fix: clang error and c++17 deprecation #34 #35 #38

* -= method for iterators

* boost -> std in multinomial statistics

* postfix operators for iterators

* prefix ++ -- return the value before application

* tests(MixtComp): change tolerance

* refactor(MixtComp): refactor deprecated std::iterator #38

* feat(RMixtCompIO): use c++17 as standard

* .clang-format added and applied on two sources

* doc

* doc

* corecting the corrections

* iterator include removed

* Correcting the corrections, once again

* missing ref

* trivial copy constructors removed

* unuglyfying

* ConstIterator(Iterator &other)

* ConstIterator(const Iterator &other)

---------

Co-authored-by: Vincent KUBICKI <vincent.kubicki@laposte.net>

Author: Quentin62

MixtComp/.clang-format

@@ -0,0 +1,14 @@
+# https://clang.llvm.org/docs/ClangFormatStyleOptions.html
+# https://llvm.org/docs/CodingStandards.html
+
+BasedOnStyle: LLVM
+
+AccessModifierOffset: -4
+AllowShortIfStatementsOnASingleLine: false
+ColumnLimit: 0
+FixNamespaceComments: false
+IndentCaseLabels: false
+IndentWidth: 4
+NamespaceIndentation: All
+TabWidth: 4
+UseTab: Always

MixtComp/README.md

@@ -29,7 +29,7 @@ brew install cmake boost eigen lcov
 
 ## Windows
 
-To install the necessary tools, user needs to install [cygwin](https://www.cygwin.com/). gcc, cmake, boost and eigen must be installed through the cygwin packages installer.
+To install the necessary tools, user needs to install [cygwin](https://www.cygwin.com/). gcc, cmake, boost and eigen must be installed through the cygwin packages installer. Note: WSL might be a better solution, but does it allows to compare with CRAN builds for example ?
 
 ## Compilation & tests
 

MixtComp/TODO.md

@@ -31,7 +31,7 @@
 ## Performances
 
 - remove regex in data parsing. Will be faster but less tolerant to data format.
-- Statistics object generate a boost::variate_generator each time a variable is sampled. It should be possible to generate a vector of value, when the parameters do not vary.
+- Statistics object generate a boost::variate_generator each time a variable is sampled. It should be possible to generate a vector of value, when the parameters do not vary. -> Use standard library for sampling, as in Multinomial Statistics.
 
 ## Long Term
 

MixtComp/docs/Graph.md

@@ -6,93 +6,88 @@ Inputs and outputs are given as Graph objects. MixtComp methods are templated wi
 - R objects (*RGraph* class, cf. [RMixtCompIO](../../RMixtCompIO/src/RGraph.h))
 - python objects (*PyGraph* class, cf. [pyMixtComp](../../pyMixtComp/src/lib/PyGraph.h))
 
-
 The different *Graph* classes must implement the following method:
 
 - `void getSubGraph(const std::vector<std::string>& path, Graph& j) const;`: get the Graph at the given path. It modifies the `j` argument.
 - `template<typename Type> void add_payload(const std::vector<std::string>& path, const std::string& name, const Type& p);`: add an object in the Graph and create the complete path to it if it does not exist yet.
-- `void addSubGraph(const std::vector<std::string>& path, const std::string& name, const Graph& p);`: add an other Graph in the Graph and create the complete path to it if it does not exist yet. 
+- `void addSubGraph(const std::vector<std::string>& path, const std::string& name, const Graph& p);`: add an other Graph in the Graph and create the complete path to it if it does not exist yet.
 - `template<typename Type> Type get_payload(const std::vector<std::string>& path, const std::string& name) const;`: get the element named `name` in `path`
 - `template<typename Type> void get_payload(const std::vector<std::string>& path, const std::string& name, Type& p);`: get the element named `name` in `path`. This version modifies the `p` argument.
 - `bool exist_payload(const std::vector<std::string>& path, const std::string& name) const;`: test if an element named `name` exists in `path`.
 - `void name_payload(const std::vector<std::string>& path, std::list<std::string>& l) const;`: get the names of all the elements in `path` It modifies the `l` argument.
 
-with `path` a vector containing the path of the element to reach or save an element (e.g. ["variable", "param", "var1", "stat"] the element in the following path: variable/param/var1/stat). `Type` can be `int`, `double`, `bool`, `vector<T>`, `vector<vector<T> >`, `NamedVector<T>`, `NamedMatrix<T>`. `NamedMatrix<T>` is a struct containing an Eigen Matrix `mat_` and two vector<string> named `colnames_` and `rownames_`. `NamedVector<T>` is a struct containing an Eigen Matrix with 1 column `vec_` and a vector<string> named `rownames_`  (see [NamedAlgebra](../src/lib/IO/NamedAlgebra.h) and [LinAlg](../src/lib/LinAlg/LinAlg.h) for mode details about `NamedVector` and `NamedMatrix`). 
-
+with `path` a vector containing the path of the element to reach or save an element (e.g. ["variable", "param", "var1", "stat"] the element in the following path: variable/param/var1/stat). `Type` can be `int`, `double`, `bool`, `vector<T>`, `vector<vector<T> >`, `NamedVector<T>`, `NamedMatrix<T>`. `NamedMatrix<T>` is a struct containing an Eigen Matrix `mat_` and two `vector<string>` named `colnames_` and `rownames_`. `NamedVector<T>` is a struct containing an Eigen Matrix with 1 column `vec_` and a `vector<string>` named `rownames_`  (see [NamedAlgebra](../src/lib/IO/NamedAlgebra.h) and [LinAlg](../src/lib/LinAlg/LinAlg.h) for mode details about `NamedVector` and `NamedMatrix`).
 
-
-# Structure of input Graphs
+## Structure of input Graphs
 
 Three Graphs for learning (and four for prediction)  (see [file](./dataFormat.md) for mdoe details):
 
 - algo
-    - nClass
-    - nInd
-    - nbBurnInIter
-    - nbIter
-    - nbGibbsBurnInIter
-    - nbGibbsIter
-    - nInitPerClass
-    - nSemTry
-    - ratioStableCriterion
-    - nStableCriterion
-    - confidenceLevel
-    - mode ("learn" or "predict")
+  - nClass
+  - nInd
+  - nbBurnInIter
+  - nbIter
+  - nbGibbsBurnInIter
+  - nbGibbsIter
+  - nInitPerClass
+  - nSemTry
+  - ratioStableCriterion
+  - nStableCriterion
+  - confidenceLevel
+  - mode ("learn" or "predict")
 
 - data
-    - var1 (array of string)
-    - var2
-    - ...
+  - var1 (array of string)
+  - var2
+  - ...
 
 - desc
-    - var1
-        - type
-        - paramStr
-    - var2
-    - ...
+  - var1
+    - type
+    - paramStr
+  - var2
+  - ...
 
 - param (output Graph of a MixtComp run. Only for prediction, see below)
 
-
-# Structure of output Graph
+## Structure of output Graph
 
 An unique Graph containing: (see [file](./objectOutput.md) for more details)
 
 - algo (copy of algo input)
-- mixture 
+- mixture
 - variable
-    - type
-        - var1: type of var1
-        - var2: type of var2
-    - data
-        - var1
-            - completed
-            - stat (to be implemented, except for LatentClass -> immediate implementation)
-        - var2
-        - ...
-    - param
-        - var1 (case 1: simple model)
-            - log 
-            - stat
-            - paramStr
-        - var2 (case 2: functional)
-            - alpha
-                - log 
-                - stat               
-            - beta
-                - log 
-                - stat 
-            - sd
-                - log 
-                - stat 
-            - paramStr
-        - var3 (case 2: rank)
-            - mu
-                - log 
-                - stat               
-            - pi
-                - log 
-                - stat 
-            - paramStr 
-        - ...
-
+  - type
+    - var1: type of var1
+    - var2: type of var2
+  - data
+    - var1
+      - completed
+      - stat (to be implemented, except for LatentClass -> immediate implementation)
+    - var2
+    - ...
+  - param
+    - var1 (case 1: simple model)
+      - log
+      - stat
+      - paramStr
+    - var2 (case 2: functional)
+      - alpha
+        - log
+        - stat
+      - beta
+        - log
+        - stat
+      - sd
+        - log
+        - stat
+      - paramStr
+    - var3 (case 2: rank)
+      - mu
+        - log
+        - stat
+      - pi
+        - log
+        - stat
+      - paramStr
+    - ...

MixtComp/docs/developmentEnvironment.md

@@ -0,0 +1,15 @@
+# Development environment
+
+## Current
+
+VS Code with the the following extensions:
+
+- clangd
+  - Disable Intellisense from Microsoft C++ extension. The formatting should be automatically handled upon detection of the `.clang-format` file at the root of the project.
+- markdownlint
+
+Enable the "Format on save" option to ensure everything is properly formatted.
+
+## Previous
+
+The general style used is K&R from Eclipse, modified for a line wrap at 200 characters.

MixtComp/docs/styleguide.md

@@ -28,17 +28,31 @@
 //#include <iostream>
 //#include <iterator>
 
-class ConstIterator: public std::iterator<std::random_access_iterator_tag,
-		Scalar, int, Scalar*, Scalar&> {
+class ConstIterator {
+
 public:
-	ConstIterator(int i, int j, const Derived& mat) :
-			i_(i), j_(j), rows_(mat.rows()), p_mat_(&mat) {
-	}
+	// iterator traits
+	using iterator_category = std::random_access_iterator_tag;
+	using value_type = Scalar;
+	using difference_type = int;
+	using pointer = Scalar *;
+	using reference = Scalar &;
 
-	ConstIterator(const Iterator& it) :
-			i_(it.i_), j_(it.j_), rows_(it.rows_), p_mat_(it.p_mat_) {
+	int i_;
+	int j_;
+	int rows_;
+	const Derived *p_mat_;
+
+	ConstIterator(int i, int j, const Derived &mat)
+		: i_(i), j_(j), rows_(mat.rows()), p_mat_(&mat) {
 	}
 
+	ConstIterator(const Iterator &other)
+		: i_(other.i_),
+		  j_(other.j_),
+		  rows_(other.rows_),
+		  p_mat_(other.p_mat_) {}
+
 	ConstIterator operator+(int i) {
 		int posP, iP, jP;
 		posP = pos();
@@ -47,11 +61,16 @@ class ConstIterator: public std::iterator<std::random_access_iterator_tag,
 		return ConstIterator(iP, jP, *p_mat_);
 	}
 
-	ConstIterator& operator+=(int i) {
+	ConstIterator operator+=(int i) {
 		posToIn(pos() + i, i_, j_);
 		return *this;
 	}
 
+	ConstIterator operator-=(int i) {
+		posToIn(pos() - i, i_, j_);
+		return *this;
+	}
+
 	ConstIterator operator-(int i) {
 		int posP, iP, jP;
 		posP = pos();
@@ -60,52 +79,50 @@ class ConstIterator: public std::iterator<std::random_access_iterator_tag,
 		return ConstIterator(iP, jP, *p_mat_);
 	}
 
-	int operator-(const ConstIterator& it) {
+	int operator-(const ConstIterator &it) {
 		return pos() - it.pos();
 	}
 
-	bool operator<(const ConstIterator& it) {
+	bool operator<(const ConstIterator &it) {
 		if (j_ < it.j_) {
 			return true;
 		} else if (j_ > it.j_) {
 			return false;
-		} else if (i_ < it.i_) // in this case, j_ == it.j_, hence comparison must be done on i_
-				{
+		} else if (i_ < it.i_) { // in this case, j_ == it.j_, hence comparison must be done on i_
 			return true;
 		}
 
 		return false;
 	}
 
-	bool operator==(const ConstIterator& it) {
+	bool operator==(const ConstIterator &it) {
 		if (i_ == it.i_ && j_ == it.j_)
 			return true;
 		else
 			return false;
 	}
 
-	bool operator>(const ConstIterator& it) {
+	bool operator>(const ConstIterator &it) {
 		if (j_ > it.j_) {
 			return true;
 		} else if (j_ > it.j_) {
 			return false;
-		} else if (i_ > it.i_) // in this case, j_ == it.j_, hence comparison must be done on i_
-				{
+		} else if (i_ > it.i_) { // in this case, j_ == it.j_, hence comparison must be done on i_
 			return true;
 		}
 
 		return false;
 	}
 
-	bool operator>=(const ConstIterator& it) {
+	bool operator>=(const ConstIterator &it) {
 		if (!(*this < it)) {
 			return true;
 		}
 
 		return false;
 	}
 
-	bool operator!=(const ConstIterator& it) {
+	bool operator!=(const ConstIterator &it) {
 		if (i_ != it.i_ || j_ != it.j_)
 			return true;
 		else
@@ -115,17 +132,17 @@ class ConstIterator: public std::iterator<std::random_access_iterator_tag,
 	/**
 	 * returns const Scalar instead of const Scalar& to avoid error with temporaries
 	 */
-	const Scalar& operator*() const {
+	const Scalar &operator*() const {
 		return (*p_mat_)(i_, j_);
 	}
 
-	const Scalar* operator->() const {
+	const Scalar *operator->() const {
 		return &(*p_mat_)(i_, j_);
 	}
 
-	const ConstIterator& operator++() {
+	const ConstIterator &operator++() {
 		if (i_ < rows_ - 1) // row increment
-				{
+		{
 			++i_;
 		} else // column increment
 		{
@@ -135,7 +152,20 @@ class ConstIterator: public std::iterator<std::random_access_iterator_tag,
 		return *this;
 	}
 
-	const ConstIterator& operator--() {
+	const ConstIterator operator++(int) {
+		ConstIterator temp(*this);
+		if (i_ < rows_ - 1) // row increment
+		{
+			++i_;
+		} else // column increment
+		{
+			i_ = 0;
+			++j_;
+		}
+		return temp;
+	}
+
+	const ConstIterator &operator--() {
 		if (i_ > 0) {
 			--i_;
 		} else {
@@ -145,12 +175,7 @@ class ConstIterator: public std::iterator<std::random_access_iterator_tag,
 		return *this;
 	}
 
-	int i_;
-	int j_;
-	int rows_;
-	const Derived* p_mat_;
-
-	void posToIn(int pos, int& i, int& j) const {
+	void posToIn(int pos, int &i, int &j) const {
 		std::div_t divresult;
 		divresult = std::div(pos, rows_);