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Merge branch 'master' into edit_bbox_refactor
2 parents 81bdf1a + 8955a0a commit 171bc8c

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‎.github/workflows/ccpp.yml‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ jobs:
2424
run: sudo apt-get update && sudo apt-get install mesa-common-dev libgl1-mesa-dev mesa-utils-extra libglapi-mesa ninja-build qt5-qmake qtbase5-dev libqt5opengl5-dev libqt5svg5-dev
2525

2626
- name: Build
27-
run: ./build.sh -DQt5_PATH=$(dpkg -L qtbase5-dev) -DUSER_PYTHON_VERSION="3.6.7" -j3
27+
run: ./build.sh -DQt5_PATH=$(dpkg -L qtbase5-dev) -j3
2828

2929
- name: Basic Test
3030
working-directory: bin/SCIRun
@@ -46,7 +46,7 @@ jobs:
4646
run: sudo apt-get update && sudo apt-get install mesa-common-dev libgl1-mesa-dev mesa-utils-extra libglapi-mesa ninja-build
4747

4848
- name: Build
49-
run: ./build.sh -DBUILD_HEADLESS:BOOL=ON -DUSER_PYTHON_VERSION="3.6.7" -DBUILD_TESTING:BOOL=ON -j3
49+
run: ./build.sh -DBUILD_HEADLESS:BOOL=ON -DBUILD_TESTING:BOOL=ON -j3
5050

5151
- name: Test
5252
working-directory: bin/SCIRun
@@ -68,7 +68,7 @@ jobs:
6868
run: sudo apt-get update && sudo apt-get install mesa-common-dev libgl1-mesa-dev mesa-utils-extra libglapi-mesa ninja-build qt5-qmake qtbase5-dev libqt5opengl5-dev libqt5svg5-dev
6969

7070
- name: Build
71-
run: ./build.sh -DQt5_PATH=$(dpkg -L qtbase5-dev) -DUSER_PYTHON_VERSION="3.6.7" -j3 -DBUILD_TESTING:BOOL=ON
71+
run: ./build.sh -DQt5_PATH=$(dpkg -L qtbase5-dev) -j3 -DBUILD_TESTING:BOOL=ON
7272

7373
- name: Test
7474
working-directory: bin/SCIRun
@@ -90,4 +90,4 @@ jobs:
9090
run: sudo apt-get update && sudo apt-get install mesa-common-dev libgl1-mesa-dev mesa-utils-extra libglapi-mesa ninja-build qt5-qmake qtbase5-dev libqt5opengl5-dev libqt5svg5-dev xorg-dev libglu1-mesa-dev
9191

9292
- name: Build
93-
run: ./build.sh -DQt5_PATH=$(dpkg -L qtbase5-dev) -DUSER_PYTHON_VERSION="3.6.7" -DWITH_OSPRAY:BOOL=ON
93+
run: ./build.sh -DQt5_PATH=$(dpkg -L qtbase5-dev) -DWITH_OSPRAY:BOOL=ON

‎.github/workflows/mac.yml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ jobs:
3434
ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers/X11/ /usr/local/include/X11
3535
3636
- name: make
37-
run: ./build.sh -DUSER_PYTHON_VERSION="3.6.7" -DQt5_PATH="${Qt5_Dir}"
37+
run: ./build.sh -DQt5_PATH="${Qt5_Dir}"
3838

3939
- name: Package
4040
working-directory: bin/SCIRun
@@ -91,7 +91,7 @@ jobs:
9191
ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers/X11/ /usr/local/include/X11
9292
9393
- name: make
94-
run: ./build.sh -DWITH_OSPRAY:BOOL=ON -DUSER_PYTHON_VERSION="3.6.7" -DQt5_PATH="${Qt5_Dir}"
94+
run: ./build.sh -DWITH_OSPRAY:BOOL=ON -DQt5_PATH="${Qt5_Dir}"
9595

9696
- name: Package
9797
working-directory: bin/SCIRun
@@ -133,7 +133,7 @@ jobs:
133133
ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers/X11/ /usr/local/include/X11
134134
135135
- name: Compile
136-
run: ./build.sh -DUSER_PYTHON_VERSION="3.6.7" -DBUILD_HEADLESS:BOOL=ON -DBUILD_TESTING:BOOL=ON
136+
run: ./build.sh -DBUILD_HEADLESS:BOOL=ON -DBUILD_TESTING:BOOL=ON
137137

138138
- name: Test
139139
working-directory: bin/SCIRun

‎.travis.yml‎

Lines changed: 17 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -55,18 +55,28 @@ matrix:
5555
dist: focal
5656
compiler: clang
5757
env: PYTHON_VERSION=3.8.2 OSPRAY_BUILD=OFF
58-
# - os: osx
59-
# osx_image: xcode9.4
60-
# env: PYTHON_VERSION=3.5.6 OSPRAY_BUILD=OFF
6158
- os: osx
6259
osx_image: xcode10.3
63-
env: PYTHON_VERSION=3.5.6 OSPRAY_BUILD=OFF
60+
env: PYTHON_VERSION=3.6.7 OSPRAY_BUILD=OFF
6461
- os: osx
65-
osx_image: xcode11
66-
env: PYTHON_VERSION=3.5.6 OSPRAY_BUILD=OFF
62+
osx_image: xcode11.3
63+
env: PYTHON_VERSION=3.6.7 OSPRAY_BUILD=OFF
64+
- os: osx
65+
osx_image: xcode11.3
66+
env: PYTHON_VERSION=3.7.9 OSPRAY_BUILD=OFF
6767
- os: osx
68-
osx_image: xcode11
68+
osx_image: xcode11.3
69+
env: PYTHON_VERSION=3.8.2 OSPRAY_BUILD=OFF
70+
- os: osx
71+
osx_image: xcode12.2
6972
env: PYTHON_VERSION=3.6.7 OSPRAY_BUILD=OFF
73+
- os: osx
74+
osx_image: xcode12.2
75+
env: PYTHON_VERSION=3.7.9 OSPRAY_BUILD=OFF
76+
- os: osx
77+
osx_image: xcode12.2
78+
env: PYTHON_VERSION=3.8.2 OSPRAY_BUILD=OFF
79+
7080

7181
before_install:
7282
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then date -u; fi

‎Superbuild/BoostExternal.cmake‎

Lines changed: 3 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -45,6 +45,7 @@ SET( boost_DEPENDENCIES )
4545
# explicitly set library list
4646
SET(boost_Libraries
4747
"atomic"
48+
"chrono"
4849
"date_time"
4950
"exception"
5051
"filesystem"
@@ -67,21 +68,12 @@ IF(UNIX)
6768
ADD_DEFINITIONS(-DBOOST_NO_CXX11_ALLOCATOR)
6869
ENDIF()
6970

71+
SET(boost_GIT_TAG "origin/v1.75.0")
72+
7073
# TODO: set up 64-bit build detection
7174
# Boost Jam needs to have 64-bit build explicitly configured
7275
IF(WIN32)
7376
SET(FORCE_64BIT_BUILD ON)
74-
SET(boost_GIT_TAG "origin/v1.67.0")
75-
ELSE()
76-
77-
if (${USER_PYTHON_VERSION} VERSION_GREATER "3.7")
78-
#message(${USER_PYTHON_VERSION} " needs a later boost")
79-
SET(boost_GIT_TAG "origin/v1.67.0")
80-
else()
81-
#message(${USER_PYTHON_VERSION} " ok with old boost")
82-
SET(boost_GIT_TAG "origin/v1.58.0")
83-
endif()
84-
8577
ENDIF()
8678

8779

‎Superbuild/PythonExternal.cmake‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -28,13 +28,14 @@
2828

2929
SET_PROPERTY(DIRECTORY PROPERTY "EP_BASE" ${ep_base})
3030

31-
SET(DEFAULT_PYTHON_VERSION "3.6.7")
32-
IF(WIN32)
33-
SET(DEFAULT_PYTHON_VERSION "3.8.2")
34-
ENDIF()
31+
SET(DEFAULT_PYTHON_VERSION "3.8.7")
32+
# TODO: check for Apple Silicon/arm64
33+
#IF(APPLE)
34+
# SET(DEFAULT_PYTHON_VERSION "3.8.7")
35+
#ENDIF()
3536

3637
set(USER_PYTHON_VERSION ${DEFAULT_PYTHON_VERSION} CACHE STRING "Branch name corresponding to Python version number")
37-
set_property(CACHE USER_PYTHON_VERSION PROPERTY STRINGS 3.4.3 3.5.6 3.6.7 3.7.1 3.8.2)
38+
set_property(CACHE USER_PYTHON_VERSION PROPERTY STRINGS 3.6.7 3.7.9 3.8.7 3.9.1)
3839

3940
string(REPLACE "." ";" USER_PYTHON_VERSION_LIST ${USER_PYTHON_VERSION})
4041
list(GET USER_PYTHON_VERSION_LIST 0 USER_PYTHON_VERSION_MAJOR)
@@ -69,7 +70,6 @@ IF(UNIX)
6970
# TODO: figure out pip package
7071
SET(python_CONFIGURE_FLAGS
7172
"--prefix=<INSTALL_DIR>"
72-
"--with-threads"
7373
"--with-ensurepip=no"
7474
)
7575
IF(APPLE)
@@ -95,7 +95,7 @@ IF(UNIX)
9595
GIT_REPOSITORY ${python_GIT_URL}
9696
GIT_TAG ${python_GIT_TAG}
9797
BUILD_IN_SOURCE ON
98-
CONFIGURE_COMMAND <SOURCE_DIR>/configure ${python_CONFIGURE_FLAGS}
98+
CONFIGURE_COMMAND ./configure ${python_CONFIGURE_FLAGS}
9999
PATCH_COMMAND ""
100100
)
101101
IF(APPLE)
@@ -154,15 +154,15 @@ IF(UNIX)
154154
SET(SCI_PYTHON_FRAMEWORK_ARCHIVE ${INSTALL_DIR}/${python_FRAMEWORK_ARCHIVE})
155155
ELSE()
156156
SET(SCI_PYTHON_ROOT_DIR ${INSTALL_DIR})
157-
SET(SCI_PYTHON_INCLUDE ${INSTALL_DIR}/include/${SCI_PYTHON_NAME}${ABIFLAGS})
157+
SET(SCI_PYTHON_INCLUDE ${INSTALL_DIR}/include/${SCI_PYTHON_NAME})
158158
SET(SCI_PYTHON_LIBRARY_DIR ${SCI_PYTHON_ROOT_DIR}/lib)
159159
SET(SCI_PYTHON_LINK_LIBRARY_DIRS ${SCI_PYTHON_LIBRARY_DIR})
160160
IF(SCIRUN_BITS MATCHES 64)
161161
LIST(APPEND SCI_PYTHON_LINK_LIBRARY_DIRS ${INSTALL_DIR}/lib64)
162162
SET(SCI_PYTHON_64BIT_MODULE_LIBRARY_PATH ${INSTALL_DIR}/lib64/${SCI_PYTHON_NAME} CACHE INTERNAL "Python modules." FORCE)
163163
ENDIF()
164164
SET(SCI_PYTHON_EXE ${INSTALL_DIR}/bin/${SCI_PYTHON_NAME})
165-
SET(SCI_PYTHON_LIBRARY ${SCI_PYTHON_NAME}${ABIFLAGS})
165+
SET(SCI_PYTHON_LIBRARY ${SCI_PYTHON_NAME})
166166

167167
# required by interpreter interface
168168
SET(PYTHON_MODULE_SEARCH_PATH ${SCI_PYTHON_MODULE_PARENT_PATH}/${SCI_PYTHON_NAME} CACHE INTERNAL "Python modules." FORCE)

‎Superbuild/UseBoost.cmake‎

Lines changed: 21 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -30,28 +30,32 @@ endif()
3030
foreach(lib ${SCI_BOOST_LIBRARY})
3131
add_library(${lib} STATIC IMPORTED GLOBAL)
3232

33-
if(CMAKE_GENERATOR MATCHES "Makefiles" AND CMAKE_BUILD_TYPE MATCHES "Debug")
33+
if((APPLE OR UNIX) AND CMAKE_BUILD_TYPE MATCHES "Debug")
3434
set(FULL_LIB_NAME "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}${lib}${DEBUG_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}")
35-
elseif(CMAKE_GENERATOR MATCHES "Makefiles")
36-
set(FULL_LIB_NAME "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}${lib}${CMAKE_STATIC_LIBRARY_SUFFIX}")
35+
elseif(APPLE OR UNIX)
36+
if(${lib} MATCHES "boost_python-mt")
37+
set(FULL_LIB_NAME "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}boost_python${USER_PYTHON_VERSION_MAJOR}${USER_PYTHON_VERSION_MINOR}-mt-x64${CMAKE_STATIC_LIBRARY_SUFFIX}")
38+
else()
39+
set(FULL_LIB_NAME "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}${lib}-x64${CMAKE_STATIC_LIBRARY_SUFFIX}")
40+
endif()
3741
else()
3842
if(${lib} MATCHES "boost_python-mt")
3943
if(WIN32)
40-
set(FULL_LIB_NAME_RELEASE "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}boost_python${USER_PYTHON_VERSION_MAJOR}${USER_PYTHON_VERSION_MINOR}-mt${CMAKE_STATIC_LIBRARY_SUFFIX}")
44+
set(FULL_LIB_NAME_RELEASE "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}boost_python${USER_PYTHON_VERSION_MAJOR}${USER_PYTHON_VERSION_MINOR}-mt-x64${CMAKE_STATIC_LIBRARY_SUFFIX}")
45+
set(FULL_LIB_NAME_DEBUG "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}boost_python${USER_PYTHON_VERSION_MAJOR}${USER_PYTHON_VERSION_MINOR}-mt${DEBUG_POSTFIX}-x64${CMAKE_STATIC_LIBRARY_SUFFIX}")
46+
else()
47+
set(FULL_LIB_NAME_RELEASE "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}boost_python${USER_PYTHON_VERSION_MAJOR}${USER_PYTHON_VERSION_MINOR}-mt${CMAKE_STATIC_LIBRARY_SUFFIX}")
4148
set(FULL_LIB_NAME_DEBUG "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}boost_python${USER_PYTHON_VERSION_MAJOR}${USER_PYTHON_VERSION_MINOR}-mt${DEBUG_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}")
42-
else(WIN32)
43-
if (${USER_PYTHON_VERSION} VERSION_GREATER "3.7")
44-
set(FULL_LIB_NAME_RELEASE "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}boost_python${USER_PYTHON_VERSION_MAJOR}${USER_PYTHON_VERSION_MINOR}-mt${CMAKE_STATIC_LIBRARY_SUFFIX}")
45-
set(FULL_LIB_NAME_DEBUG "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}boost_python${USER_PYTHON_VERSION_MAJOR}${USER_PYTHON_VERSION_MINOR}-mt${DEBUG_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}")
46-
else()
47-
set(FULL_LIB_NAME_RELEASE "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}boost_python3-mt${CMAKE_STATIC_LIBRARY_SUFFIX}")
48-
set(FULL_LIB_NAME_DEBUG "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}boost_python3-mt${DEBUG_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}")
49-
endif()
50-
endif(WIN32)
51-
else() # non-python libraries
52-
set(FULL_LIB_NAME_RELEASE "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}${lib}${CMAKE_STATIC_LIBRARY_SUFFIX}")
53-
set(FULL_LIB_NAME_DEBUG "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}${lib}${DEBUG_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}")
54-
endif()
49+
endif()
50+
else() # non-python libraries
51+
if(WIN32)
52+
set(FULL_LIB_NAME_RELEASE "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}${lib}-x64${CMAKE_STATIC_LIBRARY_SUFFIX}")
53+
set(FULL_LIB_NAME_DEBUG "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}${lib}${DEBUG_POSTFIX}$-x64${CMAKE_STATIC_LIBRARY_SUFFIX}")
54+
else()
55+
set(FULL_LIB_NAME_RELEASE "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}${lib}${CMAKE_STATIC_LIBRARY_SUFFIX}")
56+
set(FULL_LIB_NAME_DEBUG "${SCI_BOOST_LIBRARY_DIR}/${boost_LIB_PREFIX}${lib}${DEBUG_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}")
57+
endif()
58+
endif()
5559
endif()
5660

5761
message(STATUS "Configure Boost library ${lib}")

‎src/Core/Algorithms/DataIO/EigenMatrixFromScirunAsciiFormatConverter.cc‎

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,6 @@
2626
*/
2727

2828

29-
#include <boost/timer.hpp>
3029
#include <boost/scoped_ptr.hpp>
3130
#include <boost/regex.hpp>
3231
#include <boost/lexical_cast.hpp>
@@ -35,7 +34,6 @@
3534

3635
#include <iostream>
3736
#include <fstream>
38-
#include <streambuf>
3937

4038
#include <Core/Algorithms/DataIO/EigenMatrixFromScirunAsciiFormatConverter.h>
4139
#include <Core/Algorithms/Base/AlgorithmPreconditions.h>

‎src/Core/Algorithms/Legacy/Inverse/SolveInverseProblemWithStandardTikhonovImpl.cc‎

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -29,21 +29,16 @@
2929
*/
3030

3131

32-
#include <boost/bind.hpp>
33-
#include <boost/lexical_cast.hpp>
34-
3532
#include <Core/Algorithms/Legacy/Inverse/TikhonovAlgoAbstractBase.h>
3633
#include <Core/Algorithms/Legacy/Inverse/SolveInverseProblemWithStandardTikhonovImpl.h>
3734

38-
#include <Core/Datatypes/Matrix.h>
3935
#include <Core/Datatypes/DenseMatrix.h>
4036
#include <Core/Datatypes/DenseColumnMatrix.h>
4137
#include <Core/Datatypes/SparseRowMatrix.h>
4238
#include <Core/Datatypes/MatrixTypeConversions.h>
4339

4440
#include <Core/Algorithms/Base/AlgorithmPreconditions.h>
4541

46-
#include <Core/Logging/LoggerInterface.h>
4742
#include <Core/Utils/Exception.h>
4843

4944
using namespace SCIRun;

‎src/Core/Algorithms/Legacy/Inverse/SolveInverseProblemWithTSVD_impl.cc‎

Lines changed: 0 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -29,17 +29,10 @@
2929
*/
3030

3131

32-
// SCIRUN lybraries
33-
#include <boost/bind.hpp>
34-
#include <boost/lexical_cast.hpp>
35-
#include <Core/Datatypes/Matrix.h>
3632
#include <Core/Datatypes/DenseMatrix.h>
3733
#include <Core/Datatypes/DenseColumnMatrix.h>
3834
#include <Core/Datatypes/SparseRowMatrix.h>
39-
#include <Core/Datatypes/MatrixTypeConversions.h>
40-
#include <Core/Algorithms/Base/AlgorithmPreconditions.h>
4135
#include <Core/Logging/LoggerInterface.h>
42-
#include <Core/Utils/Exception.h>
4336

4437
// Tikhonov inverse libraries
4538
#include <Core/Algorithms/Legacy/Inverse/TikhonovAlgoAbstractBase.h>

‎src/Core/Algorithms/Legacy/Inverse/SolveInverseProblemWithTikhonovSVD_impl.cc‎

Lines changed: 0 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -29,23 +29,14 @@
2929
*/
3030

3131

32-
// SCIRUN lybraries
33-
#include <boost/bind.hpp>
34-
#include <boost/lexical_cast.hpp>
3532
#include <Core/Datatypes/Matrix.h>
3633
#include <Core/Datatypes/DenseMatrix.h>
3734
#include <Core/Datatypes/DenseColumnMatrix.h>
38-
#include <Core/Datatypes/SparseRowMatrix.h>
39-
#include <Core/Datatypes/MatrixTypeConversions.h>
40-
#include <Core/Algorithms/Base/AlgorithmPreconditions.h>
4135
#include <Core/Logging/LoggerInterface.h>
42-
#include <Core/Utils/Exception.h>
4336

4437
// Tikhonov inverse libraries
45-
#include <Core/Algorithms/Legacy/Inverse/TikhonovAlgoAbstractBase.h>
4638
#include <Core/Algorithms/Legacy/Inverse/SolveInverseProblemWithTikhonovSVD_impl.h>
4739

48-
// EIGEN LIBRARY
4940
#include <Eigen/Eigen>
5041
#include <Eigen/SVD>
5142

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