Merge v3.2.4 release candidate for final release

.github/workflows/windows_build_test.yml

@@ -3,33 +3,33 @@ name: Windows Build/Test
 on:
   # allows us to run workflows manually
   workflow_dispatch:
-  pull_request:
-    branches:
-      - develop
-    paths-ignore:
-      - '.github/workflows/docker_publish.yml'
-      - '.github/workflows/linux_build_test.yml'
-      - '.github/workflows/linux_upstream_test_*'
-      - '.github/workflows/mac_build_test.yml'
-      - '.github/workflows/housekeeping.yml'
-      - '.github/workflows/changelog_test.yml'
-      - '.github/actions/**'
-      - 'CI/**'
-      - 'doc/**'
+  # pull_request:
+  #   branches:
+  #     - develop
+  #   paths-ignore:
+  #     - '.github/workflows/docker_publish.yml'
+  #     - '.github/workflows/linux_build_test.yml'
+  #     - '.github/workflows/linux_upstream_test_*'
+  #     - '.github/workflows/mac_build_test.yml'
+  #     - '.github/workflows/housekeeping.yml'
+  #     - '.github/workflows/changelog_test.yml'
+  #     - '.github/actions/**'
+  #     - 'CI/**'
+  #     - 'doc/**'
 
-  push:
-    branches:
-      - develop
-    paths-ignore:
-      - '.github/workflows/docker_publish.yml'
-      - '.github/workflows/linux_build_test.yml'
-      - '.github/workflows/linux_upstream_test_*'
-      - '.github/workflows/mac_build_test.yml'
-      - '.github/workflows/housekeeping.yml'
-      - '.github/workflows/changelog_test.yml'
-      - '.github/actions/**'
-      - 'CI/**'
-      - 'doc/**'
+  # push:
+  #   branches:
+  #     - develop
+  #   paths-ignore:
+  #     - '.github/workflows/docker_publish.yml'
+  #     - '.github/workflows/linux_build_test.yml'
+  #     - '.github/workflows/linux_upstream_test_*'
+  #     - '.github/workflows/mac_build_test.yml'
+  #     - '.github/workflows/housekeeping.yml'
+  #     - '.github/workflows/changelog_test.yml'
+  #     - '.github/actions/**'
+  #     - 'CI/**'
+  #     - 'doc/**'
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -41,16 +41,16 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          auto-activate-base: true
+          auto-update-conda: true
+          auto-activate-base: false
           activate-environment: ""
 
       # yaml-cpp package has conflicting gtest headers and is not needed for this project
       - name: Conda dependencies
         shell:  bash -l {0}
         run: |
           conda install curl eigen
-          conda install -c conda-forge hdf5=1.10.6
-          conda remove -y yaml-cpp
+          conda install -c conda-forge hdf5==1.10.6
 
       - name: Environment Variables
         shell: bash -l {0}
@@ -114,12 +114,15 @@ jobs:
                 -DMOAB_DIR=../install_dir \
                 -DHDF5_ROOT="${CONDA_LOC}" \
                 -DHDF5_hdf5_LIBRARY_RELEASE="${CONDA_LOC}/lib/libhdf5_hl.lib;${CONDA_LOC}/lib/libhdf5.lib;${CONDA_LOC}/lib/zlib.lib;${CONDA_LOC}/lib/libhdf5_cpp.lib" \
-                -DCMAKE_INSTALL_PREFIX=../install_dir/ \
-                -DCMAKE_EXE_LINKER_FLAGS="" \
-                -DCMAKE_MODULE_LINKER_FLAGS="" \
-                -DCMAKE_SHARED_LINKER_FLAGS="" \
+                -DCMAKE_EXE_LINKER_FLAGS="/std:c++latest -DH5_BUILT_AS_DYNAMIC_LIB" \
+                -DCMAKE_MODULE_LINKER_FLAGS="/std:c++latest" \
+                -DCMAKE_SHARED_LINKER_FLAGS="/std:c++latest" \
                 -DCMAKE_STATIC_LINKER_FLAGS="" \
-                -DCMAKE_BUILD_TYPE=Release
+                -DCMAKE_EXE_LINKER_FLAGS="" \
+                -DCMAKE_INSTALL_PREFIX=../install_dir/ \
+                -DCMAKE_BUILD_TYPE=Release \
+                -DCMAKE_C_COMPILER="C:/Program Files (x86)/Microsoft Visual Studio/2019/Community/VC/Tools/MSVC/14.27.29110/bin/Hostx64/x64/cl.exe" \
+                -DCMAKE_CXX_COMPILER="C:/Program Files (x86)/Microsoft Visual Studio/2019/Community/VC/Tools/MSVC/14.27.29110/bin/Hostx64/x64/cl.exe"                
           cmake --build . --config Release
           cmake --install . --config Release
 

CMakeLists.txt

@@ -1,15 +1,16 @@
 project(DAGMC)
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 3.18)
 enable_language(CXX)
 
 # Set DAGMC version
 set(DAGMC_MAJOR_VERSION 3)
 set(DAGMC_MINOR_VERSION 2)
-set(DAGMC_PATCH_VERSION 3)
+set(DAGMC_PATCH_VERSION 4)
 set(DAGMC_VERSION ${DAGMC_MAJOR_VERSION}.${DAGMC_MINOR_VERSION}.${DAGMC_PATCH_VERSION})
 
 if(MSVC)
   set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+  add_definitions( -DH5_BUILT_AS_DYNAMIC_LIB )
 endif()
 
 
@@ -29,22 +30,6 @@ if(GIT_FOUND AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
   endif()
 
   option(GIT_SUBMODULE "Check submodules during build" ON)
-  if(GIT_SUBMODULE)
-    message(STATUS "Submodule update")
-    execute_process(COMMAND ${GIT_EXECUTABLE} "submodule" "update" "--init" "--recursive"
-                    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-                    RESULT_VARIABLE GIT_SUBMOD_RESULT)
-    if(NOT GIT_SUBMOD_RESULT EQUAL 0)
-      message(FATAL_ERROR "git submodule update --init --recursive failed with \
-        ${GIT_SUBMOD_RESULT}, please checkout submodules")
-    endif()
-  endif()
-endif()
-
-# Check to see if submodules exist (by checking one)
-if(NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/src/pyne/pyne/readme.rst")
-  message(FATAL_ERROR "The git submodules were not downloaded! GIT_SUBMODULE was \
-    turned off or failed. Please update submodules and try again.")
 endif()
 
 # Make the scripts in the "cmake" directory available to CMake

doc/CHANGELOG.rst

@@ -7,10 +7,13 @@ DAGMC Changelog
 Next version
 ====================
 
+v3.2.4
+====================
+
 **Changed:**
 
   * Adding info messages to CMake output for double down (#962)
-  * Update hdf5 to v1.14.3 from v1.10.4 (#931 #933)
+  * Update hdf5 to v1.14.3 from v1.10.4 for linux builds (#931 #933)
   * Ensure implicit complement handle is placed at the back of DAGMC volume indices (#935)
   * Update MOAB to 5.5.1 from 5.3.0 (#939 #940)
   * Update README regarding OpenMC (#938)
@@ -21,6 +24,9 @@ Next version
   * Update github actions to newer versions as necessary (#958)
   * CMake error message update (#960)
   * Updated documentation to build dependencies (#963)
+  * Pause support for Windows (#966)
+  * Localize invocation of git submodule for PyNE (#968)
+  * Fixed the name of the Graveyard and the Vaccuum to mat:Graveyard and mat:Vacuum (and lower case) (#971)
 
 v3.2.3
 ====================

src/CMakeLists.txt

@@ -15,6 +15,23 @@ if (BUILD_MCNP5 OR BUILD_MCNP6 OR BUILD_GEANT4 OR BUILD_FLUKA OR BUILD_CI_TESTS)
 endif ()
 if (BUILD_UWUW)
   add_subdirectory(uwuw)
+
+  if(GIT_SUBMODULE)
+    message(STATUS "Submodule update")
+    execute_process(COMMAND ${GIT_EXECUTABLE} "submodule" "update" "--init" "--recursive"
+                    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+                    RESULT_VARIABLE GIT_SUBMOD_RESULT)
+    if(NOT GIT_SUBMOD_RESULT EQUAL 0)
+      message(FATAL_ERROR "git submodule update --init --recursive failed with \
+        ${GIT_SUBMOD_RESULT}, please checkout submodules")
+    endif()
+  endif()
+
+  # Check to see if submodules exist (by checking one)
+  if(NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/pyne/pyne/readme.rst")
+    message(FATAL_ERROR "The git submodules were not downloaded! GIT_SUBMODULE was \
+      turned off or failed. Please update submodules and try again.")
+  endif()
   add_subdirectory(pyne)
 endif ()
 

src/dagmc/dagmcmetadata.cpp

@@ -209,32 +209,30 @@ void dagmcMetaData::parse_material_data() {
 
     // set the material value
     volume_material_property_data_eh[eh] = grp_name;
-
-    bool is_graveyard =
-        to_lower(grp_name).find(to_lower(graveyard_str)) != std::string::npos;
-    bool is_vacuum =
-        to_lower(grp_name).find(to_lower(vacuum_str)) != std::string::npos;
+    logger.message("Group name -- " + grp_name);
+    bool is_graveyard = (to_lower(grp_name) == to_lower(graveyard_mat_str()));
+    bool is_vacuum = (to_lower(grp_name) == to_lower(vacuum_mat_str()));
 
     // not graveyard or vacuum or implicit compliment
     if (!is_graveyard && !is_vacuum && !DAG->is_implicit_complement(eh)) {
       volume_material_data_eh[eh] = material_props[0];
     }
     // found graveyard
     else if (is_graveyard) {
-      volume_material_property_data_eh[eh] = "mat:Graveyard";
-      volume_material_data_eh[eh] = graveyard_str;
+      volume_material_property_data_eh[eh] = graveyard_mat_str();
+      volume_material_data_eh[eh] = graveyard_str();
     }
     // vacuum
     else if (is_vacuum) {
-      volume_material_property_data_eh[eh] = "mat:Vacuum";
-      volume_material_data_eh[eh] = vacuum_str;
+      volume_material_property_data_eh[eh] = vacuum_mat_str();
+      volume_material_data_eh[eh] = vacuum_str();
     }
     // implicit complement
     else if (DAG->is_implicit_complement(eh)) {
       if (implicit_complement_material == "") {
         logger.message("Implicit Complement assumed to be Vacuum");
-        volume_material_property_data_eh[eh] = "mat:Vacuum";
-        volume_material_data_eh[eh] = vacuum_str;
+        volume_material_property_data_eh[eh] = vacuum_mat_str();
+        volume_material_data_eh[eh] = vacuum_str();
       } else {
         volume_material_property_data_eh[eh] =
             "mat:" + implicit_complement_material;
@@ -379,18 +377,18 @@ void dagmcMetaData::parse_boundary_data() {
       exit(EXIT_FAILURE);
     }
     // 2d entities have been tagged with the boundary condition property
-    // ie. both surfaces and its members triangles,
+    // ie. both surfaces and its member triangles
 
     std::string bc_string = to_lower(boundary_assignment[0]);
 
-    if (bc_string.find(to_lower(reflecting_str)) != std::string::npos)
-      surface_boundary_data_eh[eh] = reflecting_str;
-    if (bc_string.find(to_lower(white_str)) != std::string::npos)
-      surface_boundary_data_eh[eh] = white_str;
-    if (bc_string.find(to_lower(periodic_str)) != std::string::npos)
-      surface_boundary_data_eh[eh] = periodic_str;
-    if (bc_string.find(to_lower(vacuum_str)) != std::string::npos)
-      surface_boundary_data_eh[eh] = vacuum_str;
+    if (bc_string.find(to_lower(reflecting_str())) != std::string::npos)
+      surface_boundary_data_eh[eh] = reflecting_str();
+    if (bc_string.find(to_lower(white_str())) != std::string::npos)
+      surface_boundary_data_eh[eh] = white_str();
+    if (bc_string.find(to_lower(periodic_str())) != std::string::npos)
+      surface_boundary_data_eh[eh] = periodic_str();
+    if (bc_string.find(to_lower(vacuum_str())) != std::string::npos)
+      surface_boundary_data_eh[eh] = vacuum_str();
   }
 }
 

src/dagmc/dagmcmetadata.hpp

@@ -316,6 +316,21 @@ class dagmcMetaData {
    */
   std::map<moab::EntityHandle, std::map<std::string, double>> importance_map;
 
+  // Getting some constant keyword values
+  const std::string& graveyard_str() const { return graveyard_str_; }
+  const std::string& vacuum_str() const { return vacuum_str_; }
+  const std::string& vacuum_mat_str() const { return vacuum_mat_str_; }
+  const std::string& graveyard_mat_str() const { return graveyard_mat_str_; }
+  const std::string& reflecting_str() const { return reflecting_str_; }
+  const std::string& white_str() const { return white_str_; }
+  const std::string& periodic_str() const { return periodic_str_; }
+
+  // Allowing modify some constant keyword values
+  void set_graveyard_str(std::string val) { graveyard_str_ = val; }
+  void set_vacuum_str(std::string val) { vacuum_str_ = val; }
+  void set_vacuum_mat_str(std::string val) { vacuum_mat_str_ = val; }
+  void set_graveyard_mat_str(std::string val) { graveyard_mat_str_ = val; }
+
   // private member variables
  private:
   /**
@@ -351,11 +366,14 @@ class dagmcMetaData {
   std::map<std::string, std::string> keyword_synonyms;
 
   // Some constant keyword values
-  const std::string graveyard_str{"Graveyard"};
-  const std::string vacuum_str{"Vacuum"};
-  const std::string reflecting_str{"Reflecting"};
-  const std::string white_str{"White"};
-  const std::string periodic_str{"Periodic"};
+  const std::string reflecting_str_{"Reflecting"};
+  const std::string white_str_{"White"};
+  const std::string periodic_str_{"Periodic"};
+  // Some less constant keyword values
+  std::string graveyard_str_{"Graveyard"};
+  std::string vacuum_str_{"Vacuum"};
+  std::string vacuum_mat_str_{"mat:Vacuum"};
+  std::string graveyard_mat_str_{"mat:Graveyard"};
 
   DagMC_Logger logger;
 };

src/dagmc/tests/dagmc_unit_tests.cpp

@@ -81,6 +81,63 @@ TEST_F(DagmcMetadataTest, TestMatAssigns) {
   }
 }
 //---------------------------------------------------------------------------//
+// FIXTURE-BASED TESTS: Tests to make sure that vacuum detection is done
+// properly
+//---------------------------------------------------------------------------//
+TEST_F(DagmcMetadataTest, TestVacuumName) {
+  // Test default behavior for vacuum name
+  {
+    // new metadata instance
+    dgm = std::make_shared<dagmcMetaData>(DAG.get());
+    // process
+    dgm->load_property_data();
+
+    int num_vol = DAG->num_entities(3);
+    std::vector<int> vol_ids = {1, 2, 3, 4};
+
+    std::vector<std::string> vacuum_names = {"Hydrogen", "Hydrogen", "Hydrogen",
+                                             "Vacuum"};
+    for (int id : vol_ids) {
+      std::string mat_prop = dgm->get_volume_property("material", id, false);
+      EXPECT_EQ(mat_prop, vacuum_names[id - 1]);
+    }
+  }
+
+  // Changing the vacuum name to detect mat:Hydrogen as the vacuum
+  {
+    dgm = std::make_shared<dagmcMetaData>(DAG.get());
+
+    dgm->set_vacuum_mat_str("mat:Hydrogen");
+    dgm->load_property_data();
+    int num_vol = DAG->num_entities(3);
+    std::vector<int> vol_ids = {1, 2, 3, 4};
+
+    std::vector<std::string> vacuum_names = {"Vacuum", "Vacuum", "Vacuum",
+                                             "Vacuum"};
+    for (int id : vol_ids) {
+      std::string mat_prop = dgm->get_volume_property("material", id, false);
+      EXPECT_EQ(mat_prop, vacuum_names[id - 1]);
+    }
+  }
+
+  // Ensuring that partial name overlap don't affect vacuum detection
+  {
+    dgm = std::make_shared<dagmcMetaData>(DAG.get());
+
+    dgm->set_vacuum_mat_str("Hydro");
+    dgm->load_property_data();
+    int num_vol = DAG->num_entities(3);
+    std::vector<int> vol_ids = {1, 2, 3, 4};
+
+    std::vector<std::string> vacuum_names = {"Hydrogen", "Hydrogen", "Hydrogen",
+                                             "Vacuum"};
+    for (int id : vol_ids) {
+      std::string mat_prop = dgm->get_volume_property("material", id, false);
+      EXPECT_EQ(mat_prop, vacuum_names[id - 1]);
+    }
+  }
+}
+//---------------------------------------------------------------------------//
 // FIXTURE-BASED TESTS: Tests to make sure that all densities have successfully
 // been assigned and successfully retreved from the metadata class
 // in this test there was no density data assigned, so it should be ""