1 |
commit: 445eb95b61c9b12481b24f962123d0f13e940ab6 |
2 |
Author: Horea Christian <chr <AT> chymera <DOT> eu> |
3 |
AuthorDate: Mon Sep 9 08:25:49 2019 +0000 |
4 |
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> |
5 |
CommitDate: Mon Sep 9 08:25:49 2019 +0000 |
6 |
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=445eb95b |
7 |
|
8 |
sci-libs/itk: version bump to 5.0.1 |
9 |
|
10 |
And removed deprecated versions on account of gccxml removal |
11 |
|
12 |
Package-Manager: Portage-2.3.72, Repoman-2.3.17 |
13 |
Signed-off-by: Horea Christian <chr <AT> chymera.eu> |
14 |
|
15 |
sci-libs/itk/files/ITKModuleRemote.patch | 45 ++++++ |
16 |
sci-libs/itk/files/tests.patch | 41 ++++++ |
17 |
sci-libs/itk/itk-4.12.0.ebuild | 136 ------------------ |
18 |
sci-libs/itk/itk-4.4.2-r1.ebuild | 135 ------------------ |
19 |
sci-libs/itk/itk-4.4.2.ebuild | 115 --------------- |
20 |
sci-libs/itk/itk-4.5.1.ebuild | 155 --------------------- |
21 |
.../itk/{itk-5.0_rc1.ebuild => itk-5.0.1.ebuild} | 50 +++++-- |
22 |
sci-libs/itk/metadata.xml | 1 - |
23 |
8 files changed, 124 insertions(+), 554 deletions(-) |
24 |
|
25 |
diff --git a/sci-libs/itk/files/ITKModuleRemote.patch b/sci-libs/itk/files/ITKModuleRemote.patch |
26 |
new file mode 100644 |
27 |
index 000000000..eb130159a |
28 |
--- /dev/null |
29 |
+++ b/sci-libs/itk/files/ITKModuleRemote.patch |
30 |
@@ -0,0 +1,45 @@ |
31 |
+Disable automatic git clone attempt for modules: |
32 |
+https://github.com/InsightSoftwareConsortium/ITK/issues/1157 |
33 |
+ |
34 |
+--- a/CMake/ITKModuleRemote.cmake 2019-08-13 18:10:33.385472767 +0200 |
35 |
++++ b/CMake/ITKModuleRemote.cmake 2019-08-13 18:12:04.020198966 +0200 |
36 |
+@@ -165,39 +165,4 @@ |
37 |
+ set(Module_${_name} ON CACHE FORCE "${_description}") |
38 |
+ endif() |
39 |
+ |
40 |
+- if(Module_${_name}) |
41 |
+- itk_download_attempt_check(Module_${_name}) |
42 |
+- include(CMakeParseArguments) |
43 |
+- cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" ${ARGN}) |
44 |
+- find_package(Git) |
45 |
+- if(NOT GIT_EXECUTABLE) |
46 |
+- message(FATAL_ERROR "error: could not find git for clone of ${_name}") |
47 |
+- endif() |
48 |
+- execute_process( |
49 |
+- COMMAND "${GIT_EXECUTABLE}" --version |
50 |
+- OUTPUT_VARIABLE ov |
51 |
+- OUTPUT_STRIP_TRAILING_WHITESPACE |
52 |
+- ) |
53 |
+- string(REGEX REPLACE "^git version (.+)$" "\\1" _version "${ov}") |
54 |
+- if("${_version}" VERSION_LESS 1.6.6) |
55 |
+- message(FATAL_ERROR "Git version 1.6.6 or later is required.") |
56 |
+- endif() |
57 |
+- |
58 |
+- set(REMOTE_GIT_TAG "${_fetch_options_GIT_TAG}") |
59 |
+- |
60 |
+- if( DEFINED REMOTE_GIT_TAG_${_name} AND NOT "${REMOTE_GIT_TAG_${_name}}" STREQUAL "${_fetch_options_GIT_TAG}") |
61 |
+- set(REMOTE_GIT_TAG "${REMOTE_GIT_TAG_${_name}}") |
62 |
+- message(STATUS "NOTE: Using override 'REMOTE_GIT_TAG_${_name}=${REMOTE_GIT_TAG}'\n" |
63 |
+- " instead of value 'GIT_TAG=${_fetch_options_GIT_TAG}'\n" |
64 |
+- " specified in file ${ITK_SOURCE_DIR}/Modules/Remote/${_name}.remote.cmake'") |
65 |
+- endif() |
66 |
+- set(REMOTE_GIT_TAG_${_name} "${REMOTE_GIT_TAG}" CACHE STRING "Override default GIT_TAG value for remote module ${_name}") |
67 |
+- mark_as_advanced(REMOTE_GIT_TAG_${_name}) |
68 |
+- |
69 |
+- _fetch_with_git("${GIT_EXECUTABLE}" |
70 |
+- "${_fetch_options_GIT_REPOSITORY}" |
71 |
+- "${REMOTE_GIT_TAG}" |
72 |
+- "${ITK_SOURCE_DIR}/Modules/Remote/${_name}" |
73 |
+- ) |
74 |
+- endif() |
75 |
+ endfunction() |
76 |
|
77 |
diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch |
78 |
new file mode 100644 |
79 |
index 000000000..c24714e4d |
80 |
--- /dev/null |
81 |
+++ b/sci-libs/itk/files/tests.patch |
82 |
@@ -0,0 +1,41 @@ |
83 |
+Known to fail by upstream: |
84 |
+https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115 |
85 |
+ |
86 |
+--- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200 |
87 |
++++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200 |
88 |
+@@ -7,8 +7,6 @@ |
89 |
+ if(NOT VTK_RENDERING_BACKEND STREQUAL "None") |
90 |
+ list(APPEND ITKVtkGlueTests |
91 |
+ itkVtkMedianFilterTest.cxx |
92 |
+- itkVtkConnectedComponentImageFilterTest.cxx |
93 |
+- QuickViewTest.cxx |
94 |
+ # ### runViewImage ### |
95 |
+ # No test generated. Use it for view images (2D or 3D) with: |
96 |
+ # ITKVtkGlueTestDriver runViewImage image_file |
97 |
+@@ -40,26 +38,3 @@ |
98 |
+ NAME itkVTKImageToImageFilterTest |
99 |
+ COMMAND ITKVtkGlueTestDriver |
100 |
+ itkVTKImageToImageFilterTest) |
101 |
+- |
102 |
+-if(NOT VTK_RENDERING_BACKEND STREQUAL "None") |
103 |
+- itk_add_test( |
104 |
+- NAME itkVtkMedianImageFilterTest |
105 |
+- COMMAND ITKVtkGlueTestDriver |
106 |
+- itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2) |
107 |
+- set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) |
108 |
+- |
109 |
+- itk_add_test( |
110 |
+- NAME QuickViewTest |
111 |
+- COMMAND ITKVtkGlueTestDriver |
112 |
+- --compare DATA{Baseline/QuickViewTest.png,:} |
113 |
+- ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png |
114 |
+- --compareNumberOfPixelsTolerance 1500 |
115 |
+- QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR}) |
116 |
+- set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) |
117 |
+- |
118 |
+- itk_add_test( |
119 |
+- NAME itkVtkConnectedComponentImageFilterTest |
120 |
+- COMMAND ITKVtkGlueTestDriver |
121 |
+- itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png}) |
122 |
+- set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) |
123 |
+-endif() |
124 |
|
125 |
diff --git a/sci-libs/itk/itk-4.12.0.ebuild b/sci-libs/itk/itk-4.12.0.ebuild |
126 |
deleted file mode 100644 |
127 |
index a9633748b..000000000 |
128 |
--- a/sci-libs/itk/itk-4.12.0.ebuild |
129 |
+++ /dev/null |
130 |
@@ -1,136 +0,0 @@ |
131 |
-# Copyright 1999-2017 Gentoo Foundation |
132 |
-# Distributed under the terms of the GNU General Public License v2 |
133 |
- |
134 |
-EAPI=6 |
135 |
- |
136 |
-PYTHON_COMPAT=( python2_7 ) |
137 |
- |
138 |
-inherit eutils toolchain-funcs cmake-utils python-single-r1 |
139 |
- |
140 |
-MYPN=InsightToolkit |
141 |
-MYP=${MYPN}-${PV} |
142 |
-DOC_PV=4.5.0 |
143 |
- |
144 |
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" |
145 |
-HOMEPAGE="http://www.itk.org" |
146 |
-SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.xz |
147 |
- doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-${DOC_PV}.tar.gz )" |
148 |
-RESTRICT="primaryuri" |
149 |
- |
150 |
-LICENSE="Apache-2.0" |
151 |
-SLOT="0" |
152 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
153 |
-IUSE="debug doc examples +fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue" |
154 |
- |
155 |
-RDEPEND=" |
156 |
- dev-libs/double-conversion:0= |
157 |
- media-libs/libpng:0= |
158 |
- media-libs/tiff:0= |
159 |
- sci-libs/dcmtk:0= |
160 |
- sci-libs/hdf5:0=[cxx] |
161 |
- sys-libs/zlib:0= |
162 |
- virtual/jpeg:0= |
163 |
- fftw? ( sci-libs/fftw:3.0= ) |
164 |
- vtkglue? ( sci-libs/vtk:0=[python?] ) |
165 |
-" |
166 |
-DEPEND="${RDEPEND} |
167 |
- python? ( |
168 |
- ${PYTHON_DEPS} |
169 |
- >=dev-lang/swig-2.0:0 |
170 |
- >=dev-cpp/gccxml-0.9.0_pre20120309 |
171 |
- ) |
172 |
- doc? ( app-doc/doxygen ) |
173 |
-" |
174 |
- |
175 |
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" |
176 |
- |
177 |
-S="${WORKDIR}/${MYP}" |
178 |
- |
179 |
-PATCHES=( |
180 |
- "${FILESDIR}/nrrdio-linking.patch" |
181 |
-) |
182 |
- |
183 |
-get_memory() { |
184 |
- free --giga | grep Mem | cut -d ' ' -f 15 || die 'unable to get memory size' |
185 |
-} |
186 |
- |
187 |
-src_configure() { |
188 |
- sed -i \ |
189 |
- -e '/find_package/d' \ |
190 |
- Modules/ThirdParty/DoubleConversion/CMakeLists.txt || die |
191 |
- |
192 |
- local mycmakeargs=( |
193 |
- -DBUILD_SHARED_LIBS=ON |
194 |
- -DITK_USE_SYSTEM_DCMTK=ON |
195 |
- -DITK_USE_SYSTEM_DOUBLECONVERSION=ON |
196 |
- -DITK_USE_SYSTEM_HDF5=ON |
197 |
- -DITK_USE_SYSTEM_JPEG=ON |
198 |
- -DITK_USE_SYSTEM_PNG=ON |
199 |
- -DITK_USE_SYSTEM_SWIG=ON |
200 |
- -DITK_USE_SYSTEM_TIFF=ON |
201 |
- -DITK_USE_SYSTEM_ZLIB=ON |
202 |
- -DITK_BUILD_DEFAULT_MODULES=ON |
203 |
- -DITK_COMPUTER_MEMORY_SIZE="$(get_memory)" |
204 |
- -DITK_WRAP_JAVA=OFF |
205 |
- -DITK_WRAP_TCL=OFF |
206 |
- -DBUILD_TESTING=$(usex test) |
207 |
- -DBUILD_EXAMPLES=$(usex examples) |
208 |
- -DITK_USE_REVIEW=$(usex review) |
209 |
- -DITKV3_COMPATIBILITY=$(usex itkv3compat) |
210 |
- -DVNL_CONFIG_ENABLE_SSE2=$(usex cpu_flags_x86_sse2) |
211 |
- ) |
212 |
- if use fftw; then |
213 |
- mycmakeargs+=( |
214 |
- -DUSE_FFTWD=ON |
215 |
- -DUSE_FFTWF=ON |
216 |
- -DUSE_SYSTEM_FFTW=ON |
217 |
- -DITK_USE_SYSTEM_FFTW=ON |
218 |
- -DITK_WRAPPING=ON |
219 |
- -DITK_WRAP_double=ON |
220 |
- -DITK_WRAP_vector_double=ON |
221 |
- -DITK_WRAP_covariant_vector_double=ON |
222 |
- -DITK_WRAP_complex_double=ON |
223 |
- ) |
224 |
- fi |
225 |
- if use vtkglue; then |
226 |
- mycmakeargs+=( |
227 |
- -DModule_ITKVtkGlue=ON |
228 |
- ) |
229 |
- fi |
230 |
- mycmakeargs+=( |
231 |
- -DITK_WRAP_PYTHON=$(usex python ON OFF) |
232 |
- ) |
233 |
- |
234 |
- cmake-utils_src_configure |
235 |
-} |
236 |
- |
237 |
-src_install() { |
238 |
- cmake-utils_src_install |
239 |
- |
240 |
- if use examples; then |
241 |
- insinto /usr/share/doc/${PF}/examples |
242 |
- docompress -x /usr/share/doc/${PF}/examples |
243 |
- doins -r "${S}"/Examples/* |
244 |
- fi |
245 |
- |
246 |
- echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN} |
247 |
- local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit" |
248 |
- if use python; then |
249 |
- echo "PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} |
250 |
- ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" |
251 |
- fi |
252 |
- echo "LDPATH=${ldpath}" >> "${T}"/40${PN} |
253 |
- doenvd "${T}"/40${PN} |
254 |
- |
255 |
- if use doc; then |
256 |
- insinto /usr/share/doc/${PF}/api-docs |
257 |
- cd "${WORKDIR}"/html |
258 |
- rm *.md5 || die "Failed to remove superfluous hashes" |
259 |
- einfo "Installing API docs. This may take some time." |
260 |
- insinto /usr/share/doc/${PF}/api-docs |
261 |
- doins -r * |
262 |
- fi |
263 |
- |
264 |
- mv "${D}/usr/lib" "${D}/usr/$(get_libdir)" || \ |
265 |
- die 'unable to fix libdir' |
266 |
-} |
267 |
|
268 |
diff --git a/sci-libs/itk/itk-4.4.2-r1.ebuild b/sci-libs/itk/itk-4.4.2-r1.ebuild |
269 |
deleted file mode 100644 |
270 |
index 93a03a5f8..000000000 |
271 |
--- a/sci-libs/itk/itk-4.4.2-r1.ebuild |
272 |
+++ /dev/null |
273 |
@@ -1,135 +0,0 @@ |
274 |
-# Copyright 1999-2015 Gentoo Foundation |
275 |
-# Distributed under the terms of the GNU General Public License v2 |
276 |
- |
277 |
-EAPI=5 |
278 |
- |
279 |
-PYTHON_COMPAT=( python2_7 ) |
280 |
- |
281 |
-inherit eutils toolchain-funcs cmake-utils python-single-r1 |
282 |
- |
283 |
-MYPN=InsightToolkit |
284 |
-MYP=${MYPN}-${PV} |
285 |
- |
286 |
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" |
287 |
-HOMEPAGE="http://www.itk.org" |
288 |
-SRC_URI=" |
289 |
- mirror://sourceforge/${PN}/${MYP}.tar.gz |
290 |
- doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-4.4.0.tar.gz )" |
291 |
-RESTRICT="primaryuri" |
292 |
- |
293 |
-LICENSE="Apache-2.0" |
294 |
-SLOT="0" |
295 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
296 |
-IUSE="debug doc examples fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue" |
297 |
- |
298 |
-RDEPEND=" |
299 |
- sci-libs/hdf5[cxx] |
300 |
- virtual/jpeg:0= |
301 |
- media-libs/libpng:0= |
302 |
- media-libs/tiff:0= |
303 |
- sys-libs/zlib |
304 |
- fftw? ( sci-libs/fftw:3.0 ) |
305 |
- vtkglue? ( sci-libs/vtk ) |
306 |
-" |
307 |
-DEPEND="${RDEPEND} |
308 |
- python? ( |
309 |
- ${PYTHON_DEPS} |
310 |
- >=dev-lang/swig-2.0:0 |
311 |
- >=dev-cpp/gccxml-0.9.0_pre20120309 |
312 |
- ) |
313 |
- doc? ( app-doc/doxygen ) |
314 |
-" |
315 |
- |
316 |
-S="${WORKDIR}/${MYP}" |
317 |
- |
318 |
-pkg_pretend() { |
319 |
- if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then |
320 |
- elog "To tune ITK to make the best use ouf working memory you can set" |
321 |
- elog " ITK_COMPUTER_MEMORY_SIZE=XX" |
322 |
- elog "in make.conf, default is 1 (unit is GB)" |
323 |
- fi |
324 |
- if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then |
325 |
- elog "For Python language bindings, you can define the dimensions" |
326 |
- elog "you want to create bindings for by setting" |
327 |
- elog " ITK_WRAP_DIMS=X;Y;Z..." |
328 |
- elog "in make.conf, default is 2;3 for 2D and 3D data" |
329 |
- fi |
330 |
-} |
331 |
- |
332 |
-src_configure() { |
333 |
- local mycmakeargs=( |
334 |
- -DWRAP_ITK_JAVA=OFF |
335 |
- -DWRAP_ITK_TCL=OFF |
336 |
- -DITK_USE_SYSTEM_HDF5=ON |
337 |
- -DITK_USE_SYSTEM_JPEG=ON |
338 |
- -DITK_USE_SYSTEM_PNG=ON |
339 |
- -DITK_USE_SYSTEM_TIFF=ON |
340 |
- -DITK_USE_SYSTEM_ZLIB=ON |
341 |
- -DITK_USE_SYSTEM_GCCXML=ON |
342 |
- -DITK_USE_SYSTEM_SWIG=ON |
343 |
- -DITK_BUILD_ALL_MODULES=ON |
344 |
- -DBUILD_SHARED_LIBS=ON |
345 |
- -DBUILD_EXAMPLES=OFF |
346 |
- -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" |
347 |
- $(cmake-utils_use_build test TESTING) |
348 |
- $(cmake-utils_use review ITK_USE_REVIEW) |
349 |
- $(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY) |
350 |
- $(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2) |
351 |
- ) |
352 |
- if use fftw; then |
353 |
- mycmakeargs+=( |
354 |
- -DUSE_FFTWD=ON |
355 |
- -DUSE_FFTWF=ON |
356 |
- -DUSE_SYSTEM_FFTW=ON |
357 |
- -DITK_WRAP_double=ON |
358 |
- -DITK_WRAP_vector_double=ON |
359 |
- -DITK_WRAP_covariant_vector_double=ON |
360 |
- -DITK_WRAP_complex_double=ON |
361 |
- ) |
362 |
- fi |
363 |
- if use vtkglue; then |
364 |
- mycmakeargs+=( |
365 |
- -DModule_ITKVtkGlue=ON |
366 |
- ) |
367 |
- fi |
368 |
- if use python; then |
369 |
- mycmakeargs+=( |
370 |
- -DITK_WRAP_PYTHON=ON |
371 |
- -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" |
372 |
- ) |
373 |
- else |
374 |
- mycmakeargs+=( |
375 |
- -DITK_WRAP_PYTHON=OFF |
376 |
- ) |
377 |
- fi |
378 |
- cmake-utils_src_configure |
379 |
-} |
380 |
- |
381 |
-src_install() { |
382 |
- cmake-utils_src_install |
383 |
- |
384 |
- if use examples; then |
385 |
- insinto /usr/share/doc/${PF}/examples |
386 |
- docompress -x /usr/share/doc/${PF}/examples |
387 |
- doins -r "${S}"/Examples/* |
388 |
- fi |
389 |
- |
390 |
- echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN} |
391 |
- local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit" |
392 |
- if use python; then |
393 |
- echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> ${T}/40${PN} |
394 |
- ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" |
395 |
- fi |
396 |
- echo "LDPATH=${ldpath}" >> ${T}/40${PN} |
397 |
- |
398 |
- if use doc; then |
399 |
- insinto "/usr/share/doc/${PF}/api-docs" |
400 |
- cd "${WORKDIR}"/html |
401 |
- rm -f *.md5 || die "Failed to remove superfluous hashes" |
402 |
- einfo "Installing API docs. This may take some time." |
403 |
- insinto "/usr/share/doc/${PF}/api-docs" |
404 |
- doins -r ./* |
405 |
- fi |
406 |
- |
407 |
- doenvd "${T}"/40${PN} |
408 |
-} |
409 |
|
410 |
diff --git a/sci-libs/itk/itk-4.4.2.ebuild b/sci-libs/itk/itk-4.4.2.ebuild |
411 |
deleted file mode 100644 |
412 |
index 2d3b9f961..000000000 |
413 |
--- a/sci-libs/itk/itk-4.4.2.ebuild |
414 |
+++ /dev/null |
415 |
@@ -1,115 +0,0 @@ |
416 |
-# Copyright 1999-2015 Gentoo Foundation |
417 |
-# Distributed under the terms of the GNU General Public License v2 |
418 |
- |
419 |
-EAPI=5 |
420 |
- |
421 |
-PYTHON_COMPAT=( python2_7 ) |
422 |
- |
423 |
-inherit eutils toolchain-funcs cmake-utils python-single-r1 |
424 |
- |
425 |
-MYP=InsightToolkit-${PV} |
426 |
- |
427 |
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" |
428 |
-HOMEPAGE="http://www.itk.org" |
429 |
-SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz" |
430 |
- |
431 |
-LICENSE="Apache-2.0" |
432 |
-SLOT="0" |
433 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
434 |
-IUSE="debug examples fftw itkv3compat python review cpu_flags_x86_sse2 test" |
435 |
- |
436 |
-RDEPEND=" |
437 |
- sci-libs/hdf5[cxx] |
438 |
- virtual/jpeg:0= |
439 |
- media-libs/libpng:0= |
440 |
- media-libs/tiff:0= |
441 |
- sys-libs/zlib |
442 |
- fftw? ( sci-libs/fftw:3.0 ) |
443 |
-" |
444 |
-DEPEND="${RDEPEND} |
445 |
- python? ( |
446 |
- ${PYTHON_DEPS} |
447 |
- >=dev-lang/swig-2.0:0 |
448 |
- >=dev-cpp/gccxml-0.9.0_pre20120309 |
449 |
- ) |
450 |
-" |
451 |
- |
452 |
-S="${WORKDIR}/${MYP}" |
453 |
- |
454 |
-pkg_pretend() { |
455 |
- if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then |
456 |
- elog "To tune ITK to make the best use ouf working memory you can set" |
457 |
- elog " ITK_COMPUTER_MEMORY_SIZE=XX" |
458 |
- elog "in make.conf, default is 1 (unit is GB)" |
459 |
- fi |
460 |
- if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then |
461 |
- elog "For Python language bindings, you can define the dimensions" |
462 |
- elog "you want to create bindings for by setting" |
463 |
- elog " ITK_WRAP_DIMS=X;Y;Z..." |
464 |
- elog "in make.conf, default is 2;3 for 2D and 3D data" |
465 |
- fi |
466 |
-} |
467 |
- |
468 |
-src_configure() { |
469 |
- local mycmakeargs=( |
470 |
- -DWRAP_ITK_JAVA=OFF |
471 |
- -DWRAP_ITK_TCL=OFF |
472 |
- -DITK_USE_SYSTEM_HDF5=ON |
473 |
- -DITK_USE_SYSTEM_JPEG=ON |
474 |
- -DITK_USE_SYSTEM_PNG=ON |
475 |
- -DITK_USE_SYSTEM_TIFF=ON |
476 |
- -DITK_USE_SYSTEM_ZLIB=ON |
477 |
- -DITK_USE_SYSTEM_GCCXML=ON |
478 |
- -DITK_USE_SYSTEM_SWIG=ON |
479 |
- -DITK_BUILD_ALL_MODULES=ON |
480 |
- -DBUILD_SHARED_LIBS=ON |
481 |
- -DBUILD_EXAMPLES=OFF |
482 |
- -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" |
483 |
- $(cmake-utils_use_build test TESTING) |
484 |
- $(cmake-utils_use review ITK_USE_REVIEW) |
485 |
- $(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY) |
486 |
- $(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2) |
487 |
- ) |
488 |
- if use fftw; then |
489 |
- mycmakeargs+=( |
490 |
- -DUSE_FFTWD=ON |
491 |
- -DUSE_FFTWF=ON |
492 |
- -DUSE_SYSTEM_FFTW=ON |
493 |
- -DITK_WRAP_double=ON |
494 |
- -DITK_WRAP_vector_double=ON |
495 |
- -DITK_WRAP_covariant_vector_double=ON |
496 |
- -DITK_WRAP_complex_double=ON |
497 |
- ) |
498 |
- fi |
499 |
- if use python; then |
500 |
- mycmakeargs+=( |
501 |
- -DITK_WRAP_PYTHON=ON |
502 |
- -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" |
503 |
- ) |
504 |
- else |
505 |
- mycmakeargs+=( |
506 |
- -DITK_WRAP_PYTHON=OFF |
507 |
- ) |
508 |
- fi |
509 |
- cmake-utils_src_configure |
510 |
-} |
511 |
- |
512 |
-src_install() { |
513 |
- cmake-utils_src_install |
514 |
- |
515 |
- if use examples; then |
516 |
- insinto /usr/share/doc/${PF}/examples |
517 |
- docompress -x /usr/share/doc/${PF}/examples |
518 |
- doins -r "${S}"/Examples/* |
519 |
- fi |
520 |
- |
521 |
- echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN} |
522 |
- local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit" |
523 |
- if use python; then |
524 |
- echo "PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> ${T}/40${PN} |
525 |
- ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" |
526 |
- fi |
527 |
- echo "LDPATH=${ldpath}" >> ${T}/40${PN} |
528 |
- |
529 |
- doenvd "${T}"/40${PN} |
530 |
-} |
531 |
|
532 |
diff --git a/sci-libs/itk/itk-4.5.1.ebuild b/sci-libs/itk/itk-4.5.1.ebuild |
533 |
deleted file mode 100644 |
534 |
index 199c03659..000000000 |
535 |
--- a/sci-libs/itk/itk-4.5.1.ebuild |
536 |
+++ /dev/null |
537 |
@@ -1,155 +0,0 @@ |
538 |
-# Copyright 1999-2015 Gentoo Foundation |
539 |
-# Distributed under the terms of the GNU General Public License v2 |
540 |
- |
541 |
-EAPI=5 |
542 |
- |
543 |
-PYTHON_COMPAT=( python2_7 ) |
544 |
- |
545 |
-inherit eutils toolchain-funcs cmake-utils python-single-r1 |
546 |
- |
547 |
-MYPN=InsightToolkit |
548 |
-MYP=${MYPN}-${PV} |
549 |
-DOC_PV=4.5.0 |
550 |
- |
551 |
-DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" |
552 |
-HOMEPAGE="http://www.itk.org" |
553 |
-SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.xz |
554 |
- doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-${DOC_PV}.tar.gz )" |
555 |
-RESTRICT="primaryuri" |
556 |
- |
557 |
-LICENSE="Apache-2.0" |
558 |
-SLOT="0" |
559 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
560 |
-IUSE="debug doc examples fftw itkv3compat python review cpu_flags_x86_sse2 test vtkglue" |
561 |
- |
562 |
-RDEPEND=" |
563 |
- dev-libs/double-conversion:0= |
564 |
- media-libs/libpng:0= |
565 |
- media-libs/tiff:0= |
566 |
- sci-libs/dcmtk:0= |
567 |
- sci-libs/hdf5:0=[cxx] |
568 |
- sys-libs/zlib:0= |
569 |
- virtual/jpeg:0= |
570 |
- fftw? ( sci-libs/fftw:3.0= ) |
571 |
- vtkglue? ( sci-libs/vtk:0=[python?] ) |
572 |
-" |
573 |
-DEPEND="${RDEPEND} |
574 |
- python? ( |
575 |
- ${PYTHON_DEPS} |
576 |
- >=dev-lang/swig-2.0:0 |
577 |
- >=dev-cpp/gccxml-0.9.0_pre20120309 |
578 |
- ) |
579 |
- doc? ( app-doc/doxygen ) |
580 |
-" |
581 |
- |
582 |
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" |
583 |
- |
584 |
-S="${WORKDIR}/${MYP}" |
585 |
- |
586 |
-PATCHES=( |
587 |
- "${FILESDIR}"/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch |
588 |
- "${FILESDIR}"/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch |
589 |
- "${FILESDIR}"/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch |
590 |
- "${FILESDIR}"/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch |
591 |
- "${FILESDIR}"/0005-make-gdcm-helper-library-static.patch |
592 |
- "${FILESDIR}"/nrrdio-linking.patch |
593 |
-) |
594 |
- |
595 |
-pkg_pretend() { |
596 |
- if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then |
597 |
- elog "To tune ITK to make the best use of working memory you can set" |
598 |
- elog " ITK_COMPUTER_MEMORY_SIZE=XX" |
599 |
- elog "in make.conf, default is 1 (unit is GB)" |
600 |
- fi |
601 |
- if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then |
602 |
- elog "For Python language bindings, you can define the dimensions" |
603 |
- elog "you want to create bindings for by setting" |
604 |
- elog " ITK_WRAP_DIMS=X;Y;Z..." |
605 |
- elog "in make.conf, default is 2;3 for 2D and 3D data" |
606 |
- fi |
607 |
-} |
608 |
- |
609 |
-src_configure() { |
610 |
- sed -i \ |
611 |
- -e '/find_package/d' \ |
612 |
- Modules/ThirdParty/DoubleConversion/CMakeLists.txt || die |
613 |
- |
614 |
- local mycmakeargs=( |
615 |
- -DBUILD_SHARED_LIBS=ON |
616 |
- -DITK_USE_SYSTEM_DCMTK=ON |
617 |
- -DITK_USE_SYSTEM_DOUBLECONVERSION=ON |
618 |
- -DITK_USE_SYSTEM_GCCXML=ON |
619 |
- -DITK_USE_SYSTEM_HDF5=ON |
620 |
- -DITK_USE_SYSTEM_JPEG=ON |
621 |
- -DITK_USE_SYSTEM_PNG=ON |
622 |
- -DITK_USE_SYSTEM_SWIG=ON |
623 |
- -DITK_USE_SYSTEM_TIFF=ON |
624 |
- -DITK_USE_SYSTEM_ZLIB=ON |
625 |
- -DITK_BUILD_DEFAULT_MODULES=ON |
626 |
- -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" |
627 |
- -DWRAP_ITK_JAVA=OFF |
628 |
- -DWRAP_ITK_TCL=OFF |
629 |
- -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" |
630 |
- -Ddouble-conversion_LIBRARIES="-ldouble-conversion" |
631 |
- $(cmake-utils_use_build test TESTING) |
632 |
- $(cmake-utils_use_build examples EXAMPLES) |
633 |
- $(cmake-utils_use review ITK_USE_REVIEW) |
634 |
- $(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY) |
635 |
- $(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2) |
636 |
- ) |
637 |
- if use fftw; then |
638 |
- mycmakeargs+=( |
639 |
- -DUSE_FFTWD=ON |
640 |
- -DUSE_FFTWF=ON |
641 |
- -DUSE_SYSTEM_FFTW=ON |
642 |
- -DITK_WRAP_double=ON |
643 |
- -DITK_WRAP_vector_double=ON |
644 |
- -DITK_WRAP_covariant_vector_double=ON |
645 |
- -DITK_WRAP_complex_double=ON |
646 |
- ) |
647 |
- fi |
648 |
- if use vtkglue; then |
649 |
- mycmakeargs+=( |
650 |
- -DModule_ITKVtkGlue=ON |
651 |
- ) |
652 |
- fi |
653 |
- if use python; then |
654 |
- mycmakeargs+=( |
655 |
- -DITK_WRAP_PYTHON=ON |
656 |
- -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" |
657 |
- ) |
658 |
- else |
659 |
- mycmakeargs+=( |
660 |
- -DITK_WRAP_PYTHON=OFF |
661 |
- ) |
662 |
- fi |
663 |
- cmake-utils_src_configure |
664 |
-} |
665 |
- |
666 |
-src_install() { |
667 |
- cmake-utils_src_install |
668 |
- |
669 |
- if use examples; then |
670 |
- insinto /usr/share/doc/${PF}/examples |
671 |
- docompress -x /usr/share/doc/${PF}/examples |
672 |
- doins -r "${S}"/Examples/* |
673 |
- fi |
674 |
- |
675 |
- echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN} |
676 |
- local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit" |
677 |
- if use python; then |
678 |
- echo "PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} |
679 |
- ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" |
680 |
- fi |
681 |
- echo "LDPATH=${ldpath}" >> "${T}"/40${PN} |
682 |
- doenvd "${T}"/40${PN} |
683 |
- |
684 |
- if use doc; then |
685 |
- insinto /usr/share/doc/${PF}/api-docs |
686 |
- cd "${WORKDIR}"/html |
687 |
- rm *.md5 || die "Failed to remove superfluous hashes" |
688 |
- einfo "Installing API docs. This may take some time." |
689 |
- insinto /usr/share/doc/${PF}/api-docs |
690 |
- doins -r * |
691 |
- fi |
692 |
-} |
693 |
|
694 |
diff --git a/sci-libs/itk/itk-5.0_rc1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild |
695 |
similarity index 69% |
696 |
rename from sci-libs/itk/itk-5.0_rc1.ebuild |
697 |
rename to sci-libs/itk/itk-5.0.1.ebuild |
698 |
index f6433e551..e1ec7166a 100644 |
699 |
--- a/sci-libs/itk/itk-5.0_rc1.ebuild |
700 |
+++ b/sci-libs/itk/itk-5.0.1.ebuild |
701 |
@@ -1,19 +1,26 @@ |
702 |
# Copyright 1999-2019 Gentoo Authors |
703 |
# Distributed under the terms of the GNU General Public License v2 |
704 |
|
705 |
-EAPI=6 |
706 |
+EAPI=7 |
707 |
|
708 |
PYTHON_COMPAT=( python2_7 python3_{5,6,7} ) |
709 |
|
710 |
-inherit eutils toolchain-funcs cmake-utils python-single-r1 |
711 |
+inherit toolchain-funcs cmake-utils python-single-r1 |
712 |
|
713 |
-MY_PV="5.0rc01" |
714 |
+MY_PN="InsightToolkit" |
715 |
+MY_P="${MY_PN}-${PV}" |
716 |
+GLI_HASH="187ab99b7d42718c99e5017f0acd3900d7469bd1" |
717 |
+GLI_TEST_HASH="57b5d5de8d777f10f269445a" |
718 |
|
719 |
DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" |
720 |
HOMEPAGE="http://www.itk.org" |
721 |
SRC_URI=" |
722 |
- https://github.com/InsightSoftwareConsortium/ITK/archive/v${MY_PV}.tar.gz |
723 |
- test? ( https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc01/InsightData-${MY_PV}.tar.gz ) |
724 |
+ https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz |
725 |
+ https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip -> ITKGenericLabelInterpolator-${PV}.zip |
726 |
+ test? ( |
727 |
+ https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip |
728 |
+ https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz |
729 |
+ ) |
730 |
" |
731 |
RESTRICT="primaryuri" |
732 |
|
733 |
@@ -21,6 +28,9 @@ LICENSE="Apache-2.0" |
734 |
SLOT="0" |
735 |
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
736 |
IUSE="debug doc examples fftw python review test vtkglue" |
737 |
+# python will not work, this is a know issue upstream: |
738 |
+# https://github.com/InsightSoftwareConsortium/ITK/issues/1229 |
739 |
+# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10 |
740 |
|
741 |
RDEPEND=" |
742 |
dev-libs/double-conversion:0= |
743 |
@@ -32,20 +42,25 @@ RDEPEND=" |
744 |
sys-libs/zlib:0= |
745 |
virtual/jpeg:0= |
746 |
fftw? ( sci-libs/fftw:3.0= ) |
747 |
- vtkglue? ( sci-libs/vtk:0=[python?] ) |
748 |
+ vtkglue? ( sci-libs/vtk:0=[rendering,python?] ) |
749 |
" |
750 |
DEPEND="${RDEPEND} |
751 |
+ sys-apps/coreutils |
752 |
python? ( |
753 |
- ${PYTHON_DEPS} |
754 |
>=dev-lang/swig-2.0:0 |
755 |
- >=dev-cpp/gccxml-0.9.0_pre20120309 |
756 |
+ dev-cpp/castxml |
757 |
) |
758 |
doc? ( app-doc/doxygen ) |
759 |
" |
760 |
|
761 |
REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" |
762 |
|
763 |
-S="${WORKDIR}/ITK-${MY_PV}" |
764 |
+S="${WORKDIR}/${MY_P}" |
765 |
+ |
766 |
+PATCHES=( |
767 |
+ "${FILESDIR}"/ITKModuleRemote.patch |
768 |
+ "${FILESDIR}"/tests.patch |
769 |
+) |
770 |
|
771 |
pkg_pretend() { |
772 |
if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then |
773 |
@@ -64,14 +79,23 @@ pkg_pretend() { |
774 |
src_prepare() { |
775 |
sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\ |
776 |
Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt |
777 |
- default |
778 |
+ ln -sr ../ITKGenericLabelInterpolator-* Modules/Remote/ITKGenericLabelInterpolator || die |
779 |
+ if use test; then |
780 |
+ for filename in ../GenericLabelInterpolator/test/*/*mha; do |
781 |
+ MD5=$(md5sum $filename) || die |
782 |
+ MD5=${MD5% *} || die |
783 |
+ cp "$filename" ".ExternalData/MD5/${MD5}" || die |
784 |
+ done |
785 |
+ fi |
786 |
+ cmake-utils_src_prepare |
787 |
} |
788 |
|
789 |
src_configure() { |
790 |
local mycmakeargs=( |
791 |
-DBUILD_SHARED_LIBS=ON |
792 |
- -DITK_USE_SYSTEM_DCMTK=ON |
793 |
-DGDCM_USE_SYSTEM_OPENJPEG=ON |
794 |
+ -DITK_FORBID_DOWNLOADS:BOOL=OFF |
795 |
+ -DITK_USE_SYSTEM_DCMTK=ON |
796 |
-DITK_USE_SYSTEM_DOUBLECONVERSION=ON |
797 |
-DITK_USE_SYSTEM_CASTXML=ON |
798 |
-DITK_USE_SYSTEM_HDF5=ON |
799 |
@@ -86,7 +110,9 @@ src_configure() { |
800 |
-DWRAP_ITK_JAVA=OFF |
801 |
-DWRAP_ITK_TCL=OFF |
802 |
-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" |
803 |
- -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${MY_PV}/.ExternalData" |
804 |
+ -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData" |
805 |
+ -DModule_GenericLabelInterpolator:BOOL=ON |
806 |
+ -DModule_ITKReview:BOOL=ON |
807 |
-DBUILD_TESTING="$(usex test ON OFF)" |
808 |
-DBUILD_EXAMPLES="$(usex examples ON OFF)" |
809 |
-DITK_USE_REVIEW="$(usex review ON OFF)" |
810 |
|
811 |
diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml |
812 |
index 8485fb7e1..7c4535324 100644 |
813 |
--- a/sci-libs/itk/metadata.xml |
814 |
+++ b/sci-libs/itk/metadata.xml |
815 |
@@ -14,7 +14,6 @@ that provides developers with an extensive suite of tools for image |
816 |
analysis. |
817 |
</longdescription> |
818 |
<use> |
819 |
- <flag name="itkv3compat">Enable compatibility with ITK version 3</flag> |
820 |
<flag name="review">Enable compilation of methods under review</flag> |
821 |
<flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag> |
822 |
</use> |