Initial import

This commit is contained in:
Guilhem Lavaux 2023-05-29 10:41:03 +02:00
commit 56a50eead3
820 changed files with 192077 additions and 0 deletions

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.aquila-modules Normal file
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.atom-build.yml Normal file
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cmd: "make"
args:
- "-C"
- "{PROJECT_PATH}/build"
sh: false
name: "Build All"
errorMatch:
- "(?<file>([A-Za-z]:[\\/])?[^:\\n]+):(?<line>\\d+):(?<col>\\d+):\\s*(fatal error|error):\\s*(?<message>.+)"
# - (?<file>[^:\\n]+):(?<line>\\d+):(?<col>\\d+):[\\s\\S]+?Error: (?<message>.+)
warningMatch:
- (?<file>([A-Za-z]:[\\/])?[^:\\n]+):(?<line>\\d+):(?<col>\\d+):\\s*(warning):\\s*(?<message>.+)
targets:
generate_build:
cmd: "bash build.sh"
args:
- --purge
- --c_compiler=/usr/bin/gcc
- --cxx_compiler=/usr/bin/g++
name: "Setup ARES build"
generate_build_mpi:
cmd: "bash build.sh"
name: "Setup ARES build with MPI"
args:
- --purge
- --with-mpi
- --c_compiler
- /usr/bin/gcc
- --cxx_compiler
- /usr/bin/g++

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BasedOnStyle: llvm
IndentWidth: 2
AlignAfterOpenBracket: AlwaysBreak
AlignEscapedNewlines: Right
Standard: Cpp11
SortIncludes: false
PointerAlignment: Right
MaxEmptyLinesToKeep: 1
ReflowComments: false
IndentPPDirectives: AfterHash
CompactNamespaces: false
IndentCaseLabels: false
AlwaysBreakTemplateDeclarations: true
NamespaceIndentation: All
BraceWrapping:
AfterControlStatement: false
AfterFunction: false
AfterNamespace: false

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* text=auto eol=lf

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# Ignore all
*
# Ignore .gitignore and .gitmodules
.gitignore
.gitmodules
!Jenkinsfile
# Unignore all with extensions
!*.*
# Unignore Dockerfile
!Dockerfile
# Unignore all dirs
!*/
### Above combination will ignore all files without extension ###
# Ignore executable files
*.[oa]
*.out
# Ignore Python bytecode file
*.pyc
# Ignore all files in these directories
.texpadtmp/
downloads/
build/
# Ignore swap files
*~
.DS_Store
extra/*/
!extra/demo/
examples/**
!examples/*.ini
!examples/2MPP.txt
!examples/completeness_*.fits
!examples/one.fits
docs/tex/
docs/sphinx/_build/
docs/sphinx/_static/
build*/
docs/doxyoutput/
docs/_build/
docs/api/
docs/_static/doxy_html/
docs/source/_generate/
!docs/source/user/building/
!build_tools/

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[submodule "external/cosmotool"]
path = external/cosmotool
url = https://bitbucket.org/glavaux/cosmotool/
ignore = dirty

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# Required
version: 2
# Build documentation in the docs/ directory with Sphinx
sphinx:
configuration: docs/source/conf.py
# Build documentation with MkDocs
#mkdocs:
# configuration: mkdocs.yml
# Optionally build your docs in additional formats such as PDF and ePub
formats: all
# Optionally set the version of Python and requirements required to build your docs
python:
version: 3.7
install:
- requirements: docs/requirements.txt

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git:
depth: 3
submodules: true
language: cpp
install:
- DEPS_DIR="${TRAVIS_BUILD_DIR}/deps"
- mkdir ${DEPS_DIR} && cd ${DEPS_DIR}
- travis_retry wget --no-check-certificates https://github.com/Kitware/CMake/releases/download/v3.17.1/cmake-3.17.1-Linux-x86_64.tar.gz
- echo "" > cmake_md5.txt
- md5sum -c cmake_md5.txt
- tar -xvf cmake-3.17.1-Linux-x86_64.tar.gz > /dev/null
- mv cmake-3.17.1-Linux-x86_64 cmake-install
- PATH=${DEPS_DIR}/cmake-install/bin:${PATH}
before_script:
- sh get-aquila-modules.sh --clone
- sh get-aquila-modules.sh --branch-set
- sh build.sh --download-deps
- sh build.sh --use-predownload --python
script:
- cd build
- make

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let g:clang_format#code_style = "file"

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.vscode/c_cpp_properties.json vendored Normal file
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{
"configurations": [
{
"name": "Linux",
"defines": [
"${default}"
],
"compilerPath": "/usr/bin/gcc",
"includePath": [
"${workspaceFolder}",
"${workspaceFolder}/extra/**",
"${env:ares_build}/",
"${env:ares_build}/external_build/eigen-prefix/src/eigen",
"${env:ares_build}/ext_install/include",
"/usr/include/eigen3"
],
"cStandard": "c11",
"cppStandard": "c++14",
"intelliSenseMode": "gcc-x64"
}
],
"version": 4
}

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{
"editor.formatOnSave": true,
"C_Cpp.default.compilerPath": "g++",
"C_Cpp.default.includePath": [
"${workspaceFolder}",
"${workspaceFolder}/extra/**",
"${env:ARES_BUILD}",
"${env:ARES_BUILD}/external_build/eigen-prefix/src/eigen",
"${env:ARES_BUILD/ext_install/include"
],
"cmake.configureOnOpen": false,
"files.associations": {
"cctype": "cpp",
"clocale": "cpp",
"cmath": "cpp",
"cstdarg": "cpp",
"cstddef": "cpp",
"cstdio": "cpp",
"cstdlib": "cpp",
"cstring": "cpp",
"ctime": "cpp",
"cwchar": "cpp",
"cwctype": "cpp",
"*.ipp": "cpp",
"array": "cpp",
"atomic": "cpp",
"strstream": "cpp",
"bit": "cpp",
"*.tcc": "cpp",
"bitset": "cpp",
"chrono": "cpp",
"complex": "cpp",
"condition_variable": "cpp",
"cstdint": "cpp",
"deque": "cpp",
"forward_list": "cpp",
"list": "cpp",
"map": "cpp",
"set": "cpp",
"unordered_map": "cpp",
"unordered_set": "cpp",
"vector": "cpp",
"exception": "cpp",
"algorithm": "cpp",
"functional": "cpp",
"iterator": "cpp",
"memory": "cpp",
"memory_resource": "cpp",
"numeric": "cpp",
"optional": "cpp",
"random": "cpp",
"ratio": "cpp",
"string": "cpp",
"string_view": "cpp",
"system_error": "cpp",
"tuple": "cpp",
"type_traits": "cpp",
"utility": "cpp",
"fstream": "cpp",
"initializer_list": "cpp",
"iomanip": "cpp",
"iosfwd": "cpp",
"iostream": "cpp",
"istream": "cpp",
"limits": "cpp",
"mutex": "cpp",
"new": "cpp",
"ostream": "cpp",
"sstream": "cpp",
"stdexcept": "cpp",
"streambuf": "cpp",
"thread": "cpp",
"cfenv": "cpp",
"cinttypes": "cpp",
"typeindex": "cpp",
"typeinfo": "cpp",
"valarray": "cpp",
"variant": "cpp",
"csetjmp": "cpp",
"csignal": "cpp",
"codecvt": "cpp",
"regex": "cpp",
"hash_map": "cpp",
"rope": "cpp",
"slist": "cpp",
"future": "cpp",
"shared_mutex": "cpp",
"hash_set": "cpp",
"scoped_allocator": "cpp",
"any": "cpp",
"compare": "cpp",
"concepts": "cpp",
"coroutine": "cpp",
"source_location": "cpp",
"ranges": "cpp",
"span": "cpp",
"stop_token": "cpp"
},
"python.formatting.provider": "yapf",
"C_Cpp.dimInactiveRegions": false,
"C_Cpp.errorSquiggles": "Enabled",
"python.linting.enabled": false,
"restructuredtext.confPath": ""
}

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{
"version": "2.0.0",
"tasks": [
{
"label": "Build ARES",
"type": "process",
"command": "nice",
"args": [
"make",
"all"
],
"options": {
"cwd": "${env:ARES_BUILD}"
},
"problemMatcher": {
"base": "$gcc",
"fileLocation": [
"absolute"
]
},
"group": {
"kind": "build",
"isDefault": true
}
}
]
}

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Release notes
=============
This file only lists the most important changes to each version. We try to follow semantic versioning:
- Major release means API incompatibilities
- Minor release means API compatibilities, but significant feature differences
- Bugfix release only fixes bugs
Release 2.1
-----------
- An option to control the verbosity in log file has been added ("system/logfile_verbose_level", v2.1.3)
Forward related
^^^^^^^^^^^^^^^
- Add a way of transforming all bias models into a forward deterministic transition. It means more flexibility at the cost of losing performance/memory by doing
more computations than required. For example, each subcatalog needs its own bias which could trigger quite a lot of recomputation and/or caching.
- PMv2 optimization when sampling.
- Implement a simple (non-MPI) haar transform.
- Add EnforceMass model element to articifially fix the mass conservation.
- Forward models may support a new behavior for adjointModel_v2. They can accumulate all adjoint vectors that are provided to them through
adjointModel_v2. The new behavior must be requested by calling BORGForwardModel::accumulateAdjoint. In that case, the user is explicitly
requested to clear the adjoint gradient when the computation is done by calling BORGForwardModel::clearAdjointGradient.
That behavior has been ported to pyborg. If the mode is not supported, an exception will be triggered.
- Merged Altair code.
- Bind ClassCosmo to ARES. Python binding is also active and vectorized for get_Tk.
Sampler related
^^^^^^^^^^^^^^^
- Add CG89 "higher order" symplectic integrator.
API related:
^^^^^^^^^^^^
- ManyPower bias model needs a likelihood info entry now to set the width of the prior on parameters. The name is ManyPower_prior_width in [info].
- Code cleanup in velocity field estimator. It also now supports Simplex-In-Cell (no adjoint gradient yet and only non-MPI).
- Models accept a broader range of parameters using BORGForwardModel::setModelParams.
Python related:
^^^^^^^^^^^^^^^
- *NEW tool* hades_python which supports a full deterministic transition written in python/tensorflow/jax. Data loading is still work in progress and
may need hacking at the moment
- Python extension is supporting LikelihoodInfo and the bias as forward model element.
- Add a 'setup.py' to support compiling the BORG python module directly with pip and packaging as a wheel file.
- Samplers fully supported from Python.
Build related
^^^^^^^^^^^^^
- build.sh only downloads the dependency if the file is not already there
- Error reporting include a full C++ stacktrace on supported platforms (cmake flag is STACKTRACE_USE_BACKTRACE=ON, experimental at the moment
It can be turned off).
- Added GIT hooks to check on basic text elements (like formatting) before running commits.
clang-formatter absence may be overridden using ARES_CLANG_OVERRIDE=1
Release 2.0alpha
----------------
- Use a prior that is purely gaussian unit variance (Fourier) in HMC now. The cosmology is completely moved as a BORGForwardModel.
- BORGForwardModel adds the v2 API to executes model: forwardModel_v2, and adjointModel_v2. This relies heavily on the mechanics of ModelIO
- Deterministic models are now self-registering and the available lists can be dynamically queried.
- Add a hook to optionally dump extra bias fields.
- Add QLPT and QLPT_RSD forward model in extra/borg
- Lots of documentation reorganization
- Added the lyman alpha model in extra/borg
- Merged the EFT likelihood effort in extra/borg
Release 1.0
-----------
Initial release

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CMakeLists.txt Normal file
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cmake_minimum_required(VERSION 3.10)
cmake_policy(SET CMP0074 NEW)
set(CMAKE_CXX_STANDARD 14)
set(CMAKE_CXX_VISIBILITY_PRESET hidden)
list(INSERT CMAKE_MODULE_PATH 0 "${CMAKE_CURRENT_SOURCE_DIR}/cmake_modules")
IF(DEFINED ARES_PREFIX_PATH)
SET(ENV{CMAKE_PREFIX_PATH} "${ARES_PREFIX_PATH}")
SET(CMAKE_PREFIX_PATH "${ARES_PREFIX_PATH}")
ENDIF()
SET(CMAKE_SKIP_BUILD_RPATH FALSE)
SET(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
option(BUILD_JULIA "Activate the Julia support" OFF)
PROJECT(ARES CXX C)
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS Debug Release RelWithDebInfo)
# Import required cmake modules
include(color_msg)
include(GetGitRevisionDescription)
include(ExternalProject)
include(CTest)
# Not used anymore
#include(GenOptMacro)
include(CheckCXXCompilerFlag)
include(CheckCCompilerFlag)
#include(FortranCInterface)
include(FindOpenMP)
include(FindPkgConfig)
include(clang-format)
include(FetchContent)
IF (CMAKE_C_COMPILER_ID MATCHES "AppleClang" OR CMAKE_CXX_COMPILER_ID MATCHES "AppleClang")
IF (NOT ${CMAKE_C_COMPILER_ID} STREQUAL ${CMAKE_CXX_COMPILER_ID})
message(WARNING "C and C++ compiler have different IDs: ${CMAKE_C_COMPILER_ID} != ${CMAKE_CXX_COMPILER_ID}")
ENDIF()
message(WARNING "AppleClang does not support OpenMP. Please use something else for more performance.")
SET(DEFAULT_ENABLE_OPENMP OFF)
ELSE()
SET(DEFAULT_ENABLE_OPENMP ON)
ENDIF()
# Options
OPTION(ENABLE_OPENMP "Activate OpenMP support" ${DEFAULT_ENABLE_OPENMP})
OPTION(DISABLE_DEBUG_OUTPUT "No debug output support (faster)" OFF)
OPTION(ENABLE_MPI "MPI support" OFF)
OPTION(CONTEXT_TIMER "Activate profiling of LibLSS contexts" OFF)
OPTION(USE_NATIVE_ARCH "Activate instruction set supported by the running system" OFF)
OPTION(ENABLE_FULL_WARNINGS "Ask the compiler to produce lots of warnings" OFF)
OPTION(BUILD_PYTHON_EXTENSION "Build the Python BORG extension" OFF)
IF(ENABLE_MPI)
find_package(MPI)
set(EXTRA_LIB ${MPI_C_LIBRARIES})
ELSE(ENABLE_MPI)
SET(EXTRA_LIB)
SET(MPI_C_INCLUDE_PATH)
ENDIF(ENABLE_MPI)
IF(USE_NATIVE_ARCH)
CHECK_CXX_COMPILER_FLAG("-march=native" COMPILER_SUPPORTS_MARCH_NATIVE)
if(COMPILER_SUPPORTS_MARCH_NATIVE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
endif()
endif()
include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
find_program(PYTHON_EXECUTABLE NAMES python3)
IF (NOT PYTHON_EXECUTABLE)
cmessage(FATAL_ERROR "Python3 interpreter to compile ARES")
ENDIF()
IF (BUILD_JULIA)
find_package(Julia)
if (NOT JULIA_EXECUTABLE)
cmessage(CWARNING "Julia not found, will not be built")
set(BUILD_JULIA OFF)
endif()
ENDIF()
IF(BUILD_PYTHON_EXTENSION)
FetchContent_MakeAvailable(pybind11)
ENDIF()
FetchContent_MakeAvailable(r3d)
# Retrieve current git revision
git_describe(GIT_VER)
IF (DEFINED CMAKE_C_COMPILER_VERSION)
cmessage(STATUS "C compiler version: ${CMAKE_C_COMPILER_VERSION}")
cmessage(STATUS "C++ compiler Version: ${CMAKE_CXX_COMPILER_VERSION}")
if (NOT ${CMAKE_C_COMPILER_VERSION} EQUAL ${CMAKE_CXX_COMPILER_VERSION})
cmessage(FATAL_ERROR "C and C++ compilers are different. Please fix parameters.")
ENDIF()
ELSE()
cmessage(WARNING "Cannot check compiler versions. Proceed with cautions.")
ENDIF()
SET(CMAKE_CXX_FLAGS_PROFILE "-O3 -pg" CACHE STRING "Flags to turn on profiling for C++ compiler")
SET(CMAKE_C_FLAGS_PROFILE "-O3 -pg" CACHE STRING "Flags to turn on profiling for C compiler" )
SET(CMAKE_EXE_LINKER_FLAGS_PROFILE "-pg" CACHE STRING "Flags to turn on profiling in linker")
mark_as_advanced(CMAKE_CXX_FLAGS_PROFILE CMAKE_C_FLAGS_PROFILE CMAKE_EXE_LINKER_FLAGS_PROFILE)
find_library(ZLIB_LIBRARY z)
find_library(_pre_RT_LIBRARY rt)
if(_pre_RT_LIBRARY)
SET(RT_LIBRARY ${_pre_RT_LIBRARY})
ENDIF()
find_library(DL_LIBRARY dl)
include_directories(
${Boost_INCLUDE_DIRS}
${GSL_INCLUDE}
${CMAKE_SOURCE_DIR}
${EIGEN_INCLUDE_DIRS}
${EXT_INSTALL}/include
${COSMOTOOL_INCLUDE}
${HDF5_INCLUDE_DIR}
${FFTW_INCLUDE_DIR}
${MPI_C_INCLUDE_PATH}
)
#
# OpenMP handling
#
IF(ENABLE_OPENMP)
IF (NOT OPENMP_FOUND)
MESSAGE(ERROR "No known compiler option for enabling OpenMP")
ENDIF(NOT OPENMP_FOUND)
SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_C_FLAGS}")
ENDIF(ENABLE_OPENMP)
IF (DISABLE_DEBUG_OUTPUT)
add_definitions(-DLIBLSS_CONSOLE_NO_DEBUG_SUPPORT)
ENDIF (DISABLE_DEBUG_OUTPUT)
IF(ENABLE_MPI)
add_definitions(-DARES_MPI_FFTW)
ENDIF (ENABLE_MPI)
IF (CONTEXT_TIMER)
add_definitions(-DLIBLSS_TIMED_CONTEXT)
ENDIF (CONTEXT_TIMER)
add_definitions(-DBOOST_ENABLE_ASSERT_DEBUG_HANDLER)
SET(ARES_INCLUDE_PATH)
# Detect extra modules
#
#
file(GLOB ARES_MODULES `LIST_DIRECTORIES false RELATIVE ${CMAKE_SOURCE_DIR}/extra ${CMAKE_SOURCE_DIR}/extra/*)
# Remove spurious contaminating OSX directories
list(REMOVE_ITEM ARES_MODULES .DS_Store)
message(STATUS "ARES modules found:")
foreach(module IN LISTS ARES_MODULES)
if (EXISTS ${CMAKE_SOURCE_DIR}/extra/${module}/DO_NOT_BUILD)
list(REMOVE_ITEM ARES_MODULES ${module})
cmessage(CWARNING " ${module} (do not build)")
else()
message(STATUS " ${module}")
endif()
endforeach()
add_subdirectory(libLSS)
add_subdirectory(src)
foreach(module IN LISTS ARES_MODULES)
if (EXISTS ${CMAKE_SOURCE_DIR}/extra/${module}/${module}.cmake)
include(${CMAKE_SOURCE_DIR}/extra/${module}/${module}.cmake)
endif()
endforeach()
setup_formatter(ARES_MODULES)

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pipeline {
agent any
options { buildDiscarder(logRotator(numToKeepStr: '5')) }
environment {
DOC_DEPLOYER = credentials('Doc deployment')
}
stages {
stage('Preparation') {
steps {
script {
branchName = 'release/2.1'
cred = '0c503fb7-7bad-459f-81f1-71467b382d39'
env.PYTHON_VENV = """${sh(
returnStdout:true,
script: 'echo "${WORKSPACE}/${BUILD_TAG}"'
)}"""
}
}
}
stage('Source') { // for display purposes
steps {
git branch: branchName, credentialsId: cred, url: 'git@bitbucket.org:aquila-consortium/borg_public.git'
sh 'python3 -m venv ${PYTHON_VENV}'
sh 'ls && echo ${PYTHON_VENV} && ls ${PYTHON_VENV}'
sh 'test -e ${PYTHON_VENV}'
sh 'git submodule init'
sh 'git submodule update --recursive'
}
}
stage('Download deps') {
steps {
ansiColor('xterm') {
sh '''
bash build.sh --download-deps
'''
}
}
}
stage('Configure') {
steps {
ansiColor('xterm') {
sh '''
. ${WORKSPACE}/${BUILD_TAG}/bin/activate
CMAKE_PREFIX_PATH=${VIRTUAL_ENV}:/opt/boost
export CMAKE_PREFIX_PATH
bash build.sh --python --use-system-boost=/opt/boost --use-system-fftw --use-system-hdf5 --native --purge --extra-flags -DINSTALL_PYTHON_LOCAL=OFF
'''
}
}
}
stage('Build') {
steps {
ansiColor('xterm') {
dir('build') {
sh 'make -j6'
}
}
}
}
stage('Tests') {
steps {
dir('build') {
sh 'make test'
}
}
}
stage('Install') {
steps {
dir('build') {
sh 'make install'
}
}
}
stage("Doc") {
steps {
dir('docs') {
sh """
. ${WORKSPACE}/${BUILD_TAG}/bin/activate
pip3 install wheel
pip3 install -r requirements.txt
rm -fr source/_generate
rm -fr _build
make SHELL=/bin/bash html
tar -C _build/html -zcvf doc.tgz .
curl -v -F filename=doc -F file=@doc.tgz http://athos.iap.fr:9595/deploy-doc2/$DOC_DEPLOYER/v2.1-public
"""
}
}
}
}
post {
failure {
notifyBuild("FAIL")
}
success {
notifyBuild("SUCCESS")
}
cleanup {
/* clean up our workspace */
//deleteDir()
/* clean up tmp directory */
//dir("${WORKSPACE}/${BUILD_TAG}") {
// deleteDir()
//}
dir("${workspace}@tmp") {
deleteDir()
}
dir("extra/hades@tmp") {
deleteDir()
}
dir("extra/borg@tmp") {
deleteDir()
}
dir("extra/ares_fg@tmp") {
deleteDir()
}
dir("extra/python@tmp") {
deleteDir()
}
}
}
}
def notifyBuild(String buildStatus = 'STARTED') {
// build status of null means successful
buildStatus = buildStatus ?: 'SUCCESS'
// Default values
def colorName = 'RED'
def colorCode = '#FF0000'
def subject = "${buildStatus}: Job '${env.JOB_NAME} [${env.BUILD_NUMBER}]'"
def summary = "${subject} (${env.BUILD_URL})"
// Override default values based on build status
if (buildStatus == 'STARTED') {
color = 'YELLOW'
colorCode = '#0000FF'
} else if (buildStatus == 'SUCCESS') {
color = 'GREEN'
colorCode = '#00FF00'
} else {
color = 'RED'
colorCode = '#FF0000'
}
def details = """<p>STARTED: Job '${env.JOB_NAME} [${env.BUILD_NUMBER}]':</p>
<p>Check console output at &QUOT;<a href='${env.BUILD_URL}'>${env.JOB_NAME} [${env.BUILD_NUMBER}]</a>&QUOT;</p>
<p>Build status: <span style='color: ${colorCode};'>${buildStatus}</span></p>"""
emailext (
mimeType: 'text/html',
subject: subject,
body: details,
recipientProviders: [developers(), requestor()]
)
}

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CeCILL FREE SOFTWARE LICENSE AGREEMENT
Version 2.1 dated 2013-06-21
Notice
This Agreement is a Free Software license agreement that is the result
of discussions between its authors in order to ensure compliance with
the two main principles guiding its drafting:
* firstly, compliance with the principles governing the distribution
of Free Software: access to source code, broad rights granted to users,
* secondly, the election of a governing law, French law, with which it
is conformant, both as regards the law of torts and intellectual
property law, and the protection that it offers to both authors and
holders of the economic rights over software.
The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
license are:
Commissariat à l'énergie atomique et aux énergies alternatives - CEA, a
public scientific, technical and industrial research establishment,
having its principal place of business at 25 rue Leblanc, immeuble Le
Ponant D, 75015 Paris, France.
Centre National de la Recherche Scientifique - CNRS, a public scientific
and technological establishment, having its principal place of business
at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
Institut National de Recherche en Informatique et en Automatique -
Inria, a public scientific and technological establishment, having its
principal place of business at Domaine de Voluceau, Rocquencourt, BP
105, 78153 Le Chesnay cedex, France.
Preamble
The purpose of this Free Software license agreement is to grant users
the right to modify and redistribute the software governed by this
license within the framework of an open source distribution model.
The exercising of this right is conditional upon certain obligations for
users so as to preserve this status for all subsequent redistributions.
In consideration of access to the source code and the rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors only have limited liability.
In this respect, the risks associated with loading, using, modifying
and/or developing or reproducing the software by the user are brought to
the user's attention, given its Free Software status, which may make it
complicated to use, with the result that its use is reserved for
developers and experienced professionals having in-depth computer
knowledge. Users are therefore encouraged to load and test the
suitability of the software as regards their requirements in conditions
enabling the security of their systems and/or data to be ensured and,
more generally, to use and operate it in the same conditions of
security. This Agreement may be freely reproduced and published,
provided it is not altered, and that no provisions are either added or
removed herefrom.
This Agreement may apply to any or all software for which the holder of
the economic rights decides to submit the use thereof to its provisions.
Frequently asked questions can be found on the official website of the
CeCILL licenses family (http://www.cecill.info/index.en.html) for any
necessary clarification.
Article 1 - DEFINITIONS
For the purpose of this Agreement, when the following expressions
commence with a capital letter, they shall have the following meaning:
Agreement: means this license agreement, and its possible subsequent
versions and annexes.
Software: means the software in its Object Code and/or Source Code form
and, where applicable, its documentation, "as is" when the Licensee
accepts the Agreement.
Initial Software: means the Software in its Source Code and possibly its
Object Code form and, where applicable, its documentation, "as is" when
it is first distributed under the terms and conditions of the Agreement.
Modified Software: means the Software modified by at least one
Contribution.
Source Code: means all the Software's instructions and program lines to
which access is required so as to modify the Software.
Object Code: means the binary files originating from the compilation of
the Source Code.
Holder: means the holder(s) of the economic rights over the Initial
Software.
Licensee: means the Software user(s) having accepted the Agreement.
Contributor: means a Licensee having made at least one Contribution.
Licensor: means the Holder, or any other individual or legal entity, who
distributes the Software under the Agreement.
Contribution: means any or all modifications, corrections, translations,
adaptations and/or new functions integrated into the Software by any or
all Contributors, as well as any or all Internal Modules.
Module: means a set of sources files including their documentation that
enables supplementary functions or services in addition to those offered
by the Software.
External Module: means any or all Modules, not derived from the
Software, so that this Module and the Software run in separate address
spaces, with one calling the other when they are run.
Internal Module: means any or all Module, connected to the Software so
that they both execute in the same address space.
GNU GPL: means the GNU General Public License version 2 or any
subsequent version, as published by the Free Software Foundation Inc.
GNU Affero GPL: means the GNU Affero General Public License version 3 or
any subsequent version, as published by the Free Software Foundation Inc.
EUPL: means the European Union Public License version 1.1 or any
subsequent version, as published by the European Commission.
Parties: mean both the Licensee and the Licensor.
These expressions may be used both in singular and plural form.
Article 2 - PURPOSE
The purpose of the Agreement is the grant by the Licensor to the
Licensee of a non-exclusive, transferable and worldwide license for the
Software as set forth in Article 5 <#scope> hereinafter for the whole
term of the protection granted by the rights over said Software.
Article 3 - ACCEPTANCE
3.1 The Licensee shall be deemed as having accepted the terms and
conditions of this Agreement upon the occurrence of the first of the
following events:
* (i) loading the Software by any or all means, notably, by
downloading from a remote server, or by loading from a physical medium;
* (ii) the first time the Licensee exercises any of the rights granted
hereunder.
3.2 One copy of the Agreement, containing a notice relating to the
characteristics of the Software, to the limited warranty, and to the
fact that its use is restricted to experienced users has been provided
to the Licensee prior to its acceptance as set forth in Article 3.1
<#accepting> hereinabove, and the Licensee hereby acknowledges that it
has read and understood it.
Article 4 - EFFECTIVE DATE AND TERM
4.1 EFFECTIVE DATE
The Agreement shall become effective on the date when it is accepted by
the Licensee as set forth in Article 3.1 <#accepting>.
4.2 TERM
The Agreement shall remain in force for the entire legal term of
protection of the economic rights over the Software.
Article 5 - SCOPE OF RIGHTS GRANTED
The Licensor hereby grants to the Licensee, who accepts, the following
rights over the Software for any or all use, and for the term of the
Agreement, on the basis of the terms and conditions set forth hereinafter.
Besides, if the Licensor owns or comes to own one or more patents
protecting all or part of the functions of the Software or of its
components, the Licensor undertakes not to enforce the rights granted by
these patents against successive Licensees using, exploiting or
modifying the Software. If these patents are transferred, the Licensor
undertakes to have the transferees subscribe to the obligations set
forth in this paragraph.
5.1 RIGHT OF USE
The Licensee is authorized to use the Software, without any limitation
as to its fields of application, with it being hereinafter specified
that this comprises:
1. permanent or temporary reproduction of all or part of the Software
by any or all means and in any or all form.
2. loading, displaying, running, or storing the Software on any or all
medium.
3. entitlement to observe, study or test its operation so as to
determine the ideas and principles behind any or all constituent
elements of said Software. This shall apply when the Licensee
carries out any or all loading, displaying, running, transmission or
storage operation as regards the Software, that it is entitled to
carry out hereunder.
5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
The right to make Contributions includes the right to translate, adapt,
arrange, or make any or all modifications to the Software, and the right
to reproduce the resulting software.
The Licensee is authorized to make any or all Contributions to the
Software provided that it includes an explicit notice that it is the
author of said Contribution and indicates the date of the creation thereof.
5.3 RIGHT OF DISTRIBUTION
In particular, the right of distribution includes the right to publish,
transmit and communicate the Software to the general public on any or
all medium, and by any or all means, and the right to market, either in
consideration of a fee, or free of charge, one or more copies of the
Software by any means.
The Licensee is further authorized to distribute copies of the modified
or unmodified Software to third parties according to the terms and
conditions set forth hereinafter.
5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
The Licensee is authorized to distribute true copies of the Software in
Source Code or Object Code form, provided that said distribution
complies with all the provisions of the Agreement and is accompanied by:
1. a copy of the Agreement,
2. a notice relating to the limitation of both the Licensor's warranty
and liability as set forth in Articles 8 and 9,
and that, in the event that only the Object Code of the Software is
redistributed, the Licensee allows effective access to the full Source
Code of the Software for a period of at least three years from the
distribution of the Software, it being understood that the additional
acquisition cost of the Source Code shall not exceed the cost of the
data transfer.
5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
When the Licensee makes a Contribution to the Software, the terms and
conditions for the distribution of the resulting Modified Software
become subject to all the provisions of this Agreement.
The Licensee is authorized to distribute the Modified Software, in
source code or object code form, provided that said distribution
complies with all the provisions of the Agreement and is accompanied by:
1. a copy of the Agreement,
2. a notice relating to the limitation of both the Licensor's warranty
and liability as set forth in Articles 8 and 9,
and, in the event that only the object code of the Modified Software is
redistributed,
3. a note stating the conditions of effective access to the full source
code of the Modified Software for a period of at least three years
from the distribution of the Modified Software, it being understood
that the additional acquisition cost of the source code shall not
exceed the cost of the data transfer.
5.3.3 DISTRIBUTION OF EXTERNAL MODULES
When the Licensee has developed an External Module, the terms and
conditions of this Agreement do not apply to said External Module, that
may be distributed under a separate license agreement.
5.3.4 COMPATIBILITY WITH OTHER LICENSES
The Licensee can include a code that is subject to the provisions of one
of the versions of the GNU GPL, GNU Affero GPL and/or EUPL in the
Modified or unmodified Software, and distribute that entire code under
the terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
The Licensee can include the Modified or unmodified Software in a code
that is subject to the provisions of one of the versions of the GNU GPL,
GNU Affero GPL and/or EUPL and distribute that entire code under the
terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
Article 6 - INTELLECTUAL PROPERTY
6.1 OVER THE INITIAL SOFTWARE
The Holder owns the economic rights over the Initial Software. Any or
all use of the Initial Software is subject to compliance with the terms
and conditions under which the Holder has elected to distribute its work
and no one shall be entitled to modify the terms and conditions for the
distribution of said Initial Software.
The Holder undertakes that the Initial Software will remain ruled at
least by this Agreement, for the duration set forth in Article 4.2 <#term>.
6.2 OVER THE CONTRIBUTIONS
The Licensee who develops a Contribution is the owner of the
intellectual property rights over this Contribution as defined by
applicable law.
6.3 OVER THE EXTERNAL MODULES
The Licensee who develops an External Module is the owner of the
intellectual property rights over this External Module as defined by
applicable law and is free to choose the type of agreement that shall
govern its distribution.
6.4 JOINT PROVISIONS
The Licensee expressly undertakes:
1. not to remove, or modify, in any manner, the intellectual property
notices attached to the Software;
2. to reproduce said notices, in an identical manner, in the copies of
the Software modified or not.
The Licensee undertakes not to directly or indirectly infringe the
intellectual property rights on the Software of the Holder and/or
Contributors, and to take, where applicable, vis-à-vis its staff, any
and all measures required to ensure respect of said intellectual
property rights of the Holder and/or Contributors.
Article 7 - RELATED SERVICES
7.1 Under no circumstances shall the Agreement oblige the Licensor to
provide technical assistance or maintenance services for the Software.
However, the Licensor is entitled to offer this type of services. The
terms and conditions of such technical assistance, and/or such
maintenance, shall be set forth in a separate instrument. Only the
Licensor offering said maintenance and/or technical assistance services
shall incur liability therefor.
7.2 Similarly, any Licensor is entitled to offer to its licensees, under
its sole responsibility, a warranty, that shall only be binding upon
itself, for the redistribution of the Software and/or the Modified
Software, under terms and conditions that it is free to decide. Said
warranty, and the financial terms and conditions of its application,
shall be subject of a separate instrument executed between the Licensor
and the Licensee.
Article 8 - LIABILITY
8.1 Subject to the provisions of Article 8.2, the Licensee shall be
entitled to claim compensation for any direct loss it may have suffered
from the Software as a result of a fault on the part of the relevant
Licensor, subject to providing evidence thereof.
8.2 The Licensor's liability is limited to the commitments made under
this Agreement and shall not be incurred as a result of in particular:
(i) loss due the Licensee's total or partial failure to fulfill its
obligations, (ii) direct or consequential loss that is suffered by the
Licensee due to the use or performance of the Software, and (iii) more
generally, any consequential loss. In particular the Parties expressly
agree that any or all pecuniary or business loss (i.e. loss of data,
loss of profits, operating loss, loss of customers or orders,
opportunity cost, any disturbance to business activities) or any or all
legal proceedings instituted against the Licensee by a third party,
shall constitute consequential loss and shall not provide entitlement to
any or all compensation from the Licensor.
Article 9 - WARRANTY
9.1 The Licensee acknowledges that the scientific and technical
state-of-the-art when the Software was distributed did not enable all
possible uses to be tested and verified, nor for the presence of
possible defects to be detected. In this respect, the Licensee's
attention has been drawn to the risks associated with loading, using,
modifying and/or developing and reproducing the Software which are
reserved for experienced users.
The Licensee shall be responsible for verifying, by any or all means,
the suitability of the product for its requirements, its good working
order, and for ensuring that it shall not cause damage to either persons
or properties.
9.2 The Licensor hereby represents, in good faith, that it is entitled
to grant all the rights over the Software (including in particular the
rights set forth in Article 5 <#scope>).
9.3 The Licensee acknowledges that the Software is supplied "as is" by
the Licensor without any other express or tacit warranty, other than
that provided for in Article 9.2 <#good-faith> and, in particular,
without any warranty as to its commercial value, its secured, safe,
innovative or relevant nature.
Specifically, the Licensor does not warrant that the Software is free
from any error, that it will operate without interruption, that it will
be compatible with the Licensee's own equipment and software
configuration, nor that it will meet the Licensee's requirements.
9.4 The Licensor does not either expressly or tacitly warrant that the
Software does not infringe any third party intellectual property right
relating to a patent, software or any other property right. Therefore,
the Licensor disclaims any and all liability towards the Licensee
arising out of any or all proceedings for infringement that may be
instituted in respect of the use, modification and redistribution of the
Software. Nevertheless, should such proceedings be instituted against
the Licensee, the Licensor shall provide it with technical and legal
expertise for its defense. Such technical and legal expertise shall be
decided on a case-by-case basis between the relevant Licensor and the
Licensee pursuant to a memorandum of understanding. The Licensor
disclaims any and all liability as regards the Licensee's use of the
name of the Software. No warranty is given as regards the existence of
prior rights over the name of the Software or as regards the existence
of a trademark.
Article 10 - TERMINATION
10.1 In the event of a breach by the Licensee of its obligations
hereunder, the Licensor may automatically terminate this Agreement
thirty (30) days after notice has been sent to the Licensee and has
remained ineffective.
10.2 A Licensee whose Agreement is terminated shall no longer be
authorized to use, modify or distribute the Software. However, any
licenses that it may have granted prior to termination of the Agreement
shall remain valid subject to their having been granted in compliance
with the terms and conditions hereof.
Article 11 - MISCELLANEOUS
11.1 EXCUSABLE EVENTS
Neither Party shall be liable for any or all delay, or failure to
perform the Agreement, that may be attributable to an event of force
majeure, an act of God or an outside cause, such as defective
functioning or interruptions of the electricity or telecommunications
networks, network paralysis following a virus attack, intervention by
government authorities, natural disasters, water damage, earthquakes,
fire, explosions, strikes and labor unrest, war, etc.
11.2 Any failure by either Party, on one or more occasions, to invoke
one or more of the provisions hereof, shall under no circumstances be
interpreted as being a waiver by the interested Party of its right to
invoke said provision(s) subsequently.
11.3 The Agreement cancels and replaces any or all previous agreements,
whether written or oral, between the Parties and having the same
purpose, and constitutes the entirety of the agreement between said
Parties concerning said purpose. No supplement or modification to the
terms and conditions hereof shall be effective as between the Parties
unless it is made in writing and signed by their duly authorized
representatives.
11.4 In the event that one or more of the provisions hereof were to
conflict with a current or future applicable act or legislative text,
said act or legislative text shall prevail, and the Parties shall make
the necessary amendments so as to comply with said act or legislative
text. All other provisions shall remain effective. Similarly, invalidity
of a provision of the Agreement, for any reason whatsoever, shall not
cause the Agreement as a whole to be invalid.
11.5 LANGUAGE
The Agreement is drafted in both French and English and both versions
are deemed authentic.
Article 12 - NEW VERSIONS OF THE AGREEMENT
12.1 Any person is authorized to duplicate and distribute copies of this
Agreement.
12.2 So as to ensure coherence, the wording of this Agreement is
protected and may only be modified by the authors of the License, who
reserve the right to periodically publish updates or new versions of the
Agreement, each with a separate number. These subsequent versions may
address new issues encountered by Free Software.
12.3 Any Software distributed under a given version of the Agreement may
only be subsequently distributed under the same version of the Agreement
or a subsequent version, subject to the provisions of Article 5.3.4
<#compatibility>.
Article 13 - GOVERNING LAW AND JURISDICTION
13.1 The Agreement is governed by French law. The Parties agree to
endeavor to seek an amicable solution to any disagreements or disputes
that may arise during the performance of the Agreement.
13.2 Failing an amicable solution within two (2) months as from their
occurrence, and unless emergency proceedings are necessary, the
disagreements or disputes shall be referred to the Paris Courts having
jurisdiction, by the more diligent Party.

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GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
To protect your rights, we need to prevent others from denying you
these rights or asking you to surrender the rights. Therefore, you have
certain responsibilities if you distribute copies of the software, or if
you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must pass on to the recipients the same
freedoms that you received. You must make sure that they, too, receive
or can get the source code. And you must show them these terms so they
know their rights.
Developers that use the GNU GPL protect your rights with two steps:
(1) assert copyright on the software, and (2) offer you this License
giving you legal permission to copy, distribute and/or modify it.
For the developers' and authors' protection, the GPL clearly explains
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authors' sake, the GPL requires that modified versions be marked as
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Some devices are designed to deny users access to install or run
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pattern of such abuse occurs in the area of products for individuals to
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Finally, every program is threatened constantly by software patents.
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The precise terms and conditions for copying, distribution and
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TERMS AND CONDITIONS
0. Definitions.
"This License" refers to version 3 of the GNU General Public License.
"Copyright" also means copyright-like laws that apply to other kinds of
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"The Program" refers to any copyrightable work licensed under this
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An interactive user interface displays "Appropriate Legal Notices"
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feature that (1) displays an appropriate copyright notice, and (2)
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The "source code" for a work means the preferred form of the work
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The Corresponding Source need not include anything that users
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The Corresponding Source for a work in source code form is that
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All rights granted under this License are granted for the term of
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You may convey verbatim copies of the Program's source code as you
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and you may offer support or warranty protection for a fee.
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"Installation Information" for a User Product means any methods,
procedures, authorization keys, or other information required to install
and execute modified versions of a covered work in that User Product from
a modified version of its Corresponding Source. The information must
suffice to ensure that the continued functioning of the modified object
code is in no case prevented or interfered with solely because
modification has been made.
If you convey an object code work under this section in, or with, or
specifically for use in, a User Product, and the conveying occurs as
part of a transaction in which the right of possession and use of the
User Product is transferred to the recipient in perpetuity or for a
fixed term (regardless of how the transaction is characterized), the
Corresponding Source conveyed under this section must be accompanied
by the Installation Information. But this requirement does not apply
if neither you nor any third party retains the ability to install
modified object code on the User Product (for example, the work has
been installed in ROM).
The requirement to provide Installation Information does not include a
requirement to continue to provide support service, warranty, or updates
for a work that has been modified or installed by the recipient, or for
the User Product in which it has been modified or installed. Access to a
network may be denied when the modification itself materially and
adversely affects the operation of the network or violates the rules and
protocols for communication across the network.
Corresponding Source conveyed, and Installation Information provided,
in accord with this section must be in a format that is publicly
documented (and with an implementation available to the public in
source code form), and must require no special password or key for
unpacking, reading or copying.
7. Additional Terms.
"Additional permissions" are terms that supplement the terms of this
License by making exceptions from one or more of its conditions.
Additional permissions that are applicable to the entire Program shall
be treated as though they were included in this License, to the extent
that they are valid under applicable law. If additional permissions
apply only to part of the Program, that part may be used separately
under those permissions, but the entire Program remains governed by
this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option
remove any additional permissions from that copy, or from any part of
it. (Additional permissions may be written to require their own
removal in certain cases when you modify the work.) You may place
additional permissions on material, added by you to a covered work,
for which you have or can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you
add to a covered work, you may (if authorized by the copyright holders of
that material) supplement the terms of this License with terms:
a) Disclaiming warranty or limiting liability differently from the
terms of sections 15 and 16 of this License; or
b) Requiring preservation of specified reasonable legal notices or
author attributions in that material or in the Appropriate Legal
Notices displayed by works containing it; or
c) Prohibiting misrepresentation of the origin of that material, or
requiring that modified versions of such material be marked in
reasonable ways as different from the original version; or
d) Limiting the use for publicity purposes of names of licensors or
authors of the material; or
e) Declining to grant rights under trademark law for use of some
trade names, trademarks, or service marks; or
f) Requiring indemnification of licensors and authors of that
material by anyone who conveys the material (or modified versions of
it) with contractual assumptions of liability to the recipient, for
any liability that these contractual assumptions directly impose on
those licensors and authors.
All other non-permissive additional terms are considered "further
restrictions" within the meaning of section 10. If the Program as you
received it, or any part of it, contains a notice stating that it is
governed by this License along with a term that is a further
restriction, you may remove that term. If a license document contains
a further restriction but permits relicensing or conveying under this
License, you may add to a covered work material governed by the terms
of that license document, provided that the further restriction does
not survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you
must place, in the relevant source files, a statement of the
additional terms that apply to those files, or a notice indicating
where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the
form of a separately written license, or stated as exceptions;
the above requirements apply either way.
8. Termination.
You may not propagate or modify a covered work except as expressly
provided under this License. Any attempt otherwise to propagate or
modify it is void, and will automatically terminate your rights under
this License (including any patent licenses granted under the third
paragraph of section 11).
However, if you cease all violation of this License, then your
license from a particular copyright holder is reinstated (a)
provisionally, unless and until the copyright holder explicitly and
finally terminates your license, and (b) permanently, if the copyright
holder fails to notify you of the violation by some reasonable means
prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is