Index Typedef (#161)

* Refactor ID types from long to index_t across the codebase

* Update clang-format action to v4.15.0 and version to 20

* Update clang-format

Author: zfergus

.clang-format

@@ -1,19 +1,148 @@
-# https://clang.llvm.org/docs/ClangFormatStyleOptions.html
-BasedOnStyle: WebKit
-ColumnLimit: 80
-AlignTrailingComments: true
-FixNamespaceComments: true
-ReflowComments: true
-BinPackParameters: false
-AllowAllParametersOfDeclarationOnNextLine: true
+---
+Language:        Cpp
+AccessModifierOffset: -4
 AlignAfterOpenBracket: AlwaysBreak
+AlignArrayOfStructures: None
+AlignConsecutiveAssignments:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  AlignFunctionDeclarations: false
+  AlignFunctionPointers: false
+  PadOperators:    true
+AlignConsecutiveBitFields:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  AlignFunctionDeclarations: false
+  AlignFunctionPointers: false
+  PadOperators:    false
+AlignConsecutiveDeclarations:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  AlignFunctionDeclarations: true
+  AlignFunctionPointers: false
+  PadOperators:    false
+AlignConsecutiveMacros:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  AlignFunctionDeclarations: false
+  AlignFunctionPointers: false
+  PadOperators:    false
+AlignConsecutiveShortCaseStatements:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCaseArrows: false
+  AlignCaseColons: false
+AlignConsecutiveTableGenBreakingDAGArgColons:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  AlignFunctionDeclarations: false
+  AlignFunctionPointers: false
+  PadOperators:    false
+AlignConsecutiveTableGenCondOperatorColons:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  AlignFunctionDeclarations: false
+  AlignFunctionPointers: false
+  PadOperators:    false
+AlignConsecutiveTableGenDefinitionColons:
+  Enabled:         false
+  AcrossEmptyLines: false
+  AcrossComments:  false
+  AlignCompound:   false
+  AlignFunctionDeclarations: false
+  AlignFunctionPointers: false
+  PadOperators:    false
+AlignEscapedNewlines: Right
+AlignOperands:   DontAlign
+AlignTrailingComments:
+  Kind:            Always
+  OverEmptyLines:  0
+AllowAllArgumentsOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowBreakBeforeNoexceptSpecifier: Never
+AllowShortBlocksOnASingleLine: Always
+AllowShortCaseExpressionOnASingleLine: true
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortCompoundRequirementOnASingleLine: true
+AllowShortEnumsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLambdasOnASingleLine: All
+AllowShortLoopsOnASingleLine: false
+AllowShortNamespacesOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AttributeMacros:
+  - __capability
+BinPackArguments: true
+BinPackParameters: false
+BitFieldColonSpacing: Both
+BraceWrapping:
+  AfterCaseLabel:  false
+  AfterClass:      false
+  AfterControlStatement: Never
+  AfterEnum:       false
+  AfterExternBlock: false
+  AfterFunction:   true
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  BeforeLambdaBody: false
+  BeforeWhile:     false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakAdjacentStringLiterals: true
+BreakAfterAttributes: Leave
+BreakAfterJavaFieldAnnotations: false
+BreakAfterReturnType: None
+BreakArrays: false
 BreakBeforeBinaryOperators: NonAssignment
-SortIncludes: true
-CommentPragmas:  '^@.+'
+BreakBeforeConceptDeclarations: Always
+BreakBeforeBraces: Custom
+BreakBeforeInlineASMColon: OnlyMultiline
+BreakBeforeTernaryOperators: true
+BreakBinaryOperations: Never
+BreakConstructorInitializers: BeforeComma
+BreakFunctionDefinitionParameters: false
+BreakInheritanceList: BeforeColon
 BreakStringLiterals: false
-PackConstructorInitializers: CurrentLine
-# Regroup includes with a priority system
-IncludeBlocks: Regroup
+BreakTemplateDeclarations: MultiLine
+ColumnLimit: 80
+CommentPragmas:  '^@.+'
+CompactNamespaces: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: false
+DerivePointerAlignment: false
+DisableFormat:   false
+EmptyLineAfterAccessModifier: Never
+EmptyLineBeforeAccessModifier: LogicalBlock
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - RANGES_FOR
+  - FOREACH
+IfMacros:
+  - IF
+IncludeBlocks:   Regroup
 IncludeCategories:
   # by default, the main header of a cpp will get priority 0
   # regex here are sorted by search pattern, not by sort priority
@@ -36,4 +165,132 @@ IncludeCategories:
   - Regex:           ".*" # catch-all for internal files
     Priority:        1    # internal file group
     SortPriority:    1
-    CaseSensitive:   true
+    CaseSensitive:   true
+IncludeIsMainRegex: '(Test)?$'
+IncludeIsMainSourceRegex: ''
+IndentAccessModifiers: false
+IndentCaseBlocks: false
+IndentCaseLabels: false
+IndentExportBlock: true
+IndentExternBlock: AfterExternBlock
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentRequiresClause: true
+IndentWidth:     4
+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
+KeepEmptyLines:
+  AtEndOfFile:     false
+  AtStartOfBlock:  true
+  AtStartOfFile:   true
+KeepFormFeed:    false
+LambdaBodyIndentation: Signature
+LineEnding:      DeriveLF
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MainIncludeChar: Quote
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: Inner
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 4
+ObjCBreakBeforeNestedBlockParam: true
+ObjCSpaceAfterProperty: true
+ObjCSpaceBeforeProtocolList: true
+PackConstructorInitializers: CurrentLine
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakBeforeMemberAccess: 150
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakOpenParenthesis: 0
+PenaltyBreakScopeResolution: 500
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyIndentedWhitespace: 0
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Left
+PPIndentWidth:   -1
+QualifierAlignment: Leave
+ReferenceAlignment: Pointer
+ReflowComments:  Always
+RemoveBracesLLVM: false
+RemoveEmptyLinesInUnwrappedLines: true
+RemoveParentheses: Leave
+RemoveSemicolon: false
+RequiresClausePosition: OwnLine
+RequiresExpressionIndentation: OuterScope
+SeparateDefinitionBlocks: Leave
+ShortNamespaceLines: 1
+SkipMacroDefinitionBody: false
+SortIncludes:    CaseInsensitive
+SortJavaStaticImport: Before
+SortUsingDeclarations: LexicographicNumeric
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: true
+SpaceAroundPointerQualifiers: Default
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCaseColon: false
+SpaceBeforeCpp11BracedList: true
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeJsonColon: false
+SpaceBeforeParens: ControlStatements
+SpaceBeforeParensOptions:
+  AfterControlStatements: true
+  AfterForeachMacros: true
+  AfterFunctionDefinitionName: false
+  AfterFunctionDeclarationName: false
+  AfterIfMacros:   true
+  AfterOverloadedOperator: false
+  AfterPlacementOperator: true
+  AfterRequiresInClause: false
+  AfterRequiresInExpression: false
+  BeforeNonEmptyParentheses: false
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceBeforeSquareBrackets: false
+SpaceInEmptyBlock: true
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  Never
+SpacesInContainerLiterals: true
+SpacesInLineCommentPrefix:
+  Minimum:         1
+  Maximum:         -1
+SpacesInParens:  Never
+SpacesInParensOptions:
+  ExceptDoubleParentheses: false
+  InCStyleCasts:   false
+  InConditionalStatements: false
+  InEmptyParentheses: false
+  Other:           false
+SpacesInSquareBrackets: false
+Standard:        Latest
+StatementAttributeLikeMacros:
+  - Q_EMIT
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TableGenBreakInsideDAGArg: DontBreak
+TabWidth:        8
+UseTab:          Never
+VerilogBreakBetweenInstancePorts: true
+WhitespaceSensitiveMacros:
+  - BOOST_PP_STRINGIZE
+  - CF_SWIFT_NAME
+  - NS_SWIFT_NAME
+  - PP_STRINGIZE
+  - STRINGIZE
+WrapNamespaceBodyWithEmptyLines: Leave
+...

.github/workflows/clang-format-check.yml

@@ -27,7 +27,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: clang-format style check
-      uses: jidicula/clang-format-action@v4.13.0
+      uses: jidicula/clang-format-action@v4.15.0
       with:
-        clang-format-version: '18'
+        clang-format-version: '20'
         check-path: ${{ matrix.path }}

python/src/barrier/adaptive_stiffness.cpp

@@ -72,10 +72,9 @@ void define_adaptive_stiffness(py::module_& m)
     m.def(
         "semi_implicit_stiffness",
         static_cast<double (*)(
-            const CollisionStencil&, const std::array<long, 4>&,
-            Eigen::ConstRef<VectorMax12d>, Eigen::ConstRef<VectorMax4d>,
-            Eigen::ConstRef<MatrixMax12d>, const double)>(
-            &semi_implicit_stiffness),
+            const CollisionStencil&, Eigen::ConstRef<VectorMax12d>,
+            Eigen::ConstRef<VectorMax4d>, Eigen::ConstRef<MatrixMax12d>,
+            const double)>(&semi_implicit_stiffness),
         R"ipc_Qu8mg5v7(
         Compute the semi-implicit stiffness for a single collision.
 
@@ -92,8 +91,8 @@ void define_adaptive_stiffness(py::module_& m)
         Returns:
             The semi-implicit stiffness.
         )ipc_Qu8mg5v7",
-        py::arg("stencil"), py::arg("vertex_ids"), py::arg("vertices"),
-        py::arg("mass"), py::arg("local_hess"), py::arg("dmin"));
+        py::arg("stencil"), py::arg("vertices"), py::arg("mass"),
+        py::arg("local_hess"), py::arg("dmin"));
 
     m.def(
         "semi_implicit_stiffness",

python/src/candidates/edge_edge.cpp

@@ -8,9 +8,11 @@ using namespace ipc;
 void define_edge_edge_candidate(py::module_& m)
 {
     py::class_<EdgeEdgeCandidate, CollisionStencil>(m, "EdgeEdgeCandidate")
-        .def(py::init<long, long>(), py::arg("edge0_id"), py::arg("edge1_id"))
         .def(
-            py::init([](std::tuple<long, long> edge_ids) {
+            py::init<index_t, index_t>(), py::arg("edge0_id"),
+            py::arg("edge1_id"))
+        .def(
+            py::init([](std::tuple<index_t, index_t> edge_ids) {
                 return std::make_unique<EdgeEdgeCandidate>(
                     std::get<0>(edge_ids), std::get<1>(edge_ids));
             }),
@@ -37,5 +39,6 @@ void define_edge_edge_candidate(py::module_& m)
         .def_readwrite(
             "edge1_id", &EdgeEdgeCandidate::edge1_id, "ID of the second edge.");
 
-    py::implicitly_convertible<std::tuple<long, long>, EdgeEdgeCandidate>();
+    py::implicitly_convertible<
+        std::tuple<index_t, index_t>, EdgeEdgeCandidate>();
 }

python/src/candidates/edge_face.cpp

@@ -9,9 +9,11 @@ using namespace ipc;
 void define_edge_face_candidate(py::module_& m)
 {
     py::class_<EdgeFaceCandidate>(m, "EdgeFaceCandidate")
-        .def(py::init<long, long>(), py::arg("edge_id"), py::arg("face_id"))
         .def(
-            py::init([](std::tuple<long, long> edge_and_face_id) {
+            py::init<index_t, index_t>(), py::arg("edge_id"),
+            py::arg("face_id"))
+        .def(
+            py::init([](std::tuple<index_t, index_t> edge_and_face_id) {
                 return std::make_unique<EdgeFaceCandidate>(
                     std::get<0>(edge_and_face_id),
                     std::get<1>(edge_and_face_id));
@@ -37,5 +39,6 @@ void define_edge_face_candidate(py::module_& m)
         .def_readwrite(
             "face_id", &EdgeFaceCandidate::face_id, "ID of the face");
 
-    py::implicitly_convertible<std::tuple<long, long>, EdgeFaceCandidate>();
+    py::implicitly_convertible<
+        std::tuple<index_t, index_t>, EdgeFaceCandidate>();
 }

python/src/candidates/edge_vertex.cpp

@@ -8,9 +8,11 @@ using namespace ipc;
 void define_edge_vertex_candidate(py::module_& m)
 {
     py::class_<EdgeVertexCandidate, CollisionStencil>(m, "EdgeVertexCandidate")
-        .def(py::init<long, long>(), py::arg("edge_id"), py::arg("vertex_id"))
         .def(
-            py::init([](std::tuple<long, long> edge_and_vertex_id) {
+            py::init<index_t, index_t>(), py::arg("edge_id"),
+            py::arg("vertex_id"))
+        .def(
+            py::init([](std::tuple<index_t, index_t> edge_and_vertex_id) {
                 return std::make_unique<EdgeVertexCandidate>(
                     std::get<0>(edge_and_vertex_id),
                     std::get<1>(edge_and_vertex_id));
@@ -39,5 +41,6 @@ void define_edge_vertex_candidate(py::module_& m)
         .def_readwrite(
             "vertex_id", &EdgeVertexCandidate::vertex_id, "ID of the vertex");
 
-    py::implicitly_convertible<std::tuple<long, long>, EdgeVertexCandidate>();
+    py::implicitly_convertible<
+        std::tuple<index_t, index_t>, EdgeVertexCandidate>();
 }