Merge pull request #74 from nextsimdg/develop

Minimum Viable Model from develop.
nextsimhub · Feb 11, 2022 · 557e45d · 557e45d
2 parents f27de8c + e839aca
commit 557e45d
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diff --git a/.clang-format b/.clang-format
@@ -0,0 +1,166 @@
+---
+Language:        Cpp
+# BasedOnStyle:  WebKit
+AccessModifierOffset: -4
+AlignAfterOpenBracket: DontAlign
+AlignConsecutiveMacros: None
+AlignConsecutiveAssignments: None
+AlignConsecutiveBitFields: None
+AlignConsecutiveDeclarations: None
+AlignEscapedNewlines: Right
+AlignOperands:   DontAlign
+AlignTrailingComments: false
+AllowAllArgumentsOnNextLine: true
+AllowAllConstructorInitializersOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortEnumsOnASingleLine: true
+AllowShortBlocksOnASingleLine: Empty
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortLambdasOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: MultiLine
+AttributeMacros:
+  - __capability
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterCaseLabel:  false
+  AfterClass:      false
+  AfterControlStatement: Never
+  AfterEnum:       false
+  AfterFunction:   true
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  AfterExternBlock: false
+  BeforeCatch:     false
+  BeforeElse:      false
+  BeforeLambdaBody: false
+  BeforeWhile:     false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: All
+BreakBeforeConceptDeclarations: true
+BreakBeforeBraces: WebKit
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeComma
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     100
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: false
+DeriveLineEnding: true
+DerivePointerAlignment: false
+DisableFormat:   false
+EmptyLineBeforeAccessModifier: LogicalBlock
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: false
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+StatementAttributeLikeMacros:
+  - Q_EMIT
+IncludeBlocks:   Preserve
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+    SortPriority:    0
+    CaseSensitive:   false
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        3
+    SortPriority:    0
+    CaseSensitive:   false
+  - Regex:           '.*'
+    Priority:        1
+    SortPriority:    0
+    CaseSensitive:   false
+IncludeIsMainRegex: '(Test)?$'
+IncludeIsMainSourceRegex: ''
+IndentCaseLabels: false
+IndentCaseBlocks: false
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentExternBlock: AfterExternBlock
+IndentRequires:  false
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+InsertTrailingCommas: None
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: Inner
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 4
+ObjCBreakBeforeNestedBlockParam: true
+ObjCSpaceAfterProperty: true
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PenaltyIndentedWhitespace: 0
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SortJavaStaticImport: Before
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCaseColon: false
+SpaceBeforeCpp11BracedList: true
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceAroundPointerQualifiers: Default
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyBlock: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpaceBeforeSquareBrackets: false
+BitFieldColonSpacing: Both
+Standard:        Latest
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth:        8
+UseCRLF:         false
+UseTab:          Never
+WhitespaceSensitiveMacros:
+  - STRINGIZE
+  - PP_STRINGIZE
+  - BOOST_PP_STRINGIZE
+  - NS_SWIFT_NAME
+  - CF_SWIFT_NAME
+...
+
diff --git a/.github/workflows/clang-compile-tests.yml b/.github/workflows/clang-compile-tests.yml
@@ -0,0 +1,128 @@
+name: compile code and tests
+
+on:
+  push:
+    branches: [ main, develop, issue15_CI_workflow ]
+  pull_request:
+    branches: [ main, develop,  issue15_CI_workflow ]
+
+jobs:
+
+  clang-on-mac:
+
+    runs-on: macos-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: clang
+      run: |
+        brew install clang-format
+        cd core/src
+        clang-format --dry-run -Werror *cpp include/*hpp
+        cd -
+        for component in physics
+        do
+          cd $component/src
+          clang-format --dry-run -Werror *cpp include/*hpp
+          cd -
+        done
+  
+
+  build-on-ubuntu:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: installs
+      run: |
+        sudo apt-get update
+        sudo apt-get install netcdf-bin libnetcdf-c++4-dev libboost-all-dev cmake
+        git clone -b v2.x https://github.com/catchorg/Catch2.git
+        cd Catch2
+        cmake -Bbuild -H. -DBUILD_TESTING=OFF
+        sudo cmake --build build/ --target install
+        cd ..
+    - name: make
+      run: |
+        cmake .
+        make
+
+  build-on-mac:
+
+    runs-on: macos-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: installs
+      run: |
+        brew install netcdf
+        brew install boost
+        brew install catch2
+        brew install cmake
+    - name: make
+      run: |
+        cmake .
+        make
+        
+        
+
+  tests-on-mac:
+
+    runs-on: macos-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: installs
+      run: |
+        brew install netcdf
+        brew install boost
+        brew install catch2
+        brew install cmake
+    - name: make
+      run: |
+        cmake .
+        make        
+    - name: run tests
+      run: |
+        cd core/test
+        for file in $(ls test*); do ./$file; done
+        cd -
+        for component in physics
+        do
+            cd $component/test
+            for file in $(ls test*); do ./$file; done
+            cd -
+        done
+
+  
+  tests-on-ubuntu:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: installs
+      run: |
+        sudo apt-get update
+        sudo apt-get install netcdf-bin libnetcdf-c++4-dev libboost-all-dev cmake
+        git clone -b v2.x https://github.com/catchorg/Catch2.git
+        cd Catch2
+        cmake -Bbuild -H. -DBUILD_TESTING=OFF
+        sudo cmake --build build/ --target install
+        cd ..
+    - name: make
+      run: |
+        cmake .
+        make
+    - name: run tests
+      run: |
+        cd core/test
+        for file in $(ls test*); do ./$file; done
+        cd -
+        for component in physics
+        do
+            cd $component/test
+            for file in $(ls test*); do ./$file; done
+            cd -
+        done
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,10 @@
 /build/
 /.cproject
 /.project
-/.settings/*
+/.pydevproject
+/.settings/*
+/src/modules/generated/moduleLoader*.ipp
+/*/src/modules/generated/moduleLoader*.ipp
+/run/restart.nc
+/run/nextsim
+/run/.DS_Store
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,22 +1,68 @@
-cmake_minimum_required(VERSION 3.1.0)
+cmake_minimum_required(VERSION 3.12)
 
 set(CMAKE_CXX_STANDARD 11)
 
 project(framework_dg)
 
+set (NETCDF_CXX "YES")
 find_package(netCDF REQUIRED)
-find_package(Boost REQUIRED)
+if ("${CMAKE_HOST_SYSTEM_NAME}" STREQUAL "Darwin")
+    set(NSDG_NetCDF_Library "netcdf-cxx4")
+else()
+    set(NSDG_NetCDF_Library "netcdf_c++4")
+endif()
+find_package(Boost COMPONENTS program_options REQUIRED)
 find_package(Catch2 REQUIRED)
 
 # To add netCDF to a target:
 # target_include_directories(target PUBLIC ${netCDF_INCLUDE_DIR})
 # target_link_directories(target PUBLIC ${netCDF_LIB_DIR})
-# target_link_libraries(target LINK_PUBLIC netcdf-cxx4)
+# target_link_libraries(target LINK_PUBLIC "${NSDG_NetCDF_Library}")
 
-# Build the main model
-add_subdirectory(src)
+# Set the location of the ipp files used by ModuleLoader for the main build
+set(ModuleLoaderIppTargetDirectory
+"${CMAKE_CURRENT_SOURCE_DIR}/core/src/modules/generated/")
 
-# Testing
-if (NOT(CMAKE_BUILD_TYPE STREQUAL "Release"))
-	add_subdirectory(test)
-endif()
+file(MAKE_DIRECTORY "${ModuleLoaderIppTargetDirectory}")
+# Set the list of components that define modules. Component subdirectories are
+# contained in this directory level and contain src/modules/ and 
+# src/modules/include/ subdirectories 
+set(ModularComponents
+"physics"
+)
+
+# Set the components which provide source or object code to the main model
+set(CodeComponents
+"physics"
+#"dynamics"
+)
+
+# Set an empty list of sources
+set(NextsimSources "")
+
+# Set an empty list of include directories
+set(NextsimIncludeDirs "")
+
+# Build the core model. Defines the 'parse_modules' target
+add_subdirectory(core)
+
+# Build all components
+foreach(compo ${CodeComponents})
+    add_subdirectory("${compo}")
+endforeach()
+
+# Link the model
+add_executable(nextsim "${NextsimSources}")
+
+target_include_directories(nextsim PRIVATE
+    "${CMAKE_CURRENT_SOURCE_DIR}"
+    "${Boost_INCLUDE_DIRS}"
+    "${ModuleLoaderIppTargetDirectory}"
+    "${NextsimIncludeDirs}"
+    "${netCDF_INCLUDE_DIR}"
+    )
+target_link_directories(nextsim PUBLIC "${netCDF_LIB_DIR}")
+target_link_libraries(nextsim LINK_PUBLIC ${Boost_LIBRARIES} "${NSDG_NetCDF_Library}")
+
+#The parse_modules target is inherited from src
+add_dependencies(nextsim parse_modules)