subject:"\[gentoo\-commits\] proj\/sci\:master commit in\: sci\-libs\/itk\/"

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2024-01-22 Thread Horea Christian

commit: 2e700f2156b19ec5346a1edd225def74b2212692
Author: Horea Christian  chymera  eu>
AuthorDate: Mon Jan 22 11:57:52 2024 +
Commit: Horea Christian  gmail  com>
CommitDate: Mon Jan 22 11:57:52 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e700f21

sci-libs/itk: updated dependency name

Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/itk-5.2.1-r2.ebuild | 2 +-
 sci-libs/itk/itk-5.3.0-r1.ebuild | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
index 1aa0dc43a..0b1f25860 100644
--- a/sci-libs/itk/itk-5.2.1-r2.ebuild
+++ b/sci-libs/itk/itk-5.2.1-r2.ebuild
@@ -71,7 +71,7 @@ DEPEND="${RDEPEND}
>=dev-lang/swig-2.0:0
dev-libs/castxml
)
-   doc? ( app-doc/doxygen )
+   doc? ( app-text/doxygen )
 "
 BDEPEND="
test? (

diff --git a/sci-libs/itk/itk-5.3.0-r1.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild
index 29a3da5d0..b2c3af801 100644
--- a/sci-libs/itk/itk-5.3.0-r1.ebuild
+++ b/sci-libs/itk/itk-5.3.0-r1.ebuild
@@ -79,7 +79,7 @@ DEPEND="${RDEPEND}
>=dev-lang/swig-2.0:0
dev-libs/castxml
)
-   doc? ( app-doc/doxygen )
+   doc? ( app-text/doxygen )
 "
 BDEPEND="
test? (

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

2023-05-12 Thread Horea Christian

commit: 3d21154c5c99a552d9a79c651f09de25594a88b0
Author: Horea Christian  chymera  eu>
AuthorDate: Sat May 13 01:29:30 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Sat May 13 01:30:58 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3d21154c

sci-libs/itk: patch for newer gcc

Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/files/itk-5.3.0-uint8.patch | 10 ++
 sci-libs/itk/itk-5.3.0-r1.ebuild |  2 ++
 2 files changed, 12 insertions(+)

diff --git a/sci-libs/itk/files/itk-5.3.0-uint8.patch 
b/sci-libs/itk/files/itk-5.3.0-uint8.patch
new file mode 100644
index 0..724314574
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.3.0-uint8.patch
@@ -0,0 +1,10 @@
+--- 
a/Modules/Filtering/MathematicalMorphology/include/itkMathematicalMorphologyEnums.h
 
b/Modules/Filtering/MathematicalMorphology/include/itkMathematicalMorphologyEnums.h
+@@ -20,6 +20,7 @@
+ 
+ #include 
+ #include "ITKMathematicalMorphologyExport.h"
++#include 
+ 
+ 
+ namespace itk

diff --git a/sci-libs/itk/itk-5.3.0-r1.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild
index 23f3341a2..29a3da5d0 100644
--- a/sci-libs/itk/itk-5.3.0-r1.ebuild
+++ b/sci-libs/itk/itk-5.3.0-r1.ebuild
@@ -92,9 +92,11 @@ BDEPEND="
 
 S="${WORKDIR}/${MY_P}"
 
+# uint patch applied by upstream for next release.
 PATCHES=(
"${FILESDIR}/${PN}-5.2.1-system-tiff-has-64.patch"
"${FILESDIR}/${PN}-5.3.0-system-openjpeg.patch"
+   "${FILESDIR}/${PN}-5.3.0-uint8.patch"
 )
 
 pkg_pretend() {

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2023-04-25 Thread Horea Christian

commit: 4b6c2d0f2f073a6ab463a6d2e0d5b64158068f63
Author: Horea Christian  chymera  eu>
AuthorDate: Tue Apr 25 15:33:37 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Tue Apr 25 15:33:37 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4b6c2d0f

sci-libs/itk: add github upstream metadata

Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/metadata.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml
index c41202e23..5da2678ec 100644
--- a/sci-libs/itk/metadata.xml
+++ b/sci-libs/itk/metadata.xml
@@ -19,6 +19,7 @@
PLEASE FIX MY DESCRIPTION


+   InsightSoftwareConsortium/ITK
itk

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2023-04-25 Thread Horea Christian

commit: fe9ed998b6cd324186a0da2f95322eea670fa666
Author: Horea Christian  chymera  eu>
AuthorDate: Tue Apr 25 15:31:01 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Tue Apr 25 15:31:01 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=fe9ed998

sci-libs/itk: sci-libs/hdf5 fixed in ::gentoo

Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/itk-5.2.1-r2.ebuild | 2 +-
 sci-libs/itk/itk-5.3.0-r1.ebuild | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
index 201f730e9..1aa0dc43a 100644
--- a/sci-libs/itk/itk-5.2.1-r2.ebuild
+++ b/sci-libs/itk/itk-5.2.1-r2.ebuild
@@ -52,7 +52,7 @@ RDEPEND="
media-libs/libpng:0=
media-libs/tiff:0=[jpeg]
sci-libs/dcmtk:0=
-

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2023-04-19 Thread Horea Christian

commit: 43e9ae1e3074b5435ed823d7121902dd95db810e
Author: Horea Christian  chymera  eu>
AuthorDate: Thu Apr 20 03:12:40 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Thu Apr 20 03:12:40 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=43e9ae1e

sci-libs/itk: enable py3.11

Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/itk-5.2.1-r2.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
index f5ddff7fd..201f730e9 100644
--- a/sci-libs/itk/itk-5.2.1-r2.ebuild
+++ b/sci-libs/itk/itk-5.2.1-r2.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..11} )
 VIRTUALX_REQUIRED="manual"
 
 inherit cmake python-single-r1 virtualx

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2023-04-19 Thread Horea Christian

commit: 3f2aee8f5efbcf9301c98133bf56daaf2767ded6
Author: Horea Christian  chymera  eu>
AuthorDate: Thu Apr 20 03:10:17 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Thu Apr 20 03:10:17 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f2aee8f

sci-libs/itk: not compatible with =sci-libs/hdf5-1.14.0

Bug #904691

Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/itk-5.2.1-r2.ebuild | 2 +-
 sci-libs/itk/itk-5.3.0-r1.ebuild | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
index c7519fb6f..f5ddff7fd 100644
--- a/sci-libs/itk/itk-5.2.1-r2.ebuild
+++ b/sci-libs/itk/itk-5.2.1-r2.ebuild
@@ -52,7 +52,7 @@ RDEPEND="
media-libs/libpng:0=
media-libs/tiff:0=[jpeg]
sci-libs/dcmtk:0=
-   sci-libs/hdf5:0=[cxx]
+

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2023-04-02 Thread Horea Christian

commit: c56ebffd2bbb74f5edd5133b89f0347a7ba72e21
Author: Horea Christian  chymera  eu>
AuthorDate: Mon Apr  3 02:57:41 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Mon Apr  3 02:57:41 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c56ebffd

sci-libs/itk: revbump fixing module build and deps

Signed-off-by: Horea Christian  chymera.eu>

 .../itk/{itk-5.3.0.ebuild => itk-5.3.0-r1.ebuild}  | 48 ++
 1 file changed, 32 insertions(+), 16 deletions(-)

diff --git a/sci-libs/itk/itk-5.3.0.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild
similarity index 89%
rename from sci-libs/itk/itk-5.3.0.ebuild
rename to sci-libs/itk/itk-5.3.0-r1.ebuild
index 54b7c89b3..23f3341a2 100644
--- a/sci-libs/itk/itk-5.3.0.ebuild
+++ b/sci-libs/itk/itk-5.3.0-r1.ebuild
@@ -8,8 +8,6 @@ VIRTUALX_REQUIRED="manual"
 
 inherit cmake python-single-r1 virtualx
 
-# rsync: [sender] link_stat 
"/distfiles/1c/itk-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
 (in gentoo) failed: No such file or directory (2)
-
 MY_PN="InsightToolkit"
 MY_P="${MY_PN}-${PV}"
 GLI_V="1.2.0"
@@ -29,7 +27,7 @@ DESCRIPTION="NLM Insight Segmentation and Registration 
Toolkit"
 HOMEPAGE="https://itk.org;
 SRC_URI="

https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
-   
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/refs/tags/v${GLI_V}.tar.gz
 -> ITKGenericLabelInterpolator-${GLI_V}
+   
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/refs/tags/v${GLI_V}.tar.gz
 -> ITKGenericLabelInterpolator-${GLI_V}.tar.gz

https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> 
ITKAdaptiveDenoising-${PV}.tar.gz
test? (

https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
@@ -50,15 +48,16 @@ RDEPEND="
dev-cpp/eigen:3
dev-libs/double-conversion:0=
dev-libs/expat:0=
-   media-libs/openjpeg:2
+   dev-libs/icu:0=
+   media-libs/libjpeg-turbo:0=
media-libs/libpng:0=
+   media-libs/openjpeg:2
media-libs/tiff:0=[jpeg]
sci-libs/dcmtk:0=
-   sci-libs/hdf5:0=[cxx]
sci-libs/gdcm:0=
-   sys-libs/zlib:0=
-   media-libs/libjpeg-turbo:0=
-   fftw? ( sci-libs/fftw:3.0= )
+   sci-libs/hdf5:0=[cxx]
+   sys-libs/zlib-ng
+   fftw? ( sci-libs/fftw:3.0=[threads] )
vtkglue? (
sci-libs/vtk:0=[rendering]
python? (
@@ -67,6 +66,13 @@ RDEPEND="
)
python? ( ${PYTHON_DEPS} )
 "
+# Might also need:
+# dev-libs/kwsys::guru
+# kwiml
+# minc
+# metaio
+# niftilib
+# sci-lib/vxl::science
 DEPEND="${RDEPEND}
sys-apps/coreutils
python? (
@@ -117,6 +123,7 @@ src_prepare() {
OpenJPEG/src/openjpeg
PNG/src/itkpng
TIFF/src/itktiff
+   ZLIB/src/itkzlib-ng
)
local x
for x in "${DROPS[@]}"; do
@@ -130,7 +137,7 @@ src_prepare() {
} | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die
 
# Remote modules
-   ln -sr "../ITKGenericLabelInterpolator-${GLI_HASH}" 
Modules/External/ITKGenericLabelInterpolator || die
+   ln -sr "../ITKGenericLabelInterpolator-${GLI_V}" 
Modules/External/ITKGenericLabelInterpolator || die
ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" 
Modules/External/ITKAdaptiveDenoising || die
 
cmake_src_prepare
@@ -158,6 +165,7 @@ src_configure() {
-DITK_FORBID_DOWNLOADS:BOOL=ON
-DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
-DITK_USE_REVIEW="$(usex review ON OFF)"
+   -DITK_USE_SYSTEM_ICU=ON
-DITK_USE_SYSTEM_DCMTK=ON
-DITK_USE_SYSTEM_DOUBLECONVERSION=ON
-DITK_USE_SYSTEM_CASTXML=ON
@@ -183,14 +191,24 @@ src_configure() {
)
if use fftw; then
mycmakeargs+=(
-   -DUSE_FFTWD=ON
-   -DUSE_FFTWF=ON
-   -DUSE_SYSTEM_FFTW=ON
+   -DITK_USE_FFTWD:BOOL=ON
+   -DITK_USE_FFTWF:BOOL=ON
+   -DITK_USE_SYSTEM_FFTW:BOOL=ON
-DITK_WRAP_double=ON
-DITK_WRAP_vector_double=ON
-DITK_WRAP_covariant_vector_double=ON
-DITK_WRAP_complex_double=ON
)
+   else
+   mycmakeargs+=(
+   -DITK_USE_FFTWD:BOOL=OFF
+   -DITK_USE_FFTWF:BOOL=OFF
+   -DITK_USE_SYSTEM_FFTW:BOOL=OFF
+   -DITK_WRAP_double=OFF
+   -DITK_WRAP_vector_double=OFF
+   -DITK_WRAP_covariant_vector_double=OFF
+

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

2023-03-24 Thread Horea Christian

commit: d23b080b9afe74c6590a9827d505e9234c00deb0
Author: Horea Christian  chymera  eu>
AuthorDate: Sat Mar 25 01:48:55 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Sat Mar 25 01:48:55 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d23b080b

sci-libs/itk: add 5.3.0

Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch | 550 +
 sci-libs/itk/itk-5.3.0.ebuild  | 251 ++
 2 files changed, 801 insertions(+)

diff --git a/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch 
b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch
new file mode 100644
index 0..27f139553
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch
@@ -0,0 +1,550 @@
+--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
 b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+@@ -1,16 +1,32 @@
+ project(ITKOpenJPEG)
+ set(ITKOpenJPEG_THIRD_PARTY 1)
+ 
+-set(ITKOpenJPEG_INCLUDE_DIRS
+-  ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
+-  ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
+-  )
+-set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" 
${ITK_USE_SYSTEM_LIBRARIES})
++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG)
++
++if(ITK_USE_SYSTEM_OPENJPEG)
++  find_package(OpenJPEG REQUIRED)
++  set(ITKOpenJPEG_INCLUDE_DIRS
++${ITKOpenJPEG_BINARY_DIR}/src
++)
++  set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS
++${OPENJPEG_INCLUDE_DIRS}
++)
++  set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}")
++  set(ITKOpenJPEG_NO_SRC 1)
++else()
++  set(ITKOpenJPEG_INCLUDE_DIRS
++${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
++${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
++)
++  set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++endif()
++
++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h)
+ set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE)
+-
+ itk_module_impl()
+ 
+-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h
++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h
+   DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR}
+   COMPONENT Development
+   )
+diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h 
b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
+rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
 b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+@@ -25,6 +25,12 @@
+ #ifndef itk_openjpeg_h
+ #define itk_openjpeg_h
+ 
+-#include 
++/* Use the openjpeg library configured for ITK.  */
++#cmakedefine ITK_USE_SYSTEM_OPENJPEG
++#ifdef ITK_USE_SYSTEM_OPENJPEG
++# include 
++#else
++# include 
++#endif
+ 
+ #endif
+--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
 b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
+@@ -27,8 +27,6 @@
+ extern "C"
+ {
+ #include "openjpeg.h"
+-#include "j2k.h"
+-#include "jp2.h"
+ }
+ 
+ 
+@@ -139,11 +137,11 @@
+ {
+   itkDebugMacro(<< "ReadImageInformation()");
+ 
+-  FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+-  /* decompression parameters */
++  /* set decoding parameters to default values */
++  
opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+ 
+-  if (!l_file)
++  opj_stream_t * cio = 
opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
++  if (!cio)
+   {
+ itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << 
this->GetFileName() << std::endl
+   << 
"Reason: "
+@@ -151,10 +149,5 @@
+   }
+ 
+-  /* set decoding parameters to default values */
+-  
opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+-
+-  opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true);
+-
+   this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */
+ 
+   opj_image_t * l_image = nullptr;
+@@ -188,9 +181,8 @@
+ 
+   /* get a decoder handle */
+-  this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++  this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+   if (!this->m_Internal->m_Dinfo)
+   {
+ opj_stream_destroy(cio);
+-fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+   << this->GetFileName() << std::endl
+@@ -202,10 +194,9 @@
+ {
+   /* JPEG 2000 compressed image data */
+   /* get a decoder handle */
+-  this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++  this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+   if (!this->m_Internal->m_Dinfo)
+   {
+ opj_stream_destroy(cio);
+-fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+   << this->GetFileName() << std::endl
+@@ -217,10 +208,9 @@
+ {
+   /* JPEG 2000, JPIP

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

2022-09-30 Thread Andrew Ammerlaan

commit: 76b20521901742c59aa823035357a3a49ebb0aad
Author: François-Xavier Carton  gmail  com>
AuthorDate: Thu Sep 29 18:08:30 2022 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Fri Sep 30 06:49:55 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=76b20521

sci-libs/itk: add upstream patch to fix building tests

Needed since commit b6218b "sci-libs/itk: add AdaptiveDenoising module"
because the commit used for that remote module is too recent and needs
that ITK commit.

Signed-off-by: François-Xavier Carton  gmail.com>
Closes: https://github.com/gentoo/sci/pull/1172
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch  | 54 ++
 .../{itk-5.2.1-r1.ebuild => itk-5.2.1-r2.ebuild}   |  0
 2 files changed, 54 insertions(+)

diff --git a/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch 
b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
index 2e547d9ca..2af8c4998 100644
--- a/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
+++ b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch
@@ -1,6 +1,7 @@
 
https://github.com/InsightSoftwareConsortium/ITK/commit/2a7f5ed199926999b67f61a97c2c9a2595a11558.patch
 
https://github.com/InsightSoftwareConsortium/ITK/commit/0c31aa688e82a34e5430873bc6176740fd09ad75.patch
 
https://github.com/InsightSoftwareConsortium/ITK/commit/28325d921a9b8793e6aaefd612f53989f951d19c.patch
+https://github.com/InsightSoftwareConsortium/ITK/commit/aafd1f9631d0fad60e1b6f53e049e95a50c48bd1.patch
 
 From 2a7f5ed199926999b67f61a97c2c9a2595a11558 Mon Sep 17 00:00:00 2001
 From: Niels Dekker 
@@ -253,3 +254,56 @@ index fca3d999b87..3b7a1d37334 100644
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py 
${python_check})
execute_process(COMMAND "${Python3_EXECUTABLE}" 
"${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py"
  OUTPUT_VARIABLE py_spp
+From aafd1f9631d0fad60e1b6f53e049e95a50c48bd1 Mon Sep 17 00:00:00 2001
+From: Hans Johnson 
+Date: Wed, 15 Dec 2021 08:10:58 -0600
+Subject: [PATCH] COMP: Remove inclusion of .hxx files as headers
+
+The ability to include either .h or .hxx files as
+header files required recursively reading the
+.h files twice.  The added complexity is
+unnecessary, costly, and can confuse static
+analysis tools that monitor header guardes (due
+to reaching the maximum depth of recursion
+limits for nested #ifdefs in checking).
+
+Co-authored-by: Simon Rit 
+---
+ CMake/ITKModuleHeaderTest.cmake  | 3 +--
+ Utilities/Maintenance/BuildHeaderTest.py | 4 
+ 2 files changed, 1 insertion(+), 6 deletions(-)
+
+diff --git a/CMake/ITKModuleHeaderTest.cmake b/CMake/ITKModuleHeaderTest.cmake
+index eb809d7e93d..82ad192a6f8 100644
+--- a/CMake/ITKModuleHeaderTest.cmake
 b/CMake/ITKModuleHeaderTest.cmake
+@@ -36,8 +36,7 @@ macro( itk_module_headertest _name )
+ # effected.
+ set( _include ${${_name}_SOURCE_DIR}/include )
+ file( GLOB _h_files ${_include}/*.h )
+-file( GLOB _hxx_files ${_include}/*.hxx )
+-set( _header_files ${_h_files} ${_hxx_files} )
++set( _header_files ${_h_files} )
+ list( LENGTH _h_files _num_headers )
+ set( _outputs ${${_name}_BINARY_DIR}/test/${_name}HeaderTest1.cxx )
+ set( _test_num 1 )
+diff --git a/Utilities/Maintenance/BuildHeaderTest.py 
b/Utilities/Maintenance/BuildHeaderTest.py
+index 26a4b6ccb3f..f8ed9f7901e 100755
+--- a/Utilities/Maintenance/BuildHeaderTest.py
 b/Utilities/Maintenance/BuildHeaderTest.py
+@@ -130,15 +130,11 @@ def main():
+ else:
+ max_idx = added_header_idx + maximum_number_of_headers
+ for i in range(added_header_idx, max_idx):
+-# Use the .hxx if possible.
+-hxx_file = h_files[i][:-1] + "hxx"
+ # Files that include VTK headers need to link to VTK.
+ if h_files[i] in BANNED_HEADERS or h_files[i].lower().find("vtk") 
!= -1:
+ to_include = (
+ '// #include "' + h_files[i] + '" // Banned in 
BuildHeaderTest.py\n'
+ )
+-elif os.path.exists(os.path.join(module_source_path, "include", 
hxx_file)):
+-to_include = '#include "' + hxx_file + '"\n'
+ else:
+ to_include = '#include "' + h_files[i] + '"\n'
+ 

diff --git a/sci-libs/itk/itk-5.2.1-r1.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
similarity index 100%
rename from sci-libs/itk/itk-5.2.1-r1.ebuild
rename to sci-libs/itk/itk-5.2.1-r2.ebuild

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

2022-09-15 Thread Andrew Ammerlaan

commit: 9ff3b1053e275f3a30fa574c79f3ee1af8cbeca0
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Thu Sep 15 11:09:45 2022 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Thu Sep 15 11:09:45 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ff3b105

Revert "sci-libs/itk: add 5.1.0"

This reverts commit 42b8aadc9ce1de416e55dba98c3ba02a0177366f.

Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-libs/itk/files/itk-5.1.0-downloads.patch  |  20 ---
 sci-libs/itk/files/itk-5.1.0-include_limits.patch |  10 --
 sci-libs/itk/files/tests.patch|  41 -
 sci-libs/itk/itk-5.1.0.ebuild | 191 --
 4 files changed, 262 deletions(-)

diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch 
b/sci-libs/itk/files/itk-5.1.0-downloads.patch
deleted file mode 100644
index 34fdb76d1..0
--- a/sci-libs/itk/files/itk-5.1.0-downloads.patch
+++ /dev/null
@@ -1,20 +0,0 @@
 a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
-+++ b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
-@@ -11,7 +11,7 @@
-
- macro(itk_download_attempt_check _name)
-   if(ITK_FORBID_DOWNLOADS)
--message(SEND_ERROR "Attempted to download ${_name} when 
ITK_FORBID_DOWNLOADS is ON")
-+message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS 
is ON")
-   endif()
- endmacro()
-
 a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 
14:30:53.0 -0400
-+++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 
14:30:53.0 -0400
-@@ -44,6 +44,4 @@
- itk_fetch_module(GenericLabelInterpolator
-   "A generic interpolator for multi-label images."
-   MODULE_COMPLIANCE_LEVEL 2
--  GIT_REPOSITORY 
${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
--  GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
-   )

diff --git a/sci-libs/itk/files/itk-5.1.0-include_limits.patch 
b/sci-libs/itk/files/itk-5.1.0-include_limits.patch
deleted file mode 100644
index 9a8fae820..0
--- a/sci-libs/itk/files/itk-5.1.0-include_limits.patch
+++ /dev/null
@@ -1,10 +0,0 @@
 
a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-+++ 
a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
-@@ -16,6 +16,7 @@
-
- #include "gdcmImageToImageFilter.h"
- #include "gdcmPhotometricInterpretation.h"
-+#include 
-
- namespace gdcm
- {

diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
deleted file mode 100644
index c24714e4d..0
--- a/sci-libs/itk/files/tests.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-Known to fail by upstream:
-https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
-
 a/Modules/Bridge/VtkGlue/test/CMakeLists.txt   2019-09-09 
00:45:14.736032139 +0200
-+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt   2019-09-09 
00:49:42.183935497 +0200
-@@ -7,8 +7,6 @@
- if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
-   list(APPEND ITKVtkGlueTests
- itkVtkMedianFilterTest.cxx
--itkVtkConnectedComponentImageFilterTest.cxx
--QuickViewTest.cxx
- # ### runViewImage ###
- # No test generated. Use it for view images (2D or 3D) with:
- # ITKVtkGlueTestDriver runViewImage image_file
-@@ -40,26 +38,3 @@
-   NAME itkVTKImageToImageFilterTest
-   COMMAND ITKVtkGlueTestDriver
- itkVTKImageToImageFilterTest)
--
--if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
--  itk_add_test(
--NAME itkVtkMedianImageFilterTest
--COMMAND ITKVtkGlueTestDriver
--  itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2)
--  set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS 
REQUIRES_DISPLAY)
--
--  itk_add_test(
--NAME QuickViewTest
--COMMAND ITKVtkGlueTestDriver
-- --compare DATA{Baseline/QuickViewTest.png,:}
--   ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png
-- --compareNumberOfPixelsTolerance 1500
--  QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} 
${ITK_TEST_OUTPUT_DIR})
--  set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
--
--  itk_add_test(
--NAME itkVtkConnectedComponentImageFilterTest
--COMMAND ITKVtkGlueTestDriver
--  itkVtkConnectedComponentImageFilterTest 
DATA{${ITK_DATA_ROOT}/Input/cthead1.png})
--  set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY 
LABELS REQUIRES_DISPLAY)
--endif()

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
deleted file mode 100644
index 34d2c215d..0
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ /dev/null
@@ -1,191 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit cmake python-single-r1
-

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2022-09-15 Thread Andrew Ammerlaan

commit: b6218b8bd67305fbc671219a8f694e29a64a5008
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Thu Sep 15 11:12:29 2022 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Thu Sep 15 11:12:29 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b6218b8b

sci-libs/itk: add AdaptiveDenoising module

Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-libs/itk/{itk-5.2.1.ebuild => itk-5.2.1-r1.ebuild} | 4 
 1 file changed, 4 insertions(+)

diff --git a/sci-libs/itk/itk-5.2.1.ebuild b/sci-libs/itk/itk-5.2.1-r1.ebuild
similarity index 95%
rename from sci-libs/itk/itk-5.2.1.ebuild
rename to sci-libs/itk/itk-5.2.1-r1.ebuild
index 25292269f..98e39935e 100644
--- a/sci-libs/itk/itk-5.2.1.ebuild
+++ b/sci-libs/itk/itk-5.2.1-r1.ebuild
@@ -11,6 +11,7 @@ inherit cmake python-single-r1 virtualx
 MY_PN="InsightToolkit"
 MY_P="${MY_PN}-${PV}"
 GLI_HASH="89da9305f5750d3990ca9fd35ecc5ce0b39c71a6"
+IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c"
 TEST_HASH="7ab9d41ad5b42ccbe8adcaf0b24416d439a264d0"
 declare -a GLI_TEST_HASHES=(

"a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a"
@@ -27,6 +28,7 @@ HOMEPAGE="https://itk.org;
 SRC_URI="

https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz

https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz
 -> ITKGenericLabelInterpolator-${PV}.tar.gz
+   
https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> 
ITKAdaptiveDenoising-${PV}.tar.gz
test? (

https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz

https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz
 -> ${P}-testingdata.tar.gz
@@ -130,6 +132,7 @@ src_prepare() {
 
# Remote modules
ln -sr "../ITKGenericLabelInterpolator-${GLI_HASH}" 
Modules/External/ITKGenericLabelInterpolator || die
+   ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" 
Modules/External/ITKAdaptiveDenoising || die
 
cmake_src_prepare
 
@@ -172,6 +175,7 @@ src_configure() {
-DITK_USE_KWSTYLE=OFF
-DITK_BUILD_DEFAULT_MODULES=ON
-DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+   -DModule_AdaptiveDenoising:BOOL=ON
-DModule_GenericLabelInterpolator:BOOL=ON
-DModule_ITKReview:BOOL=ON
-DWRAP_ITK_JAVA=OFF

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/files/, sci-libs/itk/

2022-09-15 Thread Horea Christian

commit: 42b8aadc9ce1de416e55dba98c3ba02a0177366f
Author: Horea Christian  chymera  eu>
AuthorDate: Thu Sep 15 07:02:53 2022 +
Commit: Horea Christian  gmail  com>
CommitDate: Thu Sep 15 07:02:53 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=42b8aadc

sci-libs/itk: add 5.1.0

Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/files/itk-5.1.0-downloads.patch  |  20 +++
 sci-libs/itk/files/itk-5.1.0-include_limits.patch |  10 ++
 sci-libs/itk/files/tests.patch|  41 +
 sci-libs/itk/itk-5.1.0.ebuild | 191 ++
 4 files changed, 262 insertions(+)

diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch 
b/sci-libs/itk/files/itk-5.1.0-downloads.patch
new file mode 100644
index 0..34fdb76d1
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.1.0-downloads.patch
@@ -0,0 +1,20 @@
+--- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
 b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
+@@ -11,7 +11,7 @@
+
+ macro(itk_download_attempt_check _name)
+   if(ITK_FORBID_DOWNLOADS)
+-message(SEND_ERROR "Attempted to download ${_name} when 
ITK_FORBID_DOWNLOADS is ON")
++message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS 
is ON")
+   endif()
+ endmacro()
+
+--- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 
14:30:53.0 -0400
 b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 
14:30:53.0 -0400
+@@ -44,6 +44,4 @@
+ itk_fetch_module(GenericLabelInterpolator
+   "A generic interpolator for multi-label images."
+   MODULE_COMPLIANCE_LEVEL 2
+-  GIT_REPOSITORY 
${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
+-  GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
+   )

diff --git a/sci-libs/itk/files/itk-5.1.0-include_limits.patch 
b/sci-libs/itk/files/itk-5.1.0-include_limits.patch
new file mode 100644
index 0..9a8fae820
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.1.0-include_limits.patch
@@ -0,0 +1,10 @@
+--- 
a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
 
a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
+@@ -16,6 +16,7 @@
+
+ #include "gdcmImageToImageFilter.h"
+ #include "gdcmPhotometricInterpretation.h"
++#include 
+
+ namespace gdcm
+ {

diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
new file mode 100644
index 0..c24714e4d
--- /dev/null
+++ b/sci-libs/itk/files/tests.patch
@@ -0,0 +1,41 @@
+Known to fail by upstream:
+https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
+
+--- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt   2019-09-09 
00:45:14.736032139 +0200
 b/Modules/Bridge/VtkGlue/test/CMakeLists.txt   2019-09-09 
00:49:42.183935497 +0200
+@@ -7,8 +7,6 @@
+ if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+   list(APPEND ITKVtkGlueTests
+ itkVtkMedianFilterTest.cxx
+-itkVtkConnectedComponentImageFilterTest.cxx
+-QuickViewTest.cxx
+ # ### runViewImage ###
+ # No test generated. Use it for view images (2D or 3D) with:
+ # ITKVtkGlueTestDriver runViewImage image_file
+@@ -40,26 +38,3 @@
+   NAME itkVTKImageToImageFilterTest
+   COMMAND ITKVtkGlueTestDriver
+ itkVTKImageToImageFilterTest)
+-
+-if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+-  itk_add_test(
+-NAME itkVtkMedianImageFilterTest
+-COMMAND ITKVtkGlueTestDriver
+-  itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2)
+-  set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS 
REQUIRES_DISPLAY)
+-
+-  itk_add_test(
+-NAME QuickViewTest
+-COMMAND ITKVtkGlueTestDriver
+- --compare DATA{Baseline/QuickViewTest.png,:}
+-   ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png
+- --compareNumberOfPixelsTolerance 1500
+-  QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} 
${ITK_TEST_OUTPUT_DIR})
+-  set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY)
+-
+-  itk_add_test(
+-NAME itkVtkConnectedComponentImageFilterTest
+-COMMAND ITKVtkGlueTestDriver
+-  itkVtkConnectedComponentImageFilterTest 
DATA{${ITK_DATA_ROOT}/Input/cthead1.png})
+-  set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY 
LABELS REQUIRES_DISPLAY)
+-endif()

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
new file mode 100644
index 0..34d2c215d
--- /dev/null
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -0,0 +1,191 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit cmake python-single-r1
+
+MY_PN="InsightToolkit"
+MY_P="${MY_PN}-${PV}"
+GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78"

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

2022-08-31 Thread Andrew Ammerlaan

commit: e183cbc1d2404c5ce6348627365cdc1aa483c375
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Wed Aug 31 10:30:15 2022 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Wed Aug 31 10:30:15 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e183cbc1

sci-libs/itk: drop 5.0.1, 5.1.0

Signed-off-by: Andrew Ammerlaan  gentoo.org>

 ...p-TransformFileReader-TransformFileWriter.patch |  50 --
 ...itkQuasiNewtonOptimizerv4-wrapping-warnin.patch |  28 ---
 ...itkGradientDescentOptimizerv4-wrapping-wa.patch |  73 
 ...OptimizerParameterScalesEstimatorTemplate.patch |  30 
 .../0005-make-gdcm-helper-library-static.patch |  11 --
 sci-libs/itk/files/ITKModuleRemote.patch   |  45 -
 sci-libs/itk/files/itk-5.1.0-downloads.patch   |  20 ---
 sci-libs/itk/files/itk-5.1.0-include_limits.patch  |  10 --
 sci-libs/itk/files/nrrdio-linking.patch|  15 --
 sci-libs/itk/files/tests.patch |  41 -
 sci-libs/itk/itk-5.0.1.ebuild  | 178 ---
 sci-libs/itk/itk-5.1.0.ebuild  | 191 -
 12 files changed, 692 deletions(-)

diff --git 
a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
 
b/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
deleted file mode 100644
index 094ee3229..0
--- 
a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-From d069b7b94287dae15fcaf707775f5dd2bbebcc38 Mon Sep 17 00:00:00 2001
-From: Matt McCormick 
-Date: Wed, 5 Feb 2014 15:52:34 -0500
-Subject: [PATCH 1/3] BUG: Wrap TransformFileReader, TransformFileWriter.
-
-Missing CMakeLists.txt in the wrapping directory.  Need to explicitly include
-the headers after "Template" was appended to the class name.
-
-Suggested-by: Sami Koho 
-
-Change-Id: I6f994bb18f37d5adf1d0f0311fa73506c41239a7

- Modules/IO/TransformBase/wrapping/CMakeLists.txt  | 3 +++
- Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap | 2 ++
- Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap | 2 ++
- 3 files changed, 7 insertions(+)
- create mode 100644 Modules/IO/TransformBase/wrapping/CMakeLists.txt
-
-diff --git a/Modules/IO/TransformBase/wrapping/CMakeLists.txt 
b/Modules/IO/TransformBase/wrapping/CMakeLists.txt
-new file mode 100644
-index 000..6072567
 /dev/null
-+++ b/Modules/IO/TransformBase/wrapping/CMakeLists.txt
-@@ -0,0 +1,3 @@
-+itk_wrap_module(ITKIOTransformBase)
-+itk_auto_load_submodules()
-+itk_end_wrap_module()
-diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap 
b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-index 9b52fbc..662df9e 100644
 a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
-@@ -1,3 +1,5 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkTransformFileReader.h")
- itk_wrap_class("itk::TransformFileReaderTemplate" POINTER)
-   foreach(t ${WRAP_ITK_REAL})
- itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
-diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap 
b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-index 4f1ac4a..356aaf3 100644
 a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
-@@ -1,3 +1,5 @@
-+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-+itk_wrap_include("itkTransformFileWriter.h")
- itk_wrap_class("itk::TransformFileWriterTemplate" POINTER)
-   foreach(t ${WRAP_ITK_REAL})
- itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
--- 
-1.8.5.3
-

diff --git 
a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
 
b/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
deleted file mode 100644
index 4c74d5451..0
--- 
a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-From 66d2955fbe5528d9df216c639277d1d2686447e5 Mon Sep 17 00:00:00 2001
-From: Michka Popoff 
-Date: Fri, 7 Feb 2014 19:24:49 +0100
-Subject: [PATCH 2/3] COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings
-
-The warning :
-/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml:
 warning(5): Unknown type type: itk::QuasiNewtonOptimizerv4 [typedef]
-/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml:
 warning(4): ITK type not wrapped, or currently not known: 
itk::QuasiNewtonOptimizerv4Template< double >

- .../Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap | 8 +++-
- 1 file changed, 7 insertions(+), 1 deletion(-)
-
-diff --git

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

2022-08-23 Thread Andrew Ammerlaan

commit: b4acbb5f52ed06ad45b5a4e877498a6c9f683d4e
Author: François-Xavier Carton  gmail  com>
AuthorDate: Fri Jun 10 13:16:57 2022 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Tue Aug 23 10:58:09 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b4acbb5f

sci-libs/itk: bump to 5.2.1

Signed-off-by: François-Xavier Carton  gmail.com>
Signed-off-by: Andrew Ammerlaan  gentoo.org>
Closes: https://github.com/gentoo/sci/pull/1154

 .../itk-5.2.1-fix-castxml-clang-attr-malloc.patch  |  25 +
 sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch | 558 +
 .../itk/files/itk-5.2.1-system-tiff-has-64.patch   |  18 +
 sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch  | 255 ++
 sci-libs/itk/itk-5.2.1.ebuild  | 246 +
 5 files changed, 1102 insertions(+)

diff --git a/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch 
b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch
new file mode 100644
index 0..05c9d5635
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch
@@ -0,0 +1,25 @@
+From: François-Xavier Carton 
+Date: Thu, 9 Jun 2022 14:56:22 +0200
+Subject: [PATCH] fix attr malloc error with recent glibc/gcc
+
+Recent GCC has support for __attribute__((__malloc__)) with arguments, but 
clang
+does not. castxml uses clang internally. And recent glibc/gcc uses the 
attribute
+with arguments. Mix all this, and you get:
+
+error: '__malloc__' attribute takes no arguments
+
+when compiling itk with python wrapping.
+
+To fix this, we add a define to castxml flags to remove the extra arguments.
+
+--- a/Wrapping/Generators/CastXML/CMakeLists.txt   2022-06-09 
14:53:15.582352715 +0200
 b/Wrapping/Generators/CastXML/CMakeLists.txt   2022-06-09 
14:54:38.182351433 +0200
+@@ -237,7 +237,7 @@
+   set(_castxml_cc ${_castxml_cc} "-D_HAS_TR1=0")
+ endif()
+   else()
+-set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" 
${_castxml_cc_flags} ))
++set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" 
${_castxml_cc_flags} -D__malloc__\(a,b\)=__malloc__ ))
+   endif()
+   set(_target)
+   if(CMAKE_CROSSCOMPILING)

diff --git a/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch 
b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch
new file mode 100644
index 0..ad717f677
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch
@@ -0,0 +1,558 @@
+--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
 b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+@@ -1,16 +1,32 @@
+ project(ITKOpenJPEG)
+ set(ITKOpenJPEG_THIRD_PARTY 1)
+ 
+-set(ITKOpenJPEG_INCLUDE_DIRS
+-  ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
+-  ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
+-  )
+-set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" 
${ITK_USE_SYSTEM_LIBRARIES})
++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG)
++
++if(ITK_USE_SYSTEM_OPENJPEG)
++  find_package(OpenJPEG REQUIRED)
++  set(ITKOpenJPEG_INCLUDE_DIRS
++${ITKOpenJPEG_BINARY_DIR}/src
++)
++  set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS
++${OPENJPEG_INCLUDE_DIRS}
++)
++  set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}")
++  set(ITKOpenJPEG_NO_SRC 1)
++else()
++  set(ITKOpenJPEG_INCLUDE_DIRS
++${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
++${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
++)
++  set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++endif()
++
++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h)
+ set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE)
+-
+ itk_module_impl()
+ 
+-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h
++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h
+   DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR}
+   COMPONENT Development
+   )
+diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h 
b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
+rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
 b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+@@ -25,6 +25,12 @@
+ #ifndef itk_openjpeg_h
+ #define itk_openjpeg_h
+ 
+-#include 
++/* Use the openjpeg library configured for ITK.  */
++#cmakedefine ITK_USE_SYSTEM_OPENJPEG
++#ifdef ITK_USE_SYSTEM_OPENJPEG
++# include 
++#else
++# include 
++#endif
+ 
+ #endif
+--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
 b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
+@@ -27,8 +27,6 @@
+ extern "C"
+ {
+ #include "openjpeg.h"
+-#include "j2k.h"
+-#include "jp2.h"
+ }
+ 
+ 
+@@ -139,11 +137,11 @@
+ {
+   itkDebugMacro(<< "ReadImageInformation()");
+ 
+-  FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+-  /* decompression parameters */
++  /* set decoding parameters to default values */
++  
opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+ 
+-  if (!l_file)
++

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2022-07-12 Thread Horea Christian

commit: 69348352919a4c305333a2ddc9e2c764d264dda1
Author: Horea Christian  chymera  eu>
AuthorDate: Tue Jul 12 13:36:21 2022 +
Commit: Horea Christian  gmail  com>
CommitDate: Tue Jul 12 13:36:21 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=69348352

sci-libs/itk: EAPI and PYTHON_COMPAT bump

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/itk-5.0.1.ebuild | 2 +-
 sci-libs/itk/itk-5.1.0.ebuild | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index bf9f0f021..4580c659a 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
 
 inherit cmake python-single-r1
 

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index 3f6c759ec..e6e0b25f9 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..10} )
 
 inherit cmake python-single-r1

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/files/, sci-libs/itk/

2022-01-09 Thread Horea Christian

commit: 3b227d5588eaac724032273e19541ee81aa53034
Author: Horea Christian  chymera  eu>
AuthorDate: Mon Jan 10 00:38:53 2022 +
Commit: Horea Christian  gmail  com>
CommitDate: Mon Jan 10 00:38:53 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b227d55

sci-libs/itk: fixed missing limits issue for newer GCC

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/files/itk-5.1.0-include_limits.patch | 10 ++
 sci-libs/itk/itk-5.0.1.ebuild | 10 +-
 sci-libs/itk/itk-5.1.0.ebuild | 11 ++-
 3 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/sci-libs/itk/files/itk-5.1.0-include_limits.patch 
b/sci-libs/itk/files/itk-5.1.0-include_limits.patch
new file mode 100644
index 0..9a8fae820
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.1.0-include_limits.patch
@@ -0,0 +1,10 @@
+--- 
a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
 
a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h
+@@ -16,6 +16,7 @@
+
+ #include "gdcmImageToImageFilter.h"
+ #include "gdcmPhotometricInterpretation.h"
++#include 
+
+ namespace gdcm
+ {

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index 9c8ce63eb..c0a74b27f 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -159,11 +159,11 @@ src_install() {
dodoc -r "${S}"/Examples/*
fi
 
-   echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN}
-   local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit"
+   echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN}
+   local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
if use python; then
-   echo 
"PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> 
"${T}"/40${PN}
-   
ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
+   echo 
"PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> 
"${T}"/40${PN}
+   
ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
fi
echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
doenvd "${T}"/40${PN}

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index d437d0298..8c9e48dba 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -72,6 +72,7 @@ S="${WORKDIR}/${MY_P}"
 PATCHES=(
"${FILESDIR}"/tests.patch
"${FILESDIR}"/${P}-downloads.patch
+   "${FILESDIR}"/${P}-include_limits.patch
 )
 
 pkg_pretend() {
@@ -171,11 +172,11 @@ src_install() {
dodoc -r "${S}"/Examples/*
fi
 
-   echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN}
-   local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit"
+   echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN}
+   local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
if use python; then
-   echo 
"PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> 
"${T}"/40${PN}
-   
ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
+   echo 
"PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> 
"${T}"/40${PN}
+   
ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
fi
echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
doenvd "${T}"/40${PN}

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2021-12-16 Thread Andrew Ammerlaan

commit: 92b82d3b728921c9281b64a1c0cb76b3aade3c17
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Thu Dec 16 10:44:51 2021 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Thu Dec 16 10:44:51 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=92b82d3b

sci-libs/itk: drop UnusedInherits

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-libs/itk/itk-5.0.1.ebuild | 2 +-
 sci-libs/itk/itk-5.1.0.ebuild | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index 622a7b019..9c8ce63eb 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 PYTHON_COMPAT=( python3_{7,8,9} )
 
-inherit toolchain-funcs cmake python-single-r1
+inherit cmake python-single-r1
 
 MY_PN="InsightToolkit"
 MY_P="${MY_PN}-${PV}"

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index ad23b6f14..d437d0298 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 PYTHON_COMPAT=( python3_{7,8,9} )
 
-inherit toolchain-funcs cmake python-single-r1
+inherit cmake python-single-r1
 
 MY_PN="InsightToolkit"
 MY_P="${MY_PN}-${PV}"

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2021-03-13 Thread Horea Christian

commit: 8ee4d009f7fdcb0f22f33dee2bf395d67868eee9
Author: Horea Christian  chymera  eu>
AuthorDate: Sat Mar 13 23:55:03 2021 +
Commit: Horea Christian  gmail  com>
CommitDate: Sat Mar 13 23:55:03 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8ee4d009

sci-libs/itk: added optional USE flag

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/itk-5.1.0.ebuild | 3 ++-
 sci-libs/itk/metadata.xml | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index f5c9cd50d..ad23b6f14 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -36,7 +36,7 @@ SRC_URI="
 LICENSE="Apache-2.0"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="debug doc examples fftw python review test vtkglue"
+IUSE="debug doc examples fftw itkv4-compat python review test vtkglue"
 RESTRICT="!test? ( test )"
 # python will not work, this is a know issue upstream:
 # https://github.com/InsightSoftwareConsortium/ITK/issues/2005
@@ -131,6 +131,7 @@ src_configure() {
-DModule_ITKReview:BOOL=ON
-DWRAP_ITK_JAVA=OFF
-DWRAP_ITK_TCL=OFF
+   -DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat)
)
if use fftw; then
mycmakeargs+=(

diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml
index 7c4535324..535ae83de 100644
--- a/sci-libs/itk/metadata.xml
+++ b/sci-libs/itk/metadata.xml
@@ -14,6 +14,7 @@ that provides developers with an extensive suite of tools for 
image
 analysis.
 

+   Compatibility for applications using 
ITKv4 API
Enable compilation of methods under 
review
PLEASE FIX MY DESCRIPTION

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2021-03-13 Thread Horea Christian

commit: f20e51268def2befef9ad5772c3bc4aeb5e14297
Author: Horea Christian  chymera  eu>
AuthorDate: Sat Mar 13 23:55:39 2021 +
Commit: Horea Christian  gmail  com>
CommitDate: Sat Mar 13 23:55:39 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f20e5126

sci-libs/itk: metadata indentation

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/metadata.xml | 10 +-
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml
index 535ae83de..c41202e23 100644
--- a/sci-libs/itk/metadata.xml
+++ b/sci-libs/itk/metadata.xml
@@ -9,11 +9,11 @@
Gentoo Biology Project


-Insight Segmentation and Registration Toolkit (ITK) is a library
-that provides developers with an extensive suite of tools for image
-analysis.
-
-   
+   Insight Segmentation and Registration Toolkit (ITK) is a library
+   that provides developers with an extensive suite of tools for 
image
+   analysis.
+   
+   
Compatibility for applications using 
ITKv4 API
Enable compilation of methods under 
review
PLEASE FIX MY DESCRIPTION

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2021-03-04 Thread Andrew Ammerlaan

commit: 404bb18d4e02a961b4d864b8b56ddb0b1851f0bc
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Thu Mar  4 20:57:28 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Thu Mar  4 20:57:28 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=404bb18d

sci-libs/itk: fix docinto path

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>

 sci-libs/itk/itk-5.0.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index d23816f2e..622a7b019 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -172,7 +172,7 @@ src_install() {
cd "${WORKDIR}"/html || die
rm  *.md5 || die "Failed to remove superfluous hashes"
einfo "Installing API docs. This may take some time."
-   docinto /usr/share/doc/${PF}/api-docs
+   docinto api-docs
dodoc -r *
fi
 }

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2021-03-04 Thread Andrew Ammerlaan

commit: 5751886ea4425766efee98c3e98e41c07b152444
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Thu Mar  4 20:55:56 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Thu Mar  4 20:55:56 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5751886e

sci-libs/itk: try to fix doc building

where do they go? currently fails to install with USE="doc"

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>

 sci-libs/itk/itk-5.0.1.ebuild | 14 +++---
 sci-libs/itk/itk-5.1.0.ebuild | 19 +--
 2 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index 707684d8a..d23816f2e 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -16,7 +16,7 @@ DESCRIPTION="NLM Insight Segmentation and Registration 
Toolkit"
 HOMEPAGE="http://www.itk.org;
 SRC_URI="

https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
-   
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip
 -> ITKGenericLabelInterpolator-${PV}.zip
+   
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz
 -> ITKGenericLabelInterpolator-${PV}.tar.gz
test? (

https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> 
ITKGenericLabelInterpolator_test-${PV}.zip

https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
@@ -118,6 +118,7 @@ src_configure() {
-DBUILD_TESTING="$(usex test ON OFF)"
-DBUILD_EXAMPLES="$(usex examples ON OFF)"
-DITK_USE_REVIEW="$(usex review ON OFF)"
+   -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
-DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
)
if use fftw; then
@@ -153,9 +154,9 @@ src_install() {
cmake_src_install
 
if use examples; then
-   insinto /usr/share/doc/${PF}/examples
+   docinto examples
docompress -x /usr/share/doc/${PF}/examples
-   doins -r "${S}"/Examples/*
+   dodoc -r "${S}"/Examples/*
fi
 
echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN}
@@ -168,11 +169,10 @@ src_install() {
doenvd "${T}"/40${PN}
 
if use doc; then
-   insinto /usr/share/doc/${PF}/api-docs
-   cd "${WORKDIR}"/html
+   cd "${WORKDIR}"/html || die
rm  *.md5 || die "Failed to remove superfluous hashes"
einfo "Installing API docs. This may take some time."
-   insinto /usr/share/doc/${PF}/api-docs
-   doins -r *
+   docinto /usr/share/doc/${PF}/api-docs
+   dodoc -r *
fi
 }

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index c7d19607a..f5c9cd50d 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -18,17 +18,17 @@ declare -a GLI_TEST_HASHES=(
 
 GLI_TEST_SRC=""
 for i in "${GLI_TEST_HASHES[@]}"; do
-   GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} 
-> ${i} "
+   GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} 
-> ${P}-test-${i} "
 done
 
 DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
 HOMEPAGE="http://www.itk.org;
 SRC_URI="

https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
-   
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip
 -> ITKGenericLabelInterpolator-${PV}.zip
+   
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz
 -> ITKGenericLabelInterpolator-${PV}.tar.gz
test? (

https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
-   
https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz
+   
https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz
 -> ${P}-testingdata.tar.gz
${GLI_TEST_SRC}
)
"
@@ -64,7 +64,6 @@ DEPEND="${RDEPEND}
)
doc? ( app-doc/doxygen )
 "
-BDEPEND="app-arch/unzip"
 
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
 
@@ -106,6 +105,7 @@ src_prepare() {
 
 src_configure() {
local mycmakeargs=(
+   -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
-DBUILD_EXAMPLES="$(usex examples ON OFF)"
-DBUILD_SHARED_LIBS=ON
-DBUILD_TESTING="$(usex test ON OFF)"
@@ -165,9 +165,9 @@ src_install() {
cmake_src_install
 
if use examples; then
-   insinto /usr/share/doc/${PF}/examples
+

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2021-01-19 Thread Andrew Ammerlaan

commit: 79deea549fdb01e0464c60b9045d6919dac49408
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Tue Jan 19 16:45:09 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Tue Jan 19 16:45:09 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=79deea54

sci-libs/itk: add python deps

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>

 sci-libs/itk/itk-5.0.1.ebuild | 11 ++-
 sci-libs/itk/itk-5.1.0.ebuild | 11 ++-
 2 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index c5ac9152f..707684d8a 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -43,6 +43,7 @@ RDEPEND="
virtual/jpeg:0=
fftw? ( sci-libs/fftw:3.0= )
vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
+   python? ( ${PYTHON_DEPS} )
 "
 DEPEND="${RDEPEND}
sys-apps/coreutils
@@ -157,11 +158,11 @@ src_install() {
doins -r "${S}"/Examples/*
fi
 
-   echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN}
-   local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit"
+   echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN}
+   local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit"
if use python; then
-   echo 
"PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> 
"${T}"/40${PN}
-   
ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
+   echo 
"PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> 
"${T}"/40${PN}
+   
ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
fi
echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
doenvd "${T}"/40${PN}

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index e09d1b7a8..c7d19607a 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -54,6 +54,7 @@ RDEPEND="
virtual/jpeg:0=
fftw? ( sci-libs/fftw:3.0= )
vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
+   python? ( ${PYTHON_DEPS} )
 "
 DEPEND="${RDEPEND}
sys-apps/coreutils
@@ -169,11 +170,11 @@ src_install() {
doins -r "${S}"/Examples/*
fi
 
-   echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN}
-   local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit"
+   echo "ITK_DATA_ROOT=${EROOT}/usr/share/${PN}/data" > ${T}/40${PN}
+   local ldpath="${EROOT}/usr/$(get_libdir)/InsightToolkit"
if use python; then
-   echo 
"PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> 
"${T}"/40${PN}
-   
ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
+   echo 
"PYTHONPATH=${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> 
"${T}"/40${PN}
+   
ldpath="${ldpath}:${EROOT}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
fi
echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
doenvd "${T}"/40${PN}

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2020-12-31 Thread Aisha Tammy

commit: 77f84a02fe90c20577e93edf68c026e85913f1b1
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Thu Dec 31 12:31:26 2020 +
Commit: Aisha Tammy  aisha  cc>
CommitDate: Thu Dec 31 15:52:08 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=77f84a02

sci-libs/itk: drop old python targets

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>
Closes: https://github.com/gentoo/sci/pull/1017
Signed-off-by: Aisha Tammy  aisha.cc>

 sci-libs/itk/itk-5.0.1.ebuild | 4 ++--
 sci-libs/itk/itk-5.1.0.ebuild | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index 721724036..c5ac9152f 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 python3_{6,7,8,9} )
+PYTHON_COMPAT=( python3_{7,8,9} )
 
 inherit toolchain-funcs cmake python-single-r1
 
@@ -25,7 +25,7 @@ SRC_URI="
 
 LICENSE="Apache-2.0"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
 IUSE="debug doc examples fftw python review test vtkglue"
 RESTRICT="!test? ( test )"
 # python will not work, this is a know issue upstream:

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index fa666053e..e09d1b7a8 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 python3_{6,7,8,9} )
+PYTHON_COMPAT=( python3_{7,8,9} )
 
 inherit toolchain-funcs cmake python-single-r1
 
@@ -35,7 +35,7 @@ SRC_URI="
 
 LICENSE="Apache-2.0"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
 IUSE="debug doc examples fftw python review test vtkglue"
 RESTRICT="!test? ( test )"
 # python will not work, this is a know issue upstream:

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2020-12-24 Thread Horea Christian

commit: d71b8611784dda298b7ae55d604d1bbf13ab7e1a
Author: Horea Christian  chymera  eu>
AuthorDate: Thu Dec 24 17:26:23 2020 +
Commit: Horea Christian  gmail  com>
CommitDate: Thu Dec 24 17:26:23 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d71b8611

sci-libs/itk: deed zip BDEPEND

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/itk-5.0.1.ebuild | 1 +
 sci-libs/itk/itk-5.1.0.ebuild | 1 +
 2 files changed, 2 insertions(+)

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index 93ad7a996..721724036 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -52,6 +52,7 @@ DEPEND="${RDEPEND}
)
doc? ( app-doc/doxygen )
 "
+BDEPEND="app-arch/unzip"
 
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
 

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index 1f7a5d3b2..fa666053e 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -63,6 +63,7 @@ DEPEND="${RDEPEND}
)
doc? ( app-doc/doxygen )
 "
+BDEPEND="app-arch/unzip"
 
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2020-12-24 Thread Horea Christian

commit: f00054d77915556aa047f78e09d3c87808991e86
Author: Horea Christian  chymera  eu>
AuthorDate: Thu Dec 24 11:02:37 2020 +
Commit: Horea Christian  gmail  com>
CommitDate: Thu Dec 24 11:02:37 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f00054d7

sci-libs/itk: conditional test restriction

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/itk-5.0.1.ebuild | 1 +
 sci-libs/itk/itk-5.1.0.ebuild | 1 +
 2 files changed, 2 insertions(+)

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index 6c0310751..93ad7a996 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -27,6 +27,7 @@ LICENSE="Apache-2.0"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="debug doc examples fftw python review test vtkglue"
+RESTRICT="!test? ( test )"
 # python will not work, this is a know issue upstream:
 # https://github.com/InsightSoftwareConsortium/ITK/issues/1229
 # 
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index 2b4b145c4..1f7a5d3b2 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -37,6 +37,7 @@ LICENSE="Apache-2.0"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="debug doc examples fftw python review test vtkglue"
+RESTRICT="!test? ( test )"
 # python will not work, this is a know issue upstream:
 # https://github.com/InsightSoftwareConsortium/ITK/issues/2005
 # https://github.com/InsightSoftwareConsortium/ITK/issues/1229

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2020-10-14 Thread Horea Christian

commit: 583cbb757d8e0e967a5c6cd1b2e64f0bc2ce44ad
Author: Horea Christian  chymera  eu>
AuthorDate: Wed Oct 14 06:52:16 2020 +
Commit: Horea Christian  gmail  com>
CommitDate: Wed Oct 14 06:52:16 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=583cbb75

sci-libs/itk: PYTHON_COMPAT update

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/itk-5.0.1.ebuild | 2 +-
 sci-libs/itk/itk-5.1.0.ebuild | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index f345e06b1..6c0310751 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+PYTHON_COMPAT=( python2_7 python3_{6,7,8,9} )
 
 inherit toolchain-funcs cmake python-single-r1
 

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index 4728ba4a4..2b4b145c4 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+PYTHON_COMPAT=( python2_7 python3_{6,7,8,9} )
 
 inherit toolchain-funcs cmake python-single-r1

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2020-10-09 Thread Horea Christian

commit: 42a90d86af7de67508087b416990dabf413955ef
Author: Horea Christian  chymera  eu>
AuthorDate: Fri Oct  9 10:04:21 2020 +
Commit: Horea Christian  gmail  com>
CommitDate: Fri Oct  9 10:04:21 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=42a90d86

sci-libs/itk: eclass and RESTRICT updates

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/itk-5.0.1.ebuild | 11 +--
 sci-libs/itk/itk-5.1.0.ebuild |  1 -
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild
index e1ec7166a..f345e06b1 100644
--- a/sci-libs/itk/itk-5.0.1.ebuild
+++ b/sci-libs/itk/itk-5.0.1.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
 PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
 
-inherit toolchain-funcs cmake-utils python-single-r1
+inherit toolchain-funcs cmake python-single-r1
 
 MY_PN="InsightToolkit"
 MY_P="${MY_PN}-${PV}"
@@ -22,7 +22,6 @@ SRC_URI="

https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
)
"
-RESTRICT="primaryuri"
 
 LICENSE="Apache-2.0"
 SLOT="0"
@@ -87,7 +86,7 @@ src_prepare() {
cp "$filename" ".ExternalData/MD5/${MD5}" || die
done
fi
-   cmake-utils_src_prepare
+   cmake_src_prepare
 }
 
 src_configure() {
@@ -144,11 +143,11 @@ src_configure() {
-DITK_WRAP_PYTHON=OFF
)
fi
-   cmake-utils_src_configure
+   cmake_src_configure
 }
 
 src_install() {
-   cmake-utils_src_install
+   cmake_src_install
 
if use examples; then
insinto /usr/share/doc/${PF}/examples

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
index 64fd555cb..4728ba4a4 100644
--- a/sci-libs/itk/itk-5.1.0.ebuild
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -32,7 +32,6 @@ SRC_URI="
${GLI_TEST_SRC}
)
"
-RESTRICT="primaryuri"
 
 LICENSE="Apache-2.0"
 SLOT="0"

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

2020-09-25 Thread Horea Christian

commit: 7112647657d76049ee42f5e2c86c05c2c1330760
Author: Horea Christian  chymera  eu>
AuthorDate: Fri Sep 25 07:33:20 2020 +
Commit: Horea Christian  gmail  com>
CommitDate: Fri Sep 25 07:33:20 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=71126476

sci-libs/itk: version bump 5.1.0

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/files/itk-5.1.0-downloads.patch |  20 +++
 sci-libs/itk/itk-5.1.0.ebuild| 188 +++
 2 files changed, 208 insertions(+)

diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch 
b/sci-libs/itk/files/itk-5.1.0-downloads.patch
new file mode 100644
index 0..34fdb76d1
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.1.0-downloads.patch
@@ -0,0 +1,20 @@
+--- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
 b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400
+@@ -11,7 +11,7 @@
+
+ macro(itk_download_attempt_check _name)
+   if(ITK_FORBID_DOWNLOADS)
+-message(SEND_ERROR "Attempted to download ${_name} when 
ITK_FORBID_DOWNLOADS is ON")
++message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS 
is ON")
+   endif()
+ endmacro()
+
+--- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 
14:30:53.0 -0400
 b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 
14:30:53.0 -0400
+@@ -44,6 +44,4 @@
+ itk_fetch_module(GenericLabelInterpolator
+   "A generic interpolator for multi-label images."
+   MODULE_COMPLIANCE_LEVEL 2
+-  GIT_REPOSITORY 
${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git
+-  GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7
+   )

diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild
new file mode 100644
index 0..64fd555cb
--- /dev/null
+++ b/sci-libs/itk/itk-5.1.0.ebuild
@@ -0,0 +1,188 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit toolchain-funcs cmake python-single-r1
+
+MY_PN="InsightToolkit"
+MY_P="${MY_PN}-${PV}"
+GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78"
+TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700"
+declare -a GLI_TEST_HASHES=(
+   
"a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a"
+   
"bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
+)
+
+GLI_TEST_SRC=""
+for i in "${GLI_TEST_HASHES[@]}"; do
+   GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} 
-> ${i} "
+done
+
+DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
+HOMEPAGE="http://www.itk.org;
+SRC_URI="
+   
https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
+   
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.zip
 -> ITKGenericLabelInterpolator-${PV}.zip
+   test? (
+   
https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
+   
https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz
+   ${GLI_TEST_SRC}
+   )
+   "
+RESTRICT="primaryuri"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug doc examples fftw python review test vtkglue"
+# python will not work, this is a know issue upstream:
+# https://github.com/InsightSoftwareConsortium/ITK/issues/2005
+# https://github.com/InsightSoftwareConsortium/ITK/issues/1229
+# 
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10
+
+RDEPEND="
+   dev-libs/double-conversion:0=
+   media-libs/openjpeg:2
+   media-libs/libpng:0=
+   media-libs/tiff:0=[jpeg]
+   sci-libs/dcmtk:0=
+   sci-libs/hdf5:0=[cxx]
+   sys-libs/zlib:0=
+   virtual/jpeg:0=
+   fftw? ( sci-libs/fftw:3.0= )
+   vtkglue? ( sci-libs/vtk:0=[rendering,python?] )
+"
+DEPEND="${RDEPEND}
+   sys-apps/coreutils
+   python? (
+   >=dev-lang/swig-2.0:0
+   dev-cpp/castxml
+   )
+   doc? ( app-doc/doxygen )
+"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+   "${FILESDIR}"/tests.patch
+   "${FILESDIR}"/${P}-downloads.patch
+)
+
+pkg_pretend() {
+   if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
+   elog "To tune ITK to make the best use of working memory you 
can set"
+   elog "ITK_COMPUTER_MEMORY_SIZE=XX"
+   elog "in make.conf, default is 1 (unit is GB)"
+   fi
+   if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
+   elog "For Python language

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

2019-09-09 Thread Horea Christian

commit: 445eb95b61c9b12481b24f962123d0f13e940ab6
Author: Horea Christian  chymera  eu>
AuthorDate: Mon Sep  9 08:25:49 2019 +
Commit: Horea Christian  gmail  com>
CommitDate: Mon Sep  9 08:25:49 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=445eb95b

sci-libs/itk: version bump to 5.0.1

And removed deprecated versions on account of gccxml removal

Package-Manager: Portage-2.3.72, Repoman-2.3.17
Signed-off-by: Horea Christian  chymera.eu>

 sci-libs/itk/files/ITKModuleRemote.patch   |  45 ++
 sci-libs/itk/files/tests.patch |  41 ++
 sci-libs/itk/itk-4.12.0.ebuild | 136 --
 sci-libs/itk/itk-4.4.2-r1.ebuild   | 135 --
 sci-libs/itk/itk-4.4.2.ebuild  | 115 ---
 sci-libs/itk/itk-4.5.1.ebuild  | 155 -
 .../itk/{itk-5.0_rc1.ebuild => itk-5.0.1.ebuild}   |  50 +--
 sci-libs/itk/metadata.xml  |   1 -
 8 files changed, 124 insertions(+), 554 deletions(-)

diff --git a/sci-libs/itk/files/ITKModuleRemote.patch 
b/sci-libs/itk/files/ITKModuleRemote.patch
new file mode 100644
index 0..eb130159a
--- /dev/null
+++ b/sci-libs/itk/files/ITKModuleRemote.patch
@@ -0,0 +1,45 @@
+Disable automatic git clone attempt for modules:
+https://github.com/InsightSoftwareConsortium/ITK/issues/1157
+
+--- a/CMake/ITKModuleRemote.cmake  2019-08-13 18:10:33.385472767 +0200
 b/CMake/ITKModuleRemote.cmake  2019-08-13 18:12:04.020198966 +0200
+@@ -165,39 +165,4 @@
+ set(Module_${_name} ON CACHE FORCE "${_description}")
+   endif()
+ 
+-  if(Module_${_name})
+-itk_download_attempt_check(Module_${_name})
+-include(CMakeParseArguments)
+-cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" 
${ARGN})
+-find_package(Git)
+-if(NOT GIT_EXECUTABLE)
+-  message(FATAL_ERROR "error: could not find git for clone of ${_name}")
+-endif()
+-execute_process(
+-  COMMAND "${GIT_EXECUTABLE}" --version
+-  OUTPUT_VARIABLE ov
+-  OUTPUT_STRIP_TRAILING_WHITESPACE
+-  )
+-string(REGEX REPLACE "^git version (.+)$" "\\1" _version "${ov}")
+-if("${_version}" VERSION_LESS 1.6.6)
+-  message(FATAL_ERROR "Git version 1.6.6 or later is required.")
+-endif()
+-
+-set(REMOTE_GIT_TAG "${_fetch_options_GIT_TAG}")
+-
+-if( DEFINED REMOTE_GIT_TAG_${_name} AND NOT "${REMOTE_GIT_TAG_${_name}}" 
STREQUAL "${_fetch_options_GIT_TAG}")
+-  set(REMOTE_GIT_TAG "${REMOTE_GIT_TAG_${_name}}")
+-  message(STATUS "NOTE: Using override 
'REMOTE_GIT_TAG_${_name}=${REMOTE_GIT_TAG}'\n"
+- "  instead of value 
'GIT_TAG=${_fetch_options_GIT_TAG}'\n"
+- "  specified in file 
${ITK_SOURCE_DIR}/Modules/Remote/${_name}.remote.cmake'")
+-endif()
+-set(REMOTE_GIT_TAG_${_name} "${REMOTE_GIT_TAG}" CACHE STRING "Override 
default GIT_TAG value for remote module ${_name}")
+-mark_as_advanced(REMOTE_GIT_TAG_${_name})
+-
+-_fetch_with_git("${GIT_EXECUTABLE}"
+-  "${_fetch_options_GIT_REPOSITORY}"
+-  "${REMOTE_GIT_TAG}"
+-  "${ITK_SOURCE_DIR}/Modules/Remote/${_name}"
+-  )
+-  endif()
+ endfunction()

diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch
new file mode 100644
index 0..c24714e4d
--- /dev/null
+++ b/sci-libs/itk/files/tests.patch
@@ -0,0 +1,41 @@
+Known to fail by upstream:
+https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115
+
+--- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt   2019-09-09 
00:45:14.736032139 +0200
 b/Modules/Bridge/VtkGlue/test/CMakeLists.txt   2019-09-09 
00:49:42.183935497 +0200
+@@ -7,8 +7,6 @@
+ if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+   list(APPEND ITKVtkGlueTests
+ itkVtkMedianFilterTest.cxx
+-itkVtkConnectedComponentImageFilterTest.cxx
+-QuickViewTest.cxx
+ # ### runViewImage ###
+ # No test generated. Use it for view images (2D or 3D) with:
+ # ITKVtkGlueTestDriver runViewImage image_file
+@@ -40,26 +38,3 @@
+   NAME itkVTKImageToImageFilterTest
+   COMMAND ITKVtkGlueTestDriver
+ itkVTKImageToImageFilterTest)
+-
+-if(NOT VTK_RENDERING_BACKEND STREQUAL "None")
+-  itk_add_test(
+-NAME itkVtkMedianImageFilterTest
+-COMMAND ITKVtkGlueTestDriver
+-  itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2)
+-  set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS 
REQUIRES_DISPLAY)
+-
+-  itk_add_test(
+-NAME QuickViewTest
+-COMMAND ITKVtkGlueTestDriver
+- --compare DATA{Baseline/QuickViewTest.png,:}
+-   ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png
+- --compareNumberOfPixelsTolerance 1500
+-  QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} 
${ITK_TEST_OUTPUT_DIR})
+-  set_property(TEST QuickViewTest APPEND PROPERTY LABELS

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2019-04-01 Thread Horea Christian

commit: b78267d25570586f0a6dfd7d8d948c974c4e2846
Author: Horea Christian  yandex  com>
AuthorDate: Tue Apr  2 01:20:09 2019 +
Commit: Horea Christian  gmail  com>
CommitDate: Tue Apr  2 01:20:09 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b78267d2

sci-libs/itk: version bump 5.0_rc1

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Horea Christian  yandex.com>

 sci-libs/itk/itk-5.0_rc1.ebuild | 150 
 1 file changed, 150 insertions(+)

diff --git a/sci-libs/itk/itk-5.0_rc1.ebuild b/sci-libs/itk/itk-5.0_rc1.ebuild
new file mode 100644
index 0..f6433e551
--- /dev/null
+++ b/sci-libs/itk/itk-5.0_rc1.ebuild
@@ -0,0 +1,150 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit eutils toolchain-funcs cmake-utils python-single-r1
+
+MY_PV="5.0rc01"
+
+DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
+HOMEPAGE="http://www.itk.org;
+SRC_URI="
+   
https://github.com/InsightSoftwareConsortium/ITK/archive/v${MY_PV}.tar.gz
+   test? ( 
https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0rc01/InsightData-${MY_PV}.tar.gz
 )
+   "
+RESTRICT="primaryuri"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug doc examples fftw python review test vtkglue"
+
+RDEPEND="
+   dev-libs/double-conversion:0=
+   media-libs/openjpeg:2
+   media-libs/libpng:0=
+   media-libs/tiff:0=
+   sci-libs/dcmtk:0=
+   sci-libs/hdf5:0=[cxx]
+   sys-libs/zlib:0=
+   virtual/jpeg:0=
+   fftw? ( sci-libs/fftw:3.0= )
+   vtkglue? ( sci-libs/vtk:0=[python?] )
+"
+DEPEND="${RDEPEND}
+   python? (
+   ${PYTHON_DEPS}
+   >=dev-lang/swig-2.0:0
+   >=dev-cpp/gccxml-0.9.0_pre20120309
+   )
+   doc? ( app-doc/doxygen )
+"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+S="${WORKDIR}/ITK-${MY_PV}"
+
+pkg_pretend() {
+   if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
+   elog "To tune ITK to make the best use of working memory you 
can set"
+   elog "ITK_COMPUTER_MEMORY_SIZE=XX"
+   elog "in make.conf, default is 1 (unit is GB)"
+   fi
+   if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
+   elog "For Python language bindings, you can define the 
dimensions"
+   elog "you want to create bindings for by setting"
+   elog "ITK_WRAP_DIMS=X;Y;Z..."
+   elog "in make.conf, default is 2;3 for 2D and 3D data"
+   fi
+}
+
+src_prepare() {
+   sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\
+   Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt
+   default
+}
+
+src_configure() {
+   local mycmakeargs=(
+   -DBUILD_SHARED_LIBS=ON
+   -DITK_USE_SYSTEM_DCMTK=ON
+   -DGDCM_USE_SYSTEM_OPENJPEG=ON
+   -DITK_USE_SYSTEM_DOUBLECONVERSION=ON
+   -DITK_USE_SYSTEM_CASTXML=ON
+   -DITK_USE_SYSTEM_HDF5=ON
+   -DITK_USE_SYSTEM_JPEG=ON
+   -DITK_USE_SYSTEM_PNG=ON
+   -DITK_USE_SYSTEM_SWIG=ON
+   -DITK_USE_SYSTEM_TIFF=ON
+   -DITK_USE_SYSTEM_ZLIB=ON
+   -DITK_USE_KWSTYLE=OFF
+   -DITK_BUILD_DEFAULT_MODULES=ON
+   -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+   -DWRAP_ITK_JAVA=OFF
+   -DWRAP_ITK_TCL=OFF
+   
-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
+   
-DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${MY_PV}/.ExternalData"
+   -DBUILD_TESTING="$(usex test ON OFF)"
+   -DBUILD_EXAMPLES="$(usex examples ON OFF)"
+   -DITK_USE_REVIEW="$(usex review ON OFF)"
+   -DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
+   )
+   if use fftw; then
+   mycmakeargs+=(
+   -DUSE_FFTWD=ON
+   -DUSE_FFTWF=ON
+   -DUSE_SYSTEM_FFTW=ON
+   -DITK_WRAP_double=ON
+   -DITK_WRAP_vector_double=ON
+   -DITK_WRAP_covariant_vector_double=ON
+   -DITK_WRAP_complex_double=ON
+   )
+   fi
+   if use vtkglue; then
+   mycmakeargs+=(
+   -DModule_ITKVtkGlue=ON
+   )
+   fi
+   if use python; then
+   mycmakeargs+=(
+   -DITK_WRAP_PYTHON=ON
+   -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
+   )
+   else
+   mycmakeargs+=(
+   -DITK_WRAP_PYTHON=OFF
+   )
+   fi
+   cmake-utils_src_configure
+}
+
+src_install() {
+

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2017-06-23 Thread Justin Lecher

commit: 039697bf6b87b07578ac626d015e71bc38901722
Author: tharvik  users  noreply  github  com>
AuthorDate: Sun Jun 18 22:31:57 2017 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Fri Jun 23 09:11:41 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=039697bf

sci-libs/itk: bump to 4.12.0

Package-Manager: Portage-2.3.5, Repoman-2.3.1
Closes: https://github.com/gentoo/sci/pull/792

 sci-libs/itk/itk-4.12.0.ebuild | 136 +
 1 file changed, 136 insertions(+)

diff --git a/sci-libs/itk/itk-4.12.0.ebuild b/sci-libs/itk/itk-4.12.0.ebuild
new file mode 100644
index 0..a9633748b
--- /dev/null
+++ b/sci-libs/itk/itk-4.12.0.ebuild
@@ -0,0 +1,136 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils toolchain-funcs cmake-utils python-single-r1
+
+MYPN=InsightToolkit
+MYP=${MYPN}-${PV}
+DOC_PV=4.5.0
+
+DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
+HOMEPAGE="http://www.itk.org;
+SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.xz
+   doc? ( mirror://sourceforge/${PN}/Doxygen${MYPN}-${DOC_PV}.tar.gz )"
+RESTRICT="primaryuri"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="debug doc examples +fftw itkv3compat python review cpu_flags_x86_sse2 
test vtkglue"
+
+RDEPEND="
+   dev-libs/double-conversion:0=
+   media-libs/libpng:0=
+   media-libs/tiff:0=
+   sci-libs/dcmtk:0=
+   sci-libs/hdf5:0=[cxx]
+   sys-libs/zlib:0=
+   virtual/jpeg:0=
+   fftw? ( sci-libs/fftw:3.0= )
+   vtkglue? ( sci-libs/vtk:0=[python?] )
+"
+DEPEND="${RDEPEND}
+   python? (
+   ${PYTHON_DEPS}
+   >=dev-lang/swig-2.0:0
+   >=dev-cpp/gccxml-0.9.0_pre20120309
+   )
+   doc? ( app-doc/doxygen )
+"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+S="${WORKDIR}/${MYP}"
+
+PATCHES=(
+   "${FILESDIR}/nrrdio-linking.patch"
+)
+
+get_memory() {
+   free --giga | grep Mem | cut -d ' ' -f 15 || die 'unable to get memory 
size'
+}
+
+src_configure() {
+   sed -i \
+   -e '/find_package/d' \
+   Modules/ThirdParty/DoubleConversion/CMakeLists.txt || die
+
+   local mycmakeargs=(
+   -DBUILD_SHARED_LIBS=ON
+   -DITK_USE_SYSTEM_DCMTK=ON
+   -DITK_USE_SYSTEM_DOUBLECONVERSION=ON
+   -DITK_USE_SYSTEM_HDF5=ON
+   -DITK_USE_SYSTEM_JPEG=ON
+   -DITK_USE_SYSTEM_PNG=ON
+   -DITK_USE_SYSTEM_SWIG=ON
+   -DITK_USE_SYSTEM_TIFF=ON
+   -DITK_USE_SYSTEM_ZLIB=ON
+   -DITK_BUILD_DEFAULT_MODULES=ON
+   -DITK_COMPUTER_MEMORY_SIZE="$(get_memory)"
+   -DITK_WRAP_JAVA=OFF
+   -DITK_WRAP_TCL=OFF
+   -DBUILD_TESTING=$(usex test)
+   -DBUILD_EXAMPLES=$(usex examples)
+   -DITK_USE_REVIEW=$(usex review)
+   -DITKV3_COMPATIBILITY=$(usex itkv3compat)
+   -DVNL_CONFIG_ENABLE_SSE2=$(usex cpu_flags_x86_sse2)
+   )
+   if use fftw; then
+   mycmakeargs+=(
+   -DUSE_FFTWD=ON
+   -DUSE_FFTWF=ON
+   -DUSE_SYSTEM_FFTW=ON
+   -DITK_USE_SYSTEM_FFTW=ON
+   -DITK_WRAPPING=ON
+   -DITK_WRAP_double=ON
+   -DITK_WRAP_vector_double=ON
+   -DITK_WRAP_covariant_vector_double=ON
+   -DITK_WRAP_complex_double=ON
+   )
+   fi
+   if use vtkglue; then
+   mycmakeargs+=(
+   -DModule_ITKVtkGlue=ON
+   )
+   fi
+   mycmakeargs+=(
+   -DITK_WRAP_PYTHON=$(usex python ON OFF)
+   )
+
+   cmake-utils_src_configure
+}
+
+src_install() {
+   cmake-utils_src_install
+
+   if use examples; then
+   insinto /usr/share/doc/${PF}/examples
+   docompress -x /usr/share/doc/${PF}/examples
+   doins -r "${S}"/Examples/*
+   fi
+
+   echo "ITK_DATA_ROOT=${EROOT%/}/usr/share/${PN}/data" > ${T}/40${PN}
+   local ldpath="${EROOT%/}/usr/$(get_libdir)/InsightToolkit"
+   if use python; then
+   echo 
"PYTHONPATH=${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> 
"${T}"/40${PN}
+   
ldpath="${ldpath}:${EROOT%/}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
+   fi
+   echo "LDPATH=${ldpath}" >> "${T}"/40${PN}
+   doenvd "${T}"/40${PN}
+
+   if use doc; then
+   insinto /usr/share/doc/${PF}/api-docs
+   cd "${WORKDIR}"/html
+   rm  *.md5 || die "Failed to remove superfluous hashes"
+   einfo "Installing API docs. This may take some time."
+   insinto /usr/share/doc/${PF}/api-docs

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2015-09-21 Thread Justin Lecher

commit: 409d2cef58b65ec5e0730c5c1d634b6e886dacba
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Sep 21 17:44:03 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Sep 21 17:44:03 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=409d2cef

sci-libs/itk: Add subslot operators

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher  gentoo.org>

 sci-libs/itk/itk-4.4.2-r1.ebuild | 14 --
 sci-libs/itk/itk-4.4.2.ebuild| 16 
 sci-libs/itk/itk-4.5.1.ebuild| 10 ++
 3 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/sci-libs/itk/itk-4.4.2-r1.ebuild b/sci-libs/itk/itk-4.4.2-r1.ebuild
index 7133d57..54c0e41 100644
--- a/sci-libs/itk/itk-4.4.2-r1.ebuild
+++ b/sci-libs/itk/itk-4.4.2-r1.ebuild
@@ -25,17 +25,19 @@ IUSE="debug doc examples fftw itkv3compat python review 
cpu_flags_x86_sse2 test
 
 RDEPEND="
sci-libs/hdf5[cxx]
-   virtual/jpeg
-   media-libs/libpng
-   media-libs/tiff:0
+   virtual/jpeg:0=
+   media-libs/libpng:0=
+   media-libs/tiff:0=
sys-libs/zlib
fftw? ( sci-libs/fftw:3.0 )
vtkglue? ( sci-libs/vtk )
 "
 DEPEND="${RDEPEND}
-   python? ( ${PYTHON_DEPS}
- >=dev-lang/swig-2.0
- >=dev-cpp/gccxml-0.9.0_pre20120309 )
+   python? (
+   ${PYTHON_DEPS}
+   >=dev-lang/swig-2.0:0
+   >=dev-cpp/gccxml-0.9.0_pre20120309
+   )
doc? ( app-doc/doxygen )
 "
 

diff --git a/sci-libs/itk/itk-4.4.2.ebuild b/sci-libs/itk/itk-4.4.2.ebuild
index 815d529..d00be94 100644
--- a/sci-libs/itk/itk-4.4.2.ebuild
+++ b/sci-libs/itk/itk-4.4.2.ebuild
@@ -14,8 +14,6 @@ DESCRIPTION="NLM Insight Segmentation and Registration 
Toolkit"
 HOMEPAGE="http://www.itk.org;
 SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz"
 
-RESTRICT="primaryuri"
-
 LICENSE="Apache-2.0"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
@@ -23,16 +21,18 @@ IUSE="debug examples fftw itkv3compat python review 
cpu_flags_x86_sse2 test"
 
 RDEPEND="
sci-libs/hdf5[cxx]
-   virtual/jpeg
-   media-libs/libpng
-   media-libs/tiff:0
+   virtual/jpeg:0=
+   media-libs/libpng:0=
+   media-libs/tiff:0=
sys-libs/zlib
fftw? ( sci-libs/fftw:3.0 )
 "
 DEPEND="${RDEPEND}
-   python? ( ${PYTHON_DEPS}
- >=dev-lang/swig-2.0
- >=dev-cpp/gccxml-0.9.0_pre20120309 )
+   python? (
+   ${PYTHON_DEPS}
+   >=dev-lang/swig-2.0:0
+   >=dev-cpp/gccxml-0.9.0_pre20120309
+   )
 "
 
 S="${WORKDIR}/${MYP}"

diff --git a/sci-libs/itk/itk-4.5.1.ebuild b/sci-libs/itk/itk-4.5.1.ebuild
index a91ebf9..88981b4 100644
--- a/sci-libs/itk/itk-4.5.1.ebuild
+++ b/sci-libs/itk/itk-4.5.1.ebuild
@@ -30,14 +30,16 @@ RDEPEND="
sci-libs/dcmtk:0=
sci-libs/hdf5:0=[cxx]
sys-libs/zlib:0=
-   virtual/jpeg
+   virtual/jpeg:0=
fftw? ( sci-libs/fftw:3.0= )
vtkglue? ( sci-libs/vtk:0=[python?] )
 "
 DEPEND="${RDEPEND}
-   python? ( ${PYTHON_DEPS}
- >=dev-lang/swig-2.0
- >=dev-cpp/gccxml-0.9.0_pre20120309 )
+   python? (
+   ${PYTHON_DEPS}
+   >=dev-lang/swig-2.0:0
+   >=dev-cpp/gccxml-0.9.0_pre20120309
+   )
doc? ( app-doc/doxygen )
 "

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

2015-02-02 Thread Justin Lecher

commit: 1bfa3886b36ee376ddfacb3ddca97481a8ffb25f
Author: Marius Brehler marbre AT linux DOT sungazer DOT de
AuthorDate: Sun Feb  1 18:10:30 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Sun Feb  1 18:10:30 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1bfa3886

sci-libs/itk: Convert sse2 to cpu_flags_x86_sse2

---
 sci-libs/itk/ChangeLog   | 7 ++-
 sci-libs/itk/itk-4.4.2-r1.ebuild | 6 +++---
 sci-libs/itk/itk-4.4.2.ebuild| 6 +++---
 sci-libs/itk/itk-4.5.1.ebuild| 6 +++---
 4 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/sci-libs/itk/ChangeLog b/sci-libs/itk/ChangeLog
index b68a4b5..f623cac 100644
--- a/sci-libs/itk/ChangeLog
+++ b/sci-libs/itk/ChangeLog
@@ -1,7 +1,12 @@
 # ChangeLog for sci-libs/itk
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  01 Feb 2015; Marius Brehler mar...@linux.sungazer.de
+  itk-4.4.2.ebuild, itk-4.4.2-r1.ebuild, itk-4.5.1.ebuild:
+  Convert sse2 to cpu_flags_x86_sse2
+
+
 *itk-4.5.1 (10 Apr 2014)
 
   10 Apr 2014; Sébastien Fabbro bicat...@gentoo.org

diff --git a/sci-libs/itk/itk-4.4.2-r1.ebuild b/sci-libs/itk/itk-4.4.2-r1.ebuild
index 7693b08..5aa31c8 100644
--- a/sci-libs/itk/itk-4.4.2-r1.ebuild
+++ b/sci-libs/itk/itk-4.4.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -21,7 +21,7 @@ RESTRICT=primaryuri
 LICENSE=Apache-2.0
 SLOT=0
 KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
-IUSE=debug doc examples fftw itkv3compat python review sse2 test vtkglue
+IUSE=debug doc examples fftw itkv3compat python review cpu_flags_x86_sse2 
test vtkglue
 
 RDEPEND=
sci-libs/hdf5[cxx]
@@ -73,7 +73,7 @@ src_configure() {
$(cmake-utils_use_build test TESTING)
$(cmake-utils_use review ITK_USE_REVIEW)
$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
-   $(cmake-utils_use sse2 VNL_CONFIG_ENABLE_SSE2)
+   $(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2)
)
if use fftw; then
mycmakeargs+=(

diff --git a/sci-libs/itk/itk-4.4.2.ebuild b/sci-libs/itk/itk-4.4.2.ebuild
index 75706d2..07c0a91 100644
--- a/sci-libs/itk/itk-4.4.2.ebuild
+++ b/sci-libs/itk/itk-4.4.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -19,7 +19,7 @@ RESTRICT=primaryuri
 LICENSE=Apache-2.0
 SLOT=0
 KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
-IUSE=debug examples fftw itkv3compat python review sse2 test
+IUSE=debug examples fftw itkv3compat python review cpu_flags_x86_sse2 test
 
 RDEPEND=
sci-libs/hdf5[cxx]
@@ -69,7 +69,7 @@ src_configure() {
$(cmake-utils_use_build test TESTING)
$(cmake-utils_use review ITK_USE_REVIEW)
$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
-   $(cmake-utils_use sse2 VNL_CONFIG_ENABLE_SSE2)
+   $(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2)
)
if use fftw; then
mycmakeargs+=(

diff --git a/sci-libs/itk/itk-4.5.1.ebuild b/sci-libs/itk/itk-4.5.1.ebuild
index ba0ca28..ed7f183 100644
--- a/sci-libs/itk/itk-4.5.1.ebuild
+++ b/sci-libs/itk/itk-4.5.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -21,7 +21,7 @@ RESTRICT=primaryuri
 LICENSE=Apache-2.0
 SLOT=0
 KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
-IUSE=debug doc examples fftw itkv3compat python review sse2 test vtkglue
+IUSE=debug doc examples fftw itkv3compat python review cpu_flags_x86_sse2 
test vtkglue
 
 RDEPEND=
dev-libs/double-conversion:0=
@@ -94,7 +94,7 @@ src_configure() {
$(cmake-utils_use_build examples EXAMPLES)
$(cmake-utils_use review ITK_USE_REVIEW)
$(cmake-utils_use itkv3compat ITKV3_COMPATIBILITY)
-   $(cmake-utils_use sse2 VNL_CONFIG_ENABLE_SSE2)
+   $(cmake-utils_use cpu_flags_x86_sse2 VNL_CONFIG_ENABLE_SSE2)
)
if use fftw; then
mycmakeargs+=(

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/files/, sci-libs/itk/

2014-04-10 Thread Sebastien Fabbro

commit: be1836449dfcf8edc09329c66bb389a879f15fac
Author: Sébastien Fabbro bicatali AT gentoo DOT org
AuthorDate: Thu Apr 10 17:59:32 2014 +
Commit: Sebastien Fabbro bicatali AT gentoo DOT org
CommitDate: Thu Apr 10 17:59:32 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=be183644

sci-libs/itk: Version bump. Reworked ebuild

Package-Manager: portage-2.2.8-prefix

---
 sci-libs/itk/ChangeLog |  11 ++
 ...p-TransformFileReader-TransformFileWriter.patch |  50 +++
 ...itkQuasiNewtonOptimizerv4-wrapping-warnin.patch |  28 
 ...itkGradientDescentOptimizerv4-wrapping-wa.patch |  73 ++
 ...OptimizerParameterScalesEstimatorTemplate.patch |  30 
 .../0005-make-gdcm-helper-library-static.patch |  11 ++
 sci-libs/itk/files/nrrdio-linking.patch|  15 ++
 sci-libs/itk/itk-4.5.1.ebuild  | 154 +
 8 files changed, 372 insertions(+)

diff --git a/sci-libs/itk/ChangeLog b/sci-libs/itk/ChangeLog
index 6aeb88a..b68a4b5 100644
--- a/sci-libs/itk/ChangeLog
+++ b/sci-libs/itk/ChangeLog
@@ -2,6 +2,17 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*itk-4.5.1 (10 Apr 2014)
+
+  10 Apr 2014; Sébastien Fabbro bicat...@gentoo.org
+  +files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch,
+  +files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch,
+  +files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch,
+  +files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch,
+  +files/0005-make-gdcm-helper-library-static.patch,
+  +files/nrrdio-linking.patch, +itk-4.5.1.ebuild:
+  sci-libs/itk: Version bump. Reworked ebuild
+
   06 Jan 2014; Justin Lecher j...@gentoo.org metadata.xml:
   Fix missing local USE
 

diff --git 
a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
 
b/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
new file mode 100644
index 000..094ee32
--- /dev/null
+++ 
b/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch
@@ -0,0 +1,50 @@
+From d069b7b94287dae15fcaf707775f5dd2bbebcc38 Mon Sep 17 00:00:00 2001
+From: Matt McCormick matt.mccorm...@kitware.com
+Date: Wed, 5 Feb 2014 15:52:34 -0500
+Subject: [PATCH 1/3] BUG: Wrap TransformFileReader, TransformFileWriter.
+
+Missing CMakeLists.txt in the wrapping directory.  Need to explicitly include
+the headers after Template was appended to the class name.
+
+Suggested-by: Sami Koho sami.k...@gmail.com
+
+Change-Id: I6f994bb18f37d5adf1d0f0311fa73506c41239a7
+---
+ Modules/IO/TransformBase/wrapping/CMakeLists.txt  | 3 +++
+ Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap | 2 ++
+ Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap | 2 ++
+ 3 files changed, 7 insertions(+)
+ create mode 100644 Modules/IO/TransformBase/wrapping/CMakeLists.txt
+
+diff --git a/Modules/IO/TransformBase/wrapping/CMakeLists.txt 
b/Modules/IO/TransformBase/wrapping/CMakeLists.txt
+new file mode 100644
+index 000..6072567
+--- /dev/null
 b/Modules/IO/TransformBase/wrapping/CMakeLists.txt
+@@ -0,0 +1,3 @@
++itk_wrap_module(ITKIOTransformBase)
++itk_auto_load_submodules()
++itk_end_wrap_module()
+diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap 
b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
+index 9b52fbc..662df9e 100644
+--- a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
 b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap
+@@ -1,3 +1,5 @@
++set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
++itk_wrap_include(itkTransformFileReader.h)
+ itk_wrap_class(itk::TransformFileReaderTemplate POINTER)
+   foreach(t ${WRAP_ITK_REAL})
+ itk_wrap_template(${ITKM_${t}} ${ITKT_${t}})
+diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap 
b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
+index 4f1ac4a..356aaf3 100644
+--- a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
 b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap
+@@ -1,3 +1,5 @@
++set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
++itk_wrap_include(itkTransformFileWriter.h)
+ itk_wrap_class(itk::TransformFileWriterTemplate POINTER)
+   foreach(t ${WRAP_ITK_REAL})
+ itk_wrap_template(${ITKM_${t}} ${ITKT_${t}})
+-- 
+1.8.5.3
+

diff --git 
a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
 
b/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
new file mode 100644
index 000..4c74d54
--- /dev/null
+++ 
b/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch
@@ -0,0 +1,28 @@
+From 66d2955fbe5528d9df216c639277d1d2686447e5 Mon Sep 17 00:00:00 2001
+From: Michka Popoff michkapop...@gmail.com
+Date: Fri, 7 Feb 2014 19:24:49 +0100
+Subject: [PATCH 2/3] COMP:

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/files/, sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/files/, sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/, sci-libs/itk/files/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/

[gentoo-commits] proj/sci:master commit in: sci-libs/itk/files/, sci-libs/itk/

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