1st full Gauss/Lorentz LF. Still room for optimization, and further testing.

Explicit passing of MnStrategy during minimizer initialization

Approved-by: Suter Andreas

.gitignore

@@ -0,0 +1,2 @@
+# ignore all files generated from an in-repo build
+build/

CMakeLists.txt

@@ -1,7 +1,7 @@
 # - musrfit
 cmake_minimum_required(VERSION 3.17)
 
-project(musrfit VERSION 1.9.1 LANGUAGES C CXX)
+project(musrfit VERSION 1.9.8 LANGUAGES C CXX)
 
 #--- musrfit specific options -------------------------------------------------
 option(nexus "build optional NeXus support. Needed for ISIS" OFF)
@@ -109,13 +109,13 @@ find_package(FFTW3 REQUIRED)
 find_package(LibXml2 REQUIRED)
 
 #--- check for OpenMP ---------------------------------------------------------
-if (try_OpenMP AND NOT APPLE)
+if (try_OpenMP)
   find_package(OpenMP)
-  if (OpenMP_FOUND)
+  if (OpenMP_CXX_FOUND)
     add_definitions(-DHAVE_GOMP)
     set(HAVE_GOMP 1 CACHE INTERNAL "Have GOMP")
-  endif (OpenMP_FOUND)
-endif (try_OpenMP AND NOT APPLE)
+  endif (OpenMP_CXX_FOUND)
+endif (try_OpenMP)
 
 #--- check for Qt -------------------------------------------------------------
 if (qt_based_tools)
@@ -200,8 +200,10 @@ endif (qt_based_tools)
 
 #--- if NeXus check also for HDF4, HDF5, and MXML -----------------------------
 if (nexus)
-  find_package(HDF5 COMPONENTS CXX REQUIRED )
-  find_package(HDF4 REQUIRED)
+  find_package(HDF5 COMPONENTS CXX REQUIRED)
+  if (HAVE_HDF4)
+    find_package(HDF4 REQUIRED)
+  endif (HAVE_HDF4)  
   find_package(NEXUS REQUIRED)
   add_definitions(-DPNEXUS_ENABLED)
 endif (nexus)
@@ -222,10 +224,48 @@ else ()
   set(IS_GIT_REPO 0)
 endif ()
 
+#--- start create git-revision.h ----------------------------------------------
+if (IS_GIT_REPO)
+  execute_process(COMMAND sh ${CMAKE_SOURCE_DIR}/src/git_revision.sh)
+
+  set(HAVE_GIT_REV_H "-DHAVE_GIT_REV_H")  
+  set(GIT_REV_H "git-revision.h")
+else (IS_GIT_REPO)
+  set(HAVE_GIT_REV_H "")  
+  set(GIT_REV_H "")
+endif (IS_GIT_REPO)
+
+#--- end create git-revision.h ------------------------------------------------
+
+#--- rpath related things -----------------------------------------------------
+# use, i.e. don't skip the full RPATH for the build tree
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+
+# add the automatically determined parts of the RPATH
+# which point to directories outside the build tree to the install RPATH
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+# the RPATH to be used when installing, but only if it's not a system directory
+list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
+if("${isSystemDir}" STREQUAL "-1")
+    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+endif("${isSystemDir}" STREQUAL "-1")
+set(rpath ${CMAKE_INSTALL_RPATH})
+string(APPEND rpath ";/usr/local/lib")
+set(CMAKE_INSTALL_RPATH "${rpath}")
+
 #--- propagate to the sub-directories -----------------------------------------
 add_subdirectory(src)
 
 #--- write summary of the installation
+cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+
 message("")
 message("|-----------------------------------------------------------------------|")
 message("|                                                                       |")
@@ -233,8 +273,9 @@ message("|                            Summary
 message("|                                                                       |")
 message("|-----------------------------------------------------------------------|")
 message("")
-message(" System: ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
-message(" -------")
+message(" System:    ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
+message(" Processor: ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})")
+message(" ----------")
 message("")
 message(" musrfit Version: ${musrfit_VERSION}")
 message(" ----------------")
@@ -260,7 +301,11 @@ endif (OpenMP_FOUND)
 
 if (nexus)
   message("")
-  message(" HDF4    found in ${HDF4_INCLUDE_DIRS}")
+  if (HAVE_HDF4)
+    message(" HDF4    found in ${HDF4_INCLUDE_DIRS}")
+  else (HAVE_HDF4)
+    message(" HDF4    not present.")	  
+  endif (HAVE_HDF4)	  
   message(" HDF5    found in ${HDF5_INCLUDE_DIRS}, Version: ${HDF5_VERSION}")
   message(" NeXus   found in ${NEXUS_INCLUDE_DIR}, Version: ${NEXUS_VERSION_STRING}")
 endif (nexus)

ChangeLog

@@ -12,6 +12,42 @@ or
 
 https://bitbucket.org/muonspin/musrfit/commits/all
 
+Release of V1.9.8, 2025/03/24
+=============================
+
+add a user interface option to export data from a msr-file view (single- or multiple files).
+
+Release of V1.9.7, 2025/01/18
+=============================
+
+allow spaces in RUN block path-filename
+
+Release of V1.9.6, 2024/12/02
+=============================
+
+added jump to block feature in musredit.
+
+
+Release of V1.9.5, 2024/06/24
+=============================
+
+yaml export of ALL fit-parameters, as initiated by R.M.L. McFadden.
+
+Release of V1.9.4, 2024/06/08
+=============================
+
+enable OpenMP for macOS.
+
+Release of V1.9.3, 2024/04/19
+=============================
+
+fix of function string generation from AST.
+
+Release of V1.9.2, 2023/10/25
+=============================
+
+switch over to smart pointers wherever possible.
+
 Release of V1.9.1, 2023/05/16
 =============================
 

README.md

@@ -32,7 +32,6 @@ For a more exhaustive user documentation see:
 
 <andreas.suter@psi.ch>
 
-For the beta-NMR related parts, please contact
-
+For the beta-NMR related parts, please contact Zaher Salman
 <zaher.salman@psi.ch>
 

cmake/configure_musrfit_version_file.cmake.in

@@ -1,30 +0,0 @@
-# configure_musrfit_version_file.cmake.in:
-set(SRC_DIR "@CMAKE_SOURCE_DIR@")
-set(BIN_DIR "@CMAKE_CURRENT_BINARY_DIR@")
-
-# Set variables
-set(CMAKE_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
-set(MUSRFIT_VERSION "@MUSRFIT_VERSION@")
-
-# Get the current working branch
-execute_process(
-  COMMAND git rev-parse --abbrev-ref HEAD
-  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-  OUTPUT_VARIABLE GIT_BRANCH
-  OUTPUT_STRIP_TRAILING_WHITESPACE
-)
-
-# Get the latest abbreviated commit hash of the working branch
-execute_process(
-  COMMAND git log -1 --pretty="%h, %ci"
-  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-  OUTPUT_VARIABLE GIT_CURRENT_SHA1
-  OUTPUT_STRIP_TRAILING_WHITESPACE
-)
-
-configure_file(
-  ${SRC_DIR}/cmake/git-revision.h.in
-  ${BIN_DIR}/git-revision.h
-  @ONLY
-)
-# EOF

doc/examples/UserFcn/PUserFcn.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2025 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

doc/examples/UserFcn/PUserFcn.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2021 by Andreas Suter                              *
+ *   Copyright (C) 2007-2025 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

doc/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ea8ddbeaec87fd554dad49f5d0917959
+config: 1c72e3ac8764a6fbfdf66c0cdf797d3d
 tags: 645f666f9bcd5a90fca523b33c5a78b7

doc/html/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.9.0',
+    VERSION: '1.9.5',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

doc/html/_static/haiku.css

@@ -1,376 +0,0 @@
-/*
- * haiku.css_t
- * ~~~~~~~~~~~
- *
- * Sphinx stylesheet -- haiku theme.
- *
- * Adapted from http://haiku-os.org/docs/Haiku-doc.css.
- * Original copyright message:
- *
- *     Copyright 2008-2009, Haiku. All rights reserved.
- *     Distributed under the terms of the MIT License.
- *
- *     Authors:
- *              Francois Revol <revol@free.fr>
- *              Stephan Assmus <superstippi@gmx.de>
- *              Braden Ewing <brewin@gmail.com>
- *              Humdinger <humdingerb@gmail.com>
- *
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-@import url("basic.css");
-
-html {
-    margin: 0px;
-    padding: 0px;
-    background: #FFF url(bg-page.png) top left repeat-x;
-}
-
-body {
-    line-height: 1.5;
-    margin: auto;
-    padding: 0px;
-    font-family: "DejaVu Sans", Arial, Helvetica, sans-serif;
-    min-width: 59em;
-    max-width: 70em;
-    color: #333333;
-}
-
-div.footer {
-    padding: 8px;
-    font-size: 11px;
-    text-align: center;
-    letter-spacing: 0.5px;
-}
-
-/* link colors and text decoration */
-
-a:link {
-    font-weight: bold;
-    text-decoration: none;
-    color: #dc3c01;
-}
-
-a:visited {
-    font-weight: bold;
-    text-decoration: none;
-    color: #892601;
-}
-
-a:hover, a:active {
-    text-decoration: underline;
-    color: #ff4500;
-}
-
-/* Some headers act as anchors, don't give them a hover effect */
-
-h1 a:hover, a:active {
-    text-decoration: none;
-    color: #0c3762;
-}
-
-h2 a:hover, a:active {
-    text-decoration: none;
-    color: #0c3762;
-}
-
-h3 a:hover, a:active {
-    text-decoration: none;
-    color: #0c3762;
-}
-
-h4 a:hover, a:active {
-    text-decoration: none;
-    color: #0c3762;
-}
-
-a.headerlink {
-    color: #a7ce38;
-    padding-left: 5px;
-}
-
-a.headerlink:hover {
-    color: #a7ce38;
-}
-
-/* basic text elements */
-
-div.content {
-    margin-top: 20px;
-    margin-left: 40px;
-    margin-right: 40px;
-    margin-bottom: 50px;
-    font-size: 0.9em;
-}
-
-/* heading and navigation */
-
-div.header {
-    position: relative;
-    left: 0px;
-    top: 0px;
-    height: 85px;
-    /* background: #eeeeee; */
-    padding: 0 40px;
-}
-div.header h1 {
-    font-size: 1.6em;
-    font-weight: normal;
-    letter-spacing: 1px;
-    color: #0c3762;
-    border: 0;
-    margin: 0;
-    padding-top: 15px;
-}
-div.header h1 a {
-    font-weight: normal;
-    color: #0c3762;
-}
-div.header h2 {
-    font-size: 1.3em;
-    font-weight: normal;
-    letter-spacing: 1px;
-    text-transform: uppercase;
-    color: #aaa;
-    border: 0;
-    margin-top: -3px;
-    padding: 0;
-}
-
-div.header img.rightlogo {
-    float: right;
-}
-
-
-div.title {
-    font-size: 1.3em;
-    font-weight: bold;
-    color: #0c3762;
-    border-bottom: dotted thin #e0e0e0;
-    margin-bottom: 25px;
-}
-div.topnav {
-    /* background: #e0e0e0; */
-}
-div.topnav p {
-    margin-top: 0;
-    margin-left: 40px;
-    margin-right: 40px;
-    margin-bottom: 0px;
-    text-align: right;
-    font-size: 0.8em;
-}
-div.bottomnav {
-    background: #eeeeee;
-}
-div.bottomnav p {
-    margin-right: 40px;
-    text-align: right;
-    font-size: 0.8em;
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-
-a.uplink {
-    font-weight: normal;
-}
-
-
-/* contents box */
-
-table.index {
-    margin: 0px 0px 30px 30px;
-    padding: 1px;
-    border-width: 1px;
-    border-style: dotted;
-    border-color: #e0e0e0;
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-    font-weight: bold;
-    font-size: 1.1em;
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-table.index a:link, table.index a:visited {
-    font-weight: normal;
-    text-decoration: none;
-    color: #dc3c01;
-}
-table.index a:hover, table.index a:active {
-    text-decoration: underline;
-    color: #ff4500;
-}
-
-
-/* Haiku User Guide styles and layout */
-
-/* Rounded corner boxes */
-/* Common declarations */
-div.admonition {
-    -webkit-border-radius: 10px;
-    -khtml-border-radius: 10px;
-    -moz-border-radius: 10px;
-    border-radius: 10px;
-    border-style: dotted;
-    border-width: thin;
-    border-color: #dcdcdc;
-    padding: 10px 15px 10px 15px;
-    margin-bottom: 15px;
-    margin-top: 15px;
-}
-div.note {
-    padding: 10px 15px 10px 80px;
-    background: #e4ffde url(alert_info_32.png) 15px 15px no-repeat;
-    min-height: 42px;
-}
-div.warning {
-    padding: 10px 15px 10px 80px;
-    background: #fffbc6 url(alert_warning_32.png) 15px 15px no-repeat;
-    min-height: 42px;
-}
-div.seealso {
-    background: #e4ffde;
-}
-
-/* More layout and styles */
-h1 {
-    font-size: 1.3em;
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-h3 {
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-    color: #0c3762;
-    margin-top: 30px;
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-h4 {
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-    font-weight: normal;
-    color: #0c3762;
-    margin-top: 30px;
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-
-p {
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-}
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-p.last {
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-ol {
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-ul {
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-li {
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-div.content ul > li {
-    -moz-background-clip:border;
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-    -moz-background-origin:padding;
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-hr {
-    border-top: 1px solid #ccc;
-    border-bottom: 0;
-    border-right: 0;
-    border-left: 0;
-    margin-bottom: 10px;
-    margin-top: 20px;
-}
-
-/* printer only pretty stuff */
-@media print {
-    .noprint {
-        display: none;
-    }
-    /* for acronyms we want their definitions inlined at print time */
-    acronym[title]:after {
-        font-size: small;
-        content: " (" attr(title) ")";
-        font-style: italic;
-    }
-    /* and not have mozilla dotted underline */
-    acronym {
-        border: none;
-    }
-    div.topnav, div.bottomnav, div.header, table.index {
-        display: none;
-    }
-    div.content {
-        margin: 0px;
-        padding: 0px;
-    }
-    html {
-        background: #FFF;
-    }
-}
-
-.viewcode-back {
-    font-family: "DejaVu Sans", Arial, Helvetica, sans-serif;
-}
-
-div.viewcode-block:target {
-    background-color: #f4debf;
-    border-top: 1px solid #ac9;
-    border-bottom: 1px solid #ac9;
-    margin: -1px -10px;
-    padding: 0 12px;
-}
-
-/* math display */
-div.math p {
-    text-align: center;
-}

doc/html/_static/style.css

@@ -0,0 +1,5 @@
+/* dynamic content width, see https://stackoverflow.com/questions/23211695/modifying-content-width-of-the-sphinx-theme-read-the-docs */
+
+.wy-nav-content {
+    max-width: none;
+}

doc/html/acknowledgement.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Acknowledgements &mdash; musrfit 1.9.0 documentation</title>
+  <title>Acknowledgements &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -30,7 +30,9 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Bugtracking" href="bugtracking.html" />
-    <link rel="prev" title="MusrRoot - an Extensible Open File Format for μSR" href="musr-root.html" /> 
+    <link rel="prev" title="MusrRoot - an Extensible Open File Format for μSR" href="musr-root.html" />
+    <link href="_static/style.css" rel="stylesheet" type="text/css">
+
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -94,6 +96,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -198,7 +201,7 @@ extremely competent way to deal with his projects as well as to deal with the ch
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -220,7 +223,7 @@ extremely competent way to deal with his projects as well as to deal with the ch
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/any2many.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>any2many - a Universal μSR-file-format converter &mdash; musrfit 1.9.0 documentation</title>
+  <title>any2many - a Universal μSR-file-format converter &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -29,8 +29,10 @@
   <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="MusrRoot - an Extensible Open File Format for μSR" href="musr-root.html" />
-    <link rel="prev" title="msr2data - A Program for Automatically Processing Multiple musrfit msr Files" href="msr2data.html" /> 
+    <link rel="next" title="Short description and references to the supported file-formats" href="file-formats.html" />
+    <link rel="prev" title="msr2data - A Program for Automatically Processing Multiple musrfit msr Files" href="msr2data.html" />
+    <link href="_static/style.css" rel="stylesheet" type="text/css">
+
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -94,6 +96,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -175,7 +178,7 @@ For a detailed description see <a class="reference internal" href="user-manual.h
   
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
       
-        <a href="musr-root.html" class="btn btn-neutral float-right" title="MusrRoot - an Extensible Open File Format for μSR" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
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@@ -188,7 +191,7 @@ For a detailed description see <a class="reference internal" href="user-manual.h
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Jun 24, 2024.
 
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@@ -210,7 +213,7 @@ For a detailed description see <a class="reference internal" href="user-manual.h
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',