From 0e96ddc5d11dd2371ab835c1dfa005b0f7753e31 Mon Sep 17 00:00:00 2001
From: Guilhem Saurel <guilhem.saurel@laas.fr>
Date: Tue, 10 Apr 2018 17:34:24 +0200
Subject: [PATCH] [Doc] Remove empty files, translate other to md

---
 .../creating-models.md}                       | 33 ++++++--------
 .../Chapters/crtp.dox => Chapters/crtp.md}    |  7 ++-
 doc/Doxyfile.extra.in                         |  2 +-
 doc/{Overview.dox => Overview.md}             | 44 ++++++++-----------
 .../Chapters/data-driven-algorithms.dox       | 27 ------------
 .../Chapters/dynamic-algorithms.dox           | 27 ------------
 doc/additionalDoc/Chapters/fcl-geometries.dox | 27 ------------
 .../Chapters/modeling-rigid-body.dox          | 27 ------------
 .../Chapters/python-bindings.dox              | 27 ------------
 .../Chapters/spatial-algebra.dox              | 27 ------------
 doc/treeview.dox                              | 10 +----
 11 files changed, 39 insertions(+), 219 deletions(-)
 rename doc/{additionalDoc/Chapters/creating-models.dox => Chapters/creating-models.md} (84%)
 rename doc/{additionalDoc/Chapters/crtp.dox => Chapters/crtp.md} (94%)
 rename doc/{Overview.dox => Overview.md} (51%)
 delete mode 100644 doc/additionalDoc/Chapters/data-driven-algorithms.dox
 delete mode 100644 doc/additionalDoc/Chapters/dynamic-algorithms.dox
 delete mode 100644 doc/additionalDoc/Chapters/fcl-geometries.dox
 delete mode 100644 doc/additionalDoc/Chapters/modeling-rigid-body.dox
 delete mode 100644 doc/additionalDoc/Chapters/python-bindings.dox
 delete mode 100644 doc/additionalDoc/Chapters/spatial-algebra.dox

diff --git a/doc/additionalDoc/Chapters/creating-models.dox b/doc/Chapters/creating-models.md
similarity index 84%
rename from doc/additionalDoc/Chapters/creating-models.dox
rename to doc/Chapters/creating-models.md
index 5b95a979a..1d82bda93 100644
--- a/doc/additionalDoc/Chapters/creating-models.dox
+++ b/doc/Chapters/creating-models.md
@@ -1,3 +1,5 @@
+# Creating models
+<!--
 //
 // Copyright (c) 2016 CNRS
 // Author: Florent Lamiraux, Justin Carpentier, Florian Valenza
@@ -15,26 +17,22 @@
 // received a copy of the GNU Lesser General Public License along with
 // Pinocchio If not, see
 // <http://www.gnu.org/licenses/>.
-
-namespace pinocchio
-{
-  
-/** \page Chapters_CreatingModels Creating models
+-->
 
 Here you can find the differents ways to create a model ( simple models, python/lua/urdf loading, Joint after Joint)
 
-\section Chapters_CreatingModels_introduction Introduction
+## Introduction
 
 In Pinocchio you can create Models in many ways. We have built-in parsers for different kind of format ( urdf, python, Lua)
 but you can also create a Model from scratch and fill it with the Joints you want.
 
-\section Chapters_CreatingModels_supported_formats Supported formats
+## Supported formats
 
 
-\subsection Chapters_CreatingModels_urdf Format urdf
+### Format urdf
 
 To load an urdf file in C++ code, copy the following lines:
-\code
+```
 #include <pinocchio/multibody/model.hpp>
 #include <pinocchio/multibody/parser/urdf.hpp>
 #include <pinocchio/multibody/parser/utils.hpp>
@@ -45,24 +43,24 @@ const std::string filename = "path/to/file/model.urdf";
 se3::JointModelFreeflyer rootJoint;
 se3::Model model = se3::urdf::buildModel (filename, rootJoint, verbose);
 se3::Data data (model);
-\endcode
+```
 
-\subsection Chapters_CreatingModels_Python Format Python
+### Format Python
 
 To load a python file in C++ code, copy the following lines:
-\code
+```
 #include <pinocchio/multibody/model.hpp>
 #include <pinocchio/multibody/parser/python.hpp>
 #include <pinocchio/multibody/parser/utils.hpp>
 #include <pinocchio/multibody/joint.hpp>
 
 //put here code to load from python
-\endcode
+```
 
-\subsection Chapters_CreatingModels_lua Format lua
+### Format lua
 
 To load an lua file in C++ code, copy the following lines:
-\code
+```
 #include <pinocchio/multibody/model.hpp>
 #include <pinocchio/multibody/parser/lua.hpp>
 #include <pinocchio/multibody/parser/utils.hpp>
@@ -72,7 +70,4 @@ bool freeflyer = true;
 const std::string filename = "path/to/file/model.lua";
 se3::Model model = se3::lua::buildModel (filename, freeflyer);
 se3::Data data (model);
-\endcode
-
-*/  
-}
\ No newline at end of file
+```
diff --git a/doc/additionalDoc/Chapters/crtp.dox b/doc/Chapters/crtp.md
similarity index 94%
rename from doc/additionalDoc/Chapters/crtp.dox
rename to doc/Chapters/crtp.md
index 4025fb9e3..669cd8b6f 100644
--- a/doc/additionalDoc/Chapters/crtp.dox
+++ b/doc/Chapters/crtp.md
@@ -1,4 +1,5 @@
-//
+# Curiously recurring template pattern
+<!--
 // Copyright (c) 2016 CNRS
 // Author: Florent Lamiraux, Justin Carpentier, Florian Valenza
 //
@@ -15,8 +16,7 @@
 // received a copy of the GNU Lesser General Public License along with
 // Pinocchio If not, see
 // <http://www.gnu.org/licenses/>.
-
-/** \page  Chapters_crtp Curiously recurring template pattern
+-->
 
 Similarly to Eigen, Pinocchio library makes intensive use of the so called CRTP design
 pattern. This pattern is used for performance reasons in the
@@ -24,4 +24,3 @@ implementation of static polymorphism, avoiding dynamic casts and calls to virtu
 All in all, CRTP plays a central role in the performance of Pinocchio.
 
 We refer to  https://en.wikipedia.org/wiki/Curiously_recurring_template_pattern for further explanations.
- */
diff --git a/doc/Doxyfile.extra.in b/doc/Doxyfile.extra.in
index f58d83027..78c18b7ae 100644
--- a/doc/Doxyfile.extra.in
+++ b/doc/Doxyfile.extra.in
@@ -308,7 +308,7 @@ RECURSIVE              = YES
 # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
 # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
 
-FILE_PATTERNS          = *.cc *.cpp *.h *.hpp *.hxx *.hh *.dox
+FILE_PATTERNS          = *.cc *.cpp *.h *.hpp *.hxx *.hh *.dox *.md
 
 # If the value of the INPUT tag contains directories, you can use the
 # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
diff --git a/doc/Overview.dox b/doc/Overview.md
similarity index 51%
rename from doc/Overview.dox
rename to doc/Overview.md
index 493c68259..a53e466ae 100644
--- a/doc/Overview.dox
+++ b/doc/Overview.md
@@ -1,6 +1,8 @@
+# Overview {#index}
+<!--
 //
-// Copyright (c) 2016 CNRS
-// Author: Florent Lamiraux, Justin Carpentier
+// Copyright (c) 2016, 2018 CNRS
+// Author: Florent Lamiraux, Justin Carpentier, Guilhem Saurel
 //
 // This file is part of Pinocchio
 // Pinocchio is free software: you can redistribute it
@@ -15,48 +17,40 @@
 // received a copy of the GNU Lesser General Public License along with
 // Pinocchio If not, see
 // <http://www.gnu.org/licenses/>.
+-->
 
-namespace pinocchio {
-
-/** \mainpage Overview
 
 This is the documentation of Pinocchio, the Eigen-like library for Rigid Body Dynamics computations.
 This library implements highly efficient kinematic and dynamic algorithms for multi-body systems making Pinocchio a versatile framework for robotics applications.
 
-\section pinocchio_section_installation Installation
+## Installation
 
 The full installation procedure can be found at https://github.com/stack-of-tasks/pinocchio/wiki/Installation.
 For further details about the project, please visit the GitHub page:
-https://github.com/stack-of-tasks/pinocchio 
+https://github.com/stack-of-tasks/pinocchio
 
-\section pinocchio_section_introduction Introduction
+## Introduction
 
 One of the main features is the separation between models (constant values representing an object) and data (used for intermediate computations).
 The two main classes are:
-\li se3::Model that represents a kinematic chain composed of joints that move
-    links with mass and inertia,
-\li se3::Data that stores intermediate data for kinematic and dynamic computations.
+- se3::Model that represents a kinematic chain composed of joints that move links with mass and inertia,
+- se3::Data that stores intermediate data for kinematic and dynamic computations.
 
-\section pinocchio_section_spatial_algebra Spatial Algebra
+## Spatial Algebra
 
 The library provides some classes to represent spatial quantities at the root of kinematic and dynamic computations. This main classes are reported below:
-\li se3::SE3Tpl represents a rigid placement, a mathematical representation of \f$ SE(3) \f$.
-\li se3::MotionTpl represents a spatial motion (linear and angular velocities), e.g. a spatial velocity or acceleration associated to a frame or a body. The spatial motion is the mathematical representation of \f$ se(3) \f$.
-\li se3::ForceTpl represents a spatial force, e.g. a spatial impulse or force associated to a body. The spatial force is the mathematical representation of \f$ se^{*}(3) \f$, the dual of \f$ se(3) \f$.
-\li se3::InertiaTpl represents a spatial inertia characterizing a rigid body and expressed in a given frame. This inertia is composed of mass, the position of the center of mass regarding to the frame and a rotational inertia.
+- se3::SE3Tpl represents a rigid placement, a mathematical representation of \f$ SE(3) \f$.
+- se3::MotionTpl represents a spatial motion (linear and angular velocities), e.g. a spatial velocity or acceleration associated to a frame or a body. The spatial motion is the mathematical representation of \f$ se(3) \f$.
+- se3::ForceTpl represents a spatial force, e.g. a spatial impulse or force associated to a body. The spatial force is the mathematical representation of \f$ se^{*}(3) \f$, the dual of \f$ se(3) \f$.
+- se3::InertiaTpl represents a spatial inertia characterizing a rigid body and expressed in a given frame. This inertia is composed of mass, the position of the center of mass regarding to the frame and a rotational inertia.
 
-\section pinocchio_section_algos Main Algorithms
+## Main Algorithms
 
-\section pinocchio_section_collision_checking Collision checking and distance computation
+## Collision checking and distance computation
 
 Collision checking between two bodies of the kinematic chain and external
 obstacles is implemented using library hpp-fcl (a modified version of
 Flexible Collision Library). The computation of the position of objects in 3D
 space for a given configuration is performed by the following classes:
-\li se3::GeometryModel that represents the collision objects associated to a joint stored in a se3::Model,
-\li se3::GeometryData that stores intermediate data like the position of objects
-in a given configuration of the kinematic chain.
-
-*/
-
-}
+- se3::GeometryModel that represents the collision objects associated to a joint stored in a se3::Model,
+- se3::GeometryData that stores intermediate data like the position of objects in a given configuration of the kinematic chain.
diff --git a/doc/additionalDoc/Chapters/data-driven-algorithms.dox b/doc/additionalDoc/Chapters/data-driven-algorithms.dox
deleted file mode 100644
index 21ad10530..000000000
--- a/doc/additionalDoc/Chapters/data-driven-algorithms.dox
+++ /dev/null
@@ -1,27 +0,0 @@
-//
-// Copyright (c) 2016 CNRS
-// Author: Florian Valenza
-//
-// This file is part of Pinocchio
-// Pinocchio is free software: you can redistribute it
-// and/or modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation, either version
-// 3 of the License, or (at your option) any later version.
-//
-// Pinocchio is distributed in the hope that it will be
-// useful, but WITHOUT ANY WARRANTY; without even the implied warranty
-// of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// General Lesser Public License for more details. You should have
-// received a copy of the GNU Lesser General Public License along with
-// Pinocchio If not, see
-// <http://www.gnu.org/licenses/>.
-
-namespace pinocchio
-{
-  
-/** \page Chapters_DataDrivenAlgorithms Data Driven Algorithms
-
-Here you can find informations about how information is stored in PInocchio and how algorithms workd
-
-*/  
-}
\ No newline at end of file
diff --git a/doc/additionalDoc/Chapters/dynamic-algorithms.dox b/doc/additionalDoc/Chapters/dynamic-algorithms.dox
deleted file mode 100644
index 8a0dfe6da..000000000
--- a/doc/additionalDoc/Chapters/dynamic-algorithms.dox
+++ /dev/null
@@ -1,27 +0,0 @@
-//
-// Copyright (c) 2016 CNRS
-// Author: Florian Valenza
-//
-// This file is part of Pinocchio
-// Pinocchio is free software: you can redistribute it
-// and/or modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation, either version
-// 3 of the License, or (at your option) any later version.
-//
-// Pinocchio is distributed in the hope that it will be
-// useful, but WITHOUT ANY WARRANTY; without even the implied warranty
-// of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// General Lesser Public License for more details. You should have
-// received a copy of the GNU Lesser General Public License along with
-// Pinocchio If not, see
-// <http://www.gnu.org/licenses/>.
-
-namespace pinocchio
-{
-  
-/** \page Chapters_DynamicAlgorithms Dynamic Algorithms
-
-Here you can find informations about dynamic algorithms
-
-*/  
-}
\ No newline at end of file
diff --git a/doc/additionalDoc/Chapters/fcl-geometries.dox b/doc/additionalDoc/Chapters/fcl-geometries.dox
deleted file mode 100644
index c7f0541de..000000000
--- a/doc/additionalDoc/Chapters/fcl-geometries.dox
+++ /dev/null
@@ -1,27 +0,0 @@
-//
-// Copyright (c) 2016 CNRS
-// Author: Florian Valenza
-//
-// This file is part of Pinocchio
-// Pinocchio is free software: you can redistribute it
-// and/or modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation, either version
-// 3 of the License, or (at your option) any later version.
-//
-// Pinocchio is distributed in the hope that it will be
-// useful, but WITHOUT ANY WARRANTY; without even the implied warranty
-// of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// General Lesser Public License for more details. You should have
-// received a copy of the GNU Lesser General Public License along with
-// Pinocchio If not, see
-// <http://www.gnu.org/licenses/>.
-
-namespace pinocchio
-{
-  
-/** \page Chapters_FclGeometries Geometry
-
-Here you can find informations about how geometries are stored ( index of parent ) and used via FCL
-
-*/  
-}
\ No newline at end of file
diff --git a/doc/additionalDoc/Chapters/modeling-rigid-body.dox b/doc/additionalDoc/Chapters/modeling-rigid-body.dox
deleted file mode 100644
index 47af9ef5c..000000000
--- a/doc/additionalDoc/Chapters/modeling-rigid-body.dox
+++ /dev/null
@@ -1,27 +0,0 @@
-//
-// Copyright (c) 2016 CNRS
-// Author: Florian Valenza
-//
-// This file is part of Pinocchio
-// Pinocchio is free software: you can redistribute it
-// and/or modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation, either version
-// 3 of the License, or (at your option) any later version.
-//
-// Pinocchio is distributed in the hope that it will be
-// useful, but WITHOUT ANY WARRANTY; without even the implied warranty
-// of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// General Lesser Public License for more details. You should have
-// received a copy of the GNU Lesser General Public License along with
-// Pinocchio If not, see
-// <http://www.gnu.org/licenses/>.
-
-namespace pinocchio
-{
-  
-/** \page Chapters_RigidBodyDynamicModel Modeling rigid bodies
-
-Here you can find informations related to how pinocchio models a rigid multi body model. (ie Joints augmented by inertias)
-
-*/  
-}
\ No newline at end of file
diff --git a/doc/additionalDoc/Chapters/python-bindings.dox b/doc/additionalDoc/Chapters/python-bindings.dox
deleted file mode 100644
index 3df4bbba6..000000000
--- a/doc/additionalDoc/Chapters/python-bindings.dox
+++ /dev/null
@@ -1,27 +0,0 @@
-//
-// Copyright (c) 2016 CNRS
-// Author: Florian Valenza
-//
-// This file is part of Pinocchio
-// Pinocchio is free software: you can redistribute it
-// and/or modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation, either version
-// 3 of the License, or (at your option) any later version.
-//
-// Pinocchio is distributed in the hope that it will be
-// useful, but WITHOUT ANY WARRANTY; without even the implied warranty
-// of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// General Lesser Public License for more details. You should have
-// received a copy of the GNU Lesser General Public License along with
-// Pinocchio If not, see
-// <http://www.gnu.org/licenses/>.
-
-namespace pinocchio
-{
-  
-/** \page Chapters_PythonBindings Python Bindings
-
-Here you can find explications concerning python bindings and calls to C++ methods + RobotWrapper Class
-
-*/  
-}
\ No newline at end of file
diff --git a/doc/additionalDoc/Chapters/spatial-algebra.dox b/doc/additionalDoc/Chapters/spatial-algebra.dox
deleted file mode 100644
index e42fc2eab..000000000
--- a/doc/additionalDoc/Chapters/spatial-algebra.dox
+++ /dev/null
@@ -1,27 +0,0 @@
-//
-// Copyright (c) 2016 CNRS
-// Author: Florian Valenza
-//
-// This file is part of Pinocchio
-// Pinocchio is free software: you can redistribute it
-// and/or modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation, either version
-// 3 of the License, or (at your option) any later version.
-//
-// Pinocchio is distributed in the hope that it will be
-// useful, but WITHOUT ANY WARRANTY; without even the implied warranty
-// of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// General Lesser Public License for more details. You should have
-// received a copy of the GNU Lesser General Public License along with
-// Pinocchio If not, see
-// <http://www.gnu.org/licenses/>.
-
-namespace pinocchio
-{
-  
-/** \page Chapters_SpatialAlgebra Spatial Algebra
-
-Here you can find informations related to Roy FeatherStone's book Rigid Body Dynamic Algorithms and spatial algebra
-
-*/  
-}
\ No newline at end of file
diff --git a/doc/treeview.dox b/doc/treeview.dox
index 607fe709d..f9767c8d2 100644
--- a/doc/treeview.dox
+++ b/doc/treeview.dox
@@ -28,14 +28,8 @@ namespace pinocchio {
   //
 
   /** \page Chapters Chapters
-       - \subpage Chapters_SpatialAlgebra
-       - \subpage Chapters_RigidBodyDynamicModel
-       - \subpage Chapters_DynamicAlgorithms
-       - \subpage Chapters_DataDrivenAlgorithms
-       - \subpage Chapters_FclGeometries
-       - \subpage Chapters_CreatingModels
-       - \subpage Chapters_PythonBindings
-       - \subpage Chapters_crtp
+       - \subpage md_doc_Chapters_creating-models
+       - \subpage md_doc_Chapters_crtp
   */
 
   //
-- 
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