Compare revisions

3243d36a · 4753c1d9 · fbd076e2 · c29dd5ac · cb37500f · fa553738
--- a/.git-blame-ignore-revs
+++ b/.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
--- a/.gitignore
+++ b/.gitignore
+_build*
+.~
+compile_commands.json
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
+include: http://rainboard.laas.fr/project/dynamic-graph/.gitlab-ci.yml
--- a/.gitmodules
+++ b/.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
+	url = https://github.com/jrl-umi3218/jrl-cmakemodules.git
--- a/.pre-commit-config.yaml
+++ b/.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
--- a/.travis.yml
+++ b/.travis.yml
-language: cpp
-compiler:
-  - clang
-  - gcc
-script: "./.travis/build"
-before_install:
-  - git submodule update --init --recursive
-  - sudo apt-get update -qq
-  - sudo apt-get install -qq doxygen doxygen-latex libboost-all-dev libeigen3-dev liblapack-dev libblas-dev gfortran
-  - sudo pip install cpp-coveralls --use-mirrors
-after_success:
-  - coveralls -e _travis/install -e tests
-  - git config --global user.name "Travis CI"
-  - git config --global user.email "thomas.moulard+travis@gmail.com"
-  - git remote set-url origin https://thomas-moulard:${GH_TOKEN}@github.com/stack-of-tasks/dynamic-graph.git
-  - git fetch origin gh-pages:gh-pages
-  - cd _travis/build/doc && ../../../cmake/github/update-doxygen-doc.sh
-notifications:
-  email:
-    - hpp-source@laas.fr
-branches:
-  only:
-    - master
-matrix:
-  allow_failures:
-    - compiler: clang
-env:
-  global:
-    secure: "Slm+HqRT+Vy0SG7E9gEShuHvNz6XWRUmBhVBLVJEaYy/0Lo2qp4OjFEWDjiJwFIiXstW2Wclds4SuewAn3Tc4x7dsY+5uaMCX7S/HPzsBCjLXUwjKasUqEGaVTIYmtFJm57hOkz6K2SLUUV4intkMiwtCiq/R0xe92QTTKkHyfo="
--- a/.travis/build
+++ b/.travis/build
-#!/bin/sh
-set -ev
-
-# Directories.
-root_dir=`pwd`
-build_dir="$root_dir/_travis/build"
-install_dir="$root_dir/_travis/install"
-jrl_mathtools_dir="$build_dir/jrl-mathtools"
-jrl_mal_dir="$build_dir/jrl-mal"
-
-# Shortcuts.
-git_clone="git clone --quiet --recursive"
-
-# Create layout.
-rm -rf "$build_dir" "$install_dir"
-mkdir -p "$build_dir"
-mkdir -p "$install_dir"
-
-# Setup environment variables.
-export LD_LIBRARY_PATH="$install_dir/lib:$LD_LIBRARY_PATH"
-export PKG_CONFIG_PATH="$install_dir/lib/pkgconfig:$PKG_CONFIG_PATH"
-
-# Retrieve jrl-mathtools
-echo "--> Compiling jrl-mathtools"
-cd "$build_dir"
-$git_clone "git://github.com/jrl-umi3218/jrl-mathtools.git"
-cd "$jrl_mathtools_dir"
-cmake . -DCMAKE_INSTALL_PREFIX:STRING="$install_dir"
-make install
-
-# Retrieve jrl-mal
-echo "--> Compiling jrl-mal"
-cd "$build_dir"
-$git_clone "git://github.com/jrl-umi3218/jrl-mal.git"
-cd "$jrl_mal_dir"
-cmake . -DCMAKE_INSTALL_PREFIX:STRING="$install_dir"
-make install
-
-# Compile metapod and run tests
-cd "$build_dir"
-cmake "$root_dir" -DCMAKE_INSTALL_PREFIX="$install_dir"		\
-		  -DCMAKE_CXX_FLAGS="--coverage"		\
-		  -DCMAKE_EXE_LINKER_FLAGS="--coverage"		\
-		  -DCMAKE_MODULE_LINKER_FLAGS="--coverage"	\
-		  -DCMAKE_INSTALL_PREFIX:STRING="$install_dir"
-make
-make test
-make install
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-# Copyright 2010, Olivier Stasse, JRL, CNRS/AIST
-#
-# This file is part of dynamic-graph.
-# dynamic-graph is free software: you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation, either version 3 of
-# the License, or (at your option) any later version.
-#
-# dynamic-graph is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Lesser Public License for more details.  You should have
-# received a copy of the GNU Lesser General Public License along with
-# dynamic-graph. If not, see <http://www.gnu.org/licenses/>.
-
-CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
-
-INCLUDE(cmake/base.cmake)
-INCLUDE(cmake/boost.cmake)
-INCLUDE(cmake/pthread.cmake)
-INCLUDE(cmake/cpack.cmake)
-
-SET(PROJECT_NAME dynamic-graph)
-SET(PROJECT_DESCRIPTION "Dynamic graph library")
-SET(PROJECT_URL "http://github.com/jrl-umi3218/dynamic-graph")
-
-SET(CUSTOM_HEADER_DIR "${PROJECT_NAME}")
-
-# Defines paths.
-SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
-
-SETUP_PROJECT()
-
-# Trigger dependency to jrl-mal
-ADD_REQUIRED_DEPENDENCY("jrl-mal >= 1.8.0")
+cmake_minimum_required(VERSION 3.1)
+
+# Project properties
+set(PROJECT_ORG stack-of-tasks)
+set(PROJECT_NAME dynamic-graph)
+set(PROJECT_DESCRIPTION "Dynamic graph library")
+set(PROJECT_URL "https://github.com/${PROJECT_ORG}/${PROJECT_NAME}")
+
+# Project options
+option(SUFFIX_SO_VERSION "Suffix library name with its version" ON)
+
+# Project configuration
+set(PROJECT_USE_CMAKE_EXPORT TRUE)
+set(CUSTOM_HEADER_DIR ${PROJECT_NAME})
+set(CXX_DISABLE_WERROR TRUE)
+
+# Doxygen setup
+set(DOXYGEN_USE_MATHJAX YES)
+set(DOXYGEN_USE_TEMPLATE_CSS YES)
+
+# JRL-cmakemodule setup
+include(cmake/base.cmake)
+include(cmake/boost.cmake)
+
+# Project definition
+compute_project_args(PROJECT_ARGS LANGUAGES CXX)
+project(${PROJECT_NAME} ${PROJECT_ARGS})
+check_minimal_cxx_standard(14 ENFORCE)
+
+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-shell-procedure.hh DG_SHELLPROCEDURE shell_procedure_EXPORTS)
-GENERATE_CONFIGURATION_HEADER(
-  ${HEADER_DIR}
-  config-contiifstream.hh DG_CONTIIFSTREAM contiifstream_EXPORTS)
-
-# FIXME: to be changed into lib/dynamic-graph
-# to avoid name collision when installing dynamic-graph in /usr.
-SET(PLUGINDIR "${CMAKE_INSTALL_LIBDIR}/plugin")
-
-# Add extra keys to pkg-config file to export the location of the
-# plug-in directory in a robust manner.
-SET(PKG_CONFIG_EXTRA
-  "plugindirname=${PLUGINDIR}
-plugindir=${CMAKE_INSTALL_PREFIX}/${PLUGINDIR}")
-
-# Add dependency toward dynamic graph library in pkg-config file.
-PKG_CONFIG_APPEND_LIBS("dynamic-graph")
-
-# Search for Boost.
-SEARCH_FOR_BOOST()
-SEARCH_FOR_PTHREAD()
-
-ADD_SUBDIRECTORY(src)
-ADD_SUBDIRECTORY(include)
-ADD_SUBDIRECTORY(doc)
-ADD_SUBDIRECTORY(tests)
-ADD_SUBDIRECTORY(share)
-
-SETUP_PROJECT_FINALIZE()
-SETUP_PROJECT_CPACK()
\ No newline at end of file
+generate_configuration_header(${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(${PROJECT_NAME}_SOURCES
+    src/debug/debug.cpp
+    src/debug/real-time-logger.cpp
+    src/debug/logger.cpp
+    src/dgraph/entity.cpp
+    src/dgraph/factory.cpp
+    src/dgraph/pool.cpp
+    src/exception/exception-abstract.cpp
+    src/exception/exception-factory.cpp
+    src/exception/exception-signal.cpp
+    src/exception/exception-traces.cpp
+    src/mt/process-list.cpp
+    src/signal/signal-array.cpp
+    src/command/value.cpp
+    src/command/command.cpp)
+
+add_library(${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)
+
+if(UNIX)
+  target_link_libraries(${PROJECT_NAME} PUBLIC ${CMAKE_DL_LIBS} pthread)
+endif(UNIX)
+
+if(SUFFIX_SO_VERSION)
+  set_target_properties(${PROJECT_NAME} PROPERTIES SOVERSION ${PROJECT_VERSION})
+endif(SUFFIX_SO_VERSION)
+
+install(
+  TARGETS ${PROJECT_NAME}
+  EXPORT ${TARGETS_EXPORT_NAME}
+  DESTINATION lib)
+
+set(DYNAMIC_GRAPH_PLUGINDIR "lib/${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)
+if(BUILD_TESTING)
+  add_subdirectory(tests)
+endif(BUILD_TESTING)
+
+pkg_config_append_libs(${PROJECT_NAME})
+install(FILES package.xml DESTINATION share/${PROJECT_NAME})
--- a/COPYING.LESSER
+++ b/COPYING.LESSER
-                   GNU LESSER GENERAL PUBLIC LICENSE
-                       Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-
-  This version of the GNU Lesser General Public License incorporates
-the terms and conditions of version 3 of the GNU General Public
-License, supplemented by the additional permissions listed below.
-
-  0. Additional Definitions.
-
-  As used herein, "this License" refers to version 3 of the GNU Lesser
-General Public License, and the "GNU GPL" refers to version 3 of the GNU
-General Public License.
-
-  "The Library" refers to a covered work governed by this License,
-other than an Application or a Combined Work as defined below.
-
-  An "Application" is any work that makes use of an interface provided
-by the Library, but which is not otherwise based on the Library.
-Defining a subclass of a class defined by the Library is deemed a mode
-of using an interface provided by the Library.
-
-  A "Combined Work" is a work produced by combining or linking an
-Application with the Library.  The particular version of the Library
-with which the Combined Work was made is also called the "Linked
-Version".
-
-  The "Minimal Corresponding Source" for a Combined Work means the
-Corresponding Source for the Combined Work, excluding any source code
-for portions of the Combined Work that, considered in isolation, are
-based on the Application, and not on the Linked Version.
-
-  The "Corresponding Application Code" for a Combined Work means the
-object code and/or source code for the Application, including any data
-and utility programs needed for reproducing the Combined Work from the
-Application, but excluding the System Libraries of the Combined Work.
-
-  1. Exception to Section 3 of the GNU GPL.
-
-  You may convey a covered work under sections 3 and 4 of this License
-without being bound by section 3 of the GNU GPL.
-
-  2. Conveying Modified Versions.
-
-  If you modify a copy of the Library, and, in your modifications, a
-facility refers to a function or data to be supplied by an Application
-that uses the facility (other than as an argument passed when the
-facility is invoked), then you may convey a copy of the modified
-version:
-
-   a) under this License, provided that you make a good faith effort to
-   ensure that, in the event an Application does not supply the
-   function or data, the facility still operates, and performs
-   whatever part of its purpose remains meaningful, or
-
-   b) under the GNU GPL, with none of the additional permissions of
-   this License applicable to that copy.
-
-  3. Object Code Incorporating Material from Library Header Files.
-
-  The object code form of an Application may incorporate material from
-a header file that is part of the Library.  You may convey such object
-code under terms of your choice, provided that, if the incorporated
-material is not limited to numerical parameters, data structure
-layouts and accessors, or small macros, inline functions and templates
-(ten or fewer lines in length), you do both of the following:
-
-   a) Give prominent notice with each copy of the object code that the
-   Library is used in it and that the Library and its use are
-   covered by this License.
-
-   b) Accompany the object code with a copy of the GNU GPL and this license
-   document.
-
-  4. Combined Works.
-
-  You may convey a Combined Work under terms of your choice that,
-taken together, effectively do not restrict modification of the
-portions of the Library contained in the Combined Work and reverse
-engineering for debugging such modifications, if you also do each of
-the following:
-
-   a) Give prominent notice with each copy of the Combined Work that
-   the Library is used in it and that the Library and its use are
-   covered by this License.
-
-   b) Accompany the Combined Work with a copy of the GNU GPL and this license
-   document.
-
-   c) For a Combined Work that displays copyright notices during
-   execution, include the copyright notice for the Library among
-   these notices, as well as a reference directing the user to the
-   copies of the GNU GPL and this license document.
-
-   d) Do one of the following:
-
-       0) Convey the Minimal Corresponding Source under the terms of this
-       License, and the Corresponding Application Code in a form
-       suitable for, and under terms that permit, the user to
-       recombine or relink the Application with a modified version of
-       the Linked Version to produce a modified Combined Work, in the
-       manner specified by section 6 of the GNU GPL for conveying
-       Corresponding Source.
-
-       1) Use a suitable shared library mechanism for linking with the
-       Library.  A suitable mechanism is one that (a) uses at run time
-       a copy of the Library already present on the user's computer
-       system, and (b) will operate properly with a modified version
-       of the Library that is interface-compatible with the Linked
-       Version.
-
-   e) Provide Installation Information, but only if you would otherwise
-   be required to provide such information under section 6 of the
-   GNU GPL, and only to the extent that such information is
-   necessary to install and execute a modified version of the
-   Combined Work produced by recombining or relinking the
-   Application with a modified version of the Linked Version. (If
-   you use option 4d0, the Installation Information must accompany
-   the Minimal Corresponding Source and Corresponding Application
-   Code. If you use option 4d1, you must provide the Installation
-   Information in the manner specified by section 6 of the GNU GPL
-   for conveying Corresponding Source.)
-
-  5. Combined Libraries.
-
-  You may place library facilities that are a work based on the
-Library side by side in a single library together with other library
-facilities that are not Applications and are not covered by this
-License, and convey such a combined library under terms of your
-choice, if you do both of the following:
-
-   a) Accompany the combined library with a copy of the same work based
-   on the Library, uncombined with any other library facilities,
-   conveyed under the terms of this License.
-
-   b) Give prominent notice with the combined library that part of it
-   is a work based on the Library, and explaining where to find the
-   accompanying uncombined form of the same work.
-
-  6. Revised Versions of the GNU Lesser General Public License.
-
-  The Free Software Foundation may publish revised and/or new versions
-of the GNU Lesser General Public License from time to time. Such new
-versions will be similar in spirit to the present version, but may
-differ in detail to address new problems or concerns.
-
-  Each version is given a distinguishing version number. If the
-Library as you received it specifies that a certain numbered version
-of the GNU Lesser General Public License "or any later version"
-applies to it, you have the option of following the terms and
-conditions either of that published version or of any later version
-published by the Free Software Foundation. If the Library as you
-received it does not specify a version number of the GNU Lesser
-General Public License, you may choose any version of the GNU Lesser
-General Public License ever published by the Free Software Foundation.
-
-  If the Library as you received it specifies that a proxy can decide
-whether future versions of the GNU Lesser General Public License shall
-apply, that proxy's public statement of acceptance of any version is
-permanent authorization for you to choose that version for the
-Library.
--- a/ChangeLog
+++ b/ChangeLog
@@ -3,6 +3,21 @@ CHANGELOG

 [Current]

+* remove shell
+
+[v3.0.0]
+ * Replace jrl-mal with eigen
+ * Add ostream and isteram operators for Eigen Classes
+
+
+[v2.5.5]
+ * Improve Travis support
+
+[v2.5.4]
+ * Update lib installation path (multiarch portability).
+ * Allow to access class name of a signal.
+ * Add Travis and coveralls.io support.
+
 [v2.5.3]
 * Synchronize.
 * Synchronize.

--- a/LICENSE
+++ b/LICENSE
+BSD 2-Clause License
+
+Copyright (c) 2019, CNRS
+Author: Stack of Tasks Development Team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
--- a/NEWS
+++ b/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.
-
--- a/README.md
+++ b/README.md
 dynamic-graph
 =============

-[![Build Status](https://travis-ci.org/stack-of-tasks/dynamic-graph.png)](https://travis-ci.org/stack-of-tasks/dynamic-graph)
-[![Coverage Status](https://coveralls.io/repos/stack-of-tasks/dynamic-graph/badge.png)](https://coveralls.io/r/stack-of-tasks/dynamic-graph)
-
+[![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.

 A dynamic graph data-flow is composed of:
- - entities (graph nodes)
- - signals (input/output of a graph action)
+ * entities (graph nodes)
+ * signals (input/output of a graph action)

 Output signals can then be plugged into input signals to data
 transmission.
@@ -17,17 +18,139 @@ transmission.
 An efficient caching mechanism avoid useless data recomputation and a
 simple built-in language can be used to control the graph actions.

+It is released under the [BSD-clause 2](COPYING.LESSER) license.
+
+
+**Warning:** this repository contains [Git
+submodules][git-submodules]. Please clone this repository using the
+`git clone --recursive` command. If you already have cloned the
+repository, you can run `git submodule init && git submodule update`
+to retrieve the submodules.
+
+
+Documentation
+-------------
+
+To get started with this library, please read the [online Doxygen
+documentation][doxygen-documentation].
+
+It can also be generated locally by running the `make doc`
+command. After the package is installed, the documentation will be
+located in the `$prefix/share/doc/dynamic-graph` directoy where
+`$prefix` is your installation prefix (`/usr/local` by default).
+
+
+Getting Help
+------------
+
+Support is provided through issues on the github interface.
+
+How can I install dynamic-graph?
+--------------------------------
+
+### Installing dependencies
+
+The matrix abstract layer depends on several packages which
+have to be available on your machine.
+
+ - Libraries:
+   - [Boost][] (>= 1.40)
+   - Doxygen
+   - Eigen3
+   - pthread
+ - System tools:
+   - [CMake][] (>=2.6)
+   - [pkg-config][]
+   - usual compilation tools (GCC/G++, make, etc.)
+     If you are using Ubuntu, these tools are gathered in the `build-essential` package.
+
+
+
+### Compiling and installing the package
+
+The manual compilation requires two steps:
+
+ 1. configuration of the build and generation of the build files
+ 2. compilation of the sources and installation of the package
+
+dynamic-graph uses [CMake][] to generate build files. It is
+recommended to create a separate build directory:
+
+```sh
+mkdir _build         # (1) Create a build directory
+cd _build            # (2) Go to the newly created build directory
+cmake [options] ..   # (3) Generate the build files
+```
+
+Options which can be passed to CMake are detailed in the next section.
+
+```sh
+make                 # (4) Compile the package
+make test            # (5) Execute the package tests
+make install         # (6) Install the package into the prefix (see step 3)
+```
+
+
+### Options
+
+Additional options can be set on the command line through the
+following command: `-D<option>=<value>`.
+
+For instance: `cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo ..` will set
+the `CMAKE_BUILD_TYPE` option to the value `RelWithDebInfo`.
+
+
+Available options are:
+
+- `CMAKE_BUILD_TYPE` set the build profile that should be used (debug,
+  release, etc.). We recommend `RelWithDebInfo` as it will provide
+  performances while keeping debugging symbols enabled.
+- `CMAKE_INSTALL_PREFIX` set the installation prefix (the directory
+  where the software will be copied to after it has been compiled).
+
+
+### Running the test suite
+
+The test suite can be run from your build directory by running:
+
+```sh
+   make test
+```
+
+Please open a ticket if some tests are failing on your computer, it
+should not be the case.
+
+
+Contributing
+------------
+
+If you want to contribute, please refer to the
+[CONTRIBUTING.md](CONTRIBUTING.md) file
+
+Credits
+-------
+
+This package authors are credited in the [AUTHORS](AUTHORS) file.
+
+
+
+Available Packages
+------------------
+
+ * RobotPkg :
+   http://robotpkg.openrobots.org/robotpkg/motion/dynamic-graph/index.html

-Setup
-----

-To compile this package, it is recommended to create a separate build
-directory:
+[doxygen-documentation]: http://stack-of-tasks.github.io/dynamic-graph/doxygen/HEAD/

-    mkdir _build
-    cd _build
-    cmake [OPTIONS] ..
-    make install
+[git-submodules]: http://git-scm.com/book/en/Git-Tools-Submodules

-Please note that CMake produces a `CMakeCache.txt` file which should
-be deleted to reconfigure a package from scratch.
+[Boost]: http://www.boost.org/
+[CMake]: htttp://www.cmake.org/
+[Doxygen]: http://www.stack.nl/~dimitri/doxygen/
+[Eigen]: http://eigen.tuxfamily.org/
+[Git]: http://git-scm.com/
+[Libtool]: https://www.gnu.org/software/libtool/
+[RobotPkg]: http://robotpkg.openrobots.org/
+[log4cxx]: https://logging.apache.org/log4cxx/
+[pkg-config]: http://www.freedesktop.org/wiki/Software/pkg-config/
--- a/cmake @ 47c0cbf0
+++ b/cmake @ 47c0cbf0
-Subproject commit 7449641387efcfdb5bf01d2d36c40a7c1c12c0b6
+Subproject commit 47c0cbf0b29433060682377dcb28266e8dc38995
--- a/cmake_uninstall.cmake.in
+++ b/cmake_uninstall.cmake.in
-# Template for uninstalling the files 
-# provided by this package.
-#
-# This file is coming straight from
-# http://www.cmake.org/Wiki/CMake_FAQ
-# O. Stasse, JRL, CNRS, 2010
-#
-
-IF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
-  MESSAGE(FATAL_ERROR "Cannot find install manifest: \"@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt\"")
-ENDIF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
-
-FILE(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files)
-STRING(REGEX REPLACE "\n" ";" files "${files}")
-FOREACH(file ${files})
-  MESSAGE(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"")
-  IF(EXISTS "$ENV{DESTDIR}${file}")
-    EXEC_PROGRAM(
-      "@CMAKE_COMMAND@" ARGS "-E remove \"$ENV{DESTDIR}${file}\""
-      OUTPUT_VARIABLE rm_out
-      RETURN_VALUE rm_retval
-      )
-    IF(NOT "${rm_retval}" STREQUAL 0)
-      MESSAGE(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"")
-    ENDIF(NOT "${rm_retval}" STREQUAL 0)
-  ELSE(EXISTS "$ENV{DESTDIR}${file}")
-    MESSAGE(STATUS "File \"$ENV{DESTDIR}${file}\" does not exist.")
-  ENDIF(EXISTS "$ENV{DESTDIR}${file}")
-ENDFOREACH(file)
--- a/debian/changelog
+++ b/debian/changelog
-dynamic-graph (1.0.0.99-3) lucid; urgency=low
-
-  * Add plug-ins to libdynamic-graph1.0.0.99.
-
- -- Thomas Moulard <thomas.moulard@gmail.com>  Wed, 28 Sep 2010 11:45:00 +0200
-
-dynamic-graph (1.0.0.99-2) lucid; urgency=low
-
-  * Add libboost-thread-dev to build requirement.
-
- -- Thomas Moulard <thomas.moulard@gmail.com>  Wed, 28 Sep 2010 10:40:00 +0200
-
-dynamic-graph (1.0.0.99-1) lucid; urgency=low
-
-  * Initial work.
-
- -- Thomas Moulard <thomas.moulard@gmail.com>  Wed, 28 Sep 2010 03:15:00 +0200
--- a/debian/compat
+++ b/debian/compat
-7
--- a/debian/control
+++ b/debian/control
-Source: dynamic-graph
-Priority: extra
-Maintainer: Thomas Moulard <thomas.moulard@gmail.com>
-Build-Depends: debhelper (>= 7.0.50~), cmake (>= 2.6),
-	       doxygen (>= 1.6.3),
-	       pkg-config (>= 0.22),
-	       perl (>= 5.10.1),
-	       libboost-dev (>= 1.33.1),
-	       libboost-thread-dev (>= 1.33.1)
-Standards-Version: 3.8.4
-#Vcs-Git:
-#Vcs-browser:
-Section: libs
-#Homepage:
-
-Package: libdynamic-graph-dev
-Section: libdevel
-Architecture: any
-Depends: libdynamic-graph1.0.0.99 (= ${binary:Version}), ${misc:Depends}
-Suggests: libdynamic-graph-doc
-Description: Dynamic graph C++ library development package
- The dynamic graph library allows the representation of data-flow in C++.
- It provides fast graph evaluation and a simple script language to manipulate
- the graph actions.
- .
- This package contains development files (headers and pkg-config file).
-
-
-Package: libdynamic-graph1.0.0.99
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Dynamic graph C++ library
- The dynamic graph library allows the representation of data-flow in C++.
- It provides fast graph evaluation and a simple script language to manipulate
- the graph actions.
-
-
-Package: libdynamic-graph-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends}
-Suggests: libjrl-mathtools-doc
-Description: documentation for the dynamic graph C++ library
- The dynamic graph library allows the representation of data-flow in C++.
- It provides fast graph evaluation and a simple script language to manipulate
- the graph actions.
- .
- This package contains the Doxygen documentation.
--- a/debian/copyright
+++ b/debian/copyright
-This work was packaged for Debian by:
-
-    Thomas Moulard <thomas.moulard@gmail.com> on Wed, 28 Sep 2010 03:13:00 +0200
-
-It was downloaded from <not yet available>
-
-Upstream Author(s):
-
-    Thomas Moulard <thomas.moulard@gmail.com>
-
-Copyright:
-
-    Copyright (C) 2010 François Bleibel, Olivier Stasse, JRL, CNRS/AIST.
-
-License:
-
-    See `/usr/share/common-licenses/LGPL-3'.
-
-The Debian packaging is:
-
-    Copyright (C) 2010 Thomas Moulard <thomas.moulard@gmail.com>
-    and is licensed under the GPL version 3,
-    see `/usr/share/common-licenses/GPL-3'.
--- a/debian/docs
+++ b/debian/docs
-AUTHORS
-NEWS
-README.md
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