[med-svn] [Git][med-team/simka][master] 8 commits: New upstream version 1.5.3
Andreas Tille
gitlab at salsa.debian.org
Thu Jan 28 11:25:59 GMT 2021
Andreas Tille pushed to branch master at Debian Med / simka
Commits:
58cf2947 by Andreas Tille at 2021-01-28T12:19:41+01:00
New upstream version 1.5.3
- - - - -
fe922b21 by Andreas Tille at 2021-01-28T12:19:41+01:00
routine-update: New upstream version
- - - - -
1369f3ce by Andreas Tille at 2021-01-28T12:19:41+01:00
Update upstream source from tag 'upstream/1.5.3'
Update to upstream version '1.5.3'
with Debian dir d274cb9cc620c19a62496b3e5aaf14e84d27ac48
- - - - -
2837f9ce by Andreas Tille at 2021-01-28T12:19:42+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
3a5fdb11 by Andreas Tille at 2021-01-28T12:19:44+01:00
routine-update: Add salsa-ci file
- - - - -
d4196343 by Andreas Tille at 2021-01-28T12:19:44+01:00
routine-update: Rules-Requires-Root: no
- - - - -
d602bce2 by Andreas Tille at 2021-01-28T12:19:45+01:00
Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
- - - - -
b03c77a6 by Andreas Tille at 2021-01-28T12:21:43+01:00
Update patches
- - - - -
19 changed files:
- + .devcontainer/Dockerfile
- + .devcontainer/devcontainer.json
- + .gitlab-ci.yml
- CMakeLists.txt
- README.md
- debian/changelog
- debian/control
- debian/patches/fix_test_path.patch
- debian/patches/use_debian_packaged_libraries.patch
- debian/rules
- + debian/salsa-ci.yml
- + doc/CMakeLists.txt
- + doc/doxygen/doxygen.css
- + doc/doxygen/gatb-simka.doxyfile
- example/simple_test.sh
- + scripts/sonarqube_diags/Dockerfile.sq
- + scripts/sonarqube_diags/analysis.sh
- + sonar-project.properties
- src/SimkaPotara.hpp
Changes:
=====================================
.devcontainer/Dockerfile
=====================================
@@ -0,0 +1,36 @@
+#-------------------------------------------------------------------------------------------------------------
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
+#-------------------------------------------------------------------------------------------------------------
+
+FROM mcr.microsoft.com/vscode/devcontainers/base:0-buster
+
+# This Dockerfile's base image has a non-root user with sudo access. Use the "remoteUser"
+# property in devcontainer.json to use it. On Linux, the container user's GID/UIDs
+# will be updated to match your local UID/GID (when using the dockerFile property).
+# See https://aka.ms/vscode-remote/containers/non-root-user for details.
+ARG USERNAME=vscode
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+
+# Configure apt and install packages
+RUN apt-get update \
+ && export DEBIAN_FRONTEND=noninteractive \
+ #
+ # Install C++ tools
+ && apt-get -y install build-essential cmake cppcheck valgrind \
+ #
+ # Additions for GATB and Simka
+ && apt-get -y install zlib1g-dev doxygen graphviz ack vim \
+ #
+ # [Optional] Update UID/GID if needed
+ && if [ "$USER_GID" != "1000" ] || [ "$USER_UID" != "1000" ]; then \
+ groupmod --gid $USER_GID $USERNAME \
+ && usermod --uid $USER_UID --gid $USER_GID $USERNAME \
+ && chown -R $USER_UID:$USER_GID /home/$USERNAME; \
+ fi \
+ #
+ # Clean up
+ && apt-get autoremove -y \
+ && apt-get clean -y \
+ && rm -rf /var/lib/apt/lists/*
=====================================
.devcontainer/devcontainer.json
=====================================
@@ -0,0 +1,27 @@
+// For format details, see https://aka.ms/vscode-remote/devcontainer.json or this file's README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.128.0/containers/cpp
+{
+ "name": "GATB/Simka remote development container",
+ "dockerFile": "Dockerfile",
+ "runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined"],
+
+ // Set *default* container specific settings.json values on container create.
+ "settings": {
+ "terminal.integrated.shell.linux": "/bin/bash"
+ },
+
+ // Add the IDs of extensions you want installed when the container is created.
+ "extensions": [
+ "ms-vscode.cpptools"
+ ]
+
+ // Use 'forwardPorts' to make a list of ports inside the container available locally.
+ // "forwardPorts": [],
+
+ // Use 'postCreateCommand' to run commands after the container is created.
+ // "postCreateCommand": "gcc -v",
+
+ // Uncomment to connect as a non-root user. See https://aka.ms/vscode-remote/containers/non-root.
+ // "remoteUser": "vscode"
+
+}
\ No newline at end of file
=====================================
.gitlab-ci.yml
=====================================
@@ -0,0 +1,92 @@
+stages:
+ - update_simka_sq_image
+ - analysis
+ - aggregate
+ - deploy
+
+variables:
+ GIT_SUBMODULE_STRATEGY: recursive
+
+#########################################################################################################
+sonar:analysis:
+ stage: analysis
+ image: $CI_REGISTRY_IMAGE/simka_sq:latest
+ script:
+ - echo "Launching sonar:analysis diagnostics..."
+ - scripts/sonarqube_diags/analysis.sh > analysis.log
+ - mkdir -p public/doc
+ - mv coverage-html public/doc/lcov # for gitlabpages publication
+ tags:
+ #- simka-igrida
+ - large
+ cache: {}
+ artifacts:
+ paths:
+ - build/
+ - analyzer_reports/
+ - simka-scan-build-cmake.log
+ - simka-scan-build-make.log
+ - gcov.xml
+ - simka-clang-tidy-report.log
+ - compile_commands.json
+ - simka-cppcheck.xml
+ - simka-rats.xml
+ - analysis.log
+ - public/
+ when: always # useful to debug
+ expire_in: 5 days
+
+
+
+#########################################################################################################
+sonar:aggregate:
+ stage: aggregate
+ image: $CI_REGISTRY_IMAGE/simka_sq:latest
+ script:
+ - echo "Launching sonar:aggregate task..."
+ - echo "====================="; pwd; ls -atlhrsF; echo "====================="
+ - ls analyzer_reports/*/*.plist
+ - sonar-scanner -X -Dsonar.login=$SONARQUBE_LOGIN -Dsonar.verbose=true &> sonar-scanner.log
+ tags:
+ #- simka-igrida
+ artifacts:
+ paths:
+ - sonar-scanner.log
+ when: always # useful to debug
+ expire_in: 5 days
+
+##################################################################################################################################################################################################################
+# Ref. https://gitlab.inria.fr/help/ci/docker/using_docker_build.md#making-docker-in-docker-builds-faster-with-docker-layer-caching
+update_simka_sq_image:
+ stage: update_simka_sq_image
+ image: docker
+ tags:
+ #- simka-igrida
+ - large
+ services:
+ - docker:19.03.12-dind
+ script:
+ - echo "Launching update_ci_image job..."
+ - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+ - docker pull $CI_REGISTRY_IMAGE/simka_sq:latest || true
+ - docker --version
+ - cd scripts/sonarqube_diags
+ - docker build -f Dockerfile.sq --cache-from $CI_REGISTRY_IMAGE/simka_sq:latest --tag $CI_REGISTRY_IMAGE/simka_sq:latest .
+ - docker push $CI_REGISTRY_IMAGE/simka_sq:latest
+ - docker image ls
+ when: manual
+
+pages:
+ image: $CI_REGISTRY_IMAGE/simka_sq:latest
+ stage: deploy
+ script:
+ - mkdir -p public/doc
+ - test -d build || mkdir build
+ - cd build
+ - cmake --target doc-gatb-simka ..
+ - make doc-gatb-simka
+ - mv doc/html ../public/doc/doxygen
+ artifacts:
+ paths:
+ - public
+
=====================================
CMakeLists.txt
=====================================
@@ -7,7 +7,7 @@ cmake_minimum_required(VERSION 2.6)
################################################################################
SET (gatb-tool_VERSION_MAJOR 1)
SET (gatb-tool_VERSION_MINOR 5)
-SET (gatb-tool_VERSION_PATCH 2)
+SET (gatb-tool_VERSION_PATCH 3)
IF (DEFINED MAJOR)
SET (gatb-tool_VERSION_MAJOR ${MAJOR})
@@ -91,6 +91,13 @@ target_link_libraries (simkaMerge ${gatb-core-libraries})
add_executable (simkaMinCore src/simkaMin/SimkaMin.cpp ${SimkaMinFiles})
target_link_libraries (simkaMinCore ${gatb-core-libraries})
+################################################################################
+# DOCUMENTATION GENERATION
+################################################################################
+IF (EXISTS "${PROJECT_SOURCE_DIR}/doc")
+ ADD_SUBDIRECTORY(doc EXCLUDE_FROM_ALL)
+ENDIF()
+
################################################################################
# PACKAGING
################################################################################
=====================================
README.md
=====================================
@@ -1,15 +1,43 @@
-# Simka & SimkaMin
+
+<details>
+ <summary markdown="span">Table of contents</summary>
+
+ [[_TOC_]]
+</details>
+
+# Simka & SimkaMin
+
+[](http://www.gnu.org/licenses/agpl-3.0.en.html)
+
+
+> This directory stores Simka and SimkaMin software. This readme focuses on Simka features. All information about SimkaMin is located in the [simkaMin](simkaMin/) directory.
+
+
+# Continuous integration status (master branch)
+
+### Build status
| **Linux** | **Mac OSX** |
|-----------|-------------|
-[](https://ci.inria.fr/gatb-core/view/Simka/job/tool-simka-build-debian7-64bits-gcc-4.7/) | [](https://ci.inria.fr/gatb-core/view/Simka/job/tool-simka-build-macos-10.9.5-gcc-4.2.1/)
+[](https://ci.inria.fr/gatb-core/view/Simka/job/tool-simka-build-debian7-64bits-gcc-4.7-gitlab/) | [](https://ci.inria.fr/gatb-core/view/Simka/job/tool-simka-build-macos-10.9.5-gcc-4.2.1-gitlab/)
-[](http://www.gnu.org/licenses/agpl-3.0.en.html)
+### SonarQube metrics
+<details>
+ <summary markdown="span">Click me to expand</summary>
-This github directory stores Simka and SimkaMin software. This readme focuses on Simka features. All information about SimkaMin is located in the [simkaMin](simkaMin/) directory.
+ [](https://sonarqube.inria.fr/sonarqube/component_measures?id=genscale%3Agatb%3Atools%3Asimka%3Agitlab%3Amaster&metric=ncloc)
+ [](https://sonarqube.inria.fr/sonarqube/component_measures?id=genscale%3Agatb%3Atools%3Asimka%3Agitlab%3Amaster&metric=comment_lines_density)
+ [](https://sonarqube.inria.fr/sonarqube/component_measures?id=genscale%3Agatb%3Atools%3Asimka%3Agitlab%3Amaster&metric=coverage)
+ [](https://sonarqube.inria.fr/sonarqube/component_measures?id=genscale%3Agatb%3Atools%3Asimka%3Agitlab%3Amaster&metric=bugs)
+ [](https://sonarqube.inria.fr/sonarqube/component_measures?id=genscale%3Agatb%3Atools%3Asimka%3Agitlab%3Amaster&metric=vulnerabilities)
+ [](https://sonarqube.inria.fr/sonarqube/component_measures?id=genscale%3Agatb%3Atools%3Asimka%3Agitlab%3Amaster&metric=code_smells)
+ [](https://sonarqube.inria.fr/sonarqube/component_measures?id=genscale%3Agatb%3Atools%3Asimka%3Agitlab%3Amaster&metric=new_bugs)
+ [](https://sonarqube.inria.fr/sonarqube/component_measures?id=genscale%3Agatb%3Atools%3Asimka%3Agitlab%3Amaster&metric=new_vulnerabilities)
+ [](https://sonarqube.inria.fr/sonarqube/component_measures?id=genscale%3Agatb%3Atools%3Asimka%3Agitlab%3Amaster&metric=new_code_smells)
+</details>
# What is Simka?
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+simka (1.5.3-1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.5.1 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Trim trailing whitespace.
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 Jan 2021 12:19:41 +0100
+
simka (1.5.2-1) unstable; urgency=medium
[ Andreas Tille ]
=====================================
debian/control
=====================================
@@ -12,10 +12,11 @@ Build-Depends: debhelper-compat (= 13),
python3-all,
dh-python,
chrpath
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/simka
Vcs-Git: https://salsa.debian.org/med-team/simka.git
Homepage: https://github.com/GATB/simka
+Rules-Requires-Root: no
Package: simka
Architecture: amd64 arm64 i386 ppc64el s390x hppa ia64 ppc64 riscv64 sparc64
=====================================
debian/patches/fix_test_path.patch
=====================================
@@ -3,9 +3,9 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-09-13
---
---- simka.orig/tests/simkaMin/test_simkaMin.py
-+++ simka/tests/simkaMin/test_simkaMin.py
-@@ -16,28 +16,28 @@
+--- a/tests/simkaMin/test_simkaMin.py
++++ b/tests/simkaMin/test_simkaMin.py
+@@ -16,28 +16,28 @@ NB_CORES = [1, 0]
def create_command(scriptFilename, outputPrefix, k, filter, nb_reads, nb_kmers, nb_cores, input_filename):
outputDir = "k" + str(k) + "_" + filter.replace("-", "") + "_" + str(nb_reads) + "-" + str(nb_kmers) + "_n" + str(nb_cores)
@@ -38,7 +38,7 @@ Last-Update: 2019-09-13
command += " -max-reads " + str(nb_reads)
command += " " + filter + " "
return command, outputDir
-@@ -48,7 +48,7 @@
+@@ -48,7 +48,7 @@ def create_truth():
for nb_reads in NB_READS:
for nb_kmers in NB_KMERS:
for nb_cores in NB_CORES:
@@ -47,7 +47,7 @@ Last-Update: 2019-09-13
print (command)
ret = os.system(command)
if ret != 0: exit(1)
-@@ -146,7 +146,7 @@
+@@ -146,7 +146,7 @@ def test():
for nb_reads in NB_READS:
for nb_kmers in NB_KMERS:
for nb_cores in NB_CORES:
@@ -56,7 +56,7 @@ Last-Update: 2019-09-13
print (command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
-@@ -166,25 +166,25 @@
+@@ -166,25 +166,25 @@ def test_append():
os.mkdir(out_dir)
merged_sketch_filename = os.path.join(out_dir, "merged_sketch.bin")
@@ -86,7 +86,7 @@ Last-Update: 2019-09-13
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
-@@ -194,12 +194,12 @@
+@@ -194,12 +194,12 @@ def test_append():
os.remove(filename_temp)
@@ -101,7 +101,7 @@ Last-Update: 2019-09-13
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
-@@ -223,10 +223,10 @@
+@@ -223,10 +223,10 @@ def test_matrix_update():
clear(out_dir)
os.mkdir(out_dir)
@@ -115,7 +115,7 @@ Last-Update: 2019-09-13
f2 = open(filename_temp2, "w")
N=2 #where to split the file
i=0
-@@ -241,13 +241,13 @@
+@@ -241,13 +241,13 @@ def test_matrix_update():
f2.close()
# init
@@ -131,9 +131,9 @@ Last-Update: 2019-09-13
print(command)
ret = os.system(command + suffix)
if ret != 0: exit(1)
---- simka.orig/tests/simple_test.py
-+++ simka/tests/simple_test.py
-@@ -91,7 +91,7 @@
+--- a/tests/simple_test.py
++++ b/tests/simple_test.py
+@@ -91,7 +91,7 @@ def test_parallelization():
#test k=31 t=0
clear()
print("TESTING k=31 t=0")
@@ -142,7 +142,7 @@ Last-Update: 2019-09-13
print(command)
os.system(command + suffix)
test_dists("results_k31_t0")
-@@ -99,7 +99,7 @@
+@@ -99,7 +99,7 @@ test_dists("results_k31_t0")
#test k=21 t=0
clear()
print("TESTING k=21 t=0")
@@ -151,7 +151,7 @@ Last-Update: 2019-09-13
print(command)
os.system(command + suffix)
test_dists("results_k21_t0")
-@@ -107,7 +107,7 @@
+@@ -107,7 +107,7 @@ test_dists("results_k21_t0")
#test k=31 t=2
clear()
print("TESTING k=31 t=2")
@@ -160,7 +160,7 @@ Last-Update: 2019-09-13
print(command)
os.system(command + suffix)
test_dists("results_k31_t2")
-@@ -115,7 +115,7 @@
+@@ -115,7 +115,7 @@ test_dists("results_k31_t2")
#test k=21 t=2
clear()
print("TESTING k=21 t=2")
@@ -169,7 +169,7 @@ Last-Update: 2019-09-13
print(command)
os.system(command + suffix)
test_dists("results_k21_t2")
-@@ -123,9 +123,9 @@
+@@ -123,9 +123,9 @@ test_dists("results_k21_t2")
#test resources 1
clear()
print("TESTING parallelization")
@@ -181,9 +181,9 @@ Last-Update: 2019-09-13
os.system(command + suffix)
test_parallelization()
---- simka.orig/example/simple_test.sh
-+++ simka/example/simple_test.sh
-@@ -3,23 +3,23 @@
+--- a/example/simple_test.sh
++++ b/example/simple_test.sh
+@@ -4,16 +4,7 @@ ADDITIONAL_SIMKA_OPTIONS=$*
# look for simka binary. In devel mode, it's in ../build/bin directory.
# In production mode, it's in ../bin directory.
@@ -197,26 +197,7 @@ Last-Update: 2019-09-13
- echo "could not find a compiled simka binary"
- exit 1
-fi
--
-+#if [ -f "../bin/simka" ]
-+#then
-+# bindir="../bin"
-+#elif [ -f "../build/bin/simka" ]
-+#then
-+# bindir="../build/bin"
-+#else
-+# echo "could not find a compiled simka binary"
-+# exit 1
-+#fi
+bindir="/usr/bin"
- # run simka
--command="$bindir/simka -in ../example/simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output"
-+command="simka -in simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output"
- #printf "$command\n\n"
-
- # DO NOT add lines between '$command' exec and 'var...' !
--$command
-+simka -in simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output
- var=$?
- printf "\n\n\n"
+ # run simka
+ command="$bindir/simka -in ../example/simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output $ADDITIONAL_SIMKA_OPTIONS"
=====================================
debian/patches/use_debian_packaged_libraries.patch
=====================================
@@ -4,11 +4,9 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-09-09
---
-Index: simka/CMakeLists.txt
-===================================================================
---- simka.orig/CMakeLists.txt 2019-09-16 14:56:48.756951860 +0100
-+++ simka/CMakeLists.txt 2019-09-16 14:57:02.785070784 +0100
-@@ -42,7 +42,10 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -42,7 +42,10 @@ SET (CMAKE_MODULE_PATH ${GATB_CORE_HOME}
SET (GATB_CORE_EXCLUDE_EXAMPLES 1)
# GATB CORE
@@ -20,7 +18,7 @@ Index: simka/CMakeLists.txt
################################################################################
# TOOL
-@@ -53,17 +56,22 @@
+@@ -53,17 +56,22 @@ add_definitions (${gatb-core-flags})
# we add a new compilation variable
if (PRINTALL)
@@ -45,7 +43,7 @@ Index: simka/CMakeLists.txt
configure_file (
${PROJECT_SOURCE_DIR}/src/core/SimkaAlgorithmTemplate.cpp.in
${PROJECT_BINARY_DIR}/src/core/template/SimkaAlgorithmTemplate_${KSIZE}.cpp
-@@ -78,18 +86,18 @@
+@@ -78,18 +86,18 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMA
set(PROJECT_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/bin)
add_executable (simka src/SimkaPotara.cpp ${ProjectFiles})
@@ -68,4 +66,4 @@ Index: simka/CMakeLists.txt
+target_link_libraries (simkaMinCore gatbcore hdf5 z pthread)
################################################################################
- # PACKAGING
+ # DOCUMENTATION GENERATION
=====================================
debian/rules
=====================================
@@ -34,4 +34,3 @@ override_dh_installman:
debian/simka/usr/share/man/man1/simkaMin_update.1
override_dh_missing:
-
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
doc/CMakeLists.txt
=====================================
@@ -0,0 +1,12 @@
+
+find_package (Doxygen)
+
+if (DOXYGEN_FOUND)
+
+ CONFIGURE_FILE (${CMAKE_CURRENT_SOURCE_DIR}/doxygen/gatb-simka.doxyfile ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+
+ ADD_CUSTOM_TARGET (doc-gatb-simka
+ ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+ )
+
+endif (DOXYGEN_FOUND)
=====================================
doc/doxygen/doxygen.css
=====================================
@@ -0,0 +1,1183 @@
+/* The standard CSS for doxygen $doxygenversion */
+
+body, table, div, p, dl {
+ font: 400 14px/19px Roboto,sans-serif;
+}
+
+/* @group Heading Levels */
+
+h1.groupheader {
+ font-size: 150%;
+}
+
+.title {
+ font-size: 250%;
+ font-weight: bold;
+ margin: 10px 2px;
+}
+
+h2.groupheader {
+ border-bottom: 1px solid ##99;
+ color: ##44;
+ font-size: 150%;
+ font-weight: normal;
+ margin-top: 1.75em;
+ padding-top: 8px;
+ padding-bottom: 4px;
+ width: 100%;
+}
+
+h3.groupheader {
+ font-size: 100%;
+}
+
+h1, h2, h3, h4, h5, h6 {
+ -webkit-transition: text-shadow 0.5s linear;
+ -moz-transition: text-shadow 0.5s linear;
+ -ms-transition: text-shadow 0.5s linear;
+ -o-transition: text-shadow 0.5s linear;
+ transition: text-shadow 0.5s linear;
+ margin-right: 15px;
+}
+
+h1.glow, h2.glow, h3.glow, h4.glow, h5.glow, h6.glow {
+ text-shadow: 0 0 15px cyan;
+}
+
+dt {
+ font-weight: bold;
+}
+
+div.multicol {
+ -moz-column-gap: 1em;
+ -webkit-column-gap: 1em;
+ -moz-column-count: 3;
+ -webkit-column-count: 3;
+}
+
+p.startli, p.startdd, p.starttd {
+ margin-top: 2px;
+}
+
+p.endli {
+ margin-bottom: 0px;
+}
+
+p.enddd {
+ margin-bottom: 4px;
+}
+
+p.endtd {
+ margin-bottom: 2px;
+}
+
+/* @end */
+
+caption {
+ font-weight: bold;
+}
+
+span.legend {
+ font-size: 70%;
+ text-align: center;
+}
+
+h3.version {
+ font-size: 90%;
+ text-align: center;
+}
+
+div.qindex, div.navtab{
+ background-color: ##ee;
+ border: 1px solid ##b0;
+ text-align: center;
+}
+
+div.qindex, div.navpath {
+ width: 100%;
+ line-height: 140%;
+}
+
+div.navtab {
+ margin-right: 15px;
+}
+
+/* @group Link Styling */
+
+a {
+ color: ##50;
+ font-weight: normal;
+ text-decoration: none;
+}
+
+.contents a:visited {
+ color: ##60;
+}
+
+a:hover {
+ text-decoration: underline;
+}
+
+a.qindex {
+ font-weight: bold;
+}
+
+a.qindexHL {
+ font-weight: bold;
+ background-color: ##AA;
+ color: #ffffff;
+ border: 1px double ##98;
+}
+
+.contents a.qindexHL:visited {
+ color: #ffffff;
+}
+
+a.el {
+ font-weight: bold;
+}
+
+a.elRef {
+}
+
+a.code, a.code:visited {
+ color: #4665A2;
+}
+
+a.codeRef, a.codeRef:visited {
+ color: #4665A2;
+}
+
+/* @end */
+
+dl.el {
+ margin-left: -1cm;
+}
+
+pre.fragment {
+ border: 1px solid #C4CFE5;
+ background-color: #FBFCFD;
+ padding: 4px 6px;
+ margin: 4px 8px 4px 2px;
+ overflow: auto;
+ word-wrap: break-word;
+ font-size: 9pt;
+ line-height: 125%;
+ font-family: monospace, fixed;
+ font-size: 105%;
+}
+
+div.fragment {
+ padding: 10px;
+ margin: 10px;
+ background-color: #FFFEFA;
+ border: 1px solid #C4CFE5;
+}
+
+div.line {
+ font-family: monospace, fixed;
+ font-size: 13px;
+ min-height: 13px;
+ line-height: 1.0;
+ text-wrap: unrestricted;
+ white-space: -moz-pre-wrap; /* Moz */
+ white-space: -pre-wrap; /* Opera 4-6 */
+ white-space: -o-pre-wrap; /* Opera 7 */
+ white-space: pre-wrap; /* CSS3 */
+ word-wrap: break-word; /* IE 5.5+ */
+ text-indent: -53px;
+ padding-left: 53px;
+ padding-bottom: 0px;
+ margin: 0px;
+ -webkit-transition-property: background-color, box-shadow;
+ -webkit-transition-duration: 0.5s;
+ -moz-transition-property: background-color, box-shadow;
+ -moz-transition-duration: 0.5s;
+ -ms-transition-property: background-color, box-shadow;
+ -ms-transition-duration: 0.5s;
+ -o-transition-property: background-color, box-shadow;
+ -o-transition-duration: 0.5s;
+ transition-property: background-color, box-shadow;
+ transition-duration: 0.5s;
+}
+
+div.line.glow {
+ background-color: cyan;
+ box-shadow: 0 0 10px cyan;
+}
+
+
+span.lineno {
+ padding-right: 4px;
+ text-align: right;
+ border-right: 2px solid #0F0;
+ background-color: #E8E8E8;
+ white-space: pre;
+}
+span.lineno a {
+ background-color: #D8D8D8;
+}
+
+span.lineno a:hover {
+ background-color: #C8C8C8;
+}
+
+div.ah {
+ background-color: black;
+ font-weight: bold;
+ color: #ffffff;
+ margin-bottom: 3px;
+ margin-top: 3px;
+ padding: 0.2em;
+ border: solid thin #333;
+ border-radius: 0.5em;
+ -webkit-border-radius: .5em;
+ -moz-border-radius: .5em;
+ box-shadow: 2px 2px 3px #999;
+ -webkit-box-shadow: 2px 2px 3px #999;
+ -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+ background-image: -webkit-gradient(linear, left top, left bottom, from(#eee), to(#000),color-stop(0.3, #444));
+ background-image: -moz-linear-gradient(center top, #eee 0%, #444 40%, #000);
+}
+
+div.groupHeader {
+ margin-left: 16px;
+ margin-top: 12px;
+ font-weight: bold;
+}
+
+div.groupText {
+ margin-left: 16px;
+ font-style: italic;
+}
+
+body {
+ background-color: white;
+ color: black;
+ margin: 0;
+}
+
+div.contents {
+ margin-top: 10px;
+ margin-left: 12px;
+ margin-right: 8px;
+}
+
+td.indexkey {
+ background-color: ##ee;
+ font-weight: bold;
+ border: 1px solid ##cc;
+ margin: 2px 0px 2px 0;
+ padding: 2px 10px;
+ white-space: nowrap;
+ vertical-align: top;
+}
+
+td.indexvalue {
+ background-color: ##ee;
+ border: 1px solid ##cc;
+ padding: 2px 10px;
+ margin: 2px 0px;
+}
+
+tr.memlist {
+ background-color: ##f0;
+}
+
+p.formulaDsp {
+ text-align: center;
+}
+
+img.formulaDsp {
+
+}
+
+img.formulaInl {
+ vertical-align: middle;
+}
+
+div.center {
+ text-align: center;
+ margin-top: 0px;
+ margin-bottom: 0px;
+ padding: 0px;
+}
+
+div.center img {
+ border: 0px;
+}
+
+address.footer {
+ text-align: right;
+ padding-right: 12px;
+}
+
+img.footer {
+ border: 0px;
+ vertical-align: middle;
+}
+
+/* @group Code Colorization */
+
+span.keyword {
+ color: #545454
+}
+
+span.keywordtype {
+ color: #545454
+}
+
+span.keywordflow {
+ color: #545454
+}
+
+span.comment {
+ color: #2B7A2B
+}
+
+span.preprocessor {
+ color: #545454
+}
+
+span.stringliteral {
+ color: #545454
+}
+
+span.charliteral {
+ color: #545454
+}
+
+span.vhdldigit {
+ color: #ff00ff
+}
+
+span.vhdlchar {
+ color: #000000
+}
+
+span.vhdlkeyword {
+ color: #700070
+}
+
+span.vhdllogic {
+ color: #ff0000
+}
+
+blockquote {
+ background-color: ##F8;
+ border-left: 2px solid ##FF;
+ margin: 0 24px 0 4px;
+ padding: 0 12px 0 16px;
+}
+
+/* @end */
+
+/*
+.search {
+ color: #003399;
+ font-weight: bold;
+}
+
+form.search {
+ margin-bottom: 0px;
+ margin-top: 0px;
+}
+
+input.search {
+ font-size: 75%;
+ color: #000080;
+ font-weight: normal;
+ background-color: #e8eef2;
+}
+*/
+
+td.tiny {
+ font-size: 75%;
+}
+
+.dirtab {
+ padding: 4px;
+ border-collapse: collapse;
+ border: 1px solid ##b0;
+}
+
+th.dirtab {
+ background: ##ee;
+ font-weight: bold;
+}
+
+hr {
+ height: 0px;
+ border: none;
+ border-top: 1px solid ##66;
+}
+
+hr.footer {
+ height: 1px;
+}
+
+/* @group Member Descriptions */
+
+table.memberdecls {
+ border-spacing: 0px;
+ padding: 0px;
+}
+
+.memberdecls td, .fieldtable tr {
+ -webkit-transition-property: background-color, box-shadow;
+ -webkit-transition-duration: 0.5s;
+ -moz-transition-property: background-color, box-shadow;
+ -moz-transition-duration: 0.5s;
+ -ms-transition-property: background-color, box-shadow;
+ -ms-transition-duration: 0.5s;
+ -o-transition-property: background-color, box-shadow;
+ -o-transition-duration: 0.5s;
+ transition-property: background-color, box-shadow;
+ transition-duration: 0.5s;
+}
+
+.memberdecls td.glow, .fieldtable tr.glow {
+ background-color: cyan;
+ box-shadow: 0 0 15px cyan;
+}
+
+.mdescLeft, .mdescRight,
+.memItemLeft, .memItemRight,
+.memTemplItemLeft, .memTemplItemRight, .memTemplParams {
+ background-color: ##FA;
+ border: none;
+ margin: 4px;
+ padding: 1px 0 0 8px;
+}
+
+.mdescLeft, .mdescRight {
+ padding: 0px 8px 4px 8px;
+ color: #555;
+}
+
+.memSeparator {
+ border-bottom: 1px solid #DEE4F0;
+ line-height: 1px;
+ margin: 0px;
+ padding: 0px;
+}
+
+.memItemLeft, .memTemplItemLeft {
+ white-space: nowrap;
+}
+
+.memItemRight {
+ width: 100%;
+}
+
+.memTemplParams {
+ color: ##60;
+ white-space: nowrap;
+ font-size: 80%;
+}
+
+/* @end */
+
+/* @group Member Details */
+
+/* Styles for detailed member documentation */
+
+.memtemplate {
+ font-size: 80%;
+ color: ##60;
+ font-weight: normal;
+ margin-left: 9px;
+}
+
+.memnav {
+ background-color: ##ee;
+ border: 1px solid ##b0;
+ text-align: center;
+ margin: 2px;
+ margin-right: 15px;
+ padding: 2px;
+}
+
+.mempage {
+ width: 100%;
+}
+
+.memitem {
+ padding: 0;
+ margin-bottom: 10px;
+ margin-right: 5px;
+ -webkit-transition: box-shadow 0.5s linear;
+ -moz-transition: box-shadow 0.5s linear;
+ -ms-transition: box-shadow 0.5s linear;
+ -o-transition: box-shadow 0.5s linear;
+ transition: box-shadow 0.5s linear;
+ display: table !important;
+ width: 100%;
+}
+
+.memitem.glow {
+ box-shadow: 0 0 15px cyan;
+}
+
+.memname {
+ font-weight: bold;
+ margin-left: 6px;
+}
+
+.memname td {
+ vertical-align: bottom;
+}
+
+.memproto, dl.reflist dt {
+ border-top: 1px solid ##B4;
+ border-left: 1px solid ##B4;
+ border-right: 1px solid ##B4;
+ padding: 6px 0px 6px 0px;
+ color: ##2b;
+ font-weight: bold;
+ text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+ background-image:url('nav_f.png');
+ background-repeat:repeat-x;
+ background-color: ##E6;
+ /* opera specific markup */
+ box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+ border-top-right-radius: 4px;
+ border-top-left-radius: 4px;
+ /* firefox specific markup */
+ -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+ -moz-border-radius-topright: 4px;
+ -moz-border-radius-topleft: 4px;
+ /* webkit specific markup */
+ -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+ -webkit-border-top-right-radius: 4px;
+ -webkit-border-top-left-radius: 4px;
+
+}
+
+.memdoc, dl.reflist dd {
+ border-bottom: 1px solid ##B4;
+ border-left: 1px solid ##B4;
+ border-right: 1px solid ##B4;
+ padding: 6px 10px 2px 10px;
+ background-color: ##FC;
+ border-top-width: 0;
+ background-image:url('nav_g.png');
+ background-repeat:repeat-x;
+ background-color: #FFFFFF;
+ /* opera specific markup */
+ border-bottom-left-radius: 4px;
+ border-bottom-right-radius: 4px;
+ box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+ /* firefox specific markup */
+ -moz-border-radius-bottomleft: 4px;
+ -moz-border-radius-bottomright: 4px;
+ -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+ /* webkit specific markup */
+ -webkit-border-bottom-left-radius: 4px;
+ -webkit-border-bottom-right-radius: 4px;
+ -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+}
+
+dl.reflist dt {
+ padding: 5px;
+}
+
+dl.reflist dd {
+ margin: 0px 0px 10px 0px;
+ padding: 5px;
+}
+
+.paramkey {
+ text-align: right;
+}
+
+.paramtype {
+ white-space: nowrap;
+}
+
+.paramname {
+ color: #602020;
+ white-space: nowrap;
+}
+.paramname em {
+ font-style: normal;
+}
+.paramname code {
+ line-height: 14px;
+}
+
+.params, .retval, .exception, .tparams {
+ margin-left: 0px;
+ padding-left: 0px;
+}
+
+.params .paramname, .retval .paramname {
+ font-weight: bold;
+ vertical-align: top;
+}
+
+.params .paramtype {
+ font-style: italic;
+ vertical-align: top;
+}
+
+.params .paramdir {
+ font-family: "courier new",courier,monospace;
+ vertical-align: top;
+}
+
+table.mlabels {
+ border-spacing: 0px;
+}
+
+td.mlabels-left {
+ width: 100%;
+ padding: 0px;
+}
+
+td.mlabels-right {
+ vertical-align: bottom;
+ padding: 0px;
+ white-space: nowrap;
+}
+
+span.mlabels {
+ margin-left: 8px;
+}
+
+span.mlabel {
+ background-color: ##88;
+ border-top:1px solid ##70;
+ border-left:1px solid ##70;
+ border-right:1px solid ##CC;
+ border-bottom:1px solid ##CC;
+ text-shadow: none;
+ color: white;
+ margin-right: 4px;
+ padding: 2px 3px;
+ border-radius: 3px;
+ font-size: 7pt;
+ white-space: nowrap;
+ vertical-align: middle;
+}
+
+
+
+/* @end */
+
+/* these are for tree view when not used as main index */
+
+div.directory {
+ margin: 10px 0px;
+ border-top: 1px solid #A8B8D9;
+ border-bottom: 1px solid #A8B8D9;
+ width: 100%;
+}
+
+.directory table {
+ border-collapse:collapse;
+}
+
+.directory td {
+ margin: 0px;
+ padding: 0px;
+ vertical-align: top;
+}
+
+.directory td.entry {
+ white-space: nowrap;
+ padding-right: 6px;
+}
+
+.directory td.entry a {
+ outline:none;
+}
+
+.directory td.entry a img {
+ border: none;
+}
+
+.directory td.desc {
+ width: 100%;
+ padding-left: 6px;
+ padding-right: 6px;
+ padding-top: 3px;
+ border-left: 1px solid rgba(0,0,0,0.05);
+}
+
+.directory tr.even {
+ padding-left: 6px;
+ background-color: ##F8;
+}
+
+.directory img {
+ vertical-align: -30%;
+}
+
+.directory .levels {
+ white-space: nowrap;
+ width: 100%;
+ text-align: right;
+ font-size: 9pt;
+}
+
+.directory .levels span {
+ cursor: pointer;
+ padding-left: 2px;
+ padding-right: 2px;
+ color: ##50;
+}
+
+div.dynheader {
+ margin-top: 8px;
+ -webkit-touch-callout: none;
+ -webkit-user-select: none;
+ -khtml-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ user-select: none;
+}
+
+address {
+ font-style: normal;
+ color: ##33;
+}
+
+table.doxtable {
+ border-collapse:collapse;
+ margin-top: 4px;
+ margin-bottom: 4px;
+}
+
+table.doxtable td, table.doxtable th {
+ border: 1px solid ##37;
+ padding: 3px 7px 2px;
+}
+
+table.doxtable th {
+ background-color: ##47;
+ color: #FFFFFF;
+ font-size: 110%;
+ padding-bottom: 4px;
+ padding-top: 5px;
+}
+
+table.fieldtable {
+ /*width: 100%;*/
+ margin-bottom: 10px;
+ border: 1px solid ##B4;
+ border-spacing: 0px;
+ -moz-border-radius: 4px;
+ -webkit-border-radius: 4px;
+ border-radius: 4px;
+ -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+ -webkit-box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+ box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+}
+
+.fieldtable td, .fieldtable th {
+ padding: 3px 7px 2px;
+}
+
+.fieldtable td.fieldtype, .fieldtable td.fieldname {
+ white-space: nowrap;
+ border-right: 1px solid ##B4;
+ border-bottom: 1px solid ##B4;
+ vertical-align: top;
+}
+
+.fieldtable td.fieldname {
+ padding-top: 5px;
+}
+
+.fieldtable td.fielddoc {
+ border-bottom: 1px solid ##B4;
+ /*width: 100%;*/
+}
+
+.fieldtable td.fielddoc p:first-child {
+ margin-top: 2px;
+}
+
+.fieldtable td.fielddoc p:last-child {
+ margin-bottom: 2px;
+}
+
+.fieldtable tr:last-child td {
+ border-bottom: none;
+}
+
+.fieldtable th {
+ background-image:url('nav_f.png');
+ background-repeat:repeat-x;
+ background-color: ##E6;
+ font-size: 90%;
+ color: ##2B;
+ padding-bottom: 4px;
+ padding-top: 5px;
+ text-align:left;
+ -moz-border-radius-topleft: 4px;
+ -moz-border-radius-topright: 4px;
+ -webkit-border-top-left-radius: 4px;
+ -webkit-border-top-right-radius: 4px;
+ border-top-left-radius: 4px;
+ border-top-right-radius: 4px;
+ border-bottom: 1px solid ##B4;
+}
+
+
+.tabsearch {
+ top: 0px;
+ left: 10px;
+ height: 36px;
+ background-image: url('tab_b.png');
+ z-index: 101;
+ overflow: hidden;
+ font-size: 13px;
+}
+
+.navpath ul
+{
+ font-size: 11px;
+ background-image:url('tab_b.png');
+ background-repeat:repeat-x;
+ background-position: 0 -5px;
+ height:30px;
+ line-height:30px;
+ color:##9b;
+ border:solid 1px ##ca;
+ overflow:hidden;
+ margin:0px;
+ padding:0px;
+}
+
+.navpath li
+{
+ list-style-type:none;
+ float:left;
+ padding-left:10px;
+ padding-right:15px;
+ background-image:url('bc_s.png');
+ background-repeat:no-repeat;
+ background-position:right;
+ color:##45;
+}
+
+.navpath li.navelem a
+{
+ height:32px;
+ display:block;
+ text-decoration: none;
+ outline: none;
+ color: ##30;
+ font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
+ text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+ text-decoration: none;
+}
+
+.navpath li.navelem a:hover
+{
+ color:##80;
+}
+
+.navpath li.footer
+{
+ list-style-type:none;
+ float:right;
+ padding-left:10px;
+ padding-right:15px;
+ background-image:none;
+ background-repeat:no-repeat;
+ background-position:right;
+ color:##45;
+ font-size: 8pt;
+}
+
+
+div.summary
+{
+ float: right;
+ font-size: 8pt;
+ padding-right: 5px;
+ width: 50%;
+ text-align: right;
+}
+
+div.summary a
+{
+ white-space: nowrap;
+}
+
+div.ingroups
+{
+ font-size: 8pt;
+ width: 50%;
+ text-align: left;
+}
+
+div.ingroups a
+{
+ white-space: nowrap;
+}
+
+div.header
+{
+ background-image:url('nav_h.png');
+ background-repeat:repeat-x;
+ background-color: ##FA;
+ margin: 0px;
+ border-bottom: 1px solid ##CC;
+}
+
+div.headertitle
+{
+ padding: 5px 5px 5px 10px;
+}
+
+dl
+{
+ padding: 0 0 0 10px;
+}
+
+/* dl.note, dl.warning, dl.attention, dl.pre, dl.post, dl.invariant, dl.deprecated, dl.todo, dl.test, dl.bug */
+dl.section
+{
+ margin-left: 0px;
+ padding-left: 0px;
+}
+
+dl.note
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #D0C000;
+}
+
+dl.warning, dl.attention
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #FF0000;
+}
+
+dl.pre, dl.post, dl.invariant
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #00D000;
+}
+
+dl.deprecated
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #505050;
+}
+
+dl.todo
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #00C0E0;
+}
+
+dl.test
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #3030E0;
+}
+
+dl.bug
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #C08050;
+}
+
+dl.section dd {
+ margin-bottom: 6px;
+}
+
+
+#projectlogo
+{
+ text-align: center;
+ vertical-align: bottom;
+ border-collapse: separate;
+}
+
+#projectlogo img
+{
+ border: 0px none;
+}
+
+#projectname
+{
+ font: 300% Tahoma, Arial,sans-serif;
+ margin: 0px;
+ padding: 2px 0px;
+}
+
+#projectbrief
+{
+ font: 120% Tahoma, Arial,sans-serif;
+ margin: 0px;
+ padding: 0px;
+}
+
+#projectnumber
+{
+ font: 50% Tahoma, Arial,sans-serif;
+ margin: 0px;
+ padding: 0px;
+}
+
+#titlearea
+{
+ padding: 0px;
+ margin: 0px;
+ width: 100%;
+ border-bottom: 1px solid ##70;
+}
+
+.image
+{
+ text-align: center;
+}
+
+.dotgraph
+{
+ text-align: center;
+}
+
+.mscgraph
+{
+ text-align: center;
+}
+
+.caption
+{
+ font-weight: bold;
+}
+
+div.zoom
+{
+ border: 1px solid ##A0;
+}
+
+dl.citelist {
+ margin-bottom:50px;
+}
+
+dl.citelist dt {
+ color:##40;
+ float:left;
+ font-weight:bold;
+ margin-right:10px;
+ padding:5px;
+}
+
+dl.citelist dd {
+ margin:2px 0;
+ padding:5px 0;
+}
+
+div.toc {
+ padding: 14px 25px;
+ background-color: ##F6;
+ border: 1px solid ##DD;
+ border-radius: 7px 7px 7px 7px;
+ float: right;
+ height: auto;
+ margin: 0 20px 10px 10px;
+ width: 200px;
+}
+
+div.toc li {
+ background: url("bdwn.png") no-repeat scroll 0 5px transparent;
+ font: 10px/1.2 Verdana,DejaVu Sans,Geneva,sans-serif;
+ margin-top: 5px;
+ padding-left: 10px;
+ padding-top: 2px;
+}
+
+div.toc h3 {
+ font: bold 12px/1.2 Arial,FreeSans,sans-serif;
+ color: ##60;
+ border-bottom: 0 none;
+ margin: 0;
+}
+
+div.toc ul {
+ list-style: none outside none;
+ border: medium none;
+ padding: 0px;
+}
+
+div.toc li.level1 {
+ margin-left: 0px;
+}
+
+div.toc li.level2 {
+ margin-left: 15px;
+}
+
+div.toc li.level3 {
+ margin-left: 30px;
+}
+
+div.toc li.level4 {
+ margin-left: 45px;
+}
+
+.inherit_header {
+ font-weight: bold;
+ color: gray;
+ cursor: pointer;
+ -webkit-touch-callout: none;
+ -webkit-user-select: none;
+ -khtml-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ user-select: none;
+}
+
+.inherit_header td {
+ padding: 6px 0px 2px 5px;
+}
+
+.inherit {
+ display: none;
+}
+
+tr.heading h2 {
+ margin-top: 12px;
+ margin-bottom: 4px;
+}
+
+ at media print
+{
+ #top { display: none; }
+ #side-nav { display: none; }
+ #nav-path { display: none; }
+ body { overflow:visible; }
+ h1, h2, h3, h4, h5, h6 { page-break-after: avoid; }
+ .summary { display: none; }
+ .memitem { page-break-inside: avoid; }
+ #doc-content
+ {
+ margin-left:0 !important;
+ height:auto !important;
+ width:auto !important;
+ overflow:inherit;
+ display:inline;
+ }
+}
=====================================
doc/doxygen/gatb-simka.doxyfile
=====================================
@@ -0,0 +1,1720 @@
+# Doxyfile 1.7.4
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project.
+#
+# All text after a hash (#) is considered a comment and will be ignored.
+# The format is:
+# TAG = value [value, ...]
+# For lists items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ").
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
+
+DOXYFILE_ENCODING = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
+# by quotes) that should identify the project.
+
+#PROJECT_NAME = SIMKA-gatb.core-API- at gatb-core-version@
+PROJECT_NAME = simka- at gatb-tool-version@
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+# This could be handy for archiving the generated documentation or
+# if some version control system is used.
+
+PROJECT_NUMBER =
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer
+# a quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF =
+
+# With the PROJECT_LOGO tag one can specify an logo or icon that is
+# included in the documentation. The maximum height of the logo should not
+# exceed 55 pixels and the maximum width should not exceed 200 pixels.
+# Doxygen will copy the logo to the output directory.
+
+PROJECT_LOGO =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+# base path where the generated documentation will be put.
+# If a relative path is entered, it will be relative to the location
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY = .
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
+# 4096 sub-directories (in 2 levels) under the output directory of each output
+# format and will distribute the generated files over these directories.
+# Enabling this option can be useful when feeding doxygen a huge amount of
+# source files, where putting all generated files in the same directory would
+# otherwise cause performance problems for the file system.
+
+CREATE_SUBDIRS = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# The default language is English, other supported languages are:
+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
+# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+
+OUTPUT_LANGUAGE = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+# include brief member descriptions after the members that are listed in
+# the file and class documentation (similar to JavaDoc).
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
+# the brief description of a member or function before the detailed description.
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator
+# that is used to form the text in various listings. Each string
+# in this list, if found as the leading text of the brief description, will be
+# stripped from the text and the result after processing the whole list, is
+# used as the annotated text. Otherwise, the brief description is used as-is.
+# If left blank, the following values are used ("$name" is automatically
+# replaced with the name of the entity): "The $name class" "The $name widget"
+# "The $name file" "is" "provides" "specifies" "contains"
+# "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# Doxygen will generate a detailed section even if there is only a brief
+# description.
+
+ALWAYS_DETAILED_SEC = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+# path before files name in the file list and in the header files. If set
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+# can be used to strip a user-defined part of the path. Stripping is
+# only done if one of the specified strings matches the left-hand part of
+# the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the
+# path to strip.
+
+STRIP_FROM_PATH =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
+# the path mentioned in the documentation of a class, which tells
+# the reader which header file to include in order to use a class.
+# If left blank only the name of the header file containing the class
+# definition is used. Otherwise one should specify the include paths that
+# are normally passed to the compiler using the -I flag.
+
+STRIP_FROM_INC_PATH =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
+# (but less readable) file names. This can be useful if your file system
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+# will interpret the first line (until the first dot) of a JavaDoc-style
+# comment as the brief description. If set to NO, the JavaDoc
+# comments will behave just like regular Qt-style comments
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
+# interpret the first line (until the first dot) of a Qt-style
+# comment as the brief description. If set to NO, the comments
+# will behave just like regular Qt-style comments (thus requiring
+# an explicit \brief command for a brief description.)
+
+QT_AUTOBRIEF = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
+# treat a multi-line C++ special comment block (i.e. a block of //! or ///
+# comments) as a brief description. This used to be the default behaviour.
+# The new default is to treat a multi-line C++ comment block as a detailed
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
+# member inherits the documentation from any documented member that it
+# re-implements.
+
+INHERIT_DOCS = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
+# a new page for each member. If set to NO, the documentation of a member will
+# be part of the file/class/namespace that contains it.
+
+SEPARATE_MEMBER_PAGES = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE = 8
+
+# This tag can be used to specify a number of aliases that acts
+# as commands in the documentation. An alias has the form "name=value".
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
+# put the command \sideeffect (or @sideeffect) in the documentation, which
+# will result in a user-defined paragraph with heading "Side Effects:".
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
+# sources only. Doxygen will then generate output that is more tailored for C.
+# For instance, some of the names that are used will be different. The list
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
+# sources only. Doxygen will then generate output that is more tailored for
+# Java. For instance, namespaces will be presented as packages, qualified
+# scopes will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources only. Doxygen will then generate output that is more tailored for
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given extension.
+# Doxygen has a built-in mapping, but you can override or extend it using this
+# tag. The format is ext=language, where ext is a file extension, and language
+# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
+# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
+# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
+# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
+# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+
+EXTENSION_MAPPING =
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should
+# set this tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
+# func(std::string) {}). This also makes the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+
+BUILTIN_STL_SUPPORT = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+
+CPP_CLI_SUPPORT = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
+# Doxygen will parse them like normal C++ but will assume all classes use public
+# instead of private inheritance when no explicit protection keyword is present.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate getter
+# and setter methods for a property. Setting this option to YES (the default)
+# will make doxygen replace the get and set methods by a property in the
+# documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
+
+IDL_PROPERTY_SUPPORT = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
+# the same type (for instance a group of public functions) to be put as a
+# subgroup of that type (e.g. under the Public Functions section). Set it to
+# NO to prevent subgrouping. Alternatively, this can be done per class using
+# the \nosubgrouping command.
+
+SUBGROUPING = YES
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
+# unions are shown inside the group in which they are included (e.g. using
+# @ingroup) instead of on a separate page (for HTML and Man pages) or
+# section (for LaTeX and RTF).
+
+INLINE_GROUPED_CLASSES = NO
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+# is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically
+# be useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penalty.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will roughly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols
+
+SYMBOL_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. When set to YES local
+# methods, which are defined in the implementation section but not in
+# the interface are included in the documentation.
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespaces are hidden.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = YES
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES = YES
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS = YES
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+# will put a list of the files that are included by a file in the documentation
+# of that file.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
+# will list include files with double quotes in the documentation
+# rather than with sharp brackets.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+# is inserted in the documentation for inline members.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+# brief documentation of file, namespace and class members alphabetically
+# by member name. If set to NO (the default) the members will appear in
+# declaration order.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
+# will sort the (brief and detailed) documentation of class members so that
+# constructors and destructors are listed first. If set to NO (the default)
+# the constructors will appear in the respective orders defined by
+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+# hierarchy of group names into alphabetical order. If set to NO (the default)
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
+# sorted by fully-qualified names, including namespaces. If set to
+# NO (the default), the class list will be sorted only by class name,
+# not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME = YES
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
+# do proper type resolution of all parameters of a function it will reject a
+# match between the prototype and the implementation of a member function even
+# if there is only one candidate or it is obvious which candidate to choose
+# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
+# will still accept a match between prototype and implementation in such cases.
+
+STRICT_PROTO_MATCHING = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or
+# disable (NO) the todo list. This list is created by putting \todo
+# commands in the documentation.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or
+# disable (NO) the bug list. This list is created by putting \bug
+# commands in the documentation.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+# disable (NO) the deprecated list. This list is created by putting
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST = YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+# the initial value of a variable or macro consists of for it to appear in
+# the documentation. If the initializer consists of more lines than specified
+# here it will be hidden. Use a value of 0 to hide initializers completely.
+# The appearance of the initializer of individual variables and macros in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES = YES
+
+# If the sources in your project are distributed over multiple directories
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
+# in the documentation. The default is NO.
+
+#SHOW_DIRECTORIES = NO
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page.
+# This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command <command> <input-file>, where <command> is the value of
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+# provided by doxygen. Whatever the program writes to standard output
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. The create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option.
+# You can optionally specify a file name after the option, if omitted
+# DoxygenLayout.xml will be used as the name of the layout file.
+
+LAYOUT_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some
+# parameters in a documented function, or documenting parameters that
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR = YES
+
+# The WARN_NO_PARAMDOC option can be enabled to get warnings for
+# functions that are documented, but have no documentation for their parameters
+# or return value. If set to NO (the default) doxygen will only warn about
+# wrong or incomplete parameter documentation, but not about the absence of
+# documentation.
+
+WARN_NO_PARAMDOC = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text. Optionally the format may contain
+# $version, which will be replaced by the version of the file (if it could
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning
+# and error messages should be written. If left blank the output is written
+# to stderr.
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT = @CMAKE_CURRENT_SOURCE_DIR@/../src/ @CMAKE_CURRENT_SOURCE_DIR@/../test/src/ @CMAKE_CURRENT_SOURCE_DIR@/../doc/doxygen
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+# also the default input encoding. Doxygen uses libiconv (or the iconv built
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+# the list of possible encodings.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank the following patterns are tested:
+# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
+# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
+# *.f90 *.f *.for *.vhd *.vhdl
+
+FILE_PATTERNS =
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories. Note that the wildcards are matched
+# against the file with absolute path, so to exclude all test directories
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or
+# directories that contain example code fragments that are included (see
+# the \include command).
+
+EXAMPLE_PATH = @CMAKE_CURRENT_SOURCE_DIR@/../examples
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude
+# commands irrespective of the value of the RECURSIVE tag.
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH = @CMAKE_CURRENT_SOURCE_DIR@/../doc/doxygen/images
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output.
+# If FILTER_PATTERNS is specified, this tag will be
+# ignored.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis.
+# Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match.
+# The filters are a list of the form:
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+# info on how filters are used. If FILTER_PATTERNS is empty or if
+# non of the patterns match the file name, INPUT_FILTER is applied.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will be used to filter the input files when producing source
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
+# and it is also possible to disable source filtering for a specific pattern
+# using *.ext= (so without naming a filter). This option only has effect when
+# FILTER_SOURCE_FILES is enabled.
+
+FILTER_SOURCE_PATTERNS =
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+# Note: To get rid of all source code in the generated output, make sure also
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES
+# then for each documented function all documented
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES
+# then for each documented function all documented entities
+# called/used by that function will be listed.
+
+REFERENCES_RELATION = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+# link to the source code.
+# Otherwise they will link to the documentation.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code
+# will point to the HTML generated by the htags(1) tool instead of doxygen
+# built-in source browser. The htags tool is part of GNU's global source
+# tagging system (see http://www.gnu.org/software/global/global.html). You
+# will need version 4.8.6 or higher.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX = YES
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all
+# classes will be put under the same header in the alphabetical index.
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard header. Note that when using a custom header you are responsible
+# for the proper inclusion of any scripts and style sheets that doxygen
+# needs, which is dependent on the configuration options used.
+# It is adviced to generate a default header using "doxygen -w html
+# header.html footer.html stylesheet.css YourConfigFile" and then modify
+# that header. Note that the header is subject to change so you typically
+# have to redo this when upgrading to a newer version of doxygen or when changing the value of configuration settings such as GENERATE_TREEVIEW!
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER =
+
+# If the HTML_TIMESTAMP tag is set to YES then the generated HTML documentation will contain the timesstamp.
+
+HTML_TIMESTAMP = YES
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If the tag is left blank doxygen
+# will generate a default style sheet. Note that doxygen will try to copy
+# the style sheet file to the HTML output directory, so don't put your own
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET = @CMAKE_CURRENT_SOURCE_DIR@/../doc/doxygen/doxygen.css
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that
+# the files will be copied as-is; there are no commands or markers available.
+
+HTML_EXTRA_FILES =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
+# Doxygen will adjust the colors in the stylesheet and background images
+# according to this color. Hue is specified as an angle on a colorwheel,
+# see http://en.wikipedia.org/wiki/Hue for more information.
+# For instance the value 0 represents red, 60 is yellow, 120 is green,
+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
+# The allowed range is 0 to 359.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
+# the colors in the HTML output. For a value of 0 the output will use
+# grayscales only. A value of 255 will produce the most vivid colors.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
+# the luminance component of the colors in the HTML output. Values below
+# 100 gradually make the output lighter, whereas values above 100 make
+# the output darker. The value divided by 100 is the actual gamma applied,
+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
+# and 100 does not change the gamma.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting
+# this to NO can help when comparing the output of multiple runs.
+
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+# files or namespaces will be aligned in HTML using tables. If set to
+# NO a bullet list will be used.
+
+#HTML_ALIGN_MEMBERS = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded. For this to work a browser that supports
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+
+GENERATE_DOCSET = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+
+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
+
+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+
+DOCSET_PUBLISHER_NAME = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+# be used to specify the file name of the resulting .chm file. You
+# can add a path in front of the file if the result should not be
+# written to the html output directory.
+
+CHM_FILE =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+# be used to specify the location (absolute path including file name) of
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+# controls if a separate .chi index file is generated (YES) or that
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+# controls whether a binary table of contents is generated (YES) or a
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
+# that can be used as input for Qt's qhelpgenerator to generate a
+# Qt Compressed Help (.qch) of the generated HTML documentation.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
+# add. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
+# Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's
+# filter section matches.
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
+# Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS =
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
+# be used to specify the location of Qt's qhelpgenerator.
+# If non-empty doxygen will try to run qhelpgenerator on the generated
+# .qhp file.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
+# will be generated, which together with the HTML files, form an Eclipse help
+# plugin. To install this plugin and make it available under the help contents
+# menu in Eclipse, the contents of the directory containing the HTML and XML
+# files needs to be copied into the plugins directory of eclipse. The name of
+# the directory within the plugins directory should be the same as
+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
+# the help appears.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have
+# this name.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+# top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it.
+
+DISABLE_INDEX = NO
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
+# (range [0,1..20]) that doxygen will group on one line in the generated HTML
+# documentation. Note that a value of 0 will completely suppress the enum
+# values from appearing in the overview section.
+
+ENUM_VALUES_PER_LINE = 4
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information.
+# If the tag value is set to YES, a side panel will be generated
+# containing a tree-like index structure (just like the one that
+# is generated for HTML Help). For this to work a browser that supports
+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
+# Windows users are probably better off using the HTML help feature.
+
+GENERATE_TREEVIEW = YES
+
+# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
+# and Class Hierarchy pages using a tree view instead of an ordered list.
+
+#USE_INLINE_TREES = NO
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+# used to set the initial width (in pixels) of the frame in which the tree
+# is shown.
+
+TREEVIEW_WIDTH = 250
+
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
+# links to external symbols imported via tag files in a separate window.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are
+# not supported properly for IE 6.0, but are supported on all modern browsers.
+# Note that when changing this option you need to delete any form_*.png files
+# in the HTML output before the changes have effect.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
+# (see http://www.mathjax.org) which uses client side Javascript for the
+# rendering instead of using prerendered bitmaps. Use this if you do not
+# have LaTeX installed or if you want to formulas look prettier in the HTML
+# output. When enabled you also need to install MathJax separately and
+# configure the path to it using the MATHJAX_RELPATH option.
+
+USE_MATHJAX = NO
+
+# When MathJax is enabled you need to specify the location relative to the
+# HTML output directory using the MATHJAX_RELPATH option. The destination
+# directory should contain the MathJax.js script. For instance, if the mathjax
+# directory is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the
+# mathjax.org site, so you can quickly see the result without installing
+# MathJax, but it is strongly recommended to install a local copy of MathJax
+# before deployment.
+
+MATHJAX_RELPATH = http://www.mathjax.org/mathjax
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box
+# for the HTML output. The underlying search engine uses javascript
+# and DHTML and should work on any modern browser. Note that when using
+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
+# (GENERATE_DOCSET) there is already a search function so this one should
+# typically be disabled. For large projects the javascript based search engine
+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+
+SEARCHENGINE = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a PHP enabled web server instead of at the web client
+# using Javascript. Doxygen will generate the search PHP script and index
+# file to put on the web server. The advantage of the server
+# based approach is that it scales better to large projects and allows
+# full text search. The disadvantages are that it is more difficult to setup
+# and does not have live searching capabilities.
+
+SERVER_BASED_SEARCH = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked. If left blank `latex' will be used as the default command name.
+# Note that when enabling USE_PDFLATEX this option is only used for
+# generating bitmaps for formulas in the HTML output, but not in the
+# Makefile that is written to the output directory.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
+# generate index for LaTeX. If left blank `makeindex' will be used as the
+# default command name.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+# LaTeX documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used
+# by the printer. Possible values are: a4, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE = a4
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+# the generated latex document. The header should contain everything until
+# the first chapter. If it is left blank doxygen will generate a
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
+# the generated latex document. The footer should contain everything after
+# the last chapter. If it is left blank doxygen will generate a
+# standard footer. Notice: only use this tag if you know what you are doing!
+
+LATEX_FOOTER =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+# contain links (just like the HTML output) instead of page references
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS = YES
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
+# higher quality PDF documentation.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+# command to the generated LaTeX files. This will instruct LaTeX to keep
+# running if errors occur, instead of asking the user for help.
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
+# include the index chapters (such as File Index, Compound Index, etc.)
+# in the output.
+
+LATEX_HIDE_INDICES = NO
+
+# If LATEX_SOURCE_CODE is set to YES then doxygen will include
+# source code with syntax highlighting in the LaTeX output.
+# Note that which sources are shown also depends on other settings
+# such as SOURCE_BROWSER.
+
+LATEX_SOURCE_CODE = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimized for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+# RTF documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+# will contain hyperlink fields. The RTF file will
+# contain links (just like the HTML output) instead of page references.
+# This makes the output suitable for online browsing using WORD or other
+# programs which support those fields.
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# config file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an rtf document.
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
+# then it will generate one additional man file for each entity
+# documented in the real man page(s). These additional files
+# only source the real man page, but without them the man command
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_SCHEMA =
+
+# The XML_DTD tag can be used to specify an XML DTD,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_DTD =
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
+# dump the program listings (including syntax highlighting
+# and cross-referencing information) to the XML output. Note that
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
+# generate an AutoGen Definitions (see autogen.sf.net) file
+# that captures the structure of the code including all
+# documentation. Note that this feature is still experimental
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
+# generate a Perl module file that captures the structure of
+# the code including all documentation. Note that this
+# feature is still experimental and incomplete at the
+# moment.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
+# nicely formatted so it can be parsed by a human reader.
+# This is useful
+# if you want to understand what is going on.
+# On the other hand, if this
+# tag is set to NO the size of the Perl module output will be much smaller
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
+# This is useful so different doxyrules.make files included by the same
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
+# files.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+# names in the source code. If set to NO (the default) only conditional
+# compilation will be performed. Macro expansion can be done in a controlled
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+# then the macro expansion is limited to the macros specified with the
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# pointed to by INCLUDE_PATH will be searched when a #include is found.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition that
+# overrules the definition found in the source code.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+# doxygen's preprocessor will remove all references to function-like macros
+# that are alone on a line, have an all uppercase name, and do not end with a
+# semicolon, because these will confuse the parser if not removed.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles.
+# Optionally an initial location of the external documentation
+# can be added for each tagfile. The format of a tag file without
+# this location is as follows:
+#
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+#
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where "loc1" and "loc2" can be relative or absolute paths or
+# URLs. If a location is present for each tag, the installdox tool
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE =
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+# in the class index. If set to NO only the inherited external classes
+# will be listed.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will
+# be listed.
+
+EXTERNAL_GROUPS = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+# or super classes. Setting the tag to NO turns the diagrams off. Note that
+# this option also works with HAVE_DOT disabled, but it is recommended to
+# install and use dot, since it yields more powerful graphs.
+
+CLASS_DIAGRAMS = NO
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# If set to YES, the inheritance and collaboration graphs will hide
+# inheritance and usage relations if the target is undocumented
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT = YES
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
+# allowed to run in parallel. When set to 0 (the default) doxygen will
+# base this on the number of processors available in the system. You can set it
+# explicitly to a value larger than 0 to get control over the balance
+# between CPU load and processing speed.
+
+DOT_NUM_THREADS = 0
+
+# By default doxygen will write a font called Helvetica to the output
+# directory and reference it in all dot files that doxygen generates.
+# When you want a differently looking font you can specify the font name
+# using DOT_FONTNAME. You need to make sure dot is able to find the font,
+# which can be done by putting it in a standard location or by setting the
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
+# containing the font.
+
+DOT_FONTNAME = Helvetica
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+# The default size is 10pt.
+
+DOT_FONTSIZE = 11
+
+# By default doxygen will tell dot to use the output directory to look for the
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a
+# different font using DOT_FONTNAME you can set the path where dot
+# can find it using this tag.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect inheritance relations. Setting this tag to YES will force the
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH = NO
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+
+UML_LOOK = YES
+
+# If set to YES, the inheritance and collaboration graphs will show the
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+# tags are set to YES then doxygen will generate a graph for each documented
+# file showing the direct and indirect include dependencies of the file with
+# other documented files.
+
+INCLUDE_GRAPH = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+# documented header file showing the documented files that directly or
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH = NO
+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# will generate a graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# then doxygen will show the dependencies a directory has on other directories
+# in a graphical way. The dependency relations are determined by the #include
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. Possible values are svg, png, jpg, or gif.
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the
+# \dotfile command).
+
+DOTFILE_DIRS =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the
+# \mscfile command).
+
+MSCFILE_DIRS =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# nodes that will be shown in the graph. If the number of nodes in a graph
+# becomes larger than this value, doxygen will truncate the graph, which is
+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
+# graphs generated by dot. A depth value of 3 means that only nodes reachable
+# from the root by following a path via at most 3 edges will be shown. Nodes
+# that lay further from the root node will be omitted. Note that setting this
+# option to 1 or 2 may greatly reduce the computation time needed for large
+# code bases. Also note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not
+# seem to support this out of the box. Warning: Depending on the platform used,
+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10)
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS = NO
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+# generate a legend page explaining the meaning of the various boxes and
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
+# remove the intermediate dot files that are used to generate
+# the various graphs.
+
+DOT_CLEANUP = YES
=====================================
example/simple_test.sh
=====================================
@@ -1,4 +1,5 @@
#!/bin/bash
+ADDITIONAL_SIMKA_OPTIONS=$*
#simple test with real data
# look for simka binary. In devel mode, it's in ../build/bin directory.
@@ -15,7 +16,7 @@ else
fi
# run simka
-command="$bindir/simka -in ../example/simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output"
+command="$bindir/simka -in ../example/simka_input.txt -out ./simka_results/ -out-tmp ./simka_temp_output $ADDITIONAL_SIMKA_OPTIONS"
#printf "$command\n\n"
# DO NOT add lines between '$command' exec and 'var...' !
=====================================
scripts/sonarqube_diags/Dockerfile.sq
=====================================
@@ -0,0 +1,104 @@
+# This Dockerfile prepares an image equipped with all necessary softwares to prepare
+# and upload SonarQube diagnostics
+#
+# Usage:
+# docker login registry.gitlab.inria.fr
+# docker build -f Dockerfile.sq -t registry.gitlab.inria.fr/gatb/simka/simka_sq .
+# docker push registry.gitlab.inria.fr/gatb/simka/simka_sq
+# NB: these tasks may be launched by gitlab-ci (manual job: update_simka_sq_image)
+#
+# References:
+# see eg https://sed-bso.gitlabpages.inria.fr/sonarqube/#sec-2-5
+
+FROM debian:10
+
+ENV FORCE_UNSAFE_CONFIGURE=1
+ENV DEBIAN_FRONTEND noninteractive
+
+LABEL maintainer="Charles Deltel <charles.deltel at inria.fr>"
+
+RUN apt-get update
+RUN apt install -y \
+ make autoconf wget unzip \
+ zlib1g-dev libcppunit-dev \
+ git build-essential cmake clang clang-tidy gcovr lcov cppcheck valgrind python-pip pylint sudo vim tree \
+ doxygen graphviz # for doxygen doc generation
+
+RUN pip install --upgrade pip
+RUN python -m pip install pytest pytest-cov setuptools scan-build
+
+RUN chmod a+rx /root && \
+ mkdir -p /root/apps
+
+ENV version_rats 2.4
+RUN cd /root/apps && \
+ wget https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/rough-auditing-tool-for-security/rats-${version_rats}.tgz && \
+ tar -xzvf rats-${version_rats}.tgz && \
+ cd rats-${version_rats} && \
+ ./configure && make && sudo make install && \
+ rm /root/apps/rats-${version_rats}.tgz
+
+ENV version_drmemory 2.2.0-1
+RUN cd /root/apps && \
+ wget https://github.com/DynamoRIO/drmemory/releases/download/release_2.2.0/DrMemory-Linux-${version_drmemory}.tar.gz && \
+ tar xf DrMemory-Linux-${version_drmemory}.tar.gz && \
+ rm /root/apps/DrMemory-Linux-${version_drmemory}.tar.gz
+
+RUN cd /root/apps && \
+ wget --no-check-certificate https://scan.coverity.com/download/linux64 --post-data "token=XEJaJ1cAnqW-9M_zkmxd7w&project=Heat" -O coverity_tool.tgz && \
+ tar xf coverity_tool.tgz && \
+ ln -s -f $PWD/cov-analysis-linux64-*/bin/cov-build /usr/local/bin/cov-build && \
+ rm /root/apps/coverity_tool.tgz
+
+RUN cd /root/apps && \
+ wget https://github.com/eriwen/lcov-to-cobertura-xml/archive/1.6.tar.gz && \
+ tar xvf 1.6.tar.gz && \
+ ln -s /root/apps/lcov-to-cobertura-xml-1.6/lcov_cobertura/lcov_cobertura.py /usr/local/bin/lcov_cobertura.py && \
+ rm /root/apps/1.6.tar.gz
+
+RUN cd /root/apps && \
+ git clone https://github.com/SonarOpenCommunity/sonar-cxx.git && \
+ chmod +x /root/apps/sonar-cxx/cxx-sensors/src/tools/vera++Report2checkstyleReport.perl && \
+ ln -s /root/apps/sonar-cxx/cxx-sensors/src/tools/vera++Report2checkstyleReport.perl /usr/local/bin/vera++Report2checkstyleReport.perl
+
+ENV version_sonar 4.2.0.1873
+RUN cd /root/apps && \
+ wget https://binaries.sonarsource.com/Distribution/sonar-scanner-cli/sonar-scanner-cli-${version_sonar}-linux.zip && \
+ unzip sonar-scanner-cli-${version_sonar}-linux.zip && \
+ ln -s /root/apps/sonar-scanner-${version_sonar}-linux/bin/sonar-scanner /usr/local/bin/sonar-scanner && \
+ rm /root/apps/sonar-scanner-cli-${version_sonar}-linux.zip
+
+# cf. https://docs.docker.com/install/linux/docker-ce/debian/
+#RUN apt-get remove docker docker-engine docker.io containerd runc
+RUN sudo apt-get install -y \
+ apt-transport-https \
+ ca-certificates \
+ curl \
+ gnupg2 \
+ software-properties-common
+
+RUN curl -fsSL https://download.docker.com/linux/debian/gpg | sudo apt-key add -
+RUN apt-key fingerprint 0EBFCD88
+RUN sudo add-apt-repository \
+ "deb [arch=amd64] https://download.docker.com/linux/debian $(lsb_release -cs) stable" && \
+ apt-get update && \
+ apt-get install -y docker-ce docker-ce-cli containerd.io
+
+RUN docker --version
+
+RUN groupadd -f -g 1000 gitlab && \
+ useradd -u 1000 -g gitlab -d /home/gitlab/ -ms /bin/bash gitlab && \
+ mkdir /builds && \
+ chown -R gitlab:gitlab /builds && \
+ echo "gitlab:gitlab" | chpasswd && adduser gitlab sudo
+
+USER gitlab
+
+# change the default shell to be bash
+SHELL ["/bin/bash", "-c"]
+
+# set DRMEMORY path (does not work without using an absolute path)
+ENV DRMEMORY /root/apps/DrMemory-Linux-${version_drmemory}/bin64
+
+# default working directory is
+WORKDIR /builds
\ No newline at end of file
=====================================
scripts/sonarqube_diags/analysis.sh
=====================================
@@ -0,0 +1,115 @@
+# This script launches several diagnostics, whose results will be uploaded to the
+# SonarQube server.
+#!/bin/bash
+set -xv
+
+echo_stderr() { echo "$@" 1>&2; }
+
+echo_stderr "===> Launching analysis script (to prepare SonarQube diagnostics)..."
+
+####################################################################################################
+# CppCheck and RATS analysis
+####################################################################################################
+
+echo_stderr "===> Launching CppCheck analysis..."
+# see e.g. https://sonarqube.inria.fr/pages/documentation.html#org4575413
+
+export CPPCHECK_INCLUDES="-Icore -Iminikc -IsimkaMin"
+export SOURCES_TO_ANALYZE="src"
+export SOURCES_TO_EXCLUDE= # ex. "-isrc/beta"
+export DEFINITIONS= # -D
+
+cppcheck -v -f --language=c++ --platform=unix64 --enable=all --suppress=missingIncludeSystem --xml --xml-version=2 \
+ ${DEFINITIONS} ${CPPCHECK_INCLUDES} ${SOURCES_TO_EXCLUDE} ${SOURCES_TO_ANALYZE} \
+ 2> simka-cppcheck.xml
+
+echo_stderr "===> Launching RATS analysis..."
+export SOURCES_TO_ANALYZE="src"
+rats -w 3 --xml ${SOURCES_TO_ANALYZE} > simka-rats.xml
+
+####################################################################################################
+# Compile the code
+####################################################################################################
+mkdir build
+cd build
+
+# compilation options
+echo_stderr "===> Compilation options"
+CFLAGS="--coverage \
+ -fPIC -fdiagnostics-show-option \
+ -Wall -Wunused-parameter -Wundef -Wno-long-long \
+ -Wsign-compare -Wmissing-prototypes -Wstrict-prototypes -Wcomment \
+ -pedantic -g"
+LDFLAGS="--coverage"
+echo_stderr "CFLAGS: $CFLAGS"
+echo_stderr "LDFLAGS: $LDFLAGS"
+
+# launch cmake
+echo_stderr "===> Launching cmake with scan-build..."
+
+scan-build -v -plist --intercept-first --analyze-headers -o analyzer_reports \
+ cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_EXPORT_COMPILE_COMMANDS=ON \
+ -DCMAKE_CXX_FLAGS="$CFLAGS" -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS" \
+ -DCMAKE_BUILD_TYPE=DEBUG \
+ -DCMAKE_CXX_OUTPUT_EXTENSION_REPLACE=ON &> simka-scan-build-cmake.log
+
+# launch make
+echo_stderr "===> Launching make with scan-build..."
+time scan-build -v -plist --intercept-first --analyze-headers -o analyzer_reports \
+ make -j 4 &> simka-scan-build-make.log
+ # make -j 4
+
+[[ -x "bin/simka" ]] || { echo "Error, simka executable not generated"; exit 111; }
+
+mv simka-scan-build-cmake.log ..
+mv simka-scan-build-make.log ..
+mv analyzer_reports ..
+
+####################################################################################################
+# Clang-tidy analysis
+####################################################################################################
+echo_stderr "===> Launching clang-tidy..."
+test -f compile_commands.json || echo "Warning, compilation database missing"
+cd ..
+#clang-tidy -p build/ $(find src/ -name *.cpp) -checks='*' > simka-clang-tidy-report.log
+clang-tidy -p build/ $(find src/ -name *.cpp) -checks=-*,clang-analyzer-*,cppcoreguidelines-* > simka-clang-tidy-report.log
+cd - # back in build/ again
+mv compile_commands.json ..
+
+####################################################################################################
+# Coverage analysis
+####################################################################################################
+
+echo_stderr "===> Launching lcov (initial)..."
+
+# run initial/baseline lcov
+lcov --capture --initial --directory . --output-file simka_coverage_base.info
+
+# run tests
+echo_stderr "===> Launching a simple test run..."
+../example/simple_test.sh -max-count 2 -max-merge 4 -nb-cores 4 -max-memory 3000
+
+# run lcov again after tests complete
+echo_stderr "===> Launching lcov (after test completion)..."
+lcov --capture --directory . --output-file simka_coverage_test.info
+
+# combine lcov tracefiles
+lcov --add-tracefile simka_coverage_base.info \
+ --add-tracefile simka_coverage_test.info \
+ --output-file simka_coverage_total.info
+
+# extract useful data
+lcov --extract simka_coverage_total.info '*simka/src/*' \
+ --output-file simka_coverage_total_filtered.info
+
+# generate the html lcov page that can be published
+echo_stderr "===> Generating coverage html pages..."
+genhtml -o coverage-html simka_coverage_total_filtered.info
+mv coverage-html ..
+
+# convert the lcov report to an xml format convertible with SonarQube
+echo_stderr "===> Generating coverage report for SonarQube..."
+cd ..
+lcov_cobertura.py build/simka_coverage_total_filtered.info --output gcov.xml --base-dir src/
+
+echo_stderr "===> Done..."
=====================================
sonar-project.properties
=====================================
@@ -0,0 +1,16 @@
+sonar.links.homepage=https://gitlab.inria.fr/GATB/simka
+sonar.links.scm=https://gitlab.inria.fr/GATB/simka.git
+sonar.projectDescription=Simka project
+sonar.host.url=https://sonarqube.inria.fr/sonarqube
+sonar.projectKey=genscale:gatb:tools:simka:gitlab:master
+sonar.sources=src
+sonar.exclusions=thirdparty/**
+sonar.language=c++
+sonar.cxx.includeDirectories=$(echo | gcc -E -Wp,-v - 2>&1 | grep "^ " | tr '\n' ',')
+sonar.cxx.gcc.reportPath=simka-scan-build.log
+sonar.cxx.gcc.regex=(?<file>.*):(?<line>[0-9]+):[0-9]+:\\x20warning:\\x20(?<message>.*)\\x20\\[(?<id>.*)\\]
+sonar.cxx.clangtidy.reportPath=simka-clang-tidy-report.log
+sonar.cxx.clangsa.reportPath=analyzer_reports/*/*.plist
+sonar.cxx.cppcheck.reportPath=simka-cppcheck.xml
+sonar.cxx.rats.reportPath=simka-rats.xml
+sonar.cxx.coverage.reportPath=gcov.xml
=====================================
src/SimkaPotara.hpp
=====================================
@@ -18,7 +18,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
-
+
#ifndef TOOLS_SIMKA_SRC_SIMKAFUSION_HPP_
#define TOOLS_SIMKA_SRC_SIMKAFUSION_HPP_
@@ -214,9 +214,18 @@ public:
//cout << "lala" << endl;
//cout << _execDir << endl;
-
- _execDir = System::file().getRealPath(execFilename);
- _execDir = System::file().getDirectory(_execDir) + "/";
+
+ if (execFilename == "simka") // i.e. simka binary is found in $PATH
+ {
+ //cout << endl << "Debug info : execFilename = simka (i.e. simka binary is found in $PATH)" << endl;
+ _execDir = "";
+ }
+ else
+ {
+ //cout << endl << "Debug info : execFilename = " << execFilename << endl;
+ _execDir = System::file().getRealPath(execFilename);
+ _execDir = System::file().getDirectory(_execDir) + "/";
+ }
//_options = options;
@@ -364,8 +373,19 @@ public:
_isClusterMode = false;
}
+ if (this->_options->getInt(STR_MAX_MEMORY) < 2000)
+ {
+ std::cout << "WARNING: running Simka with low memory is risky. Simka may hang because of that. Consider running with -max-memory X where X > 2000" << std::endl;
+ }
+
+ if (this->_options->getInt(STR_MAX_MEMORY) < 500)
+ {
+ std::cout << "Please run Simka with higher memory usage than 500 MB" << std::endl;
+ exit(1);
+ }
+
//_isClusterMode = true;
@@ -601,6 +621,13 @@ public:
IBank* bank = Bank::open(inputDir + this->_bankNames[i]);
LOCAL(bank);
+ // Check that data files are not empty
+ int64_t nbItems = bank->estimateNbItems();
+ if (nbItems==0) {
+ cerr << "ERROR: Dataset is empty: " << this->_bankNames[i] << endl;
+ exit(1);
+ }
+
//size_t nbBank_ = bank->getCompositionNb();
SimkaBankTemp* simkaBank = new SimkaBankTemp(bank, this->_maxNbReads*this->_nbBankPerDataset[i]);
//banksToDelete.push_back(simkaBank);
@@ -817,7 +844,7 @@ public:
string tempDir = this->_outputDirTemp + "/temp/" + this->_bankNames[i];
- string command = "nohup " + _execDir + "/simkaCountProcess " + _execDir + "/simkaCount ";
+ string command = "nohup " + _execDir + "simkaCountProcess " + _execDir + "simkaCount ";
command += " " + string(STR_KMER_SIZE) + " " + SimkaAlgorithm<>::toString(this->_kmerSize);
command += " " + string("-out-tmp-simka") + " " + this->_outputDirTemp;
command += " " + string("-out-tmp") + " " + tempDir;
@@ -983,7 +1010,7 @@ public:
filenameQueue.push_back(datasetId);
- string command = "nohup " + _execDir + "/simkaMerge ";
+ string command = "nohup " + _execDir + "simkaMerge ";
command += " " + string(STR_KMER_SIZE) + " " + SimkaAlgorithm<>::toString(this->_kmerSize);
command += " " + string(STR_URI_INPUT) + " " + this->_inputFilename;
command += " " + string("-out-tmp-simka") + " " + this->_outputDirTemp;
View it on GitLab: https://salsa.debian.org/med-team/simka/-/compare/1536404c4bce899c022489142d4c8a53a7f198a5...b03c77a69cda244e354ccddccaf63453680effc3
--
View it on GitLab: https://salsa.debian.org/med-team/simka/-/compare/1536404c4bce899c022489142d4c8a53a7f198a5...b03c77a69cda244e354ccddccaf63453680effc3
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