Merge branch 'SCIInstitute/master'

Author: allywarner

.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

@@ -1,3 +1,4 @@
+sudo: required
 language:
 - cpp
 
@@ -34,10 +35,8 @@ install:
 # 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 -j8
 #  make SCIRunTestData_external
 #  && make test
 

README.md

@@ -37,6 +37,7 @@ For documentation, please see: http://sciinstitute.github.io/SCIRun/
   - Apple clang 5.1
   - Qt 4.8
     + Download from http://releases.qt-project.org/qt4/source/qt-mac-opensource-4.8.4.dmg.
+    + 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)
   - Visual Studio 2013
   - Qt 4.8

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/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

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

build.sh

@@ -63,6 +63,7 @@ printhelp() {
     echo -e "--verbose\t\tTurn on verbose build"
 #    echo -e "--set-osx-version-min\tTarget a minimum Mac OS X version (currently ${OSX_TARGET_VERSION}, ${OSX_TARGET_ARCH}) [OS X only]"
 #    echo -e "--xcode-build\t\tConfigure and build Xcode project against ALL_BUILD target [OS X only]"
+    echo -e "--with-tetgen\t\tBuild SCIRun with Tetgen library"
     echo -e "--cmake=<path to cmake>\t\tUse given CMake"
     echo -e "--cmake-args=<cmake args>\t\tUse given CMake args"
     echo -e "--documentation\t\tEnable building documentation (requires LaTeX)"
@@ -169,7 +170,7 @@ find_cmake() {
 
 # handle both types of OS X generators
 configure_scirun_osx() {
-    local build_opts=$1
+    local build_opts=$@
 
     if [[ $setosxmin -eq 1 ]]; then
         build_opts="${build_opts} -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=${OSX_TARGET_VERSION} -DCMAKE_OSX_SYSROOT:PATH=${OSX_TARGET_VERSION_SDK} -DCMAKE_OSX_ARCHITECTURES:STRING=${OSX_TARGET_ARCH}"
@@ -184,7 +185,7 @@ configure_scirun_osx() {
 
 # generic Unix makefile build
 configure_scirun_make() {
-    local build_opts=$1
+    local build_opts=$@
 
     build_opts="${build_opts} -DCMAKE_BUILD_TYPE:STRING=${buildtype} -DCMAKE_VERBOSE_MAKEFILE:BOOL=${verbosebuild}"
 
@@ -198,7 +199,7 @@ configure_scirun() {
     fi
     try cd $builddir
 
-    local COMMON_BUILD_OPTS="-DBUILD_DOCUMENTATION:BOOL=$documentation"
+    local COMMON_BUILD_OPTS="-DWITH_TETGEN:BOOL=$tetgenbuild -DBUILD_DOCUMENTATION:BOOL=$documentation"
 
     if [[ $osx -eq 1 ]]; then
         configure_scirun_osx $COMMON_BUILD_OPTS
@@ -268,6 +269,8 @@ verbosebuild="OFF"
 builddir="$DIR/bin"
 xcodebuild=0
 documentation="OFF"
+# currently off by default
+tetgenbuild="OFF"
 
 echo "Parsing arguments..."
 while [[ $1 != "" ]]; do
@@ -308,6 +311,8 @@ while [[ $1 != "" ]]; do
             else
               echo "WARNING: Only OS X supports the --xcode-build flag."
             fi;;
+        --with-tetgen)
+            tetgenbuild="ON";;
         --documentation)
             documentation="ON";;
         -j*)

src/CMake/Modules/MacOSXBundleInfo.plist.in

@@ -32,6 +32,8 @@
 	<true/>
 	<key>NSHumanReadableCopyright</key>
 	<string>${MACOSX_BUNDLE_COPYRIGHT}</string>
+        <key>NSHighResolutionCapable</key>
+        <true/>
 	<key>CFBundleDocumentTypes</key>
 	<array>
 		<dict>