Clean up repository for release. (#142)

Adding clang-format style and tidying up bits and pieces.

.clang-format

@@ -0,0 +1,225 @@
+---
+Language:        Cpp
+# BasedOnStyle:  LLVM
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignArrayOfStructures: None
+AlignConsecutiveAssignments:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  PadOperators:    true
+AlignConsecutiveBitFields:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  PadOperators:    false
+AlignConsecutiveDeclarations:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  PadOperators:    false
+AlignConsecutiveMacros:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  PadOperators:    false
+AlignEscapedNewlines: Right
+AlignOperands:   Align
+AlignTrailingComments:
+  Kind:            Always
+  OverEmptyLines:  0
+AllowAllArgumentsOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: Never
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortEnumsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLambdasOnASingleLine: All
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: MultiLine
+AttributeMacros:
+  - __capability
+BinPackArguments: true
+BinPackParameters: true
+BitFieldColonSpacing: Both
+BraceWrapping:
+  AfterCaseLabel:  false
+  AfterClass:      false
+  AfterControlStatement: Never
+  AfterEnum:       false
+  AfterExternBlock: false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  BeforeLambdaBody: false
+  BeforeWhile:     false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakAfterAttributes: Never
+BreakAfterJavaFieldAnnotations: false
+BreakArrays:     true
+BreakBeforeBinaryOperators: None
+BreakBeforeConceptDeclarations: Always
+BreakBeforeBraces: Attach
+BreakBeforeInlineASMColon: OnlyMultiline
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializers: BeforeColon
+BreakInheritanceList: BeforeColon
+BreakStringLiterals: true
+ColumnLimit:     80
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+EmptyLineAfterAccessModifier: Never
+EmptyLineBeforeAccessModifier: LogicalBlock
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IfMacros:
+  - KJ_IF_MAYBE
+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: ''
+IndentAccessModifiers: false
+IndentCaseBlocks: false
+IndentCaseLabels: false
+IndentExternBlock: AfterExternBlock
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentRequiresClause: true
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+InsertBraces:    false
+InsertNewlineAtEOF: false
+InsertTrailingCommas: None
+IntegerLiteralSeparator:
+  Binary:          0
+  BinaryMinDigits: 0
+  Decimal:         0
+  DecimalMinDigits: 0
+  Hex:             0
+  HexMinDigits:    0
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+LambdaBodyIndentation: Signature
+LineEnding:      DeriveLF
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 2
+ObjCBreakBeforeNestedBlockParam: true
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PackConstructorInitializers: BinPack
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakOpenParenthesis: 0
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyIndentedWhitespace: 0
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Right
+PPIndentWidth:   -1
+QualifierAlignment: Leave
+ReferenceAlignment: Pointer
+ReflowComments:  true
+RemoveBracesLLVM: false
+RemoveSemicolon: false
+RequiresClausePosition: OwnLine
+RequiresExpressionIndentation: OuterScope
+SeparateDefinitionBlocks: Leave
+ShortNamespaceLines: 1
+SortIncludes:    CaseSensitive
+SortJavaStaticImport: Before
+SortUsingDeclarations: LexicographicNumeric
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: true
+SpaceAroundPointerQualifiers: Default
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCaseColon: false
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeParensOptions:
+  AfterControlStatements: true
+  AfterForeachMacros: true
+  AfterFunctionDefinitionName: false
+  AfterFunctionDeclarationName: false
+  AfterIfMacros:   true
+  AfterOverloadedOperator: false
+  AfterRequiresInClause: false
+  AfterRequiresInExpression: false
+  BeforeNonEmptyParentheses: false
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceBeforeSquareBrackets: false
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  Never
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInLineCommentPrefix:
+  Minimum:         1
+  Maximum:         -1
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Latest
+StatementAttributeLikeMacros:
+  - Q_EMIT
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth:        8
+UseTab:          Never
+WhitespaceSensitiveMacros:
+  - BOOST_PP_STRINGIZE
+  - CF_SWIFT_NAME
+  - NS_SWIFT_NAME
+  - PP_STRINGIZE
+  - STRINGIZE
+...
+

.github/workflows/build.yml

@@ -18,17 +18,19 @@ env:
 
 jobs:
   build:
-    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
+    # The CMake configure and build commands are platform-agnostic and should work equally well on Windows or Mac.
     # You can convert this to a matrix build if you need cross-platform coverage.
     # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
     runs-on: ubuntu-20.04
     strategy:
       fail-fast: false
       matrix:
+        mpi_enabled: [ON, OFF]
         compiler: [
           {c: gcc-10, cpp: g++-10, fortran: gfortran-10},
           {c: clang-12, cpp: clang++-12, fortran: gfortran-10}
         ]
+    name: Compiler ${{ matrix.compiler.cpp }} with MPI ${{matrix.mpi_enabled}}
 
     steps:
     - uses: actions/checkout@v3
@@ -62,6 +64,7 @@ jobs:
         -DUSE_SANITIZERS=ON
         -DENABLE_DOXYGEN=OFF
         -DBUILD_DOCS=OFF
+        -DENABLE_MPI=${{ matrix.mpi_enabled }}
 
     - name: Build
       # Build your program with the given configuration

.github/workflows/documentation.yml

@@ -12,7 +12,7 @@ on:
     paths:
       - 'src/**.h'
       - 'src/**.cpp'
-      - 'documentation/**.md'
+      - 'documentation/**'
       - '.github/workflows/documentation.yml'
 
 env:

.github/workflows/format-check.yml

@@ -0,0 +1,19 @@
+name: Format Check
+on:
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  check:
+    runs-on: ubuntu-24.04
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Check style with clang-format
+      # Use clang-format to check all C++ files for code style errors.
+      # The .clang-format file was created using clang-format 16, not all
+      # checks are available in earlier versions so the --Wno-error=unknown flag
+      # is used. Users should use clang-format 16 or later if possible.
+      run: >
+        find ${{github.workspace}} -iname '*.cpp' -o -iname '*.h' | xargs 
+        clang-format --dry-run --Werror --Wno-error=unknown 2>&1

CMakeLists.txt

@@ -46,11 +46,6 @@ if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
         include(cmake/Doxygen.cmake)
         include(cmake/Sphinx.cmake)
 
-        # Make sphinx target depend on builing doxygen docs first
-        if(ENABLE_SPHINX)
-                add_dependencies(sphinxdocs doxygendocs)
-        endif()
-
         # Include option to build with/without OpenMP
         include(cmake/BuildOptions.cmake)