merging with master

Author: jessdtate

.github/CONTRIBUTING.md

@@ -0,0 +1,9 @@
+TODO: Contribution guide. Follow this example:
+
+https://github.com/atom/atom/blob/master/CONTRIBUTING.md
+
+TODO add contribution guidelines. These could include:
+
+    Steps for creating good issues or pull requests.
+    Links to external documentation, mailing lists, or a code of conduct.
+    Community and behavioral expectations.

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,31 @@
+### Prerequisites
+
+* [ ] Are you running the [latest version of SCIRun](https://github.com/SCIInstitute/SCIRun/releases)?
+[//]: # (* [ ] TODO: Did you check the [debugging guide](http://flight-manual.atom.io/hacking-atom/sections/debugging/)?)
+[//]: # (* [ ] TODO: Did you check the [FAQs on Discuss](https://discuss.atom.io/c/faq)?)
+* [ ] Are you reporting to the [correct repository](https://github.com/SCIInstitute/SCIRun)?
+* [ ] Did you [perform a cursory search](https://github.com/SCIInstitute/SCIRun/issues) to see if your bug or enhancement is already reported?
+
+For more information on how to write a good [bug report](https://github.com/atom/atom/blob/master/CONTRIBUTING.md#how-do-i-submit-a-good-bug-report) or [enhancement request](https://github.com/atom/atom/blob/master/CONTRIBUTING.md#how-do-i-submit-a-good-enhancement-suggestion), see the `CONTRIBUTING` guide. These links point to another project, but most of the advice holds in general.
+
+### Description
+
+[Description of the bug or feature]
+
+For Mac crash bugs, please *DO NOT* paste an entire MacOS crash report here. Edit it down to just the stack trace of the thread that crashed, along with the general system info on the top.
+
+**In all bug cases, some combination of screenshots, sample network(s), and input data should be attached. You can use any cloud storage links you want for networks and data.**
+
+### Steps to Reproduce
+
+1. [First Step]
+2. [Second Step]
+3. [and so on...]
+
+**Expected behavior:** [What you expected to happen]
+
+**Actual behavior:** [What actually happened]
+
+### Versions
+
+You can get this information from executing `SCIRun --version` at the command line, or clicking on the version button in the bottom right corner of the GUI (which copies the version to the clipboard). Also, please include the OS and what version of the OS you're running.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,8 @@
+TODO
+
+In the new file, add your pull request template. This could include:
+
+    A reference to a related issue in your repository.
+    A description of the changes proposed in the pull request.
+    @mentions of the person or team responsible for reviewing proposed changes.
+

.travis.yml

@@ -1,43 +1,31 @@
-language:
-- cpp
+language: c++
 
-os:
-#Too many slow builds on Travis OSX images causing build errors. Turning off to speed up turn around. We can investigate later. For now, main developers should build on Mac before merging.
-#- osx
-- linux
-
-compiler:
-- clang
-# TODO: gcc chokes on a boost pthread usage, disabling for now.
-#- gcc
-
-#matrix:
-#  exclude:
-#  - os: osx
-#    compiler: g++
+matrix:
+  include:
+    - os: linux
+      dist: trusty
+      sudo: required
+      compiler: gcc
+    - os: linux
+      dist: trusty
+      sudo: required
+      compiler: clang
+#   - os: osx
+#     osx_image: xcode7.2
 
 # check environment (copied from libgit2sharp)
 before_install:
 - date -u
 - uname -a
-- if [ "${TRAVIS_OS_NAME}" = "linux" ]; then ./ci/linux_before_install.sh; fi
-- if [ "${TRAVIS_OS_NAME}" = "osx" ]; then ./ci/osx_before_install.sh; fi
-
-# make sure cmake is installed, set up latest GCC C++ compiler if necessary
-install:
- - if [ "${TRAVIS_OS_NAME}" = "linux" ]; then ./ci/linux_install.sh; fi
-# - if [ "${TRAVIS_OS_NAME}" = "linux" -a "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
- - if [ "${TRAVIS_OS_NAME}" = "osx" ]; then ./ci/osx_install.sh; fi
+#- sudo apt-get update -qq
 
 # TODO: could move script to separate file
 # Not running unit tests at the moment, so turn off testing, which will
 # hopefully make OS X builds a bit faster
 script:
   - cd bin
-  - cmake -DDOWNLOAD_TOOLKITS:BOOL=OFF -DRUN_BASIC_REGRESSION_TESTS:BOOL=OFF ../Superbuild
-  - make -j4
-  - cmake -DDOWNLOAD_TOOLKITS:BOOL=OFF -DRUN_BASIC_REGRESSION_TESTS:BOOL=OFF ../Superbuild # factory config needs 2 cmakes ?!?
-  - make -j4
+  - cmake -DDOWNLOAD_TOOLKITS:BOOL=OFF -DBUILD_TESTING:BOOL=OFF ../Superbuild
+  - make -j4 1> /dev/null
 #  make SCIRunTestData_external
 #  && make test
 

README.md

@@ -33,24 +33,24 @@ For documentation, please see: http://sciinstitute.github.io/SCIRun/
 
 ### Platform Notes
 #### Build requirements
-* OS X (tested on 10.7 and 10.8)
+* OS X (tested on 10.7-10.11)
   - Apple clang 5.1
   - Qt 4.8
     + Download from http://releases.qt-project.org/qt4/source/qt-mac-opensource-4.8.4.dmg.
-* Windows (tested on Windows 7, 8)
-  - Visual Studio 2013
+    + The above dmg will not work if using OS X 10.11. In this case Qt 4.8 can be acquired through macports using the command 'sudo port install qt4-mac' - more on macports here: https://www.macports.org/install.php
+* Windows (tested on Windows 7, 8, 10)
+  - Visual Studio 2013, 2015
   - Qt 4.8
     + Build from source (see http://scirundocwiki.sci.utah.edu/SCIRunDocs/index.php/CIBC:Seg3D2:Building_Releases#Installing_Qt_on_your_system_and_building_from_scratch for instructions), but be sure to download http://releases.qt-project.org/qt4/source/qt-everywhere-opensource-src-4.8.4.tar.gz.
-* Linux (tested on Ubuntu 12.10)
-  - gcc 4.6, 4.7
+* Linux (tested on Ubuntu 12.10, OpenSUSE Leap)
+  - gcc 4.6, 4.7, 4.8
   - Qt 4.8
     + Build from source (http://releases.qt-project.org/qt4/source/qt-everywhere-opensource-src-4.8.4.tar.gz), or use system libraries if available.
 * All platforms
   - CMake 2.8
-    + Root cmake file is SCIRun/src/CMakeLists.txt.
+    + Root cmake file is SCIRun/Superbuild/CMakeLists.txt.
     + Building in the source directory is not permitted.
     + Make sure BUILD_SHARED_LIBS is on (default setting).
-    + BUILD_WITH_PYTHON works on Windows, not yet (easily) on MacOS.
 
 #### CMake Build Generators
 * Windows
@@ -62,9 +62,11 @@ For documentation, please see: http://sciinstitute.github.io/SCIRun/
   - Unix Makefiles
 
 #### Unix Makefiles notes
-* Boost must be built before the SCIRun libraries.
-* Parallel make builds can be used as long the Boost target is built first, for example:
-  - make -j4 Boost_external && make -j4
+* Build Superbuild first (src/Superbuild), then subsequently, SCIRun can be built by itself (src/).
+* Included `build.sh` takes care of all this for you.
+
+### Tagging releases
+On an OSX system, run script `release.sh` in the `src` directory with the release name in format `alpha.XX` as a parameter.
 
 ### Questions and Answers
 For help, email the testing mailing list at [email protected].
@@ -74,7 +76,7 @@ For help, email the testing mailing list at [email protected].
 
   The MIT License
 
-  Copyright (c) 2015 Scientific Computing and Imaging Institute,
+  Copyright (c) 2016 Scientific Computing and Imaging Institute,
   University of Utah.
 
 

Superbuild/CMakeLists.txt

@@ -27,7 +27,10 @@
 CMAKE_MINIMUM_REQUIRED(VERSION 2.8.7 FATAL_ERROR)
 #CMAKE_MINIMUM_REQUIRED(VERSION 3.0 FATAL_ERROR)
 
-IF(CMAKE_VERSION VERSION_EQUAL 3.1 OR CMAKE_VERSION VERSION_GREATER 3.1)
+IF(POLICY CMP0043)
+  CMAKE_POLICY(SET CMP0043 OLD)
+ENDIF()
+IF(POLICY CMP0054)
   CMAKE_POLICY(SET CMP0054 NEW)
 ENDIF()
 

Superbuild/FreetypeExternal.cmake

@@ -0,0 +1,47 @@
+#  For more information, please see: http://software.sci.utah.edu
+# 
+#  The MIT License
+# 
+#  Copyright (c) 2015 Scientific Computing and Imaging Institute,
+#  University of Utah.
+# 
+#  
+#  Permission is hereby granted, free of charge, to any person obtaining a
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+# 
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software. 
+# 
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+#  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+#  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+#  DEALINGS IN THE SOFTWARE.
+
+SET_PROPERTY(DIRECTORY PROPERTY "EP_BASE" ${ep_base})
+SET(freetype_GIT_TAG "origin/seg3d_external_test")
+
+# If CMake ever allows overriding the checkout command or adding flags,
+# git checkout -q will silence message about detached head (harmless).
+ExternalProject_Add(Freetype_external
+  GIT_REPOSITORY "https://github.com/CIBC-Internal/freetype.git"
+  GIT_TAG ${freetype_GIT_TAG}
+  PATCH_COMMAND ""
+  INSTALL_DIR ""
+  INSTALL_COMMAND ""
+  CMAKE_CACHE_ARGS
+    -DCMAKE_VERBOSE_MAKEFILE:BOOL=${CMAKE_VERBOSE_MAKEFILE}
+    -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
+    -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON
+)
+
+ExternalProject_Get_Property(Freetype_external BINARY_DIR)
+SET(Freetype_DIR ${BINARY_DIR} CACHE PATH "")
+
+MESSAGE(STATUS "Freetype_DIR: ${Freetype_DIR}")

Superbuild/PythonExternal.cmake

@@ -137,7 +137,7 @@ IF(UNIX)
     IF(BUILD_HEADLESS)
       SET(PYTHON_MODULE_SEARCH_PATH Python.framework/Versions/${SCI_PYTHON_VERSION_SHORT}/${SCI_PYTHON_MODULE_PARENT_PATH}/${SCI_PYTHON_NAME} CACHE INTERNAL "Python modules." FORCE)
     ELSE()
-      SET(PYTHON_MODULE_SEARCH_PATH ../Frameworks/Python.framework/Versions/${SCI_PYTHON_VERSION_SHORT}/${SCI_PYTHON_MODULE_PARENT_PATH}/${SCI_PYTHON_NAME} CACHE INTERNAL "Python modules." FORCE)
+      SET(PYTHON_MODULE_SEARCH_PATH Frameworks/Python.framework/Versions/${SCI_PYTHON_VERSION_SHORT}/${SCI_PYTHON_MODULE_PARENT_PATH}/${SCI_PYTHON_NAME} CACHE INTERNAL "Python modules." FORCE)
     ENDIF()
     SET(SCI_PYTHON_FRAMEWORK_ARCHIVE ${INSTALL_DIR}/${python_FRAMEWORK_ARCHIVE})
   ELSE()

Superbuild/Superbuild.cmake

@@ -71,9 +71,8 @@ OPTION(BUILD_TESTING "Build with tests." ON)
 OPTION(BUILD_WITH_PYTHON "Build with python support." ON)
 
 ###########################################
-# Configure python
-OPTION(WITH_TETGEN "Build Tetgen." ON)
-MARK_AS_ADVANCED(WITH_TETGEN)
+# Configure tetgen
+OPTION(WITH_TETGEN "Build Tetgen." OFF)
 
 ###########################################
 # Configure Windows executable to run with
@@ -144,6 +143,7 @@ ADD_EXTERNAL( ${SUPERBUILD_DIR}/ZlibExternal.cmake Zlib_external )
 ADD_EXTERNAL( ${SUPERBUILD_DIR}/SQLiteExternal.cmake SQLite_external )
 ADD_EXTERNAL( ${SUPERBUILD_DIR}/LibPNGExternal.cmake LibPNG_external )
 ADD_EXTERNAL( ${SUPERBUILD_DIR}/TeemExternal.cmake Teem_external )
+ADD_EXTERNAL( ${SUPERBUILD_DIR}/FreetypeExternal.cmake Freetype_external )
 
 IF(BUILD_WITH_PYTHON)
   ADD_EXTERNAL( ${SUPERBUILD_DIR}/PythonExternal.cmake Python_external )
@@ -185,6 +185,7 @@ SET(SCIRUN_CACHE_ARGS
     "-DBoost_DIR:PATH=${Boost_DIR}"
     "-DTeem_DIR:PATH=${Teem_DIR}"
     "-DTetgen_DIR:PATH=${Tetgen_DIR}"
+    "-DFreetype_DIR:PATH=${Freetype_DIR}"
 )
 
 IF(BUILD_WITH_PYTHON)

Superbuild/TetgenExternal.cmake

@@ -26,7 +26,7 @@
 
 SET_PROPERTY(DIRECTORY PROPERTY "EP_BASE" ${ep_base})
 ExternalProject_Add(Tetgen_external
-  URL "http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz"
+  URL "http://www.tetgen.org/1.5/src/tetgen1.5.1-beta1.tar.gz"
   PATCH_COMMAND ""
   INSTALL_COMMAND ""
   CMAKE_CACHE_ARGS