Merge remote-tracking branch 'upstream/master'

Author: jessdtate

.travis.yml

@@ -1,42 +1,31 @@
-sudo: required
-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 -DBUILD_TESTING:BOOL=OFF ../Superbuild
-  - make -j8
+  - make -j4 1> /dev/null
 #  make SCIRunTestData_external
 #  && make test
 

ci/linux_before_install.sh

@@ -43,32 +43,17 @@ using namespace SCIRun;
 
 ReportFieldInfoAlgorithm::Outputs ReportFieldInfoAlgorithm::update_input_attributes(FieldHandle f) const
 {
-  VField* vfield = f->vfield();
-  VMesh*  vmesh  = f->vmesh();
+  auto vfield = f->vfield();
+  auto vmesh  = f->vmesh();
 
-  ReportFieldInfoAlgorithm::Outputs output;
+  Outputs output;
 
   if (vfield && vmesh)
   {
-    // Get name of field
-    //std::string fldname;
-    //if (f->get_property("name",fldname))
-    //{
-    //  gui_fldname_.set(fldname);
-    //}
-    //else
-    //{
-    //  gui_fldname_.set("--- Name Not Assigned ---");
-    //}
-    
-    // Generation
-    //gui_generation_.set(to_string(f->generation));
-    
-    // Typename
     auto td = f->get_type_description();
     if (td)
     {
-      const std::string &tname = td->get_name();
+      const auto& tname = td->get_name();
       output.type = tname;
     }
     else
@@ -99,7 +84,7 @@ ReportFieldInfoAlgorithm::Outputs ReportFieldInfoAlgorithm::update_input_attribu
     Point center;
     Vector size;
 
-    const BBox bbox = vmesh->get_bounding_box();
+    const auto bbox = vmesh->get_bounding_box();
     if (bbox.valid())
     {
       size = bbox.diagonal();
@@ -111,7 +96,7 @@ ReportFieldInfoAlgorithm::Outputs ReportFieldInfoAlgorithm::update_input_attribu
     {
       warning("Input Field is empty.");
 
-      const double nan = std::numeric_limits<double>::quiet_NaN();
+      const auto nan = std::numeric_limits<double>::quiet_NaN();
       output.center = Point(nan,nan,nan);
       output.size = Vector(nan, nan, nan);
 
@@ -133,7 +118,7 @@ ReportFieldInfoAlgorithm::Outputs ReportFieldInfoAlgorithm::update_input_attribu
       output.dims[p] = static_cast<double>(dim[p]);
 
     output.geometricSize = 0.0;
-    for (VMesh::Elem::index_type idx=0; idx< output.numelements_; idx++)
+    for (VMesh::Elem::index_type idx=0; idx< output.numelements_; ++idx)
     {
       output.geometricSize += vmesh->get_size(idx);
     }

ci/linux_install.sh

@@ -30,7 +30,6 @@
 #define ALGORITHMS_MATH_REPORTFIELDINFO_H
 
 #include <Core/Algorithms/Base/AlgorithmBase.h>
-#include <Core/Algorithms/Base/AlgorithmMacros.h>
 #include <Core/GeometryPrimitives/Vector.h>
 #include <Core/GeometryPrimitives/Point.h>
 #include <Core/Algorithms/Field/share.h>
@@ -43,7 +42,7 @@ namespace Fields {
   class SCISHARE ReportFieldInfoAlgorithm : public AlgorithmBase
   {
   public:
-    typedef SCIRun::FieldHandle Inputs;
+    typedef FieldHandle Inputs;
 
     struct SCISHARE Outputs
     {
@@ -61,10 +60,10 @@ namespace Fields {
 
     static std::string summarize(const Outputs& info);
 
-    AlgorithmOutput run(const AlgorithmInput& input) const;
+    AlgorithmOutput run(const AlgorithmInput& input) const override;
 
   private:
-    Outputs update_input_attributes(SCIRun::FieldHandle f) const;
+    Outputs update_input_attributes(FieldHandle f) const;
   };
 
 }}}}

ci/osx_before_install.sh

@@ -31,6 +31,7 @@
 #include <Core/Datatypes/Legacy/Field/FieldInformation.h>
 #include <Core/Datatypes/MatrixTypeConversions.h>
 #include <Core/Algorithms/Base/AlgorithmPreconditions.h>
+#include <Core/Algorithms/Base/AlgorithmVariableNames.h>
 #include <Core/Algorithms/Legacy/FiniteElements/BuildMatrix/BuildFEMatrix.h>
 #include <Core/Algorithms/DataIO/ReadMatrix.h>
 #include <Testing/Utils/SCIRunUnitTests.h>
@@ -70,18 +71,16 @@ namespace FEInputData
 
   DenseMatrixHandle nullConductivityMatrix()
   {
-    return DenseMatrixHandle();
+    return nullptr;
   }
 }
 
 TEST(BuildFEMatrixAlgorithmTests, ThrowsForNullMesh)
 {
   using namespace FEInputData;
   BuildFEMatrixAlgo algo;
-  SparseRowMatrixHandle output;
 
-  EXPECT_FALSE(algo.run(FieldHandle(), nullConductivityMatrix(), output));
-  /// @todo: consider throwing an exception instead of returning false
+  EXPECT_THROW(algo.run(withInputData((Variables::InputField, nullptr))), AlgorithmProcessingException);
 }
 
 TEST(BuildFEMatrixAlgorithmTests, TestMeshSize1e1)
@@ -94,7 +93,10 @@ TEST(BuildFEMatrixAlgorithmTests, TestMeshSize1e1)
 
   BuildFEMatrixAlgo algo;
   SparseRowMatrixHandle output;
-  ASSERT_TRUE(algo.run(mesh, nullConductivityMatrix(), output));
+  ASSERT_NO_THROW(
+    auto out = algo.run(withInputData((Variables::InputField, mesh)));
+    output = out.get<SparseRowMatrix>(BuildFEMatrixAlgo::Stiffness_Matrix);
+  );
 
   ASSERT_THAT(output, NotNull());
 
@@ -117,7 +119,10 @@ TEST(BuildFEMatrixAlgorithmTests, TestMeshSize1e3)
 
   BuildFEMatrixAlgo algo;
   SparseRowMatrixHandle output;
-  ASSERT_TRUE(algo.run(mesh, nullConductivityMatrix(), output));
+  ASSERT_NO_THROW(
+    auto out = algo.run(withInputData((Variables::InputField, mesh)));
+    output = out.get<SparseRowMatrix>(BuildFEMatrixAlgo::Stiffness_Matrix);
+  );
 
   ASSERT_THAT(output, NotNull());
 
@@ -140,7 +145,10 @@ TEST(BuildFEMatrixAlgorithmTests, TestMeshSize1e4)
 
   BuildFEMatrixAlgo algo;
   SparseRowMatrixHandle output;
-  ASSERT_TRUE(algo.run(mesh, nullConductivityMatrix(), output));
+  ASSERT_NO_THROW(
+    auto out = algo.run(withInputData((Variables::InputField, mesh)));
+    output = out.get<SparseRowMatrix>(BuildFEMatrixAlgo::Stiffness_Matrix);
+  );
 
   ASSERT_THAT(output, NotNull());
 
@@ -164,7 +172,10 @@ TEST(BuildFEMatrixAlgorithmTests, DISABLED_TestMeshSize1e5)
 
   BuildFEMatrixAlgo algo;
   SparseRowMatrixHandle output;
-  ASSERT_TRUE(algo.run(mesh, nullConductivityMatrix(), output));
+  ASSERT_NO_THROW(
+    auto out = algo.run(withInputData((Variables::InputField, mesh)));
+    output = out.get<SparseRowMatrix>(BuildFEMatrixAlgo::Stiffness_Matrix);
+  );
 
   ASSERT_THAT(output, NotNull());
 
@@ -188,7 +199,10 @@ TEST(BuildFEMatrixAlgorithmTests, DISABLED_TestMeshSize1e6)
 
   BuildFEMatrixAlgo algo;
   SparseRowMatrixHandle output;
-  ASSERT_TRUE(algo.run(mesh, nullConductivityMatrix(), output));
+  ASSERT_NO_THROW(
+    auto out = algo.run(withInputData((Variables::InputField, mesh)));
+    output = out.get<SparseRowMatrix>(BuildFEMatrixAlgo::Stiffness_Matrix);
+  );
 
   ASSERT_THAT(output, NotNull());