.clang-format

----
-ColumnLimit:     80
-...

.git-blame-ignore-revs

+# pre-commit run -a (Guilhem Saurel, 2022-07-27)
+e9a222fb0a1f236e534e21c66cb623fd8d25b8d6
+
+# pre-commit: details (Guilhem Saurel, 2022-04-14)
+1c0f3cc1048a8b2a8206510a51a237b2f1e68a34
+
+# pre-commit run -a (Guilhem Saurel, 2022-03-30)
+0c1e6fb50735d4d6cc93e15d3bef202392d47c5b
+
+# clang format defaults + pre-commit (Guilhem Saurel, 2022-03-30)
+b6fc5d81e645a84fa8f4d656371adfb27c2b2b23
+
+# [value] Clang format. (Olivier Stasse, 2022-01-09)
+b852eef0d56de04ae91a43b1ddbd837ec69ddbe6
+
+# linters: fix clang-check-12 (Guilhem Saurel, 2021-09-14)
+ca1b2fc51540b4fcb2cd0b4fccaa33b02738af41
+
+# reformat for clang-format-12 (Guilhem Saurel, 2021-09-07)
+ed5899076b7b11c16d9517295e3826dd9b9d80d2
+
+# format (Guilhem Saurel, 2020-11-13)
+c54add29f80f6bcd1d05ca741d472491cf74c180
+
+# format (Guilhem Saurel, 2020-07-22)
+f4def3bfeaf0f9c9a6d5c5eb01c3a3b2fbb04b2f
+
+# clang format. (Olivier Stasse, 2020-02-03)
+70864112c87365af645f0404f881edf36c1ec734
+
+# [clang] Update format. (Olivier Stasse, 2019-08-26)
+384b2078e4962d762db4293bf3396be17df4e5c7
+
+# [clang-format] Comply to Google style. (Olivier Stasse, 2019-08-20)
+df48199dd436ba8341ae93c7b1f87eb30d0f457a

.gitignore

 _build*
-*~
+.~
\ No newline at end of file
+compile_commands.json

.gitmodules

-[submodule "jrl-cmakemodules"]
-	   path = jrl-cmakemodules
-	   url = git://github.com/jrl-umi3218/jrl-cmakemodules.git
 [submodule "cmake"]
 	path = cmake
-	url = git://github.com/jrl-umi3218/jrl-cmakemodules.git
-[submodule ".travis"]
-	path = .travis
-	url = git://github.com/jrl-umi3218/jrl-travis.git
+	url = https://github.com/jrl-umi3218/jrl-cmakemodules.git

.pre-commit-config.yaml

+ci:
+    autoupdate_branch: 'devel'
+repos:
+-   repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v14.0.6
+    hooks:
+    -   id: clang-format
+        args: [--style=Google]
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    -   id: check-added-large-files
+    -   id: check-ast
+    -   id: check-executables-have-shebangs
+    -   id: check-json
+    -   id: check-merge-conflict
+    -   id: check-symlinks
+    -   id: check-toml
+    -   id: check-yaml
+    -   id: debug-statements
+    -   id: destroyed-symlinks
+    -   id: detect-private-key
+    -   id: end-of-file-fixer
+    -   id: fix-byte-order-marker
+    -   id: mixed-line-ending
+    -   id: trailing-whitespace
+-   repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+    - id: cmake-format

.travis @ 083fa2cb

-Subproject commit 083fa2cb0fa4ad594926d9bb3d246075e62ce9ee

.travis.yml

-language: cpp
-sudo: required
-compiler:
-  - gcc
-  - clang
-env:
-  global:
-  - DEBSIGN_KEYID=5AE5CD75
-  - secure: "lEJYxth3fNsmvNS7Ern9+kEpHk4X3Tjo51GBUQBNL6g+YyZJKm4xwBEfwK+sewlmhY3oLUds+5H/2zE27q517kIcpP2Tlp4sRfooJfnBS7YYyF+1boxbvOXrZ2aqev3rzkyvKKMBg0UJTvAiSf7JgVCkMv33GeAX3/I+djEh23U="
-  - secure: "QTw5QQDaeQWBz6APcUCyl9P9UPI/T3j1++9o9fPxygS9R/7bQYNCrSH++owcAVCJgUI5oY3RmnYk/PjVygOLM0vbFqB2mMySibAhO/U3pSLtZ/HyPjqI9fX0TV/Cf7ji7soeXKk8p6kI2InMILpODLBaLdfm/jgCdAfecr5sGQI="
-  - secure: "JEcGQsUgEND64cAGVEHSxg8j7SlwofuYtLamANszs/h8FGYZ82rEjmG7r2zqSfBj/i1WsnSbTSsh8WJuXzvV8fw8enkcLEuJG9scQJzuzY8hnLe81o1fhEkclML0SLkLQ2Fu6rIqlKKeYwmJFFhSIj69ESRIkDhkjA1OrV7szzc="
-  - APT_DEPENDENCIES="doxygen libboost-dev libboost-test-dev libboost-filesystem-dev libboost-system-dev libboost-thread-dev libboost-program-options-dev liblapack-dev gfortran libeigen3-dev"
-  - GIT_DEPENDENCIES="jrl-umi3218/jrl-mathtools jrl-umi3218/jrl-mal"
-  - PPA_URI="stack-of-tasks/snapshot"
-  - NSIQCPPSTYLE_FILEFILTERPATH=cmake/filefilter.txt
-notifications:
-  hipchat:
-    rooms:
-      - secure: "SP8KX6gPzBT0BCpcL3ybK4Cgx7a7rmK3Hv/fD2lIf/RUdTwtzLh/J/l9xSYuMZisLe1tM+12vfP7r6t1RNdXrB7pSpYvFRNIWmyfBC7KnUFVn5rwxUnDPhKY3D/XaJ1cycbBJqJdUjYjFKCGEm4x6cpRRN61Ii66RAUvm1h9aHQ="
-  email:
-  - hpp-source@laas.fr
-branches:
-  only:
-  - master
-  - debian
-script: ./.travis/run build
-after_success: ./.travis/run after_success
-after_failure: ./.travis/run after_failure
-before_install: ./.travis/run  before_install
-matrix:
-  allow_failures:
-    - compiler: clang

CMakeLists.txt

-# Copyright 2010, Olivier Stasse, JRL, CNRS/AIST
+cmake_minimum_required(VERSION 3.1)
 
-CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
+# Project properties
+set(PROJECT_ORG stack-of-tasks)
+set(PROJECT_NAME dynamic-graph)
+set(PROJECT_DESCRIPTION "Dynamic graph library")
+set(PROJECT_URL "https://github.com/${PROJECT_ORG}/${PROJECT_NAME}")
 
-INCLUDE(cmake/base.cmake)
-INCLUDE(cmake/boost.cmake)
-INCLUDE(cmake/eigen.cmake)
-INCLUDE(cmake/pthread.cmake)
+# Project options
+option(SUFFIX_SO_VERSION "Suffix library name with its version" ON)
 
-SET(PROJECT_ORG stack-of-tasks)
-SET(PROJECT_NAME dynamic-graph)
-SET(PROJECT_DESCRIPTION "Dynamic graph library")
-SET(PROJECT_URL "http://github.com/${PROJECT_ORG}/${PROJECT_NAME}")
-SET(PROJECT_SUFFIX "-v3")
+# Project configuration
+set(PROJECT_USE_CMAKE_EXPORT TRUE)
+set(CUSTOM_HEADER_DIR ${PROJECT_NAME})
+set(CXX_DISABLE_WERROR TRUE)
 
-SET(CUSTOM_HEADER_DIR "${PROJECT_NAME}")
+# Doxygen setup
+set(DOXYGEN_USE_MATHJAX YES)
+set(DOXYGEN_USE_TEMPLATE_CSS YES)
 
-SET(DOXYGEN_USE_MATHJAX YES)
+# JRL-cmakemodule setup
+include(cmake/base.cmake)
+include(cmake/boost.cmake)
 
-# Defines paths.
-SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
+# Project definition
+compute_project_args(PROJECT_ARGS LANGUAGES CXX)
+project(${PROJECT_NAME} ${PROJECT_ARGS})
+check_minimal_cxx_standard(14 ENFORCE)
 
-SETUP_PROJECT()
+include(cmake/pthread.cmake) # needs to be included after the CXX definition
+
+# Project dependencies
+if(BUILD_TESTING)
+  find_package(Boost REQUIRED COMPONENTS unit_test_framework)
+endif()
+add_project_dependency(Boost REQUIRED COMPONENTS serialization system thread)
+add_project_dependency(Eigen3 REQUIRED)
+search_for_pthread()
+
+if(Boost_VERSION GREATER 107299 OR Boost_VERSION_MACRO GREATER 107299)
+  # Silence a warning about a deprecated use of boost bind by boost >= 1.73
+  # without dropping support for boost < 1.73
+  add_definitions(-DBOOST_BIND_GLOBAL_PLACEHOLDERS)
+endif()
 
 # Add configuration headers for plug-ins.
-GENERATE_CONFIGURATION_HEADER(
-  ${HEADER_DIR} config-tracer.hh DG_TRACER tracer_EXPORTS)
-GENERATE_CONFIGURATION_HEADER(
-  ${HEADER_DIR}
-  config-tracer-real-time.hh DG_TRACERREALTIME tracer_real_time_EXPORTS)
+generate_configuration_header(${HEADER_DIR} config-tracer.hh DG_TRACER
+                              tracer_EXPORTS)
+generate_configuration_header(${HEADER_DIR} config-tracer-real-time.hh
+                              DG_TRACERREALTIME tracer_real_time_EXPORTS)
+
+# Verbosity level
+if(NOT (\"${CMAKE_VERBOSITY_LEVEL}\" STREQUAL \"\"))
+  add_definitions(-DVP_DEBUG_MODE=${CMAKE_VERBOSITY_LEVEL} -DVP_DEBUG)
+endif(NOT (\"${CMAKE_VERBOSITY_LEVEL}\" STREQUAL \"\"))
+
+# Main Library
+set(${PROJECT_NAME}_HEADERS
+    include/${CUSTOM_HEADER_DIR}/fwd.hh
+    include/${CUSTOM_HEADER_DIR}/debug.h
+    include/${CUSTOM_HEADER_DIR}/real-time-logger.h
+    include/${CUSTOM_HEADER_DIR}/real-time-logger-def.h
+    include/${CUSTOM_HEADER_DIR}/dynamic-graph-api.h
+    include/${CUSTOM_HEADER_DIR}/entity.h
+    include/${CUSTOM_HEADER_DIR}/factory.h
+    include/${CUSTOM_HEADER_DIR}/pool.h
+    include/${CUSTOM_HEADER_DIR}/exception-abstract.h
+    include/${CUSTOM_HEADER_DIR}/exception-factory.h
+    include/${CUSTOM_HEADER_DIR}/exception-signal.h
+    include/${CUSTOM_HEADER_DIR}/exception-traces.h
+    include/${CUSTOM_HEADER_DIR}/signal.h
+    include/${CUSTOM_HEADER_DIR}/signal-array.h
+    include/${CUSTOM_HEADER_DIR}/signal-base.h
+    include/${CUSTOM_HEADER_DIR}/signal-ptr.h
+    include/${CUSTOM_HEADER_DIR}/signal-time-dependent.h
+    include/${CUSTOM_HEADER_DIR}/signal-ptr.t.cpp
+    include/${CUSTOM_HEADER_DIR}/signal.t.cpp
+    include/${CUSTOM_HEADER_DIR}/time-dependency.h
+    include/${CUSTOM_HEADER_DIR}/time-dependency.t.cpp
+    # Kept for a brittle backward compatiblity.
+    include/${CUSTOM_HEADER_DIR}/signal-caster.h
+    include/${CUSTOM_HEADER_DIR}/signal-cast-helper.h
+    include/${CUSTOM_HEADER_DIR}/all-signals.h
+    include/${CUSTOM_HEADER_DIR}/signal-helper.h
+    include/${CUSTOM_HEADER_DIR}/entity-helper.h
+    include/${CUSTOM_HEADER_DIR}/tracer.h
+    include/${CUSTOM_HEADER_DIR}/tracer-real-time.h
+    include/${CUSTOM_HEADER_DIR}/command.h
+    include/${CUSTOM_HEADER_DIR}/eigen-io.h
+    include/${CUSTOM_HEADER_DIR}/linear-algebra.h
+    include/${CUSTOM_HEADER_DIR}/value.h
+    include/${CUSTOM_HEADER_DIR}/command-setter.h
+    include/${CUSTOM_HEADER_DIR}/command-setter.t.cpp
+    include/${CUSTOM_HEADER_DIR}/command-getter.h
+    include/${CUSTOM_HEADER_DIR}/command-getter.t.cpp
+    include/${CUSTOM_HEADER_DIR}/command-direct-getter.h
+    include/${CUSTOM_HEADER_DIR}/command-direct-setter.h
+    include/${CUSTOM_HEADER_DIR}/command-bind.h
+    include/${CUSTOM_HEADER_DIR}/all-commands.h
+    include/${CUSTOM_HEADER_DIR}/logger.h)
+
+set(${PROJECT_NAME}_SOURCES
+    src/debug/debug.cpp
+    src/debug/real-time-logger.cpp
+    src/debug/logger.cpp
+    src/dgraph/entity.cpp
+    src/dgraph/factory.cpp
+    src/dgraph/pool.cpp
+    src/exception/exception-abstract.cpp
+    src/exception/exception-factory.cpp
+    src/exception/exception-signal.cpp
+    src/exception/exception-traces.cpp
+    src/mt/process-list.cpp
+    src/signal/signal-array.cpp
+    src/command/value.cpp
+    src/command/command.cpp)
 
-# FIXME: to be changed into lib/dynamic-graph
-# to avoid name collision when installing dynamic-graph in /usr.
-SET(PLUGINDIR "${CMAKE_INSTALL_FULL_LIBDIR}/plugin")
+add_library(${PROJECT_NAME} SHARED ${${PROJECT_NAME}_SOURCES}
+                                   ${${PROJECT_NAME}_HEADERS})
+modernize_target_link_libraries(
+  ${PROJECT_NAME}
+  SCOPE
+  PUBLIC
+  TARGETS
+  Eigen3::Eigen
+  INCLUDE_DIRS
+  ${EIGEN3_INCLUDE_DIR})
+target_include_directories(${PROJECT_NAME} PUBLIC $<INSTALL_INTERFACE:include>)
+target_link_libraries(${PROJECT_NAME} PUBLIC Boost::serialization Boost::system
+                                             Boost::thread)
 
-# Add extra keys to pkg-config file to export the location of the
-# plug-in directory in a robust manner.
-SET(PKG_CONFIG_EXTRA "plugindir=${PLUGINDIR}")
+if(UNIX)
+  target_link_libraries(${PROJECT_NAME} PUBLIC ${CMAKE_DL_LIBS} pthread)
+endif(UNIX)
 
-# Add dependency toward dynamic graph library in pkg-config file.
-PKG_CONFIG_APPEND_LIBS(${PROJECT_NAME})
+if(SUFFIX_SO_VERSION)
+  set_target_properties(${PROJECT_NAME} PROPERTIES SOVERSION ${PROJECT_VERSION})
+endif(SUFFIX_SO_VERSION)
 
-# Search for Boost.
-SET(BOOST_COMPONENTS serialization system unit_test_framework thread)
-SEARCH_FOR_BOOST()
-SEARCH_FOR_PTHREAD()
+install(
+  TARGETS ${PROJECT_NAME}
+  EXPORT ${TARGETS_EXPORT_NAME}
+  DESTINATION lib)
 
-# Search for Boost.
-SEARCH_FOR_EIGEN()
+set(DYNAMIC_GRAPH_PLUGINDIR "lib/${PROJECT_NAME}-plugins")
+set(PACKAGE_EXTRA_MACROS
+    "set(DYNAMIC_GRAPH_PLUGINDIR ${DYNAMIC_GRAPH_PLUGINDIR})")
+set(PKG_CONFIG_EXTRA "plugindir=${DYNAMIC_GRAPH_PLUGINDIR}")
 
-ADD_SUBDIRECTORY(src)
-ADD_SUBDIRECTORY(include/${PROJECT_NAME})
-ADD_SUBDIRECTORY(tests)
+add_subdirectory(src)
+if(BUILD_TESTING)
+  add_subdirectory(tests)
+endif(BUILD_TESTING)
 
-SETUP_PROJECT_FINALIZE()
+pkg_config_append_libs(${PROJECT_NAME})
+install(FILES package.xml DESTINATION share/${PROJECT_NAME})

NEWS

@@ -129,4 +129,3 @@ stasse (3):
       Reinforce the dependant->dependent policy.     Merge the florent branch.     Makes the test_depend.cpp test works.
       Reinforce the dependant->dependent policy.
       Adding documentation to cmdPlug.
-

README.md

 dynamic-graph
 =============
 
-[![Building Status](https://travis-ci.org/stack-of-tasks/dynamic-graph.svg?branch=master)](https://travis-ci.org/stack-of-tasks/dynamic-graph)
-[![Pipeline status](https://gepgitlab.laas.fr/stack-of-tasks/dynamic-graph/badges/master/pipeline.svg)](https://gepgitlab.laas.fr/stack-of-tasks/dynamic-graph/commits/master)
-[![Coverage report](https://gepgitlab.laas.fr/stack-of-tasks/dynamic-graph/badges/master/coverage.svg?job=doc-coverage)](http://projects.laas.fr/stack-of-tasks/doc/stack-of-tasks/dynamic-graph/master/coverage/)
+[![Building status](https://gitlab.laas.fr/stack-of-tasks/dynamic-graph/badges/master/pipeline.svg)](https://gitlab.laas.fr/stack-of-tasks/dynamic-graph/commits/master)
+[![Coverage report](https://gitlab.laas.fr/stack-of-tasks/dynamic-graph/badges/master/coverage.svg?job=doc-coverage)](http://projects.laas.fr/stack-of-tasks/doc/stack-of-tasks/dynamic-graph/master/coverage/)
+[![License](https://img.shields.io/badge/License-BSD%202--Clause-green.svg)](https://opensource.org/licenses/BSD-2-Clause)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/stack-of-tasks/dynamic-graph/master.svg)](https://results.pre-commit.ci/latest/github/stack-of-tasks/dynamic-graph)
 
 This software provides an efficient way to modelize a C++ data-flow.
 
@@ -42,10 +43,7 @@ located in the `$prefix/share/doc/dynamic-graph` directoy where
 Getting Help
 ------------
 
-Support is provided through:
- * the HPP mailing-list: hpp@laas.fr
- * the following HipChat room: http://www.hipchat.com/gh4wQrZeV
-
+Support is provided through issues on the github interface.
 
 How can I install dynamic-graph?
 --------------------------------
@@ -57,13 +55,9 @@ have to be available on your machine.
 
  - Libraries:
    - [Boost][] (>= 1.40)
-     Its detection is controlled by the `BOOST_ROOT` variable, see next section
-     for more information.
-   - [Lapack][] library
-     Use the generic purpose `CMAKE_CXX_FLAGS` and `CMAKE_EXE_LINKER_FLAGS`
-     to insert the flags required for the compiler to find your Lapack library
-     if it is installed in a non-standard directory.
-   - [jrl-mal][] library
+   - Doxygen
+   - Eigen3
+   - pthread
  - System tools:
    - [CMake][] (>=2.6)
    - [pkg-config][]
@@ -143,15 +137,12 @@ This package authors are credited in the [AUTHORS](AUTHORS) file.
 Available Packages
 ------------------
 
- * RobotPkg (Release 2.5.3r1):
+ * RobotPkg :
    http://robotpkg.openrobots.org/robotpkg/motion/dynamic-graph/index.html
 
 
 [doxygen-documentation]: http://stack-of-tasks.github.io/dynamic-graph/doxygen/HEAD/
 
-[jrl-mathtools]: https://github.com/jrl-umi3218/jrl-mathtools
-[jrl-mal]: https://github.com/jrl-umi3218/jrl-mal
-
 [git-submodules]: http://git-scm.com/book/en/Git-Tools-Submodules
 
 [Boost]: http://www.boost.org/
@@ -159,7 +150,6 @@ Available Packages
 [Doxygen]: http://www.stack.nl/~dimitri/doxygen/
 [Eigen]: http://eigen.tuxfamily.org/
 [Git]: http://git-scm.com/
-[Lapack]: http://www.netlib.org/lapack/
 [Libtool]: https://www.gnu.org/software/libtool/
 [RobotPkg]: http://robotpkg.openrobots.org/
 [log4cxx]: https://logging.apache.org/log4cxx/

cmake @ 47c0cbf0

-Subproject commit 429af97fe0b858bd73a1747768cc1ac735386140
+Subproject commit 47c0cbf0b29433060682377dcb28266e8dc38995

doc/additionalDoc/debug-doc.h

@@ -3,14 +3,15 @@
 
 They are several ways to perform debugging in dynamic-graph depending on your
 needs or situation:
-- Programmatically inside the entity in C++ will write inside a buffer in a
+- Programmatically inside the entity in C++, a logger will
+write inside a buffer in a
 different thread and output in a stream (either std::cout or a file). It is
 detailed in \subpage subp_debug_rt_logger.
-- Programmatically inside the entity in C++ using a member of the entities and
-the previous real-time mechanism. It provides 4 levels of messags :(DEBUG,INFO,
+It provides 4 levels of messags :(DEBUG,INFO,
 WARNING, ERROR). It is described in details here: \subpage subp_logger
+
 - Programmatically in C++ to avoid overhead with macros and handling level as an
-int: \subpage subp_dbg_trace
+int: \subpage subp_dbg_trace .
 - If you just need to collect informations from signals (like rosbag). You can
 use an entity called Tracer inside the graph:\subpage tracerdoc . <br> A real
 time version exists to write directly inside a memory buffer

doc/additionalDoc/debug-logger.h

 /**
 \page subp_logger Loggers
 
-\section sec_logger Initialization of the logger
+\section sec_init_rt_logger Initialization of the logger
 
-\subsection subsec_logger_hcpp Header and preprocessor variable
+\subsection subsec_init_rt_logger_hcpp Header and preprocessor variable
 
 In order to activate the logger you need to add the following lines:
 \code
@@ -22,57 +22,20 @@ It is possible to set the output stream of the messages inside a file:
 
   dynamicgraph::RealTimeLogger::destroy();
 \endcode
-Here the file is "/tmp/dg-LOGS.txt".
 
-\subsection subsec_logger_init Initialization of the logger
+\section sec_use_rt_logger Using the rt_logger
+
 
-Inside the constructor of the entity:
 \code
-      logger_.setTimeSample(0.001);
-      logger_.setStreamPrintPeriod(0.005);
-      logger_.setVerbosity(VERBOSITY_ALL);
-      LoggerVerbosity alv = logger_.getVerbosity();
+// Somewhere in your library
+dgRTLOG() << "your message. Prefer to use \n than std::endl."
 \endcode
 
-The first line sets the frequency at which the logger will be updated.<br>
-The second line specifies at which frequency the STREAM messages should be
-printed.<br>
-The third line specifies the level of message to accept.<br>
-The fourth line returns the level of verbosity.
-In this case, all messages are accepted and the STREAM message are displayed on
-the output streams once on five. <br>
-
-The full list of options are:
-<ul>
-<li>VERBOSITY_ALL: Accept all messages</li>
-<li>VERBOSITY_INFO_WARNING_ERROR: Accept messages at minimum level : INFO,
-WARNING, ERROR</li> <li>VERBOSITY_WARNING_ERROR: Accept messages at minimum
-level : WARNING, ERROR</li> <li>VERBOSITY_ERROR: Accept messages at minimum
-level : ERROR</li>
-</ul>
-
 
-\section sec_logger_tests Displaying messages
+Here the output file is "/tmp/dg-LOGS.txt".
 
-Here is some example on how to display or record some information.
-\code
-      sendMsg("This is a message of level MSG_TYPE_DEBUG",MSG_TYPE_DEBUG,
-__FILE__,__LINE__); sendMsg("This is a message of level
-MSG_TYPE_INFO",MSG_TYPE_INFO, __FILE__,__LINE__); sendMsg("This is a message of
-level MSG_TYPE_WARNING",MSG_TYPE_WARNING, __FILE__,__LINE__); sendMsg("This is a
-message of level MSG_TYPE_ERROR",MSG_TYPE_ERROR, __FILE__,__LINE__);
-      sendMsg("This is a message of level
-MSG_TYPE_DEBUG_STREAM",MSG_TYPE_DEBUG_STREAM, __FILE__,__LINE__); sendMsg("This
-is a message of level MSG_TYPE_INFO_STREAM",MSG_TYPE_INFO_STREAM,
-__FILE__,__LINE__); sendMsg("This is a message of level
-MSG_TYPE_WARNING_STREAM",MSG_TYPE_WARNING_STREAM, __FILE__,__LINE__);
-      sendMsg("This is a message of level
-MSG_TYPE_ERROR_STREAM",MSG_TYPE_ERROR_STREAM, __FILE__,__LINE__);
-
-      logger_.countdown();
-\endcode
 
 Specifying the file with __FILE__ and the line inside the file by __LINE__ are
 necessary for the STREAM messages. Indeed they are indexed using the two values.
-As the default value are "" and 0 the counting will be confused.
+The default values "" and 0 for the counting are not well understood.
 */

doc/additionalDoc/debug-real-time-logger.h

-/**
-\page subp_debug_rt_logger Real-time Logger
-
- It is intended to be used like this:
-   \code
-   #define ENABLE_RT_LOG
-   #include <dynamic-graph/real-time-logger.h>
-
-   // Somewhere in the main function of your executable
-   int main (int argc, char** argv) {
-     dgADD_OSTREAM_TO_RTLOG (std::cout);
-   }
-
-   // Somewhere in your library
-   dgRTLOG() << "your message. Prefer to use \n than std::endl."
-   \endcode
-
-   \note Thread safety. This class expects to have:
-   - only one reader: the one who take the log entries and write them somewhere.
-   - one writer at a time. Writing to the logs is **never** a blocking
-     operation. If the resource is busy, the log entry is discarded.
-*/

doc/additionalDoc/doc-command.h

+/** \page subpage_command Commands
+
+\section subpage_command_intro Quick introduction
+
+Commands are allowing to expand the entities.
+It has no real interest in C++, and is mostly targeted to scripting languages
+used to manipulate the control graph.
+dynamic-graph-python provides a mecanism which is automatically binding command
+to python. The main interest for a programmer is that there is no additional
+lines to add. It is realized through CMake rules provided by the submodule
+jrl-cmakemodules.
+
+\section subpage_command_using Extending entities
+
+\subsection subpage_command_setters_and_getters Setters and getters
+
+To modify a quantity with a special method of your class, it is recommanded to
+use Setter.
+
+For instance to specify the size of the state in one entity and calls the
+method setStateSize it is possible to write:
+
+\code
+    docstring = "\n"
+                "    Set size of state vector\n"
+                "\n";
+    addCommand("resize", new command::Setter<Device, unsigned int>(
+                             *this, &Device::setStateSize, docstring));
+\endcode
+
+Getting the information of the member of the class can be realized with
+the following snippet:
+
+\code
+    addCommand("getTimeStep",
+               command::makeDirectGetter(
+                   *this, &this->timestep_,
+                   command::docDirectGetter("Time step", "double")));
+\endcode
+
+\subsubsection subsubpage_command_void_multiple_args Implementing a command
+
+Templates are provided to create commands returning no value, but with up to
+4 arguments.
+
+In order to call the following method:
+\code
+  void four_args(const int &, const int &, const int &, const int &) {
+    test_four_args_ = true;
+  }
+\endcode
+
+It is sufficient to add in the constructor:
+\code
+    addCommand("4_args",
+               makeCommandVoid4(
+                   *this, &CustomEntity::four_args,
+                   docCommandVoid4("four args", "int", "int", "int", "int")));
+\endcode
+
+The arguments are limited to the types provided by the class Value.
+
+\subsection subpage_command_void_multiple_args Commands returning a value
+
+The templates with the prefix makeCommandReturnType are allowing to return
+a type.
+
+For instance to add a command returning a type with two arguments:
+\code
+  std::string two_args_ret(const int &, const int &)
+  { test_two_args_ = true; return std::string("return");}
+\endcode
+
+In the constructor, the following snippet shows to create the command:
+\code
+    addCommand("2_args_r",
+               makeCommandReturnType2(
+                 *this, &CustomEntity::two_args_ret,
+                 docCommandVoid2("two args", "int","int")));
+\endcode
+
+\section section_calling_a_generic_command Calling a generic command
+
+Of course calling in C++ a command amounts to call directly the method.
+However in the context of writing a wrapper for another language,
+one may wants to find a command and build the call.
+
+All the commands of an entity are store in a map. The strings storing the
+commands name are the map keys.
+
+Therefore calling the previous command can be done with the following snippet:
+\code
+
+std::map<const std::string, Command *> aCommandMap =
+ this->getNewStyleCommandMap();
+
+std::string cmd_name = "4_args";
+
+std::map<const std::string, Command *>::iterator it_map;
+
+it_map = aCommandMap.find(cmd_name);
+if (it_map == aCommandMap.end())
+
+int first_arg = 1;
+Value aValue(first_arg);
+std::vector<Value> values;
+
+for (unsigned int i = 0; i < 4; i++)
+  values.push_back(aValue);
+
+it_map->second->setParameterValues(values);
+it_map->second->execute();
+it_map->second->owner();
+it_map->second->getDocstring();
+
+\endcode
+
+when returning a value the line with the call to execute is :
+\code
+Value aValue =it_map->second->execute();
+\endcode
+
+*/

doc/additionalDoc/doc-debug-real-time-logger.h

+/**
+\page subp_debug_rt_logger Real-time Logger
+
+ \section real_time_logger_quick_intro Quick introduction
+ Each entity has a protected logger_ object.
+ The simplest way to have information while running your graph is to initialize
+ it in the constructor, and then display information in the methods.
+
+ You can then change the level of information you want to display using
+ either the entity method setLoggerVerbosityLevel()
+ or the corresponding python bindings.
+
+ \section real_time_logger_modifying_entities Putting information in your
+entity.
+
+ It is possible to define the periodicity of the logger:
+ \code
+ logger_.setTimeSample(0.001);
+ \endcode
+
+ To define the periodicity at which one wants to print information:
+ \code
+ logger_.setStreamPrintPeriod(0.005);
+ \endcode
+
+ Several level of verbosity are possible:
+ \code
+ logger_.setVerbosity(VERBOSITY_ALL);
+ \endcode
+ The full list of options are:
+<ul>
+<li>VERBOSITY_ALL: Accept all messages</li>
+<li>VERBOSITY_INFO_WARNING_ERROR: Accept messages at minimum level : INFO,
+WARNING, ERROR</li> <li>VERBOSITY_WARNING_ERROR: Accept messages at minimum
+level : WARNING, ERROR</li> <li>VERBOSITY_ERROR: Accept messages at minimum
+level : ERROR</li>
+</ul>
+
+It is specified by the enum LoggerVerbosity
+
+ It is possible to display information according to various level of debug:
+ \code
+ sendMsg("This is a message of level MSG_TYPE_DEBUG", MSG_TYPE_DEBUG);
+ \endcode
+ or
+ \code
+ DYNAMIC_GRAPH_ENTITY_DEBUG   (*this) << "This is a message of level
+MSG_TYPE_DEBUG\n"; DYNAMIC_GRAPH_ENTITY_INFO    (*this) << "This is a message of
+level MSG_TYPE_INFO\n"; DYNAMIC_GRAPH_ENTITY_WARNING (*this) << "This is a
+message of level MSG_TYPE_WARNING\n"; DYNAMIC_GRAPH_ENTITY_ERROR   (*this) <<
+"This is a message of level MSG_TYPE_ERROR\n"; DYNAMIC_GRAPH_ENTITY_DEBUG_STREAM
+(*this) << "This is a message of level MSG_TYPE_DEBUG_STREAM\n";
+ DYNAMIC_GRAPH_ENTITY_INFO_STREAM    (*this) << "This is a message of level
+MSG_TYPE_INFO_STREAM\n"; DYNAMIC_GRAPH_ENTITY_WARNING_STREAM (*this) << "This is
+a message of level MSG_TYPE_WARNING_STREAM\n"; DYNAMIC_GRAPH_ENTITY_ERROR_STREAM
+(*this) << "This is a message of level MSG_TYPE_ERROR_STREAM\n"; \endcode
+
+
+   \note Thread safety. This class expects to have:
+   - only one reader: the one who take the log entries and write them somewhere.
+   - one writer at a time. Writing to the logs is **never** a blocking
+     operation. If the resource is busy, the log entry is discarded.
+*/

doc/additionalDoc/entity.h

@@ -24,7 +24,7 @@ To add flexibility to a node, it is possible to add command with arguments to
 modify the internal behavior of the entity or get information from the entity.
 As a command is in general asynchronous and rare with respect to the data-flow
 scheme for the signals the command is in general executed in a \b none-real-time
-thread.
+thread. For more details on command see \subpage subpage_command .
 
 \subsection entity_classes Entity class
 Entities are implemented as C++ classes and compiled as dynamic libraries. They
@@ -34,9 +34,9 @@ to load the library, it is not advised to do that during a control-law
 computation. Entity instanciation also implies memory allocation which is also
 time consuming and thus not advised inside a real-time thread.
 
-The entities will be placed in ${PREFIX}/lib/plugin (since this may change, it
-is advised to check the install log or the CMakeLists.txt file to check the
-installation path).
+The entities will be placed in ${PREFIX}/lib/dynamic-graph-plugin
+(since this may change, it is advised to check the install log or the
+CMakeLists.txt file to check the installation path).
 
 \subsection entities List of entities in this package
 Since most of the functionality in projects using the dynamic-graph framework

doc/additionalDoc/graph.h

@@ -8,6 +8,8 @@ In dynamic-graph a graph is build with:
 - computational nodes which are entities \subpage subpage_entities.
 - directed edges which are created by connecting input and output signals
 \subpage subp_signals.
+- commands which are expanding the capabilities of the entity
+\subpage subpage_command
 - managing the nodes is done through a factory \subpage subp_factory providing
 classes and a way to create instances from this list of classes.
 - the instances of node are handled through a pool \subpage subp_pool

doc/additionalDoc/installation.h

@@ -17,7 +17,7 @@ The sources are available through github at the following URL:
 href="https://github.com/stack-of-tasks/dynamic-graph">https://github.com/stack-of-tasks/dynamic-graph</a>
 
 To clone:
-\code
+\code{.sh}
 git clone https://github.com/stack-of-tasks/dynamic-graph.git
 \endcode