Compare revisions

77943866 · d7f41933 · 9daf8bd7 · 57a519db · 671c0e94 · 42bdac08
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
+# # pre-commit run -a (Guilhem Saurel, 2022-09-05)
+f3f2efc3fee4179e170e76e5f983baf004d7e109
+
+# pre-commit run -a (Guilhem Saurel, 2022-07-27)
+2a9fbd70d4fc47ed41e0ad25fb90e241865a341b
+
+# yapf (Guilhem Saurel, 2021-02-09)
+cf574bd33e0bb0cb5a54b83f8f434efe8951cd0e
+
+# format (Guilhem Saurel, 2020-11-13)
+5921e17ab3a8db2a98ae94d228283db924d2e140
+
+# clang-format (Olivier Stasse, 2020-08-28)
+2ea1fba7f262c07652dc060361c98af856d4d935
+
+# [format] Apply clang (Olivier Stasse, 2020-08-26)
+d59a58ec2de3a192da13c59ebce92e704f9d00c4
--- a/.gitignore
+++ b/.gitignore
+build*
+vsbld*
+include/sot-core/import-default-paths.h
+unitTesting/test-paths.h
+*~
+_build*
+*__pycache__*
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
+include: http://rainboard.laas.fr/project/sot-core/.gitlab-ci.yml
--- a/.gitmodules
+++ b/.gitmodules
+[submodule "cmake"]
+	path = cmake
+	url = https://github.com/jrl-umi3218/jrl-cmakemodules.git
--- a/.mailmap
+++ b/.mailmap
+#
+# This list is used by git-shortlog to fix a few botched name translations
+# in the git archive, either because the author's full name was messed up
+# and/or not always written the same way, making contributions from the
+# same person appearing not to be so or badly displayed.
+
+Anthony Mallet <anthony.mallet@laas.fr>
+
+Olivier Stasse <grxuser@jrl005.a01.aist.go.jp>
+Olivier Stasse <olivier.stasse@aist.go.jp>
+Olivier Stasse <stasse@dhcpt1243.a02.aist.go.jp>
+Olivier Stasse <stasse@jrl005.a01.aist.go.jp>
+Olivier Stasse <olivier.stasse@aist.go.jp>
+Olivier Stasse <stasse@stasse-laptop.(none)>
+Olivier Stasse <olivier.stasse@aist.go.jp>
+Olivier Stasse <stasse@dhcpt1059.a02.aist.go.jp>
+Olivier Stasse <stasse@jrl005.a01.aist.go.jp>
+Olivier Stasse <stasse@jrl005.a02.aist.go.jp>
+Olivier Stasse <olivier.stasse@aist.go.jp>
+Olivier Stasse <stasse@jrl006.(none)>
+Olivier Stasse <stasse@stasse-laptop.(none)>
+
+
+Nicolas Mansard <nmansard@devgiri.(none)>
+Nicolas Mansard <nmansard@jorasse.(none)>
+Nicolas Mansard <nmansard@laas.fr>
+
+
+Florent Lamiraux <florent@big-laptop.(none)>
+Florent Lamiraux <florent@dhcpt1253.a02.aist.go.jp>
+Florent Lamiraux <florent@florent-laptop.laas.fr>
+Florent Lamiraux <florent@florent-laptop.(none)>
+Florent Lamiraux <florent@laas.fr>
+Florent Lamiraux <Florent Lamiraux florent@laas.fr>
+Florent Lamiraux <florent@florent-laptop.(none)>
+Florent Lamiraux <Florent Lamiraux florent@laas.fr>
+Florent Lamiraux <florent@localhost.localdomain>
+Florent Lamiraux <florent@poullenc.laas.fr>
+Florent Lamiraux <florent@poullenc.(none)>
--- 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/psf/black
+    rev: 22.8.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/PyCQA/flake8
+    rev: 5.0.4
+    hooks:
+    -   id: flake8
+-   repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+    - id: cmake-format
--- a/AUTHORS
+++ b/AUTHORS
-Authors: Nicolas Mansard, Olivier Stasse, François Keith, François Bleibel 
\ No newline at end of file
+This package was written by and with the assistance of
+
+* François Bleibel              fbleibel@gmail.com
+* François Keith                francois.keith@aist.go.jp
+* Nicolas Mansard               FIXME
+* Thomas Moulardd               thomas.moulard@gmail.com
+* Olivier Stasse                olivier.stasse@aist.go.jp
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-#
-#  Copyright
-#
-
-CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
-
-SET(PROJECT_NAME sot-core)
-project(${PROJECT_NAME})
-
-SET(PROJECT_VERSION 1.0.0)
-
-SET(CMAKE_VERBOSE_MAKEFILE true)
-
-IF(WIN32)
-  SET(LIBDIR_KW "/LIBPATH:")
-  SET(LIBINCL_KW "")
-  SET(LIB_EXT ".lib")
-ENDIF(WIN32)
-
-IF(UNIX)
-  SET(LIBDIR_KW "-L")
-  SET(LIBINCL_KW "-l")
-  SET(LIB_EXT "")
-ENDIF(UNIX)
-
-# Languages
-# Fortran has, sadly, to be used for LAPACK libraries
-# Visual Studio uses precompiled libs so there is no
-# need to enable the Fortran language.
-enable_language(CXX)
-IF( 
-	(NOT "${CMAKE_GENERATOR}" MATCHES "Visual Studio.*") )
-enable_language(Fortran)
-ENDIF( 
-	(NOT "${CMAKE_GENERATOR}" MATCHES "Visual Studio.*")
-)	
-
-enable_testing()
-
-#
-# Look for dependencies
-#
-
-# Load Pkgconfig macros
-INCLUDE(FindPkgConfig)
-SET(PACKAGE_REQUIREMENTS "")
-#enable_language(Fortran)
-# --- LAPACK --------------------------------------------------
-FIND_PACKAGE(LAPACK)
-IF(LAPACK_FOUND)
-  foreach(lapack_lib ${LAPACK_LIBRARIES})
-    LIST(APPEND ${PROJECT_NAME}_LINK_SRC_FLAGS ${lapack_lib})
-    LIST(APPEND ${PROJECT_NAME}_LINK_FLAGS ${lapack_lib})
-  endforeach(lapack_lib)
-  IF (WIN32)
-    LIST(APPEND ${PROJECT_NAME}_CXX_FLAGS "-DBOOST_NUMERIC_BINDINGS_USE_CLAPACK" )
-  ENDIF (WIN32)
-ENDIF(LAPACK_FOUND)
-
-#
-#  Dependency to package MatrixAbstractLayer
-#
-SET(MATRIXABSTRACTLAYER_FOUND 0)
-SET(MATRIXABSTRACTLAYER_REQUIRED "MatrixAbstractLayer >= 1.8.0")
-PKG_CHECK_MODULES(MATRIXABSTRACTLAYER REQUIRED ${MATRIXABSTRACTLAYER_REQUIRED})
-EXEC_PROGRAM(${PKG_CONFIG_EXECUTABLE} ARGS  --variable=docdir MatrixAbstractLayer
-  OUTPUT_VARIABLE MATRIXABSTRACTLAYER_DOCDIR)
-MESSAGE(STATUS "pkg-config: ${PKG_CONFIG_EXECUTABLE}")
-MESSAGE(STATUS "MATRIXABSTRACTLAYER_DOCDIR=${MATRIXABSTRACTLAYER_DOCDIR}")
-SET(MATRIXABSTRACTLAYER_FOUND 1)
-
-IF(NOT ${MATRIXABSTRACTLAYER_FOUND})
-  MESSAGE(FATAL_ERROR "Check that package MatrixAbstractLayer is installed in a directory pointed out by PKG_CONFIG_PATH.")
-ENDIF(NOT ${MATRIXABSTRACTLAYER_FOUND})
-  
-IF(PACKAGE_REQUIREMENTS STREQUAL "")
-  SET(PACKAGE_REQUIREMENTS ${MATRIXABSTRACTLAYER_REQUIRED})
-ELSE(PACKAGE_REQUIREMENTS STREQUAL "")
-  SET(PACKAGE_REQUIREMENTS "${PACKAGE_REQUIREMENTS}, ${MATRIXABSTRACTLAYER_REQUIRED}")
-ENDIF(PACKAGE_REQUIREMENTS STREQUAL "")
-
-#
-#  Dependency to package dynamic-graph
-#
-SET(DYNAMIC_GRAPH_FOUND 0)
-SET(DYNAMIC_GRAPH_REQUIRED "dynamic-graph >= 1.0.0")
-PKG_CHECK_MODULES(DYNAMIC_GRAPH REQUIRED ${DYNAMIC_GRAPH_REQUIRED})
-EXEC_PROGRAM(${PKG_CONFIG_EXECUTABLE} ARGS  --variable=docdir dynamic-graph
-  OUTPUT_VARIABLE DYNAMIC_GRAPH_DOCDIR)
-MESSAGE(STATUS "pkg-config: ${PKG_CONFIG_EXECUTABLE}")
-MESSAGE(STATUS "DYNAMIC_GRAPH_DOCDIR=${DYNAMIC_GRAPH_DOCDIR}")
-SET(DYNAMIC_GRAPH_FOUND 1)
-
-IF(NOT ${DYNAMIC_GRAPH_FOUND})
-  MESSAGE(FATAL_ERROR "Check that package dynamic-graph is installed in a directory pointed out by PKG_CONFIG_PATH.")
-ENDIF(NOT ${DYNAMIC_GRAPH_FOUND})
-  
-IF(PACKAGE_REQUIREMENTS STREQUAL "")
-  SET(PACKAGE_REQUIREMENTS ${DYNAMIC_GRAPH_REQUIRED})
-ELSE(PACKAGE_REQUIREMENTS STREQUAL "")
-  SET(PACKAGE_REQUIREMENTS "${PACKAGE_REQUIREMENTS}, ${DYNAMIC_GRAPH_REQUIRED}")
-ENDIF(PACKAGE_REQUIREMENTS STREQUAL "")
-
-#
-# Boost
-#
-FIND_PACKAGE(Boost COMPONENTS filesystem REQUIRED)
-include_directories(${Boost_INCLUDE_DIRS})
-LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-
-#
-# pkg-config file
-#
-
-SET(install_pkg_prefix "\${prefix}")
-SET(install_pkg_exec_prefix "\${exec_prefix}")
-SET(install_pkg_libdir "\${libdir}")
-SET(install_pkg_datarootdir "\${datarootdir}")
-SET(install_pkg_include_dir "\${includedir}")
-
-IF(UNIX)
-  SET (${PROJECT_NAME}_LDFLAGS "-Wl,-R${install_pkg_libdir} ${LIBINCL_KW}${PROJECT_NAME}${LIB_EXT} ${${PROJECT_NAME}_LDFLAGS}")
-ENDIF(UNIX)
-
-IF(WIN32)
-  SET (${PROJECT_NAME}_LDFLAGS "${LIBINCL_KW}${PROJECT_NAME}${LIB_EXT} ${${PROJECT_NAME}_LDFLAGS}")
-ENDIF(WIN32)
-
-# Install the file in the appropriate place.
-SET(install_libdir_pkgconfig ${CMAKE_INSTALL_PREFIX}/lib/pkgconfig)
-
-CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}.pc.cmake
-  ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}.pc)
-
-INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}.pc
-  DESTINATION ${install_libdir_pkgconfig}	
-  PERMISSIONS OWNER_READ GROUP_READ WORLD_READ OWNER_WRITE)
-
-# Uninstall target.
-CONFIGURE_FILE(
-  "${CMAKE_CURRENT_SOURCE_DIR}/cmake_uninstall.cmake.in"
-  "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
-  IMMEDIATE @ONLY)
-
-ADD_CUSTOM_TARGET(uninstall
-  "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake")
-
-IF(WIN32)
-  ADD_DEFINITIONS("-D_CRT_SECURE_NO_WARNINGS -D_SCL_SECURE_NO_WARNINGS /wd4251 /wd4275 /wd4101 /wd4355")
-ENDIF(WIN32)
-
-ADD_SUBDIRECTORY(src)
-ADD_SUBDIRECTORY(include)
-ADD_SUBDIRECTORY(unitTesting)
-ADD_SUBDIRECTORY(tools)
-
-
-#
-# Documentation produced by doxygen
-#
-IF(GENERATE_DOC)
-  INCLUDE(FindDoxygen)
-  IF(DOXYGEN_FOUND)
-    MESSAGE(STATUS "Doxygen found")
-    add_subdirectory(doc)
-  ENDIF(DOXYGEN_FOUND)
-ENDIF(GENERATE_DOC)
+# Copyright 2010, 2019 JRL, CNRS/AIST, LAAS CNRS See LICENSE file.
+
+cmake_minimum_required(VERSION 3.1)
+
+# Project properties
+set(PROJECT_ORG stack-of-tasks)
+set(PROJECT_NAME sot-core)
+set(PROJECT_DESCRIPTION "Hierarchical task solver plug-in for dynamic-graph.")
+set(PROJECT_URL "https://github.com/${PROJECT_ORG}/${PROJECT_NAME}")
+
+# Project options
+option(SUFFIX_SO_VERSION "Suffix library name with its version" ON)
+
+# Project configuration
+set(PROJECT_USE_CMAKE_EXPORT TRUE)
+set(CUSTOM_HEADER_DIR "sot/core")
+set(CXX_DISABLE_WERROR TRUE)
+set(DOXYGEN_USE_MATHJAX YES)
+set(DOXYGEN_USE_TEMPLATE_CSS YES)
+
+# JRL-cmakemodule setup
+include(cmake/base.cmake)
+include(cmake/boost.cmake)
+include(cmake/sphinx.cmake)
+
+# Project definition
+compute_project_args(PROJECT_ARGS LANGUAGES CXX)
+project(${PROJECT_NAME} ${PROJECT_ARGS})
+check_minimal_cxx_standard(14 ENFORCE)
+
+# Project dependencies
+add_project_dependency(dynamic-graph-python 4.0.6 REQUIRED)
+add_project_dependency(pinocchio REQUIRED)
+add_project_dependency(Boost REQUIRED COMPONENTS regex program_options)
+if(BUILD_TESTING)
+  add_project_dependency(example-robot-data 3.8.0)
+  find_package(Boost REQUIRED COMPONENTS unit_test_framework)
+endif()
+
+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()
+
+string(REGEX REPLACE "-" "_" PYTHON_DIR ${CUSTOM_HEADER_DIR})
+
+# Verbosity level
+if(NOT (\"${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}/abstract-sot-external-interface.hh
+    include/${CUSTOM_HEADER_DIR}/additional-functions.hh
+    include/${CUSTOM_HEADER_DIR}/api.hh
+    include/${CUSTOM_HEADER_DIR}/binary-int-to-uint.hh
+    include/${CUSTOM_HEADER_DIR}/binary-op.hh
+    include/${CUSTOM_HEADER_DIR}/causal-filter.hh
+    include/${CUSTOM_HEADER_DIR}/clamp-workspace.hh
+    include/${CUSTOM_HEADER_DIR}/com-freezer.hh
+    include/${CUSTOM_HEADER_DIR}/contiifstream.hh
+    include/${CUSTOM_HEADER_DIR}/debug.hh
+    include/${CUSTOM_HEADER_DIR}/derivator.hh
+    include/${CUSTOM_HEADER_DIR}/device.hh
+    include/${CUSTOM_HEADER_DIR}/double-constant.hh
+    include/${CUSTOM_HEADER_DIR}/event.hh
+    include/${CUSTOM_HEADER_DIR}/exception-abstract.hh
+    include/${CUSTOM_HEADER_DIR}/exception-dynamic.hh
+    include/${CUSTOM_HEADER_DIR}/exception-factory.hh
+    include/${CUSTOM_HEADER_DIR}/exception-feature.hh
+    include/${CUSTOM_HEADER_DIR}/exception-signal.hh
+    include/${CUSTOM_HEADER_DIR}/exception-task.hh
+    include/${CUSTOM_HEADER_DIR}/exception-tools.hh
+    include/${CUSTOM_HEADER_DIR}/exp-moving-avg.hh
+    include/${CUSTOM_HEADER_DIR}/factory.hh
+    include/${CUSTOM_HEADER_DIR}/feature-1d.hh
+    include/${CUSTOM_HEADER_DIR}/feature-abstract.hh
+    include/${CUSTOM_HEADER_DIR}/feature-generic.hh
+    include/${CUSTOM_HEADER_DIR}/feature-joint-limits.hh
+    include/${CUSTOM_HEADER_DIR}/feature-line-distance.hh
+    include/${CUSTOM_HEADER_DIR}/feature-point6d-relative.hh
+    include/${CUSTOM_HEADER_DIR}/feature-point6d.hh
+    include/${CUSTOM_HEADER_DIR}/feature-pose.hh
+    include/${CUSTOM_HEADER_DIR}/feature-posture.hh
+    include/${CUSTOM_HEADER_DIR}/feature-task.hh
+    include/${CUSTOM_HEADER_DIR}/feature-vector3.hh
+    include/${CUSTOM_HEADER_DIR}/feature-visual-point.hh
+    include/${CUSTOM_HEADER_DIR}/filter-differentiator.hh
+    include/${CUSTOM_HEADER_DIR}/fir-filter.hh
+    include/${CUSTOM_HEADER_DIR}/flags.hh
+    include/${CUSTOM_HEADER_DIR}/fwd.hh
+    include/${CUSTOM_HEADER_DIR}/gain-adaptive.hh
+    include/${CUSTOM_HEADER_DIR}/gain-hyperbolic.hh
+    include/${CUSTOM_HEADER_DIR}/gripper-control.hh
+    include/${CUSTOM_HEADER_DIR}/integrator-abstract.hh
+    include/${CUSTOM_HEADER_DIR}/integrator-euler.hh
+    include/${CUSTOM_HEADER_DIR}/joint-limitator.hh
+    include/${CUSTOM_HEADER_DIR}/kalman.hh
+    include/${CUSTOM_HEADER_DIR}/latch.hh
+    include/${CUSTOM_HEADER_DIR}/macros.hh
+    include/${CUSTOM_HEADER_DIR}/macros-signal.hh
+    include/${CUSTOM_HEADER_DIR}/mailbox-vector.hh
+    include/${CUSTOM_HEADER_DIR}/mailbox.hh
+    include/${CUSTOM_HEADER_DIR}/mailbox.hxx
+    include/${CUSTOM_HEADER_DIR}/matrix-constant.hh
+    include/${CUSTOM_HEADER_DIR}/matrix-geometry.hh
+    include/${CUSTOM_HEADER_DIR}/matrix-svd.hh
+    include/${CUSTOM_HEADER_DIR}/memory-task-sot.hh
+    include/${CUSTOM_HEADER_DIR}/motion-period.hh
+    include/${CUSTOM_HEADER_DIR}/multi-bound.hh
+    include/${CUSTOM_HEADER_DIR}/neck-limitation.hh
+    include/${CUSTOM_HEADER_DIR}/op-point-modifier.hh
+    include/${CUSTOM_HEADER_DIR}/parameter-server.hh
+    include/${CUSTOM_HEADER_DIR}/periodic-call.hh
+    include/${CUSTOM_HEADER_DIR}/periodic-call-entity.hh
+    include/${CUSTOM_HEADER_DIR}/pool.hh
+    include/${CUSTOM_HEADER_DIR}/reader.hh
+    include/${CUSTOM_HEADER_DIR}/robot-simu.hh
+    include/${CUSTOM_HEADER_DIR}/robot-utils.hh
+    include/${CUSTOM_HEADER_DIR}/sot-loader.hh
+    include/${CUSTOM_HEADER_DIR}/sot.hh
+    include/${CUSTOM_HEADER_DIR}/stop-watch.hh
+    include/${CUSTOM_HEADER_DIR}/switch.hh
+    include/${CUSTOM_HEADER_DIR}/task.hh
+    include/${CUSTOM_HEADER_DIR}/task-abstract.hh
+    include/${CUSTOM_HEADER_DIR}/task-conti.hh
+    include/${CUSTOM_HEADER_DIR}/task-pd.hh
+    include/${CUSTOM_HEADER_DIR}/task-unilateral.hh
+    include/${CUSTOM_HEADER_DIR}/time-stamp.hh
+    include/${CUSTOM_HEADER_DIR}/timer.hh
+    include/${CUSTOM_HEADER_DIR}/trajectory.hh
+    include/${CUSTOM_HEADER_DIR}/unary-op.hh
+    include/${CUSTOM_HEADER_DIR}/utils-windows.hh
+    include/${CUSTOM_HEADER_DIR}/variadic-op.hh
+    include/${CUSTOM_HEADER_DIR}/vector-constant.hh
+    include/${CUSTOM_HEADER_DIR}/vector-to-rotation.hh
+    include/${CUSTOM_HEADER_DIR}/visual-point-projecter.hh)
+
+set(${PROJECT_NAME}_SOURCES
+    src/debug/debug.cpp
+    src/debug/contiifstream.cpp
+    src/exception/exception-abstract.cpp
+    src/exception/exception-dynamic.cpp
+    src/exception/exception-factory.cpp
+    src/exception/exception-feature.cpp
+    src/exception/exception-signal.cpp
+    src/exception/exception-task.cpp
+    src/exception/exception-tools.cpp
+    src/signal/signal-cast.cpp
+    src/feature/feature-abstract.cpp
+    src/task/task-abstract.cpp
+    src/task/multi-bound.cpp
+    src/sot/flags.cpp
+    src/sot/memory-task-sot.cpp
+    src/factory/pool.cpp
+    src/tools/utils-windows.cpp
+    src/tools/periodic-call.cpp
+    src/tools/device.cpp
+    src/tools/sot-loader.cpp
+    src/tools/trajectory.cpp
+    src/tools/robot-utils.cpp
+    src/matrix/matrix-svd.cpp
+    src/filters/causal-filter.cpp
+    src/utils/stop-watch.cpp)
+
+add_library(${PROJECT_NAME} SHARED ${${PROJECT_NAME}_SOURCES}
+                                   ${${PROJECT_NAME}_HEADERS})
+target_include_directories(${PROJECT_NAME} PUBLIC $<INSTALL_INTERFACE:include>)
+target_link_libraries(
+  ${PROJECT_NAME}
+  PUBLIC Boost::regex Boost::program_options
+         dynamic-graph-python::dynamic-graph-python pinocchio::pinocchio)
+
+if(SUFFIX_SO_VERSION)
+  set_target_properties(${PROJECT_NAME} PROPERTIES SOVERSION ${PROJECT_VERSION})
+endif(SUFFIX_SO_VERSION)
+
+install(
+  TARGETS ${PROJECT_NAME}
+  EXPORT ${TARGETS_EXPORT_NAME}
+  DESTINATION lib)
+
+add_subdirectory(src)
+if(BUILD_TESTING)
+  add_subdirectory(tests)
+endif(BUILD_TESTING)
+add_subdirectory(doc)
+
+install(FILES package.xml DESTINATION share/${PROJECT_NAME})
--- a/COPYING
+++ b/COPYING
-#
-# Copyright (c) 
-#
-# Permission to use, copy, modify, and distribute this software for any
-# purpose with or without fee is hereby granted, provided that the above
-# copyright notice and this permission notice appear in all copies.
-#
-# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
-# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
-# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
-# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
-# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
-# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
-# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
-
--- a/ChangeLog
+++ b/ChangeLog
--- a/INSTALL
+++ b/INSTALL
@@ -9,7 +9,7 @@ It is recommended to create a specific directory to install this package.
 mkdir build
 cd build
 cmake [Options] ..
-make 
+make
 make install

 Options:

--- a/LICENSE
+++ b/LICENSE
+BSD 2-Clause License
+
+Copyright (c) 2010-2019, 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
-Write in this file the news related to package sot-core.
+New in version 2.5.1 - 2011/12/08
+    Headers are installed in include/sot/core
+    Fix compilation issues on x86_64 architectures.
+    Do not define PYTHON_SITELIB.
+    Do not link to gfortran.
+    Synchronize cmake submodule.
+    Correct the link with Boost for Apple
+    Correct the definition of isnan for not unix systems: use Boost's one
+    The access to reference features has been modified.
+
+New in version 2.5 - 2011/06/21
+    Python now replaces the ad hoc scripting language.
+
+New in version 1.1 - 2010/09/30
+      Created package sot-core.
+      Added source files for library sot-core taken from sot.
+      Renamed exceptions, signals and debug to conform to new naming convention.
+      Renamed factory files
+      Renamed math and matrix files. Added files forgotten in last commit.
+      Renaming of sot and tasks (renaming complete).
+      Begin renamind classes and putting them into namespace sot.
+      Put everything in namespace sot (global objects included). Corrected some resulting bugs.
+      Some bug fixes.
+      Changed order of compilation of some .cpp files to prevent mysterious Segmentation Fault(s) from appearing.
+      Added forgotten cpp files.
+      Added forgotten file test_signal.cpp
+      Only generate documentation if GENERATE_DOC is ON.
+      Removed test test_shell which was already included in dynamic graph.
+      Finished renaming of SOT objects.
+      More refactoring. Removed undertermination between sot::Pool and dynamicgraph::Pool in pool.cpp. Added cmake configure for import-default-paths.
+      Added LAPACK library dependencies in FORTRAN.     Adjusted for a change in singletons names from dynamicgraph.
+      Added plugins compilation and installation to CMakeFiles. Started separating plugins from sot-core.
+      Corrected installation path and name of plugins. Some minor bugfixes.
+      Added tools/ directory for... tools.     Some corrections in the unit testing facility.
+      Added tools in sot-core
+      Added forgotten test file test_dep.cpp
+      Added forgotten test file test_depend.cpp
+      Added forgotten test file test_ptr.cpp
+      Removed "using dynamicgraph" directives in headers, implemented resulting changes.
+      Added two unit tests, removed a tool
+      Added new test test_factory
+      Corrected an error in test_factory
+      Changed all instances of 'dependancy' to 'dependency'
+      Corrected typo in op-point-modifier.
+      Corrected typo in gain-adaptative and related names.
+      Added plugin "Reader" to read files generated by "Tracer".
+      Corrected a bug that stemmed from the renaming of GainAdaptive (thanks unit testing!)     Added unit tests for filesystem and tracing.
+      Task-related unit tests and corrections.
+      Modified CMakeLists.txt to remove multiple definitions and include dirs.
+      Added 3 tools. Some minor corrections (such as correctly exporting classes in plugins)
+      Added uninstall.
+      Added three tools.
+      Added MotionPeriod, NeckLimitation and PeriodicCallEntity plugins.
+      Added plugins and exceptions.
+      Added forgotten file.
+      Got some tools out of the main library and into plugins, as they should have been.
+      Merge branch 'master' of git+ssh://softs.laas.fr/git/jrl/sot/sot-core
+      Added some necessary comments in Cmakelists
+      Revert "clamp must use the API of sot-core"
+      Revert "com-freezer must use the API of sot-core"
+      Revert "Distant-shell must use the API of sot-core"
+      Revert "Gripper-control must use the API of sot-core"
+      Revert "joint-limitator must use the API of sot-core"
+      Revert "kalman must use the API of sot-core"
+      Added three tests for tools and renamed one.
+      Removed wrong include in CMakeLists.
+      Made boost_thread inclusion optional and dependent on HAVE_LIBBOOST_THREAD
+      Added control entities to sot-core.
+      Added boost thread library.     Added pthread library and compilation & link flags.     Corrected multiple small bugs.     Added CMakeModules for pthread and boost numeric bindings.     Corrected some tests.
+      Made sure pthreads were included.     Simplified the unit test test_mailbox that previously *required user input*.
+      Modified pthread linking following compilation error with boost::thread.
+      Added pthread *compilation* flag; for UNIX.
+      Added pthread definition on UNIX.
+      Removed redundant definition -pthread
+      Settled down the case of mailbox.
+      Merge branch 'master' of git+ssh://softs.laas.fr/git/jrl/sot/sot-core
+      Removed distant shell (now in dg-middleware)
+      Renamed sotVectorRotation
+      Ported commit 53ef45d27b77 from StackOfTasks.
+      Revert "Ported commit 53ef45d27b77 from StackOfTasks."
+      sotFeatureTask depends on sotTask, not sotAbstractTask
+      Changed import-default-paths configuration to generate the file in source include directory *then* install.
+      Added gfortran as a link library.
+      Added gfortran CMake linking.
+      Removed CMAKE_INSTALL_PREFIX in INSTALL directive.
+      - Removed last occurences of CMAKE_INSTALL_PREFIX     - Updated documentation pictures
+      Added documentation to sot-core
+      Added doxytag reference to dynamic-graph.
+      Removed VP_DEBUG references.
+      Corrected opening of trace files.
+      Namespace missing.
+      Namespace missing.
+      Changed MatrixRotation in signal cast.
+      Removed debug trace initiator which caused a segfault.
+      Added helper entity "MatrixRotToMatrix" to convert types where the dynamic type verification system fails.
+      - Added new test test_ptrcast to try (and fail) to reproduce signal casting issue in simulation     - Added 2 new entities, HomoToRotation/Twist2 whose output is a ('standard') ml::Matrix
+      Re-added deleted overload of Matrixhomo::extract
+      Re-added accidentally deleted entity.
+      Removed all references to new entities.
+      Made exceptions derive from std::exception
+      Merge branch 'master' of git+ssh://softs.laas.fr/git/jrl/sot/sot-core
+      Contiifstream must use the API of sot-API
+      Memory-task must use the API of sot-API
+      Correct typo in macro name
+      Correct typo in macro name
+      Rotation-simple must use the API of sot-core
+      Correct typo in macro name
+      SHI must use the API of sot-core
+      Correct typo in macro name
+      Correct the inclusion and use of utils-windows.h
+      Remove a header generated by cmake from git repository
+      Win32: add definitions that disable verbose warnings
+      The boost library 'system' is also required
+      In this specific case, link_directories is only for UNIX
+      Add dependencies between plugins
+      Inter-plugins dependency: set the compilation order
+      Win32: correct the linkage
+      Win32: Correct link flags for unittesting
+      These commands are unix specific
+      The dependency in tracer is OS specific
+      Add a gitignore file.
+      Merge branch 'master' of git+ssh://git.laas.fr/git/jrl///sot/sot-core
+      clamp must use the API of sot-core
+      com-freezer must use the API of sot-core
+      Distant-shell must use the API of sot-core
+      Gripper-control must use the API of sot-core
+      joint-limitator must use the API of sot-core
+      kalman must use the API of sot-core
+      Remove warning (fabsf -> fabs)
+      Remove warnings (during conversion unsigned -> bool)
+      Correct the declaration of operator <<
+      Correct the inclusion of utils-windows.h
+      Correct the inclusion of utils-windows.h
+      Correct inclusions for win32
+      Clean the unitTesting/CMakeLists
+      Win32: the command link_directories has a wrong behaviour
+      Settle the case of Mailbox
+      Correct macro name
+      Still fighting with mailbox
+      Split the declaration and the imnplementation in mailbox
+      More tests for test_mailbox
+      Add missing CXX flags for the unit tests.
+      There is no reason to define mailvect in the template file
+      Clean the code
+      Fix Mailbox once and for all
+      Win32: LoadLibrary loads *dynamic* libraries.
+      Fix dependancy to dependency
+      Remove obsolete autogen.sh file.
+      Rewrite AUTHORS file.
+      Uniformize NEWS file.
+      Enhance README using Markdown syntax.
+      Add license file.
+      Add mailmap file.
+      Add license header.
+      Debianize package.
+      Clean documentation CMakeLists.txt
+      Update version number to 1.0.0.99.
+      Fix dependency version number in Debian package.
+      Disable test and enable doc while building debian package.
+      Fix documentation generation.
+      Fix debian rules file.
+      Fix debian package.
+      Packages libraries in Debian package.
+      Extend description of Debian package.
+      Add missing build dependencies.
--- a/README
+++ b/README
-See INSTALL for installation instruction.
--- a/README.md
+++ b/README.md
+# sot-core
+
+[![License](https://img.shields.io/badge/License-BSD%202--Clause-green.svg)](https://opensource.org/licenses/BSD-2-Clause)
+[![Pipeline status](https://gitlab.laas.fr/stack-of-tasks/sot-core/badges/master/pipeline.svg)](https://gitlab.laas.fr/stack-of-tasks/sot-core/commits/master)
+[![Coverage report](https://gitlab.laas.fr/stack-of-tasks/sot-core/badges/master/coverage.svg?job=doc-coverage)](https://gepettoweb.laas.fr/doc/stack-of-tasks/sot-core/master/coverage/)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/stack-of-tasks/sot-core/master.svg)](https://results.pre-commit.ci/latest/github/stack-of-tasks/sot-core)
+
+
+This software provides a set of dynamic graph plug-ins which can be
+used to define and solve hierarchical tasks.
+
+
+## Setup
+
+To compile this package, it is recommended to create a separate build
+directory:
+
+    mkdir _build
+    cd _build
+    cmake [OPTIONS] ..
+    make install
+
+Please note that CMake produces a `CMakeCache.txt` file which should
+be deleted to reconfigure a package from scratch.
--- a/autogen.sh
+++ b/autogen.sh
-echo ""
-echo "This package is installed through cmake. Please read INSTALL for instructions."
-echo ""
--- a/cmake @ 47c0cbf0
+++ b/cmake @ 47c0cbf0
+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}${file}")
-ENDFOREACH(file)
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
-# 
-#  Copyright 
-# 
-
-# Configure package.dox file
-CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/package.dox.cmake
-  ${CMAKE_CURRENT_BINARY_DIR}/package.dox
-)
-
-
-ADD_CUSTOM_COMMAND(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
-  COMMAND ${DOXYGEN_EXECUTABLE} \"${CMAKE_CURRENT_BINARY_DIR}/package.dox\"
-)
-
-ADD_CUSTOM_TARGET(documentation ALL
-  DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/html/index.html)
-
 #
-# Install html documentation
+# Copyright 2010 CNRS Author: Florent Lamiraux
 #

-# html files
-INSTALL(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html
-  DESTINATION ${CMAKE_INSTALL_PREFIX}/share/doc/${PROJECT_NAME})
-
-# doxytag
-INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}.doxytag
-  DESTINATION ${CMAKE_INSTALL_PREFIX}/share/doc/${PROJECT_NAME}/html)
+# get the python script install path

-# pictures
-INSTALL(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/pictures
-  DESTINATION ${CMAKE_INSTALL_PREFIX}/share/doc/${PROJECT_NAME}/html)
+if(INSTALL_DOCUMENTATION)
+  install(FILES pictures/feature.png pictures/task.png
+          DESTINATION ${_PKG_CONFIG_DOXYGENDOCDIR}/pictures)
+endif(INSTALL_DOCUMENTATION)
--- a/doc/Doxyfile.extra.in
+++ b/doc/Doxyfile.extra.in
+INPUT                  = @CMAKE_SOURCE_DIR@/include \
+                         @CMAKE_SOURCE_DIR@/doc/additionalDoc
+IMAGE_PATH             = @CMAKE_SOURCE_DIR@/doc/pictures
+
+FILE_PATTERNS          = *.cc *.cpp *.h *.hh *.hxx
+
+COLLABORATION_GRAPH    = NO
+
+CITE_BIB_FILES         = @CMAKE_SOURCE_DIR@/doc/references.bib
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