Refactored DNASim library

.clang-format

@@ -0,0 +1,92 @@
+---
+# clang-format style definition
+# Nicolas Clauvelin, Sendyne Corp. 2019
+Language:        Cpp
+BasedOnStyle: Google
+AccessModifierOffset: '-4'
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: 'false'
+AlignConsecutiveDeclarations: 'false'
+AlignEscapedNewlines: Right
+AlignOperands: 'true'
+AlignTrailingComments: 'true'
+AllowAllParametersOfDeclarationOnNextLine: 'false'
+AllowShortBlocksOnASingleLine: 'false'
+AllowShortCaseLabelsOnASingleLine: 'false'
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: 'false'
+AllowShortLoopsOnASingleLine: 'false'
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: 'false'
+AlwaysBreakTemplateDeclarations: 'true'
+BinPackArguments: 'false'
+BinPackParameters: 'false'
+BreakBeforeBraces: Custom
+BraceWrapping:
+  AfterClass: 'false'
+  AfterControlStatement: 'false'
+  AfterEnum: 'false'
+  AfterFunction: 'false'
+  AfterNamespace: 'false'
+  AfterStruct: 'false'
+  AfterUnion: 'false'
+  AfterExternBlock: 'false'
+  BeforeCatch: 'true'
+  BeforeElse: 'true'
+  IndentBraces: 'false'
+  SplitEmptyFunction: 'false'
+  SplitEmptyRecord: 'false'
+  SplitEmptyNamespace: 'false'
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeInheritanceComma: 'false'
+BreakBeforeTernaryOperators: 'true'
+BreakConstructorInitializers: BeforeColon
+BreakInheritanceList: BeforeColon
+BreakStringLiterals: 'true'
+ColumnLimit: '80'
+CompactNamespaces: 'false'
+ConstructorInitializerAllOnOneLineOrOnePerLine: 'true'
+ConstructorInitializerIndentWidth: '4'
+ContinuationIndentWidth: '4'
+Cpp11BracedListStyle: 'true'
+DerivePointerAlignment: 'false'
+DisableFormat: 'false'
+ExperimentalAutoDetectBinPacking: 'false'
+FixNamespaceComments: 'true'
+IncludeBlocks: Regroup
+IndentCaseLabels: 'true'
+IndentPPDirectives: AfterHash
+IndentWidth: '4'
+IndentWrappedFunctionNames: 'false'
+KeepEmptyLinesAtTheStartOfBlocks: 'true'
+MaxEmptyLinesToKeep: '2'
+NamespaceIndentation: None
+PointerAlignment: Left
+ReflowComments: 'true'
+SortIncludes: 'true'
+SortUsingDeclarations: 'true'
+SpaceAfterCStyleCast: 'false'
+SpaceAfterTemplateKeyword: 'true'
+SpaceBeforeAssignmentOperators: 'true'
+SpaceBeforeCpp11BracedList: 'false'
+SpaceBeforeCtorInitializerColon: 'true'
+SpaceBeforeInheritanceColon: 'true'
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: 'true'
+SpaceInEmptyParentheses: 'false'
+SpacesBeforeTrailingComments: '4'
+SpacesInAngles: 'false'
+SpacesInContainerLiterals: 'false'
+SpacesInCStyleCastParentheses: 'false'
+SpacesInParentheses: 'false'
+SpacesInSquareBrackets: 'false'
+Standard: Cpp11
+TabWidth: '4'
+UseTab: Never
+IncludeCategories:
+  - Regex:           '^".*'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+
+...

.gitignore

@@ -1,18 +1,46 @@
-# Ignore these files/directories and do not add to git project
+### Generic git ignore file ###
 
-### Clion specific directories ###
-*.idea
-build
-cmake-build-debug
-
-### Compiled Object files ###
-*.slo
-*.lo
+# Object files
 *.o
+*.ko
 *.obj
+*.elf
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
+*.a
+*.la
+*.lo
 
-### Compiled Dynamic libraries ###
+# Shared objects (inc. Windows DLLs)
+*.dll
 *.so
+*.so.*
 *.dylib
-*.dll
 
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+*.bin
+
+# Mac specific
+.DS_Store
+
+# CLion specific
+**/.idea/workspace.xml
+**/.idea/tasks.xml
+**/.idea/*.iml
+**/.idea/modules.xml
+**/.idea/vcs.xml
+
+# Build directories
+**/build
+**/cmake-build-*/

.gitmodules

@@ -0,0 +1,12 @@
+[submodule "deps/googletest"]
+	path = deps/googletest
+	url = git@github.com:google/googletest.git
+[submodule "deps/cereal"]
+	path = deps/cereal
+	url = git@github.com:USCiLab/cereal.git
+[submodule "deps/nanoflann"]
+	path = deps/nanoflann
+	url = git@github.com:jlblancoc/nanoflann.git
+[submodule "deps/eigen"]
+	path = deps/eigen
+	url = git@github.com:eigenteam/eigen-git-mirror.git

CMakeLists.txt

@@ -0,0 +1,43 @@
+# ---------------------------------------------------------------------------- #
+# emDNA CMake project
+#
+# Nicolas Clauvelin (n.clauvelin@gmail.com)
+#
+# ---------------------------------------------------------------------------- #
+
+
+# --- Project setup ---
+
+# CMake minimal version.
+cmake_minimum_required(VERSION 3.13)
+
+# Support for ccache.
+find_program(CCACHE_PROGRAM ccache)
+if(CCACHE_PROGRAM)
+    set(CMAKE_C_COMPILER_LAUNCHER ${CCACHE_PROGRAM}
+        CACHE STRING "(emDNA) C compiler ccache program" FORCE)
+    set(CMAKE_CXX_COMPILER_LAUNCHER ${CCACHE_PROGRAM}
+        CACHE STRING "(emDNA) C++ compiler ccache program" FORCE)
+    message("C/C++ compiler ccache: ${CCACHE_PROGRAM}")
+endif()
+
+# Define project.
+project(emDNA C CXX)
+
+# Enforce C++14 standard.
+set(CMAKE_CXX_STANDARD 14)
+
+# Enforce C99 standard.
+set(CMAKE_C_STANDARD 99)
+
+
+# --- Project components ---
+
+# Dependencies.
+include(deps/cereal.cmake)
+include(deps/eigen.cmake)
+include(deps/googletest.cmake)
+include(deps/nanoflann.cmake)
+
+# DNASim
+add_subdirectory(DNASim/)