Merge pull request #53 from mathLab/v9.5.0

No warnings. New VERSION. Github.

.clang-format

@@ -1,5 +1,5 @@
 #
-# The clang-format (Clang 6) style file used by deal.II.
+# The clang-format (Clang 11) style file used by deal.II.
 #
 
 AccessModifierOffset: -2
@@ -26,8 +26,9 @@ BinPackArguments: false
 BinPackParameters: false
 
 BraceWrapping:
+  AfterCaseLabel: true
   AfterClass: true
-  AfterControlStatement: true
+  AfterControlStatement: Always
   AfterEnum: true
   AfterExternBlock: true
   AfterFunction: true
@@ -36,6 +37,8 @@ BraceWrapping:
   AfterUnion: true
   BeforeCatch: true
   BeforeElse: true
+  BeforeLambdaBody: false
+  BeforeWhile: true
   IndentBraces: true
   SplitEmptyFunction: false
   SplitEmptyRecord: false
@@ -69,6 +72,8 @@ IncludeCategories:
     Priority: -1
 # deal.II folders in sorted order:
   - Regex:    "deal.II/algorithms/.*\\.h"
+    Priority: 100
+  - Regex:    "deal.II/arborx/.*\\.h"
     Priority: 110
   - Regex:    "deal.II/base/.*\\.h"
     Priority: 120
@@ -112,6 +117,8 @@ IncludeCategories:
     Priority: 300
   - Regex:    "deal.II/sundials/.*\\.h"
     Priority: 310
+  - Regex:    "deal.II/trilinos/.*\\.h"
+    Priority: 320
 # put boost right after deal:
   - Regex: "<boost.*>"
     Priority: 500
@@ -127,6 +134,10 @@ IncludeCategories:
 # should not be caught here
   - Regex: "<[a-z_]+>"
     Priority: 100000
+# make sure that "../tests.h" appears before all other local include files
+# such that replacing Assert in tests also applies to the testing header files.
+  - Regex: "\\.\\./tests\\.h"
+    Priority: 200000
 
 IndentCaseLabels: true
 IndentPPDirectives: AfterHash

.github/workflows/doxygen.yml

@@ -0,0 +1,28 @@
+name: Doxygen
+
+on:
+  push:
+    branches: [ master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Get deal.tag
+      run: |
+        wget https://www.dealii.org/developer/doxygen/deal.tag
+        
+    - name: Build Doxygen documentation
+      uses: mattnotmitt/[email protected]
+      with:
+        doxyfile-path: "./docs/Doxyfile"
+        working-directory: "."
+
+    - name: Publish Doxygen documentation
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./doc/html/
+

.github/workflows/indentation.yml

@@ -0,0 +1,22 @@
+name: Indent
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    container:
+      image: dealii/dealii:v9.5.0-jammy
+      options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Check indentation
+      run: |
+        git config --global --add safe.directory /__w/pi-BEM/pi-BEM
+        ./scripts/check_indentation.sh 

.github/workflows/tests.yml

@@ -0,0 +1,48 @@
+name: GitHub CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  debug:
+
+    runs-on: ubuntu-latest
+
+    container:
+      image: dealii/dealii:v9.5.0-jammy
+      options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Test debug
+      run: |
+         rm -rf build_linux_debug
+         mkdir build_linux_debug
+         cd build_linux_debug
+         cmake .. -GNinja -DCMAKE_BUILD_TYPE=Debug
+         ninja
+         ctest -N
+         ctest --output-on-failure
+
+  release:
+
+    runs-on: ubuntu-latest
+
+    container:
+      image: dealii/dealii:v9.5.0-jammy
+      options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Test release
+      run: |
+          rm -rf build_linux_release
+          mkdir build_linux_release
+          cd build_linux_release
+          cmake .. -GNinja -DCMAKE_BUILD_TYPE=Release
+          ninja
+          ctest -N
+          ctest --output-on-failure

CMakeLists.txt

@@ -36,7 +36,7 @@ IF(NOT "${_main}" STREQUAL "")
 ENDIF()
 
 
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8.8)
+CMAKE_MINIMUM_REQUIRED(VERSION 3.13.4)
 
 FIND_PACKAGE(deal.II 9.5 REQUIRED
   HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
@@ -61,6 +61,8 @@ if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
 set(CMAKE_MACOSX_RPATH 1)
 endif()
 
+OPTION(BEM_ENABLE_TESTING 
+"Enable deal.II style tests in this application." ON)
 
 
 # We one library and one target for each type of deal.II library
@@ -111,13 +113,12 @@ endif()
 
 
 # Doxygen
-if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in)
+if(EXISTS ${CMAKE_SOURCE_DIR}/docs/Doxyfile)
     find_package(Doxygen)
     if(DOXYGEN_FOUND)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
     add_custom_target(doc
-    ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    ${DOXYGEN_EXECUTABLE} ${CMAKE_SOURCE_DIR}/docs/Doxyfile
+    WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
     COMMENT "Generating API documentation with Doxygen" VERBATIM
     )
     endif(DOXYGEN_FOUND)
@@ -130,5 +131,3 @@ ADD_CUSTOM_TARGET(indent
   WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
   COMMAND ./scripts/indent
 )
-
-

VERSION

@@ -1 +1 @@
-9.1.1
+9.5.0

docker/debug-release/Dockerfile → docker/Dockerfile

@@ -1,14 +1,9 @@
-FROM heltai/deal2lkit:debug-release
-
-MAINTAINER [email protected]
+FROM dealii/dealii:v9.5.0-jammy
 
 # pi-BEM master image
 RUN git clone https://github.com/mathLab/pi-BEM/ &&\
     mkdir pi-BEM/build && cd pi-BEM/build &&\
     cmake -DCMAKE_BUILD_TYPE=DebugRelease \
-	  -GNinja \
-          ../ && \
-    ninja -j4 
-
-# Need this for Travis!
-USER root
+    -GNinja \
+    ../ && \
+    ninja