Refactored entire microbe stage to switch to an ECS approach for performance reasons

.clang-format

@@ -1,75 +1,164 @@
 ---
 Language: Cpp
-AccessModifierOffset: '-4'
+AccessModifierOffset: -4
 AlignAfterOpenBracket: DontAlign
-AlignConsecutiveAssignments: 'false'
-AlignConsecutiveDeclarations: 'false'
-AlignEscapedNewlinesLeft: Left
-AlignTrailingComments: 'false'
-AllowAllParametersOfDeclarationOnNextLine: 'false'
-AllowShortBlocksOnASingleLine: 'false'
-AllowShortCaseLabelsOnASingleLine: 'true'
-AllowShortFunctionsOnASingleLine: Empty
-AllowShortIfStatementsOnASingleLine: 'false'
-AllowShortLoopsOnASingleLine: 'false'
-AlwaysBreakAfterReturnType: All
-AlwaysBreakBeforeMultilineStrings: 'false'
-AlwaysBreakTemplateDeclarations: 'false'
-BinPackArguments: 'true'
-BinPackParameters: 'false'
+AlignArrayOfStructures: None
+AlignConsecutiveAssignments: None
+AlignConsecutiveBitFields: None
+AlignConsecutiveDeclarations: None
+AlignConsecutiveMacros: None
+AlignEscapedNewlines: Right
+AlignOperands: DontAlign
+AlignTrailingComments: false
+AllowAllArgumentsOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: Never
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortEnumsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: None
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLambdasOnASingleLine: All
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: true
+BinPackParameters: true
+BitFieldColonSpacing: Both
+BreakBeforeBraces: Allman
+#BreakBeforeBraces: Custom
+#BraceWrapping:
+#    AfterClass: false
+#    AfterControlStatement: false
+#    AfterEnum: false
+#    AfterFunction: true
+#    AfterNamespace: false
+#    AfterStruct: false
+#    AfterUnion: false
+#    # AfterExternBlock: false
+#    BeforeCatch: false
+#    BeforeElse: false
+#    IndentBraces: false
+#    SplitEmptyFunction: true
+#    SplitEmptyRecord: false
+#    SplitEmptyNamespace: true
+BreakAfterAttributes: Never
 BreakBeforeBinaryOperators: None
-# BreakBeforeBraces: Attach
-BreakBeforeBraces: Custom
-BraceWrapping:
-    AfterClass: false
-    AfterControlStatement: false
-    AfterEnum: false
-    AfterFunction: true
-    AfterNamespace: false
-    AfterStruct: false
-    AfterUnion: false
-    # AfterExternBlock: false
-    BeforeCatch: false
-    BeforeElse: false
-    IndentBraces: false
-    SplitEmptyFunction: true
-    SplitEmptyRecord: false
-    SplitEmptyNamespace: true
-BreakBeforeInheritanceComma: 'false'
-BreakBeforeTernaryOperators: 'false'
+BreakBeforeConceptDeclarations: Never
+BreakBeforeInlineASMColon: OnlyMultiline
+BreakBeforeTernaryOperators: false
 BreakConstructorInitializers: AfterColon
+BreakInheritanceList: AfterComma
+BreakStringLiterals: false
+ColumnLimit: 120
 # Works fine even without this
 # CommentPragmas: '^! \\'
-CompactNamespaces: 'true'
-ConstructorInitializerAllOnOneLineOrOnePerLine: 'false'
-Cpp11BracedListStyle: 'true'
-DerivePointerAlignment: 'false'
-IndentCaseLabels: 'false'
-IndentWidth: '4'
-IndentWrappedFunctionNames: 'true'
-KeepEmptyLinesAtTheStartOfBlocks: 'true'
-MaxEmptyLinesToKeep: '3'
+CompactNamespaces: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+EmptyLineAfterAccessModifier: Never
+EmptyLineBeforeAccessModifier: LogicalBlock
+FixNamespaceComments: true
+IncludeBlocks: Regroup
+IncludeCategories:
+  - Regex: "(<|\")(Jolt|boost)\/.*"
+    Priority: 2
+  - Regex: "<.*>"
+    Priority: 1
+  - Regex: "\"Include\\.h.*"
+    Priority: 3
+    SortPriority: 3
+  - Regex: "\"(core\/ForwardDefinitions\\.hpp).*"
+    Priority: 3
+    SortPriority: 4
+  - Regex: "\".*\/"
+    Priority: 5
+  - Regex: ".*"
+    Priority: 6
+IndentAccessModifiers: false
+IndentCaseLabels: true
+IndentCaseBlocks: false
+IndentExternBlock: AfterExternBlock
+IndentGotoLabels: false
+IndentPPDirectives: None
+IndentRequiresClause: false
+IndentWidth: 4
+IndentWrappedFunctionNames: true
+InsertBraces: false
+InsertNewlineAtEOF: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+LambdaBodyIndentation: Signature
+LineEnding: DeriveLF
+# MacroBlockBegin:
+# MacroBlockEnd:
+# Macros:
+MaxEmptyLinesToKeep: 1
 NamespaceIndentation: None
+# NamespaceMacros:
+#   -
+PPIndentWidth: 1
+PackConstructorInitializers: BinPack
+PenaltyExcessCharacter: 100
+PenaltyReturnTypeOnItsOwnLine: 20
 PointerAlignment: Left
-ReflowComments: 'true'
-SortIncludes: 'true'
-SortUsingDeclarations: 'true'
-SpaceAfterCStyleCast: 'false'
-SpaceAfterTemplateKeyword: 'false'
-SpaceBeforeAssignmentOperators: 'true'
-SpaceBeforeParens: Never
-# This is also a new setting not yet available
-# SpaceBeforeRangeBasedForLoopColon: 'true'
-SpaceInEmptyParentheses: 'false'
-SpacesBeforeTrailingComments: '1'
-SpacesInAngles: 'false'
-SpacesInCStyleCastParentheses: 'false'
-SpacesInParentheses: 'false'
-SpacesInContainerLiterals: 'false'
-SpacesInParentheses: 'false'
-SpacesInSquareBrackets: 'false'
-Standard: Cpp11
-TabWidth: '4'
+QualifierAlignment: Custom
+QualifierOrder:
+  - static
+  - constexpr
+  - inline
+  - const
+  - volatile
+  - restrict
+  - friend
+  - type
+# This needs to be left as otherwise functions will look ugly
+ReferenceAlignment: Left
+ReflowComments: true
+RemoveSemicolon: true
+RequiresClausePosition: OwnLine
+RequiresExpressionIndentation: OuterScope
+SeparateDefinitionBlocks: Always
+ShortNamespaceLines: 0
+SortIncludes: CaseInsensitive
+SortUsingDeclarations: Lexicographic
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: false
+SpaceAroundPointerQualifiers: Before
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCaseColon: false
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatementsExceptControlMacros
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceBeforeSquareBrackets: false
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: false
+SpacesInLineCommentPrefix:
+  Minimum: 1
+  Maximum: 1
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard: c++17
+# StatementAttributeLikeMacros:
+#   -
+StatementMacros:
+  - JPH_ADD_ATTRIBUTE
+  - JPH_ADD_BASE_CLASS
+TabWidth: 4
+# TypenameMacros:
+#   -
 UseTab: Never
+# WhitespaceSensitiveMacros:
+#   -
 
 ...

.clang-tidy

@@ -0,0 +1,5 @@
+---
+Checks: '-*,boost-*,bugprone-*,cert-*,clang-analyzer-*,concurrency-*,cppcoreguidelines-*,hicpp-*,
+  llvm-*,-llvm-header-guard,misc-*,-misc-no-recursion,modernize-*,-modernize-use-trailing-return-type,
+  performance-*,portability-*,readability-*'
+ShortStatementLines: 1

.gitignore

@@ -2,6 +2,7 @@
 /.import
 export.cfg
 /builds
+/cmake-build*
 
 /inspect_results.xml
 /files_to_check.txt
@@ -67,7 +68,6 @@ _ReSharper*/
 *.vssscc
 $tf*/
 [Bb]in
-[Dd]ebug*/
 
 # Libraries
 *.lib

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "RevolutionaryGamesCommon"]
 	path = RevolutionaryGamesCommon
 	url = https://github.com/Revolutionary-Games/RevolutionaryGamesCommon.git
+[submodule "third_party/JoltPhysics"]
+	path = third_party/JoltPhysics
+	url = https://github.com/jrouwe/JoltPhysics.git

CIConfiguration.yml

@@ -5,15 +5,15 @@ jobs:
     image: thrive/godot-ci:v21
     cache:
       loadFrom:
-        - v7-{Branch}-build
-        - v7-master-build
-      writeTo: v7-{Branch}-build
+        - v8-{Branch}-build
+        - v8-master-build
+      writeTo: v8-{Branch}-build
       shared:
-        .git/lfs: v4-lfs
-        .import: v7-import
-        builds: v3-builds
+        .git/lfs: v5-lfs
+        .import: v8-import
+        builds: v4-builds
       system:
-        /root/.nuget: v3-nuget
+        /root/.nuget: v4-nuget
     steps:
       - run:
           name: Make project valid for compile
@@ -33,15 +33,15 @@ jobs:
     image: thrive/godot-ci:v21
     cache:
       loadFrom:
-        - v4-{Branch}-jetbrains
-        - v4-master-jetbrains
-      writeTo: v4-{Branch}-jetbrains
+        - v5-{Branch}-jetbrains
+        - v5-master-jetbrains
+      writeTo: v5-{Branch}-jetbrains
       shared:
-        .git/lfs: v4-lfs
-        .import: v7-import
-        builds: v3-jetbrains-dummy-builds
+        .git/lfs: v5-lfs
+        .import: v8-import
+        builds: v4-jetbrains-dummy-builds
       system:
-        /root/.nuget: v3-nuget
+        /root/.nuget: v4-nuget
     artifacts:
       paths:
         - files_to_check.txt
@@ -94,13 +94,13 @@ jobs:
     image: thrive/godot-ci:v21
     cache:
       loadFrom:
-        - v4-{Branch}-format
-        - v4-master-format
-      writeTo: v4-{Branch}-format
+        - v5-{Branch}-format
+        - v5-master-format
+      writeTo: v5-{Branch}-format
       shared:
-        .git/lfs: v4-lfs
+        .git/lfs: v5-lfs
       system:
-        /root/.nuget: v3-nuget
+        /root/.nuget: v4-nuget
     artifacts:
       paths:
         - format_diff.patch

CMakeLists.txt

@@ -0,0 +1,75 @@
+# Native code side of Thrive
+cmake_minimum_required(VERSION 3.10)
+
+project(Thrive)
+
+# If you want to get compile commands run cmake with
+# "-DCMAKE_EXPORT_COMPILE_COMMANDS=ON"
+
+# Options
+option(USE_OBJECT_POOLS
+  "Use object pools instead of direct memory allocation (can be turned off for memory debugging)"
+  ON)
+
+option(LOCK_FREE_COLLISION_RECORDING
+  "If on uses lock free collision data recording which is hopefully faster than with locks" ON)
+
+option(USE_SMALL_VECTOR_POOLS
+  "If on uses also pools for small list allocations in physics" OFF)
+
+option(WARNINGS_AS_ERRORS "When on treat compiler warnings as errors" ON)
+
+option(NULL_HAS_UNUSUAL_REPRESENTATION
+  "When on it is not assumed that null equals numeric 0" OFF)
+
+# set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/CMake")
+
+# Also use a lib prefix on windows for consistency
+if(WIN32)
+  set(CMAKE_SHARED_LIBRARY_PREFIX_CXX "lib")
+endif()
+
+# static building
+set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+set(BUILD_SHARED_LIBS OFF)
+
+# Common options
+if(CMAKE_BUILD_TYPE STREQUAL "")
+  set(CMAKE_BUILD_TYPE Release CACHE STRING
+    "Set the build type, usually Debug or Distribution" FORCE)
+endif()
+
+# A bit unneeded Jolt hack
+# # This and the following hack is required due to Jolt being very debug-y in
+# # release mode
+# elseif(CMAKE_BUILD_TYPE STREQUAL "Release")
+# set(CMAKE_BUILD_TYPE Distribution)
+# elseif(CMAKE_BUILD_TYPE STREQUAL "RelWithDebInfo")
+# set(CMAKE_BUILD_TYPE Distribution)
+
+if(CMAKE_BUILD_TYPE STREQUAL "Debug")
+  set(CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/debug")
+else()
+  set(CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/release")
+endif()
+
+# Detect library version
+file(READ "src/native/NativeConstants.cs" versionFile)
+
+string(REGEX MATCH "Version = ([0-9]+);" _ "${versionFile}")
+set(NATIVE_LIBRARY_VERSION ${CMAKE_MATCH_1})
+
+if(NOT NATIVE_LIBRARY_VERSION)
+  message(FATAL_ERROR "Failed to parse native library version")
+endif()
+
+message(STATUS "Configured native library version ${NATIVE_LIBRARY_VERSION}")
+
+# Configure include file
+configure_file("src/native/Include.h.in" "${PROJECT_BINARY_DIR}/Include.h")
+include_directories(${PROJECT_BINARY_DIR})
+
+# Add the subfolders that define the actual things to build
+add_subdirectory(third_party)
+
+add_subdirectory(src/native)