
276 |
- |
277 |
- %warnfilter(503) OpenBabel::OBBitVec; // Not wrapping any of the overloaded operators |
278 |
- %include <openbabel/bitvec.h> |
279 |
--# Ignore shadowed method |
280 |
-+// Ignore shadowed method |
281 |
- %ignore OpenBabel::OBRotor::GetRotAtoms() const; |
282 |
- %include <openbabel/rotor.h> |
283 |
- %ignore OpenBabel::Swab; |
284 |
-@@ -321,13 +321,13 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue |
285 |
- %include <openbabel/math/align.h> |
286 |
- #endif |
287 |
- |
288 |
--# The following %ignores avoid warning messages due to shadowed classes. |
289 |
--# This does not imply a loss of functionality as (in this case) |
290 |
--# the shadowed class is identical (from the point of view of SWIG) to |
291 |
--# the shadowing class. |
292 |
--# This is because C++ references (&) are transformed by SWIG back into |
293 |
--# pointers, so that OBAtomIter(OBMol &) would be treated the same as |
294 |
--# OBAtomIter(OBMol *). |
295 |
-+// The following %ignores avoid warning messages due to shadowed classes. |
296 |
-+// This does not imply a loss of functionality as (in this case) |
297 |
-+// the shadowed class is identical (from the point of view of SWIG) to |
298 |
-+// the shadowing class. |
299 |
-+// This is because C++ references (&) are transformed by SWIG back into |
300 |
-+// pointers, so that OBAtomIter(OBMol &) would be treated the same as |
301 |
-+// OBAtomIter(OBMol *). |
302 |
- |
303 |
- %ignore OBAtomAtomIter(OBAtom &); |
304 |
- %ignore OBAtomBondIter(OBAtom &); |
305 |
-@@ -346,9 +346,9 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue |
306 |
- %ignore OBResidueIter(OBMol &); |
307 |
- %ignore OBResidueAtomIter(OBResidue &); |
308 |
- |
309 |
--# These classes are renamed so that they can be replaced by Python |
310 |
--# classes of the same name which provide Pythonic iterators |
311 |
--# (see %pythoncode section below) |
312 |
-+// These classes are renamed so that they can be replaced by Python |
313 |
-+// classes of the same name which provide Pythonic iterators |
314 |
-+// (see %pythoncode section below) |
315 |
- |
316 |
- %rename(_OBAtomAtomIter) OpenBabel::OBAtomAtomIter; |
317 |
- %rename(_OBAtomBondIter) OpenBabel::OBAtomBondIter; |
318 |
-@@ -367,8 +367,8 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue |
319 |
- |
320 |
- %include <openbabel/obiter.h> |
321 |
- |
322 |
--# The following class, OBiter, is subclassed to provide Python iterators |
323 |
--# equivalent to the C++ iterators in obiter.h and the plugin iterators |
324 |
-+// The following class, OBiter, is subclassed to provide Python iterators |
325 |
-+// equivalent to the C++ iterators in obiter.h and the plugin iterators |
326 |
- |
327 |
- %pythoncode %{ |
328 |
- class OBIter(object): |
329 |
-@@ -459,7 +459,7 @@ def double_array(mylist): |
330 |
- return c |
331 |
- %} |
332 |
- |
333 |
--# Copy some of the global variables in cvar into the openbabel namespace |
334 |
-+// Copy some of the global variables in cvar into the openbabel namespace |
335 |
- |
336 |
- %pythoncode %{ |
337 |
- obErrorLog = cvar.obErrorLog |
338 |
-@@ -470,7 +470,7 @@ atomtyper = cvar.atomtyper |
339 |
- aromtyper = cvar.aromtyper |
340 |
- %} |
341 |
- |
342 |
--# Functions to set the log file to std::cout and std::cerr |
343 |
-+// Functions to set the log file to std::cout and std::cerr |
344 |
- |
345 |
- %ignore OBForceField::SetLogFile(std::ostream *pos); |
346 |
- %extend OpenBabel::OBForceField { |
347 |
|
348 |
diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch |
349 |
deleted file mode 100644 |
350 |
index 7a0114975ff..00000000000 |
351 |
--- a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch |
352 |
+++ /dev/null |
353 |
@@ -1,28 +0,0 @@ |
354 |
-From b34edb6de512e5735d87cb0893804a4abd14f9b7 Mon Sep 17 00:00:00 2001 |
355 |
-From: baoilleach <baoilleach@71e0b675-c112-0410-beda-96664073b5c2> |
356 |
-Date: Mon, 1 Oct 2012 20:40:36 +0000 |
357 |
-Subject: [PATCH] scripts/python/testpybel.py: Minor fix to enable failing |
358 |
- test to pass. Failures due to the new MOL Chiral Flag data |
359 |
- that I stored a while ago. |
360 |
- |
361 |
-git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk@5022 71e0b675-c112-0410-beda-96664073b5c2 |
362 |
---- |
363 |
- scripts/python/examples/testpybel.py | 2 +- |
364 |
- 1 file changed, 1 insertion(+), 1 deletion(-) |
365 |
- |
366 |
-diff --git a/scripts/python/examples/testpybel.py b/scripts/python/examples/testpybel.py |
367 |
-index aa5fcd4..7951851 100644 |
368 |
---- a/scripts/python/examples/testpybel.py |
369 |
-+++ b/scripts/python/examples/testpybel.py |
370 |
-@@ -336,7 +336,7 @@ class TestPybel(TestToolkit): |
371 |
- tpsaname = "TPSA" |
372 |
- Nbits = 3 |
373 |
- Nfpbits = 32 |
374 |
-- datakeys = ['NSC', 'Comment', 'OpenBabel Symmetry Classes'] |
375 |
-+ datakeys = ['NSC', 'Comment', 'OpenBabel Symmetry Classes', 'MOL Chiral Flag'] |
376 |
- |
377 |
- def testFP_FP3(self): |
378 |
- "Checking the results from FP3" |
379 |
--- |
380 |
-1.7.12.3 |
381 |
- |
382 |
|
383 |
diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild |
384 |
deleted file mode 100644 |
385 |
index 999a73bc794..00000000000 |
386 |
--- a/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild |
387 |
+++ /dev/null |
388 |
@@ -1,93 +0,0 @@ |
389 |
-# Copyright 1999-2017 Gentoo Foundation |
390 |
-# Distributed under the terms of the GNU General Public License v2 |
391 |
- |
392 |
-EAPI=5 |
393 |
- |
394 |
-PYTHON_COMPAT=( python2_7 python3_4 ) |
395 |
- |
396 |
-inherit cmake-utils eutils multilib python-r1 |
397 |
- |
398 |
-DESCRIPTION="Python bindings for OpenBabel (including Pybel)" |
399 |
-HOMEPAGE="http://openbabel.sourceforge.net/" |
400 |
-SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" |
401 |
- |
402 |
-KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" |
403 |
-SLOT="0" |
404 |
-LICENSE="GPL-2" |
405 |
-IUSE="" |
406 |
- |
407 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
408 |
- |
409 |
-RDEPEND="${PYTHON_DEPS} |
410 |
- ~sci-chemistry/openbabel-${PV} |
411 |
- sys-libs/zlib" |
412 |
-DEPEND="${RDEPEND} |
413 |
- >=dev-lang/swig-2" |
414 |
- |
415 |
-S="${WORKDIR}"/openbabel-${PV} |
416 |
- |
417 |
-PATCHES=( |
418 |
- "${FILESDIR}"/${P}-testpybel.patch |
419 |
- "${FILESDIR}"/${P}-bindings_only.patch |
420 |
- "${FILESDIR}"/${P}-swig-3.0.3.patch |
421 |
- "${FILESDIR}"/${P}-gcc-6_and_7-backport.patch |
422 |
- ) |
423 |
- |
424 |
-src_prepare() { |
425 |
- cmake-utils_src_prepare |
426 |
- sed \ |
427 |
- -e "s:\"\.\.\":\"${EPREFIX}/usr\":g" \ |
428 |
- -i test/testbabel.py || die |
429 |
- swig -python -c++ -small -O -templatereduce -naturalvar \ |
430 |
- -I"${EPREFIX}/usr/include/openbabel-2.0" \ |
431 |
- -o scripts/python/openbabel-python.cpp \ |
432 |
- -DHAVE_EIGEN \ |
433 |
- -outdir scripts/python \ |
434 |
- scripts/openbabel-python.i \ |
435 |
- || die "Regeneration of openbabel-python.cpp failed" |
436 |
- sed \ |
437 |
- -e '/__GNUC__/s:== 4:>= 4:g' \ |
438 |
- -i include/openbabel/shared_ptr.h || die |
439 |
-} |
440 |
- |
441 |
-src_configure() { |
442 |
- my_impl_src_configure() { |
443 |
- local mycmakeargs=( |
444 |
- -DCMAKE_INSTALL_RPATH= |
445 |
- -DBINDINGS_ONLY=ON |
446 |
- -DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so" |
447 |
- -DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}" |
448 |
- -DLIB_INSTALL_DIR="${D}$(python_get_sitedir)" |
449 |
- -DPYTHON_BINDINGS=ON |
450 |
- -DPYTHON_EXECUTABLE=${PYTHON} |
451 |
- -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" |
452 |
- -DPYTHON_INCLUDE_PATH="$(python_get_includedir)" |
453 |
- -DPYTHON_LIBRARY="$(python_get_library_path)" |
454 |
- -DENABLE_TESTS=ON |
455 |
- ) |
456 |
- |
457 |
- cmake-utils_src_configure |
458 |
- } |
459 |
- |
460 |
- python_foreach_impl my_impl_src_configure |
461 |
-} |
462 |
- |
463 |
-src_compile() { |
464 |
- python_foreach_impl cmake-utils_src_make bindings_python |
465 |
-} |
466 |
- |
467 |
-src_test() { |
468 |
- python_foreach_impl cmake-utils_src_test -R py |
469 |
-} |
470 |
- |
471 |
-src_install() { |
472 |
- my_impl_src_install() { |
473 |
- cd "${BUILD_DIR}" || die |
474 |
- |
475 |
- cmake -DCOMPONENT=bindings_python -P cmake_install.cmake |
476 |
- |
477 |
- python_optimize |
478 |
- } |
479 |
- |
480 |
- python_foreach_impl my_impl_src_install |
481 |
-} |