Merge branch 'master' into 160-add-pre-compiled-postprocessings-based-on-mgisfunction

Author: thelfer

.github/workflows/doxygen.yml

@@ -0,0 +1,43 @@
+name: Doxygen
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+
+jobs:
+
+  doc-html:
+    
+    runs-on: ubuntu-latest
+    
+    steps:
+
+    - uses: actions/checkout@v2
+    
+    - name: Install Doxygen
+      run: sudo apt-get install doxygen graphviz -y
+      shell: bash
+    
+    - name: Configure CMake
+      run: |
+        cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} \
+              -Denable-doxygen-doc=ON                                               \
+              -Denable-parallel-stl-algorithms=OFF
+    
+    - name: Generate doxygen
+      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} --target doc-html 
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        personal_token: ${{ secrets.DEPLOY_TO_THELFER_GITHUB_IO }}
+        publish_branch: master
+        publish_dir: ${{github.workspace}}/build/docs/doxygen/html/ 
+        external_repository: thelfer/thelfer.github.io
+        destination_dir: mgis/doxygen/

CMakeLists.txt

@@ -75,6 +75,24 @@ if(enable-python-bindings)
   set(CPACK_COMPONENT_PYTHON_BINDINGS_DESCRIPTION
     "Contains the python bindings for MGIS")
   set(CPACK_COMPONENT_PYTHON_BINDINGS_DEPENDS mgis)
+  # store the location of the python modules in the MGIS_PYTHON_MODULES_INSTALL_DIRECTORY variable
+  if(MGIS_APPEND_SUFFIX)
+    if(WIN32)
+      set(MGIS_PYTHON_MODULES_INSTALL_DIRECTORY
+          bin/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages/mgis_${MGIS_SUFFIX_FOR_PYTHON_MODULES})
+    else(WIN32)
+      set(MGIS_PYTHON_MODULES_INSTALL_DIRECTORY
+          "lib${LIB_SUFFIX}/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages/mgis_${MGIS_SUFFIX_FOR_PYTHON_MODULES}")
+    endif(WIN32)
+  else(MGIS_APPEND_SUFFIX)
+    if(WIN32)
+      set(MGIS_PYTHON_MODULES_INSTALL_DIRECTORY
+          "bin/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages/mgis")
+    else(WIN32)
+      set(MGIS_PYTHON_MODULES_INSTALL_DIRECTORY
+          "lib${LIB_SUFFIX}/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages/mgis")
+    endif(WIN32)
+  endif(MGIS_APPEND_SUFFIX)
 endif(enable-python-bindings)
 
 # fenics-bindings (placed before compiler detection)
@@ -96,6 +114,26 @@ if(enable-julia-bindings)
   set(CMAKE_CXX_STANDARD "${_CMAKE_CXX_STANDARD}")
 endif(enable-julia-bindings)
 
+# HDF5 support (optional)
+
+option(enable-hdf5-support "enable HDF5 support" OFF)
+option(enable-hdf5-automatic-support "if set, try to support HDF5, even if not explicitly requested by enable-hdf5-support" ON)
+if(enable-hdf5-support)
+  find_package(HDF5 REQUIRED COMPONENTS CXX)
+else(enable-hdf5-support)
+  if(enable-hdf5-automatic-support)
+    find_package(HDF5 COMPONENTS CXX)
+  endif(enable-hdf5-automatic-support)
+endif(enable-hdf5-support)
+if(HDF5_FOUND)
+  set(MGIS_HDF5_SUPPORT ON)
+  MESSAGE(STATUS "hdf5 headers     : " ${HDF5_INCLUDE_DIRS})
+  MESSAGE(STATUS "hdf5 librairies  : " ${HDF5_LIBRARIES})
+  MESSAGE(STATUS "hdf5 definitions : " ${HDF5_DEFINITIONS})
+else(HDF5_FOUND)
+  set(MGIS_HDF5_SUPPORT OFF)
+endif(HDF5_FOUND)
+
 # summary
 
 if(enable-c-bindings)
@@ -114,6 +152,10 @@ if(enable-fenics-bindings)
   message(STATUS "FEniCS bindings support enabled")
 endif(enable-fenics-bindings)
 
+if(MGIS_HDF5_SUPPORT)
+  message(STATUS "HDF5 support enabled")
+endif(MGIS_HDF5_SUPPORT)
+
 find_package(Threads)
 # if(MINGW)
 #   file(WRITE "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/thread-mingw.cxx"
@@ -189,7 +231,7 @@ if(enable-doxygen-doc)
     list(APPEND CPACK_COMPONENTS_ALL doxygen)
     set(CPACK_COMPONENT_DOXYGEN_DESCRIPTION
       "Contains MGIS' doxygen documentation")
-    set(GENERATE_DOXYGEN ON)
+    set(MGIS_GENERATE_DOXYGEN ON)
   else(DOXYGEN_FOUND)
     message(FATAL_ERROR "doxygen is required")
   endif(DOXYGEN_FOUND)
@@ -241,6 +283,8 @@ add_subdirectory(include)
 add_subdirectory(src)
 add_subdirectory(tests)
 add_subdirectory(bindings)
+# shall be included after the other directories
+add_subdirectory(env)
 
 # Packaging
 if(MFrontGenericInterfaceSupportDevelopmentVersion)

Doxyfile.in

@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = @PACKAGE_NAME@
+PROJECT_NAME           = MGIS
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -1117,7 +1117,7 @@ HTML_STYLESHEET        =
 # list). For an example see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  = 
+HTML_EXTRA_STYLESHEET  = @PROJECT_SOURCE_DIR@/docs/doxygen/doxygen-awesome-css/doxygen-awesome.css
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
@@ -1129,35 +1129,7 @@ HTML_EXTRA_STYLESHEET  =
 
 HTML_EXTRA_FILES       = 
 
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
-# will adjust the colors in the style sheet and background images according to
-# this color. Hue is specified as an angle on a colorwheel, see
-# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
-# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
-# purple, and 360 is red again.
-# Minimum value: 0, maximum value: 359, default value: 220.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_HUE    = 220
-
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
-# in the HTML output. For a value of 0 the output will use grayscales only. A
-# value of 255 will produce the most vivid colors.
-# Minimum value: 0, maximum value: 255, default value: 100.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_SAT    = 100
-
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
-# luminance component of the colors in the HTML output. Values below 100
-# gradually make the output lighter, whereas values above 100 make the output
-# darker. The value divided by 100 is the actual gamma applied, so 80 represents
-# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
-# change the gamma.
-# Minimum value: 40, maximum value: 240, default value: 80.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_GAMMA  = 80
+HTML_COLORSTYLE = LIGHT
 
 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
 # page will contain the date and time when the page was generated. Setting this
@@ -1403,7 +1375,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.

INSTALL-cmake.md

@@ -66,6 +66,13 @@ Options
 - `enable-exceptions`: use exceptions to report contract violation and error reporting.
    By default, contract violation leads to abort the program.
 - `enable-parallel-stl-algorithms`: by default, STL algorithms are used if available
+- `enable-hdf5-support`: enable HDF5 support for save/restore
+  operations. Note that if this support is not explicitely requested,
+  `MGIS` still tries by default to support `HDF5` but configuration will
+  not fail if the `HDF5` library is not found. See
+  `enable-hdf5-automatic-support` for details.
+- `enable-hdf5-automatic-support`: if set, `MGIS` tries by default to
+  support `HDF5` even if enable-hdf5-support` is not set.
 
 `cmake` usefull variables
 =======================

bindings/c/include/MGIS/Behaviour/MaterialStateManager.h

@@ -46,6 +46,12 @@ typedef enum {
   MGIS_BV_LOCAL_STORAGE = 0,
   MGIS_BV_EXTERNAL_STORAGE = 1
 } mgis_bv_MaterialStateManagerStorageMode;
+
+typedef enum {
+  MGIS_BV_NO_UPDATE_POLICY = 0,
+  MGIS_BV_UPDATE_POLICY = 1
+} mgis_bv_MaterialStateManagerUpdatePolicy;
+
 /*!
  * \brief bind the gradients to the given array
  * \param[in,out] s: initializer
@@ -155,6 +161,19 @@ mgis_bv_material_state_manager_get_internal_state_variables_stride(
 MGIS_C_EXPORT mgis_status
 mgis_bv_material_state_manager_set_uniform_scalar_material_property(
     mgis_bv_MaterialStateManager* const, const char* const, const mgis_real);
+/*!
+ * \brief set the value of an uniform scalar material property
+ * \param[in] s: state manager
+ * \param[in] n: name of the material property
+ * \param[in] v: value of the material property
+ * \param[in] p: update policy
+ */
+MGIS_C_EXPORT mgis_status
+mgis_bv_material_state_manager_set_uniform_scalar_material_property2(
+    mgis_bv_MaterialStateManager* const,
+    const char* const,
+    const mgis_real,
+    const mgis_bv_MaterialStateManagerUpdatePolicy);
 /*!
  * \brief set the value of an uniform material property
  * \param[in] s: state manager
@@ -168,6 +187,21 @@ mgis_bv_material_state_manager_set_uniform_material_property(
     const char* const,
     mgis_real* const,
     const mgis_bv_MaterialStateManagerStorageMode);
+/*!
+ * \brief set the value of an uniform material property
+ * \param[in] s: state manager
+ * \param[in] n: name of the material property
+ * \param[in] v: values of the material property
+ * \param[in] sm: storage mode
+ * \param[in] p: update policy
+ */
+MGIS_C_EXPORT mgis_status
+mgis_bv_material_state_manager_set_uniform_material_property2(
+    mgis_bv_MaterialStateManager* const,
+    const char* const,
+    mgis_real* const,
+    const mgis_bv_MaterialStateManagerStorageMode,
+    const mgis_bv_MaterialStateManagerUpdatePolicy);
 /*!
  * \brief set the value of an uniform material property
  * \param[in] s: state manager
@@ -181,6 +215,21 @@ mgis_bv_material_state_manager_set_non_uniform_material_property(
     const char* const,
     mgis_real* const,
     const mgis_bv_MaterialStateManagerStorageMode);
+/*!
+ * \brief set the value of an uniform material property
+ * \param[in] s: state manager
+ * \param[in] n: name of the material property
+ * \param[in] v: values of the material property
+ * \param[in] sm: storage mode
+ * \param[in] p: update policy
+ */
+MGIS_C_EXPORT mgis_status
+mgis_bv_material_state_manager_set_non_uniform_material_property2(
+    mgis_bv_MaterialStateManager* const,
+    const char* const,
+    mgis_real* const,
+    const mgis_bv_MaterialStateManagerStorageMode,
+    const mgis_bv_MaterialStateManagerUpdatePolicy);
 
 MGIS_C_EXPORT mgis_status
 mgis_bv_material_state_manager_is_material_property_defined(
@@ -206,6 +255,17 @@ mgis_bv_material_state_manager_get_non_uniform_material_property(
 MGIS_C_EXPORT mgis_status
 mgis_bv_material_state_manager_set_uniform_scalar_mass_density(
     mgis_bv_MaterialStateManager* const, const mgis_real);
+/*!
+ * \brief set the value of an uniform scalar mass density
+ * \param[in] s: state manager
+ * \param[in] v: value of the mass density
+ * \param[in] p: update policy
+ */
+MGIS_C_EXPORT mgis_status
+mgis_bv_material_state_manager_set_uniform_scalar_mass_density2(
+    mgis_bv_MaterialStateManager* const,
+    const mgis_real,
+    const mgis_bv_MaterialStateManagerUpdatePolicy);
 /*!
  * \brief set the value of an uniform mass density
  * \param[in] s: state manager
@@ -217,6 +277,19 @@ mgis_bv_material_state_manager_set_non_uniform_mass_density(
     mgis_bv_MaterialStateManager* const,
     mgis_real* const,
     const mgis_bv_MaterialStateManagerStorageMode);
+/*!
+ * \brief set the value of an uniform mass density
+ * \param[in] s: state manager
+ * \param[in] v: values of the mass density
+ * \param[in] sm: storage mode
+ * \param[in] p: update policy
+ */
+MGIS_C_EXPORT mgis_status
+mgis_bv_material_state_manager_set_non_uniform_mass_density2(
+    mgis_bv_MaterialStateManager* const,
+    mgis_real* const,
+    const mgis_bv_MaterialStateManagerStorageMode,
+    const mgis_bv_MaterialStateManagerUpdatePolicy);
 
 MGIS_C_EXPORT mgis_status
 mgis_bv_material_state_manager_is_mass_density_defined(
@@ -240,20 +313,43 @@ MGIS_C_EXPORT mgis_status
 mgis_bv_material_state_manager_set_uniform_scalar_external_state_variable(
     mgis_bv_MaterialStateManager* const, const char* const, const mgis_real);
 
+MGIS_C_EXPORT mgis_status
+mgis_bv_material_state_manager_set_uniform_scalar_external_state_variable2(
+    mgis_bv_MaterialStateManager* const,
+    const char* const,
+    const mgis_real,
+    const mgis_bv_MaterialStateManagerUpdatePolicy);
+
 MGIS_C_EXPORT mgis_status
 mgis_bv_material_state_manager_set_uniform_external_state_variable(
     mgis_bv_MaterialStateManager* const,
     const char* const,
     mgis_real* const,
     const mgis_bv_MaterialStateManagerStorageMode);
 
+MGIS_C_EXPORT mgis_status
+mgis_bv_material_state_manager_set_uniform_external_state_variable2(
+    mgis_bv_MaterialStateManager* const,
+    const char* const,
+    mgis_real* const,
+    const mgis_bv_MaterialStateManagerStorageMode,
+    const mgis_bv_MaterialStateManagerUpdatePolicy);
+
 MGIS_C_EXPORT mgis_status
 mgis_bv_material_state_manager_set_non_uniform_external_state_variable(
     mgis_bv_MaterialStateManager* const,
     const char* const,
     mgis_real* const,
     const mgis_bv_MaterialStateManagerStorageMode);
 
+MGIS_C_EXPORT mgis_status
+mgis_bv_material_state_manager_set_non_uniform_external_state_variable2(
+    mgis_bv_MaterialStateManager* const,
+    const char* const,
+    mgis_real* const,
+    const mgis_bv_MaterialStateManagerStorageMode,
+    const mgis_bv_MaterialStateManagerUpdatePolicy);
+
 MGIS_C_EXPORT mgis_status
 mgis_bv_material_state_manager_is_external_state_variable_defined(
     int* const, const mgis_bv_MaterialStateManager* const, const char* const);