path-run-name in RUN block of the msr-file can now handle spaces.

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 1.9.3 LANGUAGES C CXX)
+project(musrfit VERSION 1.9.7 LANGUAGES C CXX)
 
 #--- musrfit specific options -------------------------------------------------
 option(nexus "build optional NeXus support. Needed for ISIS" OFF)
@@ -249,6 +249,8 @@ set(CMAKE_INSTALL_RPATH "${rpath}")
 add_subdirectory(src)
 
 #--- write summary of the installation
+cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+
 message("")
 message("|-----------------------------------------------------------------------|")
 message("|                                                                       |")
@@ -256,8 +258,9 @@ message("|                            Summary
 message("|                                                                       |")
 message("|-----------------------------------------------------------------------|")
 message("")
-message(" System: ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
+message(" System:    ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
-message(" -------")
+message(" Processor: ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})")
+message(" ----------")
 message("")
 message(" musrfit Version: ${musrfit_VERSION}")
 message(" ----------------")

ChangeLog

@@ -12,6 +12,27 @@ or
 
 https://bitbucket.org/muonspin/musrfit/commits/all
 
+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
 =============================
 

cmake/configure_musrfit_version_file.cmake.in

@@ -9,7 +9,7 @@ set(MUSRFIT_VERSION "@MUSRFIT_VERSION@")
 # Get the current working branch
 execute_process(
   COMMAND git rev-parse --abbrev-ref HEAD
-  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+  WORKING_DIRECTORY ${SRC_DIR}
   OUTPUT_VARIABLE GIT_BRANCH
   OUTPUT_STRIP_TRAILING_WHITESPACE
 )
@@ -17,7 +17,7 @@ execute_process(
 # Get the latest abbreviated commit hash of the working branch
 execute_process(
   COMMAND git log -1 --pretty="%h, %ci"
-  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+  WORKING_DIRECTORY ${SRC_DIR}
   OUTPUT_VARIABLE GIT_CURRENT_SHA1
   OUTPUT_STRIP_TRAILING_WHITESPACE
 )

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: 28c8d31b3d0d7429fcebb7bd0074bdd3
+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: '1.9.3',
+    VERSION: '1.9.5',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

doc/html/acknowledgement.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Acknowledgements &mdash; musrfit 1.9.3 documentation</title>
+  <title>Acknowledgements &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -201,7 +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 Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -223,7 +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:'1.9.3',
+            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 1.9.3 documentation</title>
+  <title>any2many - a Universal μSR-file-format converter &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -191,7 +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 Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -213,7 +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:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/bugtracking.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Bugtracking &mdash; musrfit 1.9.3 documentation</title>
+  <title>Bugtracking &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -189,7 +189,7 @@ or send an e-mail to A. Suter at PSI.</p>
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -211,7 +211,7 @@ or send an e-mail to A. Suter at PSI.</p>
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/cite.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>How to Cite musrfit? &mdash; musrfit 1.9.3 documentation</title>
+  <title>How to Cite musrfit? &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -203,7 +203,7 @@
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -225,7 +225,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/file-formats.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Short description and references to the supported file-formats &mdash; musrfit 1.9.3 documentation</title>
+  <title>Short description and references to the supported file-formats &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -503,7 +503,7 @@ Between detectors, there will be an empty line.</p>
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -525,7 +525,7 @@ Between detectors, there will be an empty line.</p>
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/genindex.html

@@ -9,7 +9,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Index &mdash; musrfit 1.9.3 documentation</title>
+  <title>Index &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -753,7 +753,7 @@
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -775,7 +775,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/index.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Welcome to the musrfit documentation! &mdash; musrfit 1.9.3 documentation</title>
+  <title>Welcome to the musrfit documentation! &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -285,7 +285,7 @@
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -307,7 +307,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/msr2data.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>msr2data - A Program for Automatically Processing Multiple musrfit msr Files &mdash; musrfit 1.9.3 documentation</title>
+  <title>msr2data - A Program for Automatically Processing Multiple musrfit msr Files &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -518,7 +518,7 @@ fit serves as template for the second and so on. The template field stays empty
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -540,7 +540,7 @@ fit serves as template for the second and so on. The template field stays empty
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/mupp.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>mupp - μSR Parameter Plotter &mdash; musrfit 1.9.3 documentation</title>
+  <title>mupp - μSR Parameter Plotter &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -408,7 +408,7 @@ SCRIPT COMMANDS:
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -430,7 +430,7 @@ SCRIPT COMMANDS:
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/musr-root.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>MusrRoot - an Extensible Open File Format for μSR &mdash; musrfit 1.9.3 documentation</title>
+  <title>MusrRoot - an Extensible Open File Format for μSR &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -1007,7 +1007,7 @@ the entry has been added. The last token, <code class="docutils literal notransl
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -1029,7 +1029,7 @@ the entry has been added. The last token, <code class="docutils literal notransl
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/musredit.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>musredit: the GUI Based Interface to musrfit &mdash; musrfit 1.9.3 documentation</title>
+  <title>musredit: the GUI Based Interface to musrfit &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -634,7 +634,7 @@ the corresponding fit parameter value, except the phases where the step will be
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -656,7 +656,7 @@ the corresponding fit parameter value, except the phases where the step will be
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/search.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Search &mdash; musrfit 1.9.3 documentation</title>
+  <title>Search &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -185,7 +185,7 @@
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -207,7 +207,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/setup-dks.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Setting up musrfit / DKS: High Speed Fitting with GPU’s &mdash; musrfit 1.9.3 documentation</title>
+  <title>Setting up musrfit / DKS: High Speed Fitting with GPU’s &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -408,7 +408,7 @@ The only thing you need <code class="docutils literal notranslate"><span class="
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -430,7 +430,7 @@ The only thing you need <code class="docutils literal notranslate"><span class="
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/setup-standard.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Setting up musrfit on Different Platforms &mdash; musrfit 1.9.3 documentation</title>
+  <title>Setting up musrfit on Different Platforms &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -264,7 +264,7 @@ Currently the <code class="docutils literal notranslate"><span class="pre">MXML<
 <p>If <em>optionally</em> the editor and graphical user interface <code class="docutils literal notranslate"><span class="pre">musrgui</span></code> / <code class="docutils literal notranslate"><span class="pre">musredit</span></code> is going to be installed there is one further requirement:</p>
 <dl class="docutils" id="index-11">
 <dt><strong>Qt</strong></dt>
-<dd>A cross-platform application and user interface framework. <em>Required version ≥ 4.6</em> (musredit) (see <a class="reference external" href="http://qt.io/">Qt</a>). Currently the <strong>Qt5</strong> is the main development part. Qt6 just kicked in, but is not widely available yet.</dd>
+<dd>A cross-platform application and user interface framework. <em>Required version ≥ 4.6</em> (musredit) (see <a class="reference external" href="http://qt.io/">Qt</a>). Currently the  <strong>Qt5</strong> is still supported since some older distributions are not yet supporting Qt6. <strong>Qt6</strong> is the <em>main</em> development part. Should be available on all new major distributions.</dd>
 </dl>
 <p>Each of the following sections focusing on the installation of <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> on the different operating systems will also give a brief introduction on the installation of the requirements before the actual musrfit installation is described.</p>
 </div>
@@ -273,9 +273,8 @@ Currently the <code class="docutils literal notranslate"><span class="pre">MXML<
 <p>Before the installation procedure will be described, please note the following restrictions:</p>
 <dl class="docutils">
 <dt><strong>GNU/Linux</strong></dt>
-<dd>No serious problems are currently known. Tested distributions: <a class="reference external" href="https://www.redhat.com/de/technologies/linux-platforms/enterprise-linux">RHEL</a>, <a class="reference external" href="https://getfedora.org/">Fedora</a>,
+<dd>No serious problems are currently known. Tested distributions: <a class="reference external" href="https://www.redhat.com/de/technologies/linux-platforms/enterprise-linux">RHEL</a> (also <a class="reference external" href="https://almalinux.org/">Alma</a>, <a class="reference external" href="https://rockylinux.org/">Rocky</a>), <a class="reference external" href="https://getfedora.org/">Fedora</a>,
-<a class="reference external" href="https://www.debian.org/">Debian</a>, <a class="reference external" href="https://www.ubuntu.com/">Ubuntu</a>, <a class="reference external" href="https://linuxmint.com/">Mint</a>, <a class="reference external" href="https://en.opensuse.org/Main_Page">openSUSE</a>,
+<a class="reference external" href="https://www.debian.org/">Debian</a>, <a class="reference external" href="https://www.ubuntu.com/">Ubuntu</a>, <a class="reference external" href="https://linuxmint.com/">Mint</a>, <a class="reference external" href="https://en.opensuse.org/Main_Page">openSUSE</a>, and <a class="reference external" href="https://de.manjaro.org/">Manjaro</a>.</dd>
-and <cite>manjaro &lt;https://de.manjaro.org/&gt;</cite>.</dd>
 <dt><strong>Mac OS X/macOS</strong></dt>
 <dd>No serious problems are currently known for macOS ≥ 10.6. <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> is ARM M1 ready.</dd>
 <dt><strong>MS Windows</strong></dt>
@@ -307,11 +306,11 @@ from the shell will do the trick (never type the ‘$’ it is the shell prompt
 <p>For <strong>Qt5/Qt6</strong>:</p>
 <blockquote>
 <div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ yum install epel-release
-$ yum install git cmake boost-devel gsl-devel fftw-devel libxml2-devel qt5-qtbase-devel qt5-qtsvg-devel
+$ yum install git cmake boost-devel gsl-devel fftw-devel libxml2-devel qt6-qtbase-devel qt6-qtsvg-devel
 </pre></div>
 </div>
 </div></blockquote>
-<p>If using <code class="docutils literal notranslate"><span class="pre">Qt6</span></code> replace <code class="docutils literal notranslate"><span class="pre">qt5-qtbase-devel</span> <span class="pre">qt5-qtsvg-devel</span></code> by <code class="docutils literal notranslate"><span class="pre">qt6-qtbase-devel</span> <span class="pre">qt6-qtsvg-devel</span></code></p>
+<p>If using <code class="docutils literal notranslate"><span class="pre">Qt5</span></code>, since e.g. Qt6 is not available, replace <code class="docutils literal notranslate"><span class="pre">qt6-qtbase-devel</span> <span class="pre">qt6-qtsvg-devel</span></code> by <code class="docutils literal notranslate"><span class="pre">qt5-qtbase-devel</span> <span class="pre">qt5-qtsvg-devel</span></code></p>
 <p>When dealing with a distribution that uses the dpkg/apt package manager like <a class="reference external" href="https://www.debian.org/">Debian</a> or <a class="reference external" href="https://www.ubuntu.com/">Ubuntu</a>
 the installation would look like:</p>
 <p>For <strong>Qt4</strong> (deprecated):</p>
@@ -322,11 +321,11 @@ the installation would look like:</p>
 </div></blockquote>
 <p>For <strong>Qt5/Qt6</strong>:</p>
 <blockquote>
-<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ apt-get install git cmake libboost-dev libboost-filesystem-dev libboost-system-dev libgsl-dev libfftw3-dev libxml2-dev qt5-default qtbase5-dev libqt5svg5-dev
+<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ apt-get install git cmake libboost-dev libboost-filesystem-dev libboost-system-dev libgsl-dev libfftw3-dev libxml2-dev qt6-base-dev qt6-svg-dev
 </pre></div>
 </div>
 </div></blockquote>
-<p>If using <code class="docutils literal notranslate"><span class="pre">Qt6</span></code> replace <code class="docutils literal notranslate"><span class="pre">qt5-default</span> <span class="pre">qtbase5-dev</span> <span class="pre">libqt5svg5-dev</span></code> by <code class="docutils literal notranslate"><span class="pre">qt6-default</span> <span class="pre">qtbase6-dev</span> <span class="pre">libqt6svg6-dev</span></code></p>
+<p>If using <code class="docutils literal notranslate"><span class="pre">Qt5</span></code>, since e.g. Qt6 is not available, replace <code class="docutils literal notranslate"><span class="pre">qt6-base-dev</span> <span class="pre">qt6-svg-dev</span></code> by <code class="docutils literal notranslate"><span class="pre">qtbase5-dev</span> <span class="pre">libqt5svg5-dev</span></code></p>
 <p>Everyone should know best himself which is the way to install distribution software on the chosen distribution.</p>
 <p>In case the distribution does not include the required software it has to be compiled from the source files. This means either to download
 the source code from the corresponding website, or to clone the git repo. If you need to follow this line, please check the install details of the corresponding package.</p>
@@ -366,8 +365,8 @@ $ mkdir build
 $ <span class="nb">cd</span> build
 $ cmake -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">1</span> -DENABLE_MXML<span class="o">=</span><span class="m">0</span> ../code
 $ cmake --build ./ --clean-first
-$ <span class="c1"># make install needs either to be carried out as root or sudo depending on your linux flavour.</span>
+$ <span class="c1"># install needs either to be carried out as root or sudo depending on your linux flavour.</span>
-$ sudo make install
+$ sudo cmake --install ./
 </pre></div>
 </div>
 </div>
@@ -412,7 +411,7 @@ $ <span class="c1"># calling it with the option -j &lt;number&gt;, where &lt;num
 $ <span class="c1"># e.g. cmake --build ./ --clean-first -- -j8</span>
 $ cmake --build ./ --clean-first
 $ <span class="c1"># as a last step of the ROOT build process we need to install it</span>
-$ make install
+$ cmake --install ./
 </pre></div>
 </div>
 <p>What is still missing is that the system should be told where to find the <code class="docutils literal notranslate"><span class="pre">ROOT</span></code> installation, therefore the following is suggested:</p>
@@ -471,7 +470,7 @@ $ git pull
 $ <span class="nb">cd</span> build
 $ xargs rm &lt; install_manifest.txt
 $ cmake --build ./ --clean-first
-$ make install
+$ cmake --install ./
 </pre></div>
 </div>
 <p>As an alternative (if git is not available), the source code can also be downloaded from the following web-page: <a class="reference external" href="https://bitbucket.org/muonspin/musrfit/downloads">musrfit at bitbucket</a></p>
@@ -511,7 +510,7 @@ $ <span class="nb">cd</span> build
 $ cmake ../ -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$ROOTSYS</span> -Dnexus<span class="o">=</span><span class="m">1</span>
 <span class="c1"># below it is assumed that multiple cores are present, hence the -j8 option</span>
 $ cmake --build ./ --clean-first -- -j8
-$ make install
+$ cmake --install ./
 $ /sbin/ldconfig                                  <span class="c1"># (as superuser)</span>
 </pre></div>
 </div>
@@ -657,7 +656,7 @@ add a new line pointing to your local copy, <em>e.g.</em></p>
 </ol>
 <p>Then the MacPorts system should be set up and can be used to install additional software.</p>
 <p>The installation of the software mentioned above is then done in the terminal:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ sudo port -v install pkgconfig autoconf automake libtool cmake fftw-3 fftw-3-single gsl boost libxml2 qt6 qt6-qtsvg
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ sudo port -v install pkgconfig autoconf automake libtool cmake libomp fftw-3 fftw-3-single gsl boost libxml2 qt6 qt6-qtsvg
 </pre></div>
 </div>
 <p>With <code class="docutils literal notranslate"><span class="pre">Qt6</span></code>, <code class="docutils literal notranslate"><span class="pre">musredit</span></code> will be installed. If it happens that you used <code class="docutils literal notranslate"><span class="pre">musrgui</span></code> in the past,
@@ -668,6 +667,7 @@ please change over to <code class="docutils literal notranslate"><span class="pr
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ sudo port -v install hdf4 hdf5
 </pre></div>
 </div>
+<p><em>hdf4</em> is likely not available anymore.</p>
 <p><strong>Only NeXus Version ≥ 4.4 is support!</strong></p>
 <p>To get things compiled do:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ <span class="c1"># get and install NeXus</span>
@@ -678,9 +678,12 @@ $ <span class="c1"># next we will build NeXus out-of-source</span>
 $ <span class="nb">cd</span> nexus
 $ mkdir build
 $ <span class="nb">cd</span> build
+$ <span class="c1"># in case hdf4 is present</span>
 $ cmake -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">1</span> -DENABLE_MXML<span class="o">=</span><span class="m">0</span> ../code
-$ make
+$ <span class="c1"># in case hdf4 is **not** present</span>
-$ sudo make install
+$ cmake -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">0</span> -DENABLE_MXML<span class="o">=</span><span class="m">0</span> ../code
+$ cmake --build ./
+$ sudo cmake --install ./
 </pre></div>
 </div>
 </div>
@@ -728,7 +731,7 @@ $ <span class="c1"># make with the option -j &lt;number&gt;, where &lt;number&gt
 $ <span class="c1"># e.g. make -j8</span>
 $ cmake --build ./ --clean-first -- -j8
 $ <span class="c1"># make will take quite a while</span>
-$ make install
+$ cmake --install ./
 </pre></div>
 </div>
 <p>For further details see <a class="reference external" href="https://root.cern.ch/building-root">Installing ROOT from Source</a>.</p>
@@ -816,10 +819,11 @@ install it.</dd>
 </dl>
 <p>After installing the <code class="docutils literal notranslate"><span class="pre">Xcode</span></code> tools go to the <a class="reference external" href="https://brew.sh/">Homebrew</a> page, and follow the installation instructions there.</p>
 <p>The essential packages (called formulae) which you will need to install are</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cmake</span> <span class="n">boost</span> <span class="n">gsl</span> <span class="n">fftw</span> <span class="n">qt6</span> <span class="n">root</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cmake</span> <span class="n">libomp</span> <span class="n">boost</span> <span class="n">gsl</span> <span class="n">fftw</span> <span class="n">qt6</span> <span class="p">(</span><span class="n">root</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>For example to install <code class="docutils literal notranslate"><span class="pre">cmake</span></code> this is done the following way:</p>
+<p>The preferred installation of root would be from source (see below), hence it is set here in parenthesis.
+For example to install <code class="docutils literal notranslate"><span class="pre">cmake</span></code> this is done the following way:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ brew install cmake
 </pre></div>
 </div>
@@ -842,7 +846,7 @@ $ mkdir build
 $ <span class="nb">cd</span> build
 $ cmake ../code -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">0</span> -DENABLE_MXML<span class="o">=</span><span class="m">0</span>
 $ cmake --build ./ --clean-first -- -j8
-$ sudo make install
+$ sudo cmake --install ./
 </pre></div>
 </div>
 </div>
@@ -880,7 +884,7 @@ $ <span class="c1"># make with the option -j &lt;number&gt;, where &lt;number&gt
 $ <span class="c1"># e.g. make -j8</span>
 $ cmake --build ./ --clean-first -- -j8
 $ <span class="c1"># make will take quite a while</span>
-$ make install
+$ cmake --install ./
 </pre></div>
 </div>
 <p>For further details see <a class="reference external" href="https://root.cern.ch/building-root">Installing ROOT from Source</a>.</p>
@@ -993,7 +997,16 @@ If the value is set to <code class="docutils literal notranslate"><span class="p
 <dd>Will check if <code class="docutils literal notranslate"><span class="pre">OpenMP</span></code> support is possible, and if yes use it. The default is enabled</dd>
 </dl>
 <p>Normally it should not be necessary to make use of any of the options except for specifying the installation path with <code class="docutils literal notranslate"><span class="pre">-DCMAKE_INSTALL_PREFIX</span></code>.
-<code class="docutils literal notranslate"><span class="pre">musrfit</span></code> build with <code class="docutils literal notranslate"><span class="pre">cmake</span></code> takes the <code class="docutils literal notranslate"><span class="pre">out-of-source</span></code> approach. Therefore a typical configuration / make / install process including
+<code class="docutils literal notranslate"><span class="pre">musrfit</span></code> build with <code class="docutils literal notranslate"><span class="pre">cmake</span></code> takes the <code class="docutils literal notranslate"><span class="pre">out-of-source</span></code> approach.</p>
+<p>In order to have <strong>OpenMP</strong> available, which allows parallel processing of the fitter, you will need to guide <code class="docutils literal notranslate"><span class="pre">cmake</span></code> to where it can find it. For a <code class="docutils literal notranslate"><span class="pre">Homebrew</span></code> installation, this would be</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ <span class="nb">export</span> <span class="nv">OpenMP_ROOT</span><span class="o">=</span><span class="k">$(</span>brew --prefix<span class="k">)</span>/opt/libomp
+</pre></div>
+</div>
+<p>and for a <code class="docutils literal notranslate"><span class="pre">MacPorts</span></code> installation, something like</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ <span class="nb">export</span> <span class="nv">OpenMP_ROOT</span><span class="o">=</span>/opt/local/include/libomp
+</pre></div>
+</div>
+<p>Therefore a typical configuration / make / install process including
 <code class="docutils literal notranslate"><span class="pre">NeXus</span></code> support would look like</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
 $ mkdir build
@@ -1001,7 +1014,24 @@ $ <span class="nb">cd</span> build
 $ cmake ../ -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$ROOTSYS</span> -Dnexus<span class="o">=</span><span class="m">1</span>
 <span class="c1"># below it is assumed that multiple cores are present, hence the -j8 option</span>
 $ cmake --build ./ --clean-first -- -j8
-$ make install
+$ cmake --install ./
+$ /sbin/ldconfig                                  <span class="c1"># (as superuser)</span>
+</pre></div>
+</div>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">If you use <code class="docutils literal notranslate"><span class="pre">MacPorts</span></code> you will likely need to guide cmake where to find <code class="docutils literal notranslate"><span class="pre">qt6</span></code>.
+You will need to provide the path to the necessary <code class="docutils literal notranslate"><span class="pre">cmake</span></code> files. This is done
+from the command line via the switch <code class="docutils literal notranslate"><span class="pre">CMAKE_PREFIX_PATH</span></code>.
+The configuration, build, and install process might look like this:</p>
+</div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
+$ mkdir build
+$ <span class="nb">cd</span> build
+$ cmake ../ -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$ROOTSYS</span> -Dnexus<span class="o">=</span><span class="m">1</span> -DCMAKE_PREFIX_PATH<span class="o">=</span>/opt/local/libexec/qt6/lib/cmake
+<span class="c1"># below it is assumed that multiple cores are present, hence the -j8 option</span>
+$ cmake --build ./ --clean-first -- -j8
+$ cmake --install ./
 $ /sbin/ldconfig                                  <span class="c1"># (as superuser)</span>
 </pre></div>
 </div>
@@ -1095,7 +1125,7 @@ $ musrview test-histo-ROOT-NPP.msr
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -1117,7 +1147,7 @@ $ musrview test-histo-ROOT-NPP.msr
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/tutorial.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Tutorial for musrfit &mdash; musrfit 1.9.3 documentation</title>
+  <title>Tutorial for musrfit &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -527,7 +527,7 @@ For a complete description please refer to the manuals of <a class="reference in
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -549,7 +549,7 @@ For a complete description please refer to the manuals of <a class="reference in
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/user-libs.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Documentation of user libs (user functions) &mdash; musrfit 1.9.3 documentation</title>
+  <title>Documentation of user libs (user functions) &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -875,7 +875,7 @@ K(m)&amp;=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -897,7 +897,7 @@ K(m)&amp;=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/user-manual.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>User manual &mdash; musrfit 1.9.3 documentation</title>
+  <title>User manual &mdash; musrfit 1.9.5 documentation</title>
   
 
   
@@ -257,6 +257,26 @@
 <dt><strong>-u, –use-no-of-threads &lt;number&gt;</strong></dt>
 <dd>&lt;number&gt;: number of threads to be used (OpenMP). Needs to be &lt;= max. number of cores.
 If OpenMP is enable, the maximal number of cores is used, if it is not limited by this option.</dd>
+<dt><strong>-r, –reset</strong></dt>
+<dd><p class="first">reset startup <code class="docutils literal notranslate"><span class="pre">musrfit_startup.xml</span></code>, i.e. rewrite a default, and quit.
+The order of which <code class="docutils literal notranslate"><span class="pre">musrfit_startup.xml</span></code> is reset is:</p>
+<blockquote class="last">
+<div><ol class="arabic simple">
+<li>if present in the current dir.</li>
+<li>if present under <code class="docutils literal notranslate"><span class="pre">$HOME/.musrfit/</span></code></li>
+<li>if present under <code class="docutils literal notranslate"><span class="pre">$MUSRFITPATH/</span></code></li>
+<li>if present under <code class="docutils literal notranslate"><span class="pre">$ROOTSYS/</span></code></li>
+</ol>
+</div></blockquote>
+</dd>
+<dt><strong>-y, –yaml</strong></dt>
+<dd><p class="first">write fit results (<code class="docutils literal notranslate"><span class="pre">MINUIT2.OUTPUT</span></code>) into a yaml-file. Output <code class="docutils literal notranslate"><span class="pre">&lt;msr-file&gt;.yaml</span></code>.</p>
+<p class="last">The motivation for storing parameter information in this (hierarchical) manner is to provide easy access to details that are cumbersome
+to store/access in tabular formats (e.g., <code class="docutils literal notranslate"><span class="pre">CSV</span></code> or <code class="docutils literal notranslate"><span class="pre">TSV</span></code>). This is especially true for the parameter covariance/correlation matrices.
+The advantage is evident when processing the contents of the <code class="docutils literal notranslate"><span class="pre">.yaml</span></code> output, which can be easily accomplished using one of the
+YAML parsers implemented in your favourite programming language (see, e.g., <a class="reference external" href="https://yaml.org/">https://yaml.org/</a> for a list of options). As an example,
+this can be achieved in <code class="docutils literal notranslate"><span class="pre">Python</span></code> using the <code class="docutils literal notranslate"><span class="pre">PyYAML</span></code>.</p>
+</dd>
 <dt><strong>–dump &lt;type&gt;</strong></dt>
 <dd>is writing a data file with the fit data and the theory; &lt;type&gt; can be ascii (data in columns) or root (data in ROOT histograms).</dd>
 <dt><strong>–timeout &lt;timeout_tag&gt;</strong></dt>
@@ -2874,7 +2894,7 @@ The syntax here is attribute driven</li>
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Apr 23, 2024.
+      Last updated on Jun 24, 2024.
 
     </p>
   </div>
@@ -2896,7 +2916,7 @@ The syntax here is attribute driven</li>
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.3',
+            VERSION:'1.9.5',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

src/classes/PFitter.cpp

@@ -39,9 +39,10 @@
 #include <iomanip>
 #include <fstream>
 #include <limits>
-
 #include <cmath>
 
+#include <boost/variant/variant.hpp>
+
 #include <sys/time.h>
 
 #include "Minuit2/FunctionMinimum.h"
@@ -54,6 +55,7 @@
 #include "Minuit2/MnPrint.h"
 #include "Minuit2/MnScan.h"
 #include "Minuit2/MnSimplex.h"
+#include "Minuit2/MnStrategy.h"
 #include "Minuit2/MnUserParameterState.h"
 #include "Minuit2/MinosError.h"
 
@@ -264,8 +266,8 @@ UInt_t PSectorChisq::GetNDF(UInt_t idx)
  * \param runListCollection pointer of the run list collection (pre-processed historgrams)
  * \param chisq_only flag: true=calculate chisq only (no fitting)
  */
-PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bool_t chisq_only) :
+PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bool_t chisq_only, Bool_t yaml_out) :
-  fChisqOnly(chisq_only), fRunInfo(runInfo), fRunListCollection(runListCollection)
+  fChisqOnly(chisq_only), fYamlOut(yaml_out), fRunInfo(runInfo), fRunListCollection(runListCollection)
 {
   // initialize variables
   fIsScanOnly = true;
@@ -1762,7 +1764,7 @@ Bool_t PFitter::ExecuteMigrad()
 
   // create migrad object
   // strategy is by default = 'default'
-  ROOT::Minuit2::MnMigrad migrad((*fFitterFcn), fMnUserParams, fStrategy);
+  ROOT::Minuit2::MnMigrad migrad((*fFitterFcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
 
   // minimize
   // maxfcn is MINUIT2 Default maxfcn
@@ -1838,7 +1840,7 @@ Bool_t PFitter::ExecuteMinimize()
 
   // create minimizer object
   // strategy is by default = 'default'
-  ROOT::Minuit2::MnMinimize minimize((*fFitterFcn), fMnUserParams, fStrategy);
+  ROOT::Minuit2::MnMinimize minimize((*fFitterFcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
 
   // minimize
   // maxfcn is MINUIT2 Default maxfcn
@@ -2473,6 +2475,122 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
       ccorr->Write("ccorr", TObject::kOverwrite, sizeof(ccorr));
       hcorr->Write("hcorr", TObject::kOverwrite, sizeof(hcorr));
       ff.Close();
+
+      if (fYamlOut) {
+        // write the fit results to an easy-to-read/parse yaml file
+        // note: the block names follow those used by Python library iminuit
+        // https://github.com/scikit-hep/iminuit
+
+        // dynamically name the yaml output file
+        // https://stackoverflow.com/a/25389052
+        std::string yaml_filename(fRunInfo->GetFileName().Data());
+        const std::string msr_ext(".msr");
+        yaml_filename.replace(yaml_filename.find(msr_ext), msr_ext.length(),
+                              ".yaml");
+
+        // define yaml's 2-space indentation
+        const std::string yaml_indent("  ");
+
+        // open the yaml file for writing
+        std::ofstream yaml_file(yaml_filename);
+
+        // number formatting of the output
+        yaml_file << std::scientific << std::setprecision(16);
+
+        // write the parameter values
+        yaml_file << "values:\n";
+        for (unsigned int i = 0; i < fParams.size(); ++i) {
+            yaml_file << yaml_indent << fParams[i].fName.Data() << ": "
+                      << fParams[i].fValue << "\n";
+        }
+
+        // write the parabolic errors
+        yaml_file << "errors:\n";
+        for (unsigned int i = 0; i < fParams.size(); ++i) {
+            yaml_file << yaml_indent << fParams[i].fName.Data() << ": "
+                      << fMnUserParams.Error(i) << "\n";
+        }
+
+        // write the minos errors
+        yaml_file << "mnerrors:\n";
+        for (unsigned int i = 0; i < fParams.size(); ++i) {
+            // use boost's implementation of a variant, which can be streamed by
+            // default - see: https://stackoverflow.com/q/47168477
+            boost::variant<double, std::string> positive_error, negative_error;
+            if (fParams[i].fPosErrorPresent) {
+                positive_error = fParams[i].fPosError;
+                negative_error = fParams[i].fStep;
+            } else {
+                positive_error = "null";
+                negative_error = "null";
+            }
+
+            yaml_file << yaml_indent << fParams[i].fName.Data() << ":\n";
+            yaml_file << yaml_indent << yaml_indent
+                      << "positive: " << positive_error << "\n";
+            yaml_file << yaml_indent << yaml_indent
+                      << "negative: " << negative_error << "\n";
+        }
+
+        // write the parameter limits
+        yaml_file << "limits:\n";
+        for (unsigned int i = 0; i < fParams.size(); ++i) {
+            // use boost's implementation of a variant, which can be streamed by
+            // default - see: https://stackoverflow.com/q/47168477
+            boost::variant<double, std::string> upper_limit, lower_limit;
+            if (fParams[i].fLowerBoundaryPresent) {
+                lower_limit = fParams[i].fLowerBoundary;
+            } else {
+                lower_limit = "null";
+            }
+            if (fParams[i].fUpperBoundaryPresent) {
+                upper_limit = fParams[i].fUpperBoundary;
+            } else {
+                upper_limit = "null";
+            }
+
+            yaml_file << yaml_indent << fParams[i].fName.Data() << ":\n";
+            yaml_file << yaml_indent << yaml_indent << "lower: " << lower_limit
+                      << "\n";
+            yaml_file << yaml_indent << yaml_indent << "upper: " << upper_limit
+                      << "\n";
+        }
+
+        // write if the parameter is fixed
+        yaml_file << "fixed:\n";
+        for (unsigned int i = 0; i < fParams.size(); ++i) {
+            std::string is_fixed = fParams[i].fStep == 0.0 ? "true" : "false";
+            yaml_file << yaml_indent << fParams[i].fName.Data() << ": " << is_fixed
+                      << "\n";
+        }
+
+        // write the covariance matrix (omitting fixed parameters)
+        yaml_file << "covariance:\n";
+        for (unsigned int i = 0; i < cov.Nrow(); ++i) {
+            yaml_file << yaml_indent << mnState.Name(parNo[i]) << ":\n";
+            for (unsigned int j = 0; j < cov.Nrow(); ++j) {
+                yaml_file << yaml_indent << yaml_indent << mnState.Name(parNo[j])
+                          << ": " << cov(i, j) << "\n";
+            }
+        }
+
+        // write the correlation matrix (omitting fixed parameters)
+        yaml_file << "correlation:\n";
+        for (unsigned int i = 0; i < cov.Nrow(); ++i) {
+            yaml_file << yaml_indent << mnState.Name(parNo[i]) << ":\n";
+            for (unsigned int j = 0; j < cov.Nrow(); ++j) {
+                double correlation =
+                        i == j ? 1.0
+                               : cov(i, j) / (fMnUserParams.Error(parNo[i]) *
+                                              fMnUserParams.Error(parNo[j]));
+                yaml_file << yaml_indent << yaml_indent << mnState.Name(parNo[j])
+                          << ": " << correlation << "\n";
+            }
+        }
+
+        // close the yaml file
+        yaml_file.close();
+      }
     }
     parNo.clear(); // clean up
   } else {
@@ -2539,7 +2657,7 @@ Bool_t PFitter::ExecuteSimplex()
 
   // create minimizer object
   // strategy is by default = 'default'
-  ROOT::Minuit2::MnSimplex simplex((*fFitterFcn), fMnUserParams, fStrategy);
+  ROOT::Minuit2::MnSimplex simplex((*fFitterFcn), fMnUserParams, ROOT::Minuit2::MnStrategy{fStrategy});
 
   // minimize
   // maxfcn is 10*MINUIT2 Default maxfcn

src/classes/PFunction.cpp

@@ -188,13 +188,28 @@ void PFunction::FillFuncEvalTree(iter_t const& i, PFuncTreeNode &node)
     node.fID = PFunctionGrammar::constGammaMuID; // keep the ID
     node.fDvalue = GAMMA_BAR_MUON; // keep the value
   } else if (i->value.id() == PFunctionGrammar::constFieldID) { // handle constant field from meta data
+    str = std::string(i->value.begin(), i->value.end()); // get string
+    boost::algorithm::trim(str);
+    if (strstr(str.c_str(), "-"))
+      node.fSign = true;
     node.fID = PFunctionGrammar::constFieldID; // keep the ID
   } else if (i->value.id() == PFunctionGrammar::constEnergyID) { // handle constant energy from meta data
+    str = std::string(i->value.begin(), i->value.end()); // get string
+    boost::algorithm::trim(str);
+    if (strstr(str.c_str(), "-"))
+      node.fSign = true;
     node.fID = PFunctionGrammar::constEnergyID; // keep the ID
   } else if (i->value.id() == PFunctionGrammar::constTempID) { // handle constant temperature from meta data
     str = std::string(i->value.begin(), i->value.end()); // get string
     boost::algorithm::trim(str);
-    status = sscanf(str.c_str(), "T%d", &ivalue); // convert string to temperature index
+    std::string pstr;
+    if (strstr(str.c_str(), "-")) {
+      node.fSign = true;
+      pstr = "-T%d";
+    } else {
+      pstr = "T%d";
+    }
+    status = sscanf(str.c_str(), pstr.c_str(), &ivalue); // convert string to temperature index
     node.fID = PFunctionGrammar::constTempID; // keep the ID
     node.fIvalue = ivalue; // Temp idx
   } else if (i->value.id() == PFunctionGrammar::parameterID) { // handle parameter number
@@ -432,21 +447,30 @@ Double_t PFunction::EvalNode(PFuncTreeNode &node)
   } else if (node.fID == PFunctionGrammar::constGammaMuID) {
     return node.fDvalue;
   } else if (node.fID == PFunctionGrammar::constFieldID) {
-    return fMetaData.fField;
+    Double_t dval = fMetaData.fField;
+    if (node.fSign)
+      dval *= -1.0;
+    return dval;
   } else if (node.fID == PFunctionGrammar::constEnergyID) {
     if (fMetaData.fEnergy == PMUSR_UNDEFINED) {
       std::cerr << std::endl << "**PANIC ERROR**: PFunction::EvalNode: energy meta data not available." << std::endl;
       std::cerr << std::endl;
       exit(0);
     }
-    return fMetaData.fEnergy;
+    Double_t dval = fMetaData.fEnergy;
+    if (node.fSign)
+      dval *= -1.0;
+    return dval;
   } else if (node.fID == PFunctionGrammar::constTempID) {
     if (node.fIvalue >= fMetaData.fTemp.size()) {
       std::cerr << std::endl << "**PANIC ERROR**: PFunction::EvalNode: Temp idx=" << node.fIvalue << " requested which is >= #Temp(s)=" << fMetaData.fTemp.size() << " available." << std::endl;
       std::cerr << std::endl;
       exit(0);
     }
-    return fMetaData.fTemp[node.fIvalue];
+    Double_t dval = fMetaData.fTemp[node.fIvalue];
+    if (node.fSign)
+      dval *= -1.0;
+    return dval;
   } else if (node.fID == PFunctionGrammar::parameterID) {
     Double_t dval;
     if (node.fSign)
@@ -609,10 +633,10 @@ void PFunction::EvalTreeForStringExpression(iter_t const& i, bool funcFlag)
     fFuncString += "Pi";
   } else if (i->value.id() == PFunctionGrammar::constGammaMuID) {
     fFuncString += "gamma_mu";
-  } else if (i->value.id() == PFunctionGrammar::constFieldID) {
+  } else if (i->value.id() == PFunctionGrammar::constFieldID) {     
-    fFuncString += "B";
+    fFuncString += boost::algorithm::trim_copy(std::string(i->value.begin(), i->value.end())).c_str();
   } else if (i->value.id() == PFunctionGrammar::constEnergyID) {
-    fFuncString += "EN";
+    fFuncString += boost::algorithm::trim_copy(std::string(i->value.begin(), i->value.end())).c_str();
   } else if (i->value.id() == PFunctionGrammar::constTempID) {
     assert(i->children.size() == 0);
     fFuncString += boost::algorithm::trim_copy(std::string(i->value.begin(), i->value.end())).c_str();

src/classes/PMsr2Data.cpp

@@ -140,29 +140,32 @@ int PMsr2Data::DetermineRunNumberDigits(unsigned int runNo, bool normalMode) con
     strLine.str(line);
     strLine >> firstOnLine;
     if (!to_lower_copy(firstOnLine).compare("run")) {
-      firstOnLine.clear();
+      // for path-names with spaces
-      strLine >> firstOnLine;
+      std::string::size_type loc{0};
-      std::string::size_type loc = firstOnLine.rfind(tempRunNumber.str());
+      while (!strLine.eof()) {
-      if ( loc != std::string::npos ) {
+        firstOnLine.clear();
-        while ( loc > 0 ) {
+        strLine >> firstOnLine;
-          if (isdigit(firstOnLine.at(--loc))) {
+        loc = firstOnLine.rfind(tempRunNumber.str());
-            ++fRunNumberDigits;
+        if ( loc != std::string::npos ) {
-          } else {
+          while ( loc > 0 ) {
-            break;
+            if (isdigit(firstOnLine.at(--loc))) {
+              ++fRunNumberDigits;
+            } else {
+              break;
+            }
           }
+          in->close();
+          fRunVectorIter = fRunVector.begin(); // set back the runlist-iterator which might have changed during the search for the correct file
+          return 0;
         }
-        in->close();
-        fRunVectorIter = fRunVector.begin(); // set back the runlist-iterator which might have changed during the search for the correct file
-        return 0;
-      } else {
-         std::cerr << std::endl << ">> msr2data: **ERROR** The first processed run file number does not match the \"file index\"!";
-         std::cerr << std::endl << ">> msr2data: **ERROR** The number of digits to be used for formatting the run numbers cannot be determined!";
-         std::cerr << std::endl << ">> msr2data: **ERROR** Please check the first msr-file that should be processed;";
-         std::cerr << std::endl << ">> msr2data: **ERROR** this is either some template or the first existing file from the run list.";
-         std::cerr << std::endl;
-         in->close();
-         return -2;
       }
+      std::cerr << std::endl << ">> msr2data: **ERROR** The first processed run file number does not match the \"file index\"!";
+      std::cerr << std::endl << ">> msr2data: **ERROR** The number of digits to be used for formatting the run numbers cannot be determined!";
+      std::cerr << std::endl << ">> msr2data: **ERROR** Please check the first msr-file that should be processed;";
+      std::cerr << std::endl << ">> msr2data: **ERROR** this is either some template or the first existing file from the run list.";
+      std::cerr << std::endl;
+      in->close();
+      return -2;
     }
   }
   std::cerr << std::endl << ">> msr2data: **ERROR** Please check the first msr-file that should be processed;";
@@ -558,11 +561,23 @@ bool PMsr2Data::PrepareNewInputFile(unsigned int tempRun, bool calledFromGlobalM
     strLine.str(line);
     strLine >> firstOnLine;
     if (!to_lower_copy(firstOnLine).compare("run")) {
-      strLine >> firstOnLine;
+      // needed for path-fln with spaces
-      std::string::size_type loc = firstOnLine.rfind(tempRunNumber.str());
+      std::string::size_type loc;
-      if ( loc != std::string::npos ) {
+      std::string sstr{""};
-        firstOnLine.replace(loc, fRunNumberDigits, newRunNumber.str());
+      firstOnLine.clear();
-      } else {
+      while (!strLine.eof()) {
+        strLine >> sstr;
+        if (firstOnLine.empty())
+          firstOnLine = sstr;
+        else
+          firstOnLine += " " + sstr;
+        loc = firstOnLine.rfind(tempRunNumber.str());
+        if ( loc != std::string::npos ) {
+          firstOnLine.replace(loc, fRunNumberDigits, newRunNumber.str());
+          break;
+        }
+      }
+      if (strLine.eof()) {
         std::cerr << std::endl << ">> msr2data: **WARNING** The template run file number does not match the \"file index\"";
         std::cerr << std::endl << ">> msr2data: **WARNING** Unexpected things will happen... (for sure)";
         std::cerr << std::endl;
@@ -694,9 +709,16 @@ bool PMsr2Data::PrepareGlobalInputFile(unsigned int tempRun, const std::string &
       msrParamList->at(i).fIsGlobal = true;
       ++fNumGlobalParam;
     }
-    // std::cout << "debug> " << msrParamList->at(i).fNo << ": " << msrParamList->at(i).fName.Data() << " is global: " << msrParamList->at(i).fIsGlobal << std::endl;
   }
 
+  // there should be at least one run specific parameter, otherwise the GLOBAL option doesn't make sense
+  if (fNumSpecParam == 0) {
+    std::cout << ">> msr2data: **ERROR** found NO run specific parameter, hence the GLOBAL option doesn't make sense." << std::endl;
+    std::cout << ">> msr2data:   Could it be, that your run specific labling is < 4 digits? Please check your msr-Input-File." << std::endl;
+    return false;
+  }
+
+
   // check if parameters have been sorted correctly from the beginning
   bool wasSorted(true);
   for (unsigned int i(0); i < fNumGlobalParam; ++i) {
@@ -1793,6 +1815,9 @@ int PMsr2Data::WriteOutput(const std::string &outfile, const std::vector<unsigne
       rawRunData = fDataHandler->GetRunData((*msrRunList)[0].GetRunName()->Data());
     }
 
+    if (rawRunData == nullptr)
+      return -1;
+
     switch (rawRunData->GetNoOfTemperatures()) {
       case 1:
         dataParamNames.push_back("dataT");

src/classes/PMsrHandler.cpp

@@ -3244,7 +3244,7 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines)
   while ((iter != lines.end()) && !error) {
     // remove potential comment at the end of lines
     str = iter->fLine;
-    Ssiz_t idx = str.Index("#");
+    Ssiz_t idx = str.Index("(");
     if (idx != -1)
       str.Remove(idx);
 
@@ -3274,23 +3274,29 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines)
       }
 
       // get run name, beamline, institute, and file-format
+      // the path/filename could potentially contain spaces! Hence the run name needs to be reconstructed from the parsing
       if (tokens->GetEntries() < 5) {
         error = true;
       } else {
         // run name
-        ostr = dynamic_cast<TObjString*>(tokens->At(1));
+        str = TString("");
-        str = ostr->GetString();
+        for (Int_t i=1; i<tokens->GetEntries()-3; i++) {
+          ostr = dynamic_cast<TObjString*>(tokens->At(i));
+          str += ostr->GetString();
+          if (i<tokens->GetEntries()-4)
+            str += TString(" ");
+        }
         param.SetRunName(str);
         // beamline
-        ostr = dynamic_cast<TObjString*>(tokens->At(2));
+        ostr = dynamic_cast<TObjString*>(tokens->At(tokens->GetEntries()-3));
         str = ostr->GetString();
         param.SetBeamline(str);
         // institute
-        ostr = dynamic_cast<TObjString*>(tokens->At(3));
+        ostr = dynamic_cast<TObjString*>(tokens->At(tokens->GetEntries()-2));
         str = ostr->GetString();
         param.SetInstitute(str);
         // data file format
-        ostr = dynamic_cast<TObjString*>(tokens->At(4));
+        ostr = dynamic_cast<TObjString*>(tokens->At(tokens->GetEntries()-1));
         str = ostr->GetString();
         param.SetFileFormat(str);
       }

src/classes/PMusrCanvas.cpp

@@ -939,6 +939,7 @@ void PMusrCanvas::HandleCmdKey(Int_t event, Int_t x, Int_t y, TObject *selected)
 
   if (fBatchMode) {
     if (fStartWithAvg) { // this is needed to get the averaging in the batch mode
+      fAveragedView = fStartWithAvg;
       HandleAverage();
       PlotAverage(true);
     }

src/classes/PRunDataHandler.cpp

@@ -3697,6 +3697,8 @@ Bool_t PRunDataHandler::ReadAsciiFile()
 {
   Bool_t success = true;
 
+std::cout << "as35> in ReadAsciiFile() ..." << std::endl;
+
   // open file
   std::ifstream f;
 
@@ -3848,7 +3850,14 @@ Bool_t PRunDataHandler::ReadAsciiFile()
           break;
         }
         ey = ostr->GetString().Atof();
+        if (ey == 0) {
+          std::cerr << std::endl << ">> PRunDataHandler::ReadAsciiFile **WARNING** line no " << lineNo << ": error y = 0 which doesn't make sense. Will set it to 1.0. Please check!!";
+          std::cerr << std::endl;
+          ey = 1.0;
+        }
       } else {
+        std::cerr << std::endl << ">> PRunDataHandler::ReadAsciiFile **WARNING** line no " << lineNo << ": error y = 0 which doesn't make sense. Will set it to 1.0. Please check!!";
+        std::cerr << std::endl;
         ey = 1.0;
       }
 
@@ -4357,7 +4366,7 @@ Bool_t PRunDataHandler::ReadDatFile()
   // open file
   std::ifstream f;
 
-  // open db-file
+  // open dat-file
   f.open(fRunPathName.Data(), std::ifstream::in);
   if (!f.is_open()) {
     std::cerr << std::endl << ">> PRunDataHandler::ReadDatFile **ERROR** Couldn't open data file (" << fRunPathName.Data() << ") for reading, sorry ...";
@@ -4456,6 +4465,12 @@ Bool_t PRunDataHandler::ReadDatFile()
           idx++;
         } else { // error value
           if (isData[i-1] == 1) { // Err or PosErr hence keep it
+            if (dval == 0.0) {
+              std::cout << std::endl << ">> PRunDataHandler::ReadDatFile **WARNING** found Err value = 0. Doesn't make sense! Will set it to 1. Please check!";
+              std::cerr << std::endl << ">>  in line: " << lineNo;
+              std::cerr << std::endl;
+              dval = 1.0;
+            }
             runData.fDataNonMusr.AppendSubErrData(idx-1, dval);
           }
         }
@@ -4470,11 +4485,11 @@ Bool_t PRunDataHandler::ReadDatFile()
 
   f.close();
 
-  // got through all the data sets and if there is NO error vector set it to '0.0'
+  // got through all the data sets and if there is NO error vector set it to '1.0'
   for (UInt_t i=0; i<noOfDataSets; i++) {
     if (runData.fDataNonMusr.GetErrData()->at(i).size() == 0) {
       for (UInt_t j=0; j<runData.fDataNonMusr.GetData()->at(i).size(); j++) {
-        runData.fDataNonMusr.AppendSubErrData(i, 0.0);
+        runData.fDataNonMusr.AppendSubErrData(i, 1.0);
       }
     }
   }

src/classes/PStartupHandler.cpp

@@ -765,7 +765,7 @@ Bool_t PStartupHandler::WriteDefaultStartupFile(bool reset_startup_file)
   fout << "            <!-- Color as RGB coded string -->" << std::endl;
   fout << "            <color>0,0,0</color>      <!-- kBlack -->" << std::endl;
   fout << "            <color>255,0,0</color>    <!-- kRed -->" << std::endl;
-  fout << "            <color>0,255,0</color>    <!-- kGreen -->" << std::endl;
+  fout << "            <color>0,153,0</color>    <!-- kGreen+2 -->" << std::endl;
   fout << "            <color>0,0,255</color>    <!-- kBlue -->" << std::endl;
   fout << "            <color>255,0,255</color>  <!-- kMagenta -->" << std::endl;
   fout << "            <color>0,255,255</color>  <!-- kCyan -->" << std::endl;

src/external/libZFRelaxation/CMakeLists.txt

@@ -53,14 +53,10 @@ target_include_directories(
 )
 
 #--- add library dependencies -------------------------------------------------
-if (OpenMP_FOUND)
-  target_compile_options(ZFRelaxation PUBLIC ${OpenMP_CXX_FLAGS})
-endif (OpenMP_FOUND)
-
 set(gomp "")
-if (OpenMP_FOUND AND (${CMAKE_HOST_SYSTEM_NAME} STREQUAL Linux))
+if (OpenMP_FOUND)
-  set(gomp gomp)
+  set(gomp OpenMP::OpenMP_CXX)
-endif (OpenMP_FOUND AND (${CMAKE_HOST_SYSTEM_NAME} STREQUAL Linux))
+endif (OpenMP_FOUND)
 target_link_libraries(ZFRelaxation 
   ${gomp} FFTW3::FFTW3 ${ROOT_LIBRARIES} PUserFcnBase cuba BMWtools
 ) 

src/include/PFitter.h

@@ -111,7 +111,7 @@ class PSectorChisq
 class PFitter
 {
   public:
-    PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bool_t chisq_only = false);
+    PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bool_t chisq_only = false, Bool_t yaml_out = false);
     virtual ~PFitter();
 
     Bool_t IsValid() { return fIsValid; }
@@ -124,6 +124,7 @@ class PFitter
     Bool_t fIsScanOnly;  ///< flag. true: scan along some parameters (no fitting).
     Bool_t fConverged;   ///< flag. true: the fit has converged.
     Bool_t fChisqOnly;   ///< flag. true: calculate chi^2 only (no fitting).
+    Bool_t fYamlOut;     ///< flag. true: generate yaml output file of the fit results (MINUIT2.OUTPUT -> yaml)
     Bool_t fUseChi2;     ///< flag. true: chi^2 fit. false: log-max-likelihood
     UInt_t fPrintLevel;  ///< tag, showing the level of messages whished. 0=minimum, 1=standard, 2=maximum
 

src/include/PFunctionGrammar.h

@@ -82,11 +82,14 @@ struct PFunctionGrammar : public grammar<PFunctionGrammar>
 
             const_gamma_mu =   leaf_node_d[ str_p("GAMMA_MU") ];
 
-            const_field    =   leaf_node_d[ str_p("B") ];
+            const_field    =   leaf_node_d[ str_p("B") ] |
+                               leaf_node_d[ str_p("-B") ];
 
-            const_energy   =   leaf_node_d[ str_p("EN") ];
+            const_energy   =   leaf_node_d[ str_p("EN") ] |
+                               leaf_node_d[ str_p("-EN") ];
 
-            const_temp    =    leaf_node_d[ ( lexeme_d[ "T" >> +digit_p ] ) ];
+            const_temp    =    leaf_node_d[ ( lexeme_d[ "T" >> +digit_p ] ) ] |
+                               leaf_node_d[ ( lexeme_d[ "-T" >> +digit_p ] ) ];
 
             fun_label      =   leaf_node_d[ ( lexeme_d[ "FUN" >> +digit_p ] ) ];
 

src/msr2data.cpp

@@ -127,6 +127,7 @@ void msr2data_syntax()
   std::cout << std::endl << "       -k, --keep-mn2-output : if fitting is used, pass the option --keep-mn2-output to musrfit";
   std::cout << std::endl << "       -t, --title-from-data-file : if fitting is used, pass the option --title-from-data-file to musrfit";
   std::cout << std::endl << "       -e, --estimateN0: estimate N0 for single histogram fits.";
+  std::cout << std::endl << "       -y, --yaml:  write fit results (MINUIT2.OUTPUT) into a yaml-file. Output <msr-file>.yaml";
   std::cout << std::endl << "       -p, --per-run-block-chisq: will per run block chisq to the msr-file.";
   std::cout << std::endl;
   std::cout << std::endl << "       global : switch on the global-fit mode";
@@ -187,6 +188,7 @@ std::string msr2data_validArguments(const std::vector<std::string> &arg)
       || (!iter->substr(0,3).compare("fit")) || (!iter->compare("-k")) || (!iter->compare("--keep-mn2-output")) \
       || (!iter->compare("-t")) || (!iter->compare("--title-from-data-file")) \
       || (!iter->compare("-e")) || (!iter->compare("--estimateN0")) \
+      || (!iter->compare("-y") || (!iter->compare("--yaml"))) \
       || (!iter->compare("-p")) || (!iter->compare("--per-run-block-chisq")) \
       || (!iter->compare("data")) || (!iter->substr(0,4).compare("msr-")) || (!iter->compare("global")) \
       || (!iter->compare("global+")) || (!iter->compare("global+!")) || (!iter->compare("new")) \
@@ -716,6 +718,8 @@ int main(int argc, char *argv[])
       musrfitOptions.append("-t ");
     if (!msr2data_useOption(arg, "-e") || !msr2data_useOption(arg, "--estimateN0"))
       musrfitOptions.append("-e ");
+    if (!msr2data_useOption(arg, "-y") || !msr2data_useOption(arg, "--yaml"))
+      musrfitOptions.append("-y ");
     if (!msr2data_useOption(arg, "-p") || !msr2data_useOption(arg, "--per-run-block-chisq"))
       musrfitOptions.append("-p ");
   }
@@ -761,7 +765,7 @@ int main(int argc, char *argv[])
 
   // Check if all given run numbers are covered by the formatting of the data file name
   status = msr2dataHandler->CheckRunNumbersInRange();
-  if(status) {
+  if (status) {
     std::cerr << std::endl;
     std::cerr << ">> msr2data: **ERROR** At least one given run number is out of range! Quitting..." << std::endl;
     return status;

src/musrFT.cpp

@@ -1437,19 +1437,18 @@ Int_t main(Int_t argc, Char_t *argv[])
     musrFT_dumpData(startupParam.dumpFln, fourier, startupParam.fourierRange[0], startupParam.fourierRange[1]);
   } else { // do Canvas
 
-    // if Fourier graphical export is whished, switch to batch mode
+    // if Fourier graphical export is wished, switch to batch mode
     Bool_t batch = false;
-    int cc=0;
+    // create list of essential arguments to pass to the ROOT application
-    char **arg;
+    std::vector<char*> args;
+    args.push_back(argv[0]); // program name
     if (startupParam.graphicFormat.Length() != 0) {
       batch = true;
-      arg[cc] = (Char_t*)malloc(16*sizeof(Char_t));
+      args.push_back((char*)"-b"); // batch mode flag
-      strcpy(arg[cc], "-b");
-      cc++;
     }
-
+    int cc = args.size();
     // plot the Fourier transform
-    TApplication app("App", &cc, arg);
+    TApplication app("App", &cc, args.data());
 
     if (startupHandler) {
       fourierCanvas = std::unique_ptr<PFourierCanvas>(new PFourierCanvas(fourier, dataSetTag, startupParam.title.Data(),

src/musredit_qt5/mupp/Pmupp.cpp

@@ -656,12 +656,17 @@ PmuppCollection PParamDataHandler::ReadColumnParamFile(const QString fln, bool &
         param.SetName(headerInfo[i]);
         param.SetValue(dval);
         if (i+1 < token.size()) {
-          if (headerCode[i+1] == PMUPP_VALUE) {
+          if ((headerCode[i+1] == PMUPP_VALUE) || (headerCode[i+1] == PMUPP_RUN)) {
             param.SetNegErr(0.0);
             param.SetPosErr(0.0);
             run.AddParam(param);
             param.ResetParam();
           }
+        } else { // last token
+          param.SetNegErr(0.0);
+          param.SetPosErr(0.0);
+          run.AddParam(param);
+          param.ResetParam();
         }
       } else if (headerCode[i] == PMUPP_POSNEGERR) {
         param.SetPosErr(dval);

src/musredit_qt5/mupp/PmuppGui.cpp

@@ -638,7 +638,7 @@ void PmuppGui::fileOpen()
          this,
          "muSR Parameter Files",
          "./",
-         "db-files (*.db);; All Params (*.msr *.db *.dat);; Msr-Files (*.msr);; dat-Files (*.dat);; All (*)");
+         "dat-files (*.dat);; db-Files (*.db);; All Params (*.msr *.db *.dat);; Msr-Files (*.msr);; All (*)");
 
   if (list.count() == 0)
     return;
@@ -985,7 +985,8 @@ void PmuppGui::refresh()
 
   for (int i=0; i<fParamDataHandler->GetNoOfCollections(); i++) {
     if (fParamDataHandler->GetCollection(i)->GetName() == label) { // found collection
-      pathName = fParamDataHandler->GetCollection(i)->GetPathName();
+      QDir dir(QDir::currentPath());
+      pathName = dir.path() + "/" + fParamDataHandler->GetCollection(i)->GetName();
       collIdx = i;
       break;
     }
@@ -1014,7 +1015,7 @@ void PmuppGui::refresh()
     }
   } else {
     QMessageBox::critical(this, "ERROR - REFRESH",
-                          QString("Couldn't refresh %1").arg(fParamDataHandler->GetCollection(collIdx)->GetName()));
+                          QString("Couldn't refresh %1?!").arg(fParamDataHandler->GetCollection(collIdx)->GetName()));
     return;
   }
 

src/musredit_qt5/musredit/PAdmin.cpp

@@ -144,6 +144,8 @@ bool PAdminXMLParser::startElement()
     fKeyWord = eMusrviewShowOneToOne;
   } else if (qName == "enable_musrt0") {
     fKeyWord = eEnableMusrT0;
+  } else if (qName == "ignore_theme_auto_detection") {
+    fKeyWord = eIgnoreThemeAutoDetection;
   } else if (qName == "dark_theme_icons_menu") {
     fKeyWord = eDarkThemeIconsMenu;
   } else if (qName == "dark_theme_icons_toolbar") {
@@ -160,6 +162,8 @@ bool PAdminXMLParser::startElement()
     fKeyWord = eDumpRoot;
   } else if (qName == "estimate_n0") {
     fKeyWord = eEstimateN0;
+  } else if (qName == "yaml_out") {
+    fKeyWord = eYamlOut;
   } else if (qName == "chisq_per_run_block") {
     fKeyWord = eChisqPreRunBlock;
   } else if (qName == "path_file_name") {
@@ -335,6 +339,13 @@ bool PAdminXMLParser::characters()
         flag = false;
       fAdmin->setEnableMusrT0Flag(flag);
       break;
+    case eIgnoreThemeAutoDetection:
+      if (str == "y")
+        flag = true;
+      else
+        flag = false;
+      fAdmin->setIgnoreThemeAutoDetection(flag);
+      break;
     case eDarkThemeIconsMenu:
       if (str == "y")
         flag = true;
@@ -389,6 +400,14 @@ bool PAdminXMLParser::characters()
       fAdmin->fMsr2DataParam.estimateN0 = flag;
       fAdmin->setEstimateN0Flag(flag);
       break;
+    case eYamlOut:
+      if (str == "y")
+        flag = true;
+      else
+        flag = false;
+      fAdmin->fMsr2DataParam.yamlOut = flag;
+      fAdmin->setYamlOutFlag(flag);
+      break;
     case eChisqPreRunBlock:
       if (str == "y")
         flag = true;
@@ -608,9 +627,11 @@ void PAdminXMLParser::dump()
   std::cout << "debug> title_from_data_file : " << fAdmin->getTitleFromDataFileFlag() << std::endl;
   std::cout << "debug> chisq_per_run_block : " << fAdmin->getChisqPerRunBlockFlag() << std::endl;
   std::cout << "debug> estimate_n0 : " << fAdmin->getEstimateN0Flag() << std::endl;
+  std::cout << "debug> yaml_out : " << fAdmin->getYamlOutFlag() << std::endl;
   std::cout << "debug> musrview_show_fourier : " << fAdmin->getMusrviewShowFourierFlag() << std::endl;
   std::cout << "debug> musrview_show_avg : " << fAdmin->getMusrviewShowAvgFlag() << std::endl;
   std::cout << "debug> enable_musrt0 : " << fAdmin->getEnableMusrT0Flag() << std::endl;
+  std::cout << "debug> ignore_theme_auto_detection : " << fAdmin->getIgnoreThemeAutoDetection() << std::endl;
   std::cout << "debug> dark_theme_icons_menu : " << fAdmin->getDarkThemeIconsMenuFlag() << std::endl;
   std::cout << "debug> dark_theme_icons_toolbar : " << fAdmin->getDarkThemeIconsToolbarFlag() << std::endl;
   std::cout << "debug> edit_w : " << fAdmin->getEditWidth() << std::endl;
@@ -725,32 +746,6 @@ QString PAdminXMLParser::expandPath(const QString &str)
  */
 PAdmin::PAdmin() : QObject()
 {
-  fTimeout = 3600;
-
-  fFontName = QString("Courier"); // default font
-  fFontSize = 11; // default font size
-
-  fPrefPathName = QString("");
-  fExecPath = QString("");
-  fDefaultSavePath = QString("");
-  fTheoFuncPixmapPath = QString("");
-
-  fBeamline   = QString("");
-  fInstitute  = QString("");
-  fFileFormat = QString("");
-
-  fMusrviewShowFourier = false;
-  fMusrviewShowAvg = false;
-
-  fTitleFromDataFile  = false;
-  fEnableMusrT0       = false;
-  fLifetimeCorrection = true;
-  fEstimateN0         = true;
-  fChisqPreRunBlock   = false;
-
-  fEditWidth = 900;
-  fEditHeight = 800;
-
   fMsr2DataParam.runList  = QString("");
   fMsr2DataParam.runListFileName = QString("");
   fMsr2DataParam.msrFileExtension = QString("");
@@ -760,6 +755,7 @@ PAdmin::PAdmin() : QObject()
   fMsr2DataParam.ignoreDataHeaderInfo = false;
   fMsr2DataParam.keepMinuit2Output = false;
   fMsr2DataParam.estimateN0 = fEstimateN0;
+  fMsr2DataParam.yamlOut = false;
   fMsr2DataParam.writeColumnData = false;
   fMsr2DataParam.recreateDbFile = false;
   fMsr2DataParam.chainFit = true;
@@ -991,6 +987,12 @@ int PAdmin::savePrefs(QString pref_fln)
         else
           data[i] = "    <estimate_n0>n</estimate_n0>";
       }
+      if (data[i].contains("<yaml_out>") && data[i].contains("</yaml_out>")) {
+        if (fYamlOut)
+          data[i] = "    <yaml_out>y</yaml_out>";
+        else
+          data[i] = "    <yaml_out>n</yaml_out>";
+      }
       if (data[i].contains("<musrview_show_fourier>") && data[i].contains("</musrview_show_fourier>")) {
         if (fMusrviewShowFourier)
           data[i] = "    <musrview_show_fourier>y</musrview_show_fourier>";
@@ -1009,17 +1011,23 @@ int PAdmin::savePrefs(QString pref_fln)
         else
           data[i] = "    <enable_musrt0>n</enable_musrt0>";
       }
+      if (data[i].contains("<ignore_theme_auto_detection>")) {
+        if (fIgnoreThemeAutoDetection)
+          data[i] = "    <ignore_theme_auto_detection>y</ignore_theme_auto_detection>";
+        else
+          data[i] = "    <ignore_theme_auto_detection>n</ignore_theme_auto_detection>";
+      }
       if (data[i].contains("<dark_theme_icons_menu>") && data[i].contains("</dark_theme_icons_menu>")) {
         if (fDarkThemeIconsMenu)
-          data[i] = "     <dark_theme_icons_menu>y</dark_theme_icons_menu>";
+          data[i] = "    <dark_theme_icons_menu>y</dark_theme_icons_menu>";
         else
-          data[i] = "     <dark_theme_icons_menu>n</dark_theme_icons_menu>";
+          data[i] = "    <dark_theme_icons_menu>n</dark_theme_icons_menu>";
       }
       if (data[i].contains("<dark_theme_icons_toolbar>") && data[i].contains("</dark_theme_icons_toolbar>")) {
         if (fDarkThemeIconsToolbar)
-          data[i] = "     <dark_theme_icons_toolbar>y</dark_theme_icons_toolbar>";
+          data[i] = "    <dark_theme_icons_toolbar>y</dark_theme_icons_toolbar>";
         else
-          data[i] = "     <dark_theme_icons_toolbar>n</dark_theme_icons_toolbar>";
+          data[i] = "    <dark_theme_icons_toolbar>n</dark_theme_icons_toolbar>";
       }
       if (data[i].contains("<font_name>") && data[i].contains("</font_name>")) {
         data[i] = QString("    <font_name>%1</font_name>").arg(fFontName);

src/musredit_qt5/musredit/PAdmin.h

@@ -71,9 +71,9 @@ class PAdminXMLParser
 
   private:
     enum EAdminKeyWords {eEmpty, eTimeout, eKeepMinuit2Output, eDumpAscii, eDumpRoot,
-                         eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0,
+                         eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0, eYamlOut,
                          eMusrviewShowFourier, eMusrviewShowAvg, eMusrviewShowOneToOne, eEnableMusrT0,
-                         eDarkThemeIconsMenu, eDarkThemeIconsToolbar, eEditW, eEditH,
+                         eDarkThemeIconsMenu, eDarkThemeIconsToolbar, eIgnoreThemeAutoDetection, eEditW, eEditH,
                          eFontName, eFontSize, eExecPath, eDefaultSavePath,
                          eRecentFile, eBeamline, eInstitute, eFileFormat, eLifetimeCorrection,
                          eTheoFuncPixmapPath, eFunc, eFuncName, eFuncComment, eFuncLabel,
@@ -129,7 +129,9 @@ class PAdmin : public QObject
     bool    getDumpAsciiFlag() { return fDumpAscii; }
     bool    getDumpRootFlag() { return fDumpRoot; }
     bool    getEstimateN0Flag() { return fEstimateN0; }
+    bool    getYamlOutFlag() { return fYamlOut; }
     bool    getChisqPerRunBlockFlag() { return fChisqPreRunBlock; }
+    bool    getIgnoreThemeAutoDetection() { return fIgnoreThemeAutoDetection; }
     bool    getDarkThemeIconsMenuFlag() { return fDarkThemeIconsMenu; }
     bool    getDarkThemeIconsToolbarFlag() { return fDarkThemeIconsToolbar; }
     int     getEditWidth() { return fEditWidth; }
@@ -157,7 +159,9 @@ class PAdmin : public QObject
     void setDumpAsciiFlag(const bool flag) { fDumpAscii = flag; }
     void setDumpRootFlag(const bool flag) { fDumpRoot = flag; }
     void setEstimateN0Flag(const bool flag) { fEstimateN0 = flag; }
+    void setYamlOutFlag(const bool flag) { fYamlOut = flag; }
     void setChisqPerRunBlockFlag(const bool flag) { fChisqPreRunBlock = flag; }
+    void setIgnoreThemeAutoDetection(const bool flag) { fIgnoreThemeAutoDetection = flag; }
     void setDarkThemeIconsMenuFlag(const bool flag) { fDarkThemeIconsMenu = flag; }
     void setDarkThemeIconsToolbarFlag(const bool flag) { fDarkThemeIconsToolbar = flag; }
     void setEditWidth(const int width) { fEditWidth = width; }
@@ -184,37 +188,39 @@ class PAdmin : public QObject
   private:
     friend class PAdminXMLParser;
 
-    int fTimeout;       ///< timeout in seconds
+    int fTimeout{3600};       ///< timeout in seconds
 
-    QString fFontName;  ///< default font name
+    QString fFontName{QString("Monospace")};  ///< default font name
-    int fFontSize;      ///< default font size
+    int fFontSize{11};      ///< default font size
 
-    QString fPrefPathName;       ///< path-name of the musredit_startup.xml
+    QString fPrefPathName{QString("")};       ///< path-name of the musredit_startup.xml
-    QString fExecPath;           ///< system path to the musrfit executables
+    QString fExecPath{QString("")};           ///< system path to the musrfit executables
-    QString fDefaultSavePath;    ///< default path where the msr-file should be saved
+    QString fDefaultSavePath{QString("")};    ///< default path where the msr-file should be saved
-    QString fTheoFuncPixmapPath; ///< path where the default pixmaps can be found
+    QString fTheoFuncPixmapPath{QString("")}; ///< path where the default pixmaps can be found
 
     QVector<QString> fRecentFile; ///< keep vector of recent path-file names
 
-    bool fMusrviewShowFourier;  ///< flag indicating if musrview should show at startup data (=false) or Fourier of data (=true).
+    bool fMusrviewShowFourier{false};  ///< flag indicating if musrview should show at startup data (=false) or Fourier of data (=true).
-    bool fMusrviewShowAvg;      ///< flag indicating if musrview should show at startup averaged (=true) or original (=false) data/Fourier.
+    bool fMusrviewShowAvg{false};      ///< flag indicating if musrview should show at startup averaged (=true) or original (=false) data/Fourier.
-    bool fMusrviewShowOneToOne; ///< flag indicating if theory points are calculate only at the data points (=true) or a higher density theory points is calculated
+    bool fMusrviewShowOneToOne{false}; ///< flag indicating if theory points are calculate only at the data points (=true) or a higher density theory points is calculated
-    bool fKeepMinuit2Output;    ///< flag indicating if the Minuit2 output shall be kept (default: no)
+    bool fKeepMinuit2Output{false};    ///< flag indicating if the Minuit2 output shall be kept (default: no)
-    bool fDumpAscii;            ///< flag indicating if musrfit shall make an ascii-dump file (for debugging purposes, default: no).
+    bool fDumpAscii{false};            ///< flag indicating if musrfit shall make an ascii-dump file (for debugging purposes, default: no).
-    bool fDumpRoot;             ///< flag indicating if musrfit shall make an root-dump file (for debugging purposes, default: no).
+    bool fDumpRoot{false};             ///< flag indicating if musrfit shall make an root-dump file (for debugging purposes, default: no).
-    bool fTitleFromDataFile;    ///< flag indicating if the title should be extracted from the data file (default: yes).
+    bool fTitleFromDataFile{true};     ///< flag indicating if the title should be extracted from the data file (default: yes).
-    bool fChisqPreRunBlock;     ///< flag indicating if musrfit shall write 'per run block' chisq to the msr-file (default: no).
+    bool fChisqPreRunBlock{false};     ///< flag indicating if musrfit shall write 'per run block' chisq to the msr-file (default: no).
-    bool fEstimateN0;           ///< flag indicating if musrfit shall estimate N0 for single histogram fits (default: yes).
+    bool fEstimateN0{true};            ///< flag indicating if musrfit shall estimate N0 for single histogram fits (default: yes).
-    bool fEnableMusrT0;         ///< flag indicating if musrT0 shall be enabled at startup from within musredit (default: yes).
+    bool fYamlOut{false};              ///< flag indicating if the MINUIT2.OUTPUT file should also be written as <msr-file>.yaml output. (default: no).
-    bool fDarkThemeIconsMenu;   ///< flag indicating if dark theme icons shall be used in the menu (default: no)
+    bool fEnableMusrT0{true};          ///< flag indicating if musrT0 shall be enabled at startup from within musredit (default: yes).
-    bool fDarkThemeIconsToolbar; ///< flag indicating if dark theme icons shall be used in the toolbar (default: no)
+    bool fIgnoreThemeAutoDetection{false}; ///< flag indicating that the theme autodetection shall be ignored. (default: no)
+    bool fDarkThemeIconsMenu{false};   ///< flag indicating if dark theme icons shall be used in the menu (default: no)
+    bool fDarkThemeIconsToolbar{false}; ///< flag indicating if dark theme icons shall be used in the toolbar (default: no)
     int  fEditWidth{900};       ///< startup edit width
     int  fEditHeight{800};      ///< startup edit height
 
-    QString fBeamline;   ///< name of the beamline. Used to generate default run header lines.
+    QString fBeamline{QString("")};   ///< name of the beamline. Used to generate default run header lines.
-    QString fInstitute;  ///< name of the institute. Used to generate default run header lines.
+    QString fInstitute{QString("")};  ///< name of the institute. Used to generate default run header lines.
-    QString fFileFormat; ///< default file format. Used to generate default run header lines.
+    QString fFileFormat{QString("")}; ///< default file format. Used to generate default run header lines.
-    bool fLifetimeCorrection; ///< flag indicating if by default the lifetime-correction-flag in a single histo file shall be set.
+    bool fLifetimeCorrection{true}; ///< flag indicating if by default the lifetime-correction-flag in a single histo file shall be set.
 
     mutable PMsr2DataParam fMsr2DataParam; ///< keeps msr2data default parameter flags
 

src/musredit_qt5/musredit/PMsr2DataDialog.cpp

@@ -84,6 +84,7 @@ PMsr2DataDialog::PMsr2DataDialog(PMsr2DataParam *msr2DataParam, const QString he
   fIgnoreDataHeaderInfo_checkBox->setChecked(fMsr2DataParam->ignoreDataHeaderInfo);
   fKeepMinuit2Output_checkBox->setChecked(fMsr2DataParam->keepMinuit2Output);
   fEstimateN0_checkBox->setChecked(fMsr2DataParam->estimateN0);
+  fYamlOut_checkBox->setChecked(fMsr2DataParam->yamlOut);
   fWriteColumnData_checkBox->setChecked(fMsr2DataParam->writeColumnData);
   fRecreateDataFile_checkBox->setChecked(fMsr2DataParam->recreateDbFile);
   fChainFit_checkBox->setChecked(fMsr2DataParam->chainFit);
@@ -121,6 +122,7 @@ PMsr2DataParam* PMsr2DataDialog::getMsr2DataParam()
   fMsr2DataParam->ignoreDataHeaderInfo = fIgnoreDataHeaderInfo_checkBox->isChecked();
   fMsr2DataParam->keepMinuit2Output = fKeepMinuit2Output_checkBox->isChecked();
   fMsr2DataParam->estimateN0 = fEstimateN0_checkBox->isChecked();
+  fMsr2DataParam->yamlOut = fYamlOut_checkBox->isChecked();
   fMsr2DataParam->writeColumnData = fWriteColumnData_checkBox->isChecked();
   fMsr2DataParam->recreateDbFile = fRecreateDataFile_checkBox->isChecked();
   fMsr2DataParam->chainFit = fChainFit_checkBox->isChecked();

src/musredit_qt5/musredit/PPrefsDialog.cpp

@@ -59,6 +59,12 @@ PPrefsDialog::PPrefsDialog(PAdmin *admin) : fAdmin(admin)
     fDarkThemeIconsToolbar_checkBox->setCheckState(Qt::Unchecked);
   }
 
+  if (fAdmin->getIgnoreThemeAutoDetection()) {
+    fIgnoreThemeAutoDetection_checkBox->setCheckState(Qt::Checked);
+  } else {
+    fIgnoreThemeAutoDetection_checkBox->setCheckState(Qt::Unchecked);
+  }
+
   fKeepMn2Output_checkBox->setChecked(fAdmin->getKeepMinuit2OutputFlag());
 
   if (fAdmin->getDumpAsciiFlag() && !fAdmin->getDumpRootFlag()) {
@@ -76,6 +82,7 @@ PPrefsDialog::PPrefsDialog(PAdmin *admin) : fAdmin(admin)
   fEnableMusrT0_checkBox->setChecked(fAdmin->getEnableMusrT0Flag());
   fPerRunBlockChisq_checkBox->setChecked(fAdmin->getChisqPerRunBlockFlag());
   fEstimateN0_checkBox->setChecked(fAdmin->getEstimateN0Flag());
+  fYamlOut_checkBox->setChecked(fAdmin->getYamlOutFlag());
   fFourier_checkBox->setChecked(fAdmin->getMusrviewShowFourierFlag());
   fAvg_checkBox->setChecked(fAdmin->getMusrviewShowAvgFlag());
   fOneToOne_checkBox->setChecked(fAdmin->getMusrviewShowOneToOneFlag());

src/musredit_qt5/musredit/PPrefsDialog.h

@@ -54,6 +54,8 @@ class PPrefsDialog : public QDialog, private Ui::PPrefsDialog
     bool getEnableMusrT0Flag()      { return fEnableMusrT0_checkBox->isChecked(); }
     bool getKeepRunPerBlockChisqFlag() { return fPerRunBlockChisq_checkBox->isChecked(); }
     bool getEstimateN0Flag()        { return fEstimateN0_checkBox->isChecked(); }
+    bool getYamlOutFlag()           { return fYamlOut_checkBox->isChecked(); }
+    bool getIgnoreThemeAutoDetection() { return fIgnoreThemeAutoDetection_checkBox->isChecked(); }
     bool getDarkThemeIconsMenuFlag()    { return fDarkThemeIconsMenu_checkBox->isChecked(); }
     bool getDarkThemeIconsToolbarFlag()    { return fDarkThemeIconsToolbar_checkBox->isChecked(); }
     bool getOneToOneFlag() { return fOneToOne_checkBox->isChecked(); }

src/musredit_qt5/musredit/PTextEdit.cpp

@@ -88,11 +88,11 @@
 PTextEdit::PTextEdit( QWidget *parent )
     : QMainWindow( parent )
 {
-  bool gotTheme = getTheme();
-
   // reads and manages the conents of the xml-startup (musredit_startup.xml) file
   fAdmin = std::make_unique<PAdmin>();
 
+  bool gotTheme = getTheme();
+
   // set default setting of the fDarkMenuIconIcons only if a theme has been recognized, otherwise take the
   // one from the xml startup file.
   if (gotTheme) {
@@ -125,6 +125,7 @@ PTextEdit::PTextEdit( QWidget *parent )
   setupEditActions();
   setupTextActions();
   setupMusrActions();
+  setupJumpToBlock();
   setupHelpActions();
 
   fTabWidget = std::make_unique<QTabWidget>( this );
@@ -133,7 +134,6 @@ PTextEdit::PTextEdit( QWidget *parent )
 
   textFamily(fAdmin->getFontName());
   textSize(QString("%1").arg(fAdmin->getFontSize()));
-  fFontChanging = false;
 
   QString iconName("");
   if (fDarkMenuIcon)
@@ -958,6 +958,31 @@ void PTextEdit::setupHelpActions()
   menu->addAction(a);
 }
 
+//----------------------------------------------------------------------------------------------------
+/**
+ * <p>Setup the JumpToBlock actions.
+ */
+void PTextEdit::setupJumpToBlock()
+{
+  QToolBar *tb = new QToolBar( this );
+  tb->setWindowTitle( "JumpToBlock Actions" );
+  addToolBar( tb );
+
+  QStringList jumpToBlockStr = {"FITPARAMETER", "THEORY", "FUNCTIONS", "GLOBAL", "RUN", "COMMANDS", "PLOT", "FOURIER", "STATISTIC"};
+  fJumpToBlock = std::make_unique<QComboBox>();
+  if (fJumpToBlock == nullptr)
+    return;
+  fJumpToBlock->addItems(jumpToBlockStr);
+  fJumpToBlock->setEditable(false);
+
+  connect( fJumpToBlock.get(), SIGNAL( activated(int) ), this, SLOT( jumpToBlock(int) ));
+
+  QLabel *jstr = new QLabel("  Jump to block: ");
+
+  tb->addWidget(jstr);
+  tb->addWidget(fJumpToBlock.get());
+}
+
 //----------------------------------------------------------------------------------------------------
 /**
  * <p>load a msr-file.
@@ -974,6 +999,7 @@ void PTextEdit::load( const QString &f, const int index )
   // create a new text edit object
   PSubTextEdit *edit = new PSubTextEdit( fAdmin.get() );
   edit->setFont(QFont(fAdmin->getFontName(), fAdmin->getFontSize()));
+  edit->setCenterOnScroll(true);
 
   // place the text edit object at the appropriate tab position
   if (index == -1)
@@ -1016,7 +1042,7 @@ PSubTextEdit *PTextEdit::currentEditor() const
     return nullptr;
 
   if ( fTabWidget->currentWidget() ) {
-    if (fTabWidget->currentWidget()->inherits( "PSubTextEdit" )) {
+    if (fTabWidget->currentWidget()->inherits( "PSubTextEdit" )) {        
       return dynamic_cast<PSubTextEdit*>(fTabWidget->currentWidget());
     }
   }
@@ -1158,6 +1184,7 @@ void PTextEdit::fileNew()
 {
   PSubTextEdit *edit = new PSubTextEdit( fAdmin.get() );
   edit->setFont(QFont(fAdmin->getFontName(), fAdmin->getFontSize()));
+  edit->setCenterOnScroll(true);
   doConnections( edit );
   fTabWidget->addTab( edit, tr( "noname" ) );
   fTabWidget->setCurrentIndex(fTabWidget->indexOf(edit));
@@ -1391,18 +1418,18 @@ void PTextEdit::fileSavePrefs()
   QString msg("");
   QMessageBox msgBox;
   msgBox.setText("Which Preferences do you want to open?");
-  msgBox.addButton("Default", QMessageBox::AcceptRole);
+  QAbstractButton *def = msgBox.addButton("Default", QMessageBox::AcceptRole);
-  msgBox.addButton("Custom", QMessageBox::AcceptRole);
+  QAbstractButton *cust = msgBox.addButton("Custom", QMessageBox::AcceptRole);
   msgBox.setStandardButtons(QMessageBox::Cancel);
   int result = msgBox.exec();
   if (result == QMessageBox::Cancel) {
     return;
-  } else if (result == 0) { // default dir
+  } else if (msgBox.clickedButton() == def) { // default dir
     fln = fAdmin->getDefaultPrefPathName();
     msg = QString("Current Default Preferences Path-Name:\n") + fln;
     if (QMessageBox::information(this, "Info", msg, QMessageBox::Ok, QMessageBox::Cancel) == QMessageBox::Cancel)
       return;
-  } else if (result == 1) { // custom dir
+  } else if (msgBox.clickedButton() == cust) { // custom dir
     fln = QFileDialog::getSaveFileName( this,
                     tr( "Save Prefs As" ), "musredit_startup.xml",
                     tr( "xml-Files (*.xml);;All Files (*)" ) );
@@ -1939,7 +1966,7 @@ void PTextEdit::editUncomment()
 
 //----------------------------------------------------------------------------------------------------
 /**
- * <p>Chances the font.
+ * <p>Changes the font.
  *
  * \param f font name
  */
@@ -1956,7 +1983,7 @@ void PTextEdit::textFamily( const QString &f )
 
 //----------------------------------------------------------------------------------------------------
 /**
- * <p>Chances the font size.
+ * <p>Changes the font size.
  *
  * \param p font size in points.
  */
@@ -2104,6 +2131,11 @@ void PTextEdit::musrFit()
     cmd.append("--estimateN0");
   }
 
+  // check yamlOut flag
+  if (fAdmin->getYamlOutFlag()) {
+    cmd.append("--yaml");
+  }
+
   // check per-run-block-chisq flag
   if (fAdmin->getChisqPerRunBlockFlag()) {
     cmd.append("--per-run-block-chisq");
@@ -2180,6 +2212,7 @@ void PTextEdit::musrMsr2Data()
   fMsr2DataParam->keepMinuit2Output = fAdmin->getKeepMinuit2OutputFlag();
   fMsr2DataParam->titleFromDataFile = fAdmin->getTitleFromDataFileFlag();
   fMsr2DataParam->estimateN0 = fAdmin->getEstimateN0Flag();
+  fMsr2DataParam->yamlOut = fAdmin->getYamlOutFlag();
   fMsr2DataParam->perRunBlockChisq = fAdmin->getChisqPerRunBlockFlag();
 
   PMsr2DataDialog *dlg = new PMsr2DataDialog(fMsr2DataParam, fAdmin->getHelpUrl("msr2data"));
@@ -2202,6 +2235,7 @@ void PTextEdit::musrMsr2Data()
     fAdmin->setKeepMinuit2OutputFlag(fMsr2DataParam->keepMinuit2Output);
     fAdmin->setTitleFromDataFileFlag(fMsr2DataParam->titleFromDataFile);
     fAdmin->setEstimateN0Flag(fMsr2DataParam->estimateN0);
+    fAdmin->setYamlOutFlag(fMsr2DataParam->yamlOut);
     fAdmin->setChisqPerRunBlockFlag(fMsr2DataParam->perRunBlockChisq);
 
     // analyze parameters
@@ -2336,6 +2370,11 @@ void PTextEdit::musrMsr2Data()
       cmd.append("-e");
     }
 
+    // yaml out. Add flag only if a fit is done
+    if (fMsr2DataParam->yamlOut && (fMsr2DataParam->fitOnly || fMsr2DataParam->templateRunNo != -1)) {
+      cmd.append("-y");
+    }
+
     // write per-run-block chisq. Add flag only if a fit is done
     if (fMsr2DataParam->perRunBlockChisq && (fMsr2DataParam->fitOnly || fMsr2DataParam->templateRunNo != -1)) {
       cmd.append("-p");
@@ -2697,6 +2736,7 @@ void PTextEdit::musrPrefs()
   }
 
   if (dlg->exec() == QDialog::Accepted) {
+    fAdmin->setIgnoreThemeAutoDetection(dlg->getIgnoreThemeAutoDetection());
     fAdmin->setDarkThemeIconsMenuFlag(dlg->getDarkThemeIconsMenuFlag());
     fAdmin->setDarkThemeIconsToolbarFlag(dlg->getDarkThemeIconsToolbarFlag());
     fAdmin->setMusrviewShowFourierFlag(dlg->getMusrviewShowFourierFlag());
@@ -2719,6 +2759,7 @@ void PTextEdit::musrPrefs()
     fAdmin->setTimeout(dlg->getTimeout());
     fAdmin->setChisqPerRunBlockFlag(dlg->getKeepRunPerBlockChisqFlag());
     fAdmin->setEstimateN0Flag(dlg->getEstimateN0Flag());
+    fAdmin->setYamlOutFlag(dlg->getYamlOutFlag());
   }
 
   delete dlg;
@@ -3293,12 +3334,35 @@ void PTextEdit::setFileSystemWatcherActive()
   fFileSystemWatcherActive = true;
 }
 
+//----------------------------------------------------------------------------------------------------
+/**
+ * <p>slot called when jumpToBlock combobox is selected
+ * @param idx
+ */
+void PTextEdit::jumpToBlock(int idx)
+{
+  QString str = fJumpToBlock->itemText(idx);
+
+  QTextDocument::FindFlags flags= QTextDocument::FindCaseSensitively | QTextDocument::FindWholeWords;
+
+  bool found = currentEditor()->find(str, flags);
+  if (found)
+    return;
+
+  // set cursor to start
+  currentEditor()->moveCursor(QTextCursor::Start);
+  currentEditor()->find(str, flags);
+}
+
 //----------------------------------------------------------------------------------------------------
 /**
  * @brief PTextEdit::getTheme
  */
 bool PTextEdit::getTheme()
 {
+  if (fAdmin->getIgnoreThemeAutoDetection())
+    return false;
+
   fDarkMenuIcon = false; // true if theme is dark
   fDarkToolBarIcon = false; // needed for ubuntu dark since there the menu icons are dark, however the toolbar icons are plain!
 
@@ -3330,10 +3394,9 @@ bool PTextEdit::getTheme()
 
   if (str.contains("dark", Qt::CaseInsensitive)) {
     fDarkMenuIcon = true;
-    if (str.contains("ubuntu", Qt::CaseInsensitive)) {
+    if (str.contains("ubuntu", Qt::CaseInsensitive) ||
-      fDarkMenuIcon = false;
+        str.contains("xfce", Qt::CaseInsensitive) ||
-      fDarkToolBarIcon = false;
+        str.contains("mx", Qt::CaseInsensitive)) {
-    } else if (str.contains("xfce", Qt::CaseInsensitive)) {
       fDarkMenuIcon = false;
       fDarkToolBarIcon = false;
     } else {

src/musredit_qt5/musredit/PTextEdit.h

@@ -86,6 +86,7 @@ private:
   void setupTextActions();
   void setupMusrActions();
   void setupHelpActions();
+  void setupJumpToBlock();
   void load( const QString &f, const int index=-1 );
   PSubTextEdit *currentEditor() const;
   void doConnections( PSubTextEdit *e );
@@ -167,16 +168,18 @@ private slots:
   void fileChanged(const QString &fileName);
   void setFileSystemWatcherActive();
 
+  void jumpToBlock(int idx);
+
 private:
-  bool fDarkMenuIcon; ///< flag indicating if a dark or plain icon shall be used in the menu pull-downs
+  bool fDarkMenuIcon{false}; ///< flag indicating if a dark or plain icon shall be used in the menu pull-downs
-  bool fDarkToolBarIcon; ///< flag indicating if a dark or plain icon shall be used in the toolbar
+  bool fDarkToolBarIcon{false}; ///< flag indicating if a dark or plain icon shall be used in the toolbar
   std::unique_ptr<PAdmin> fAdmin; ///< pointer to the xml-startup file informations. Needed for different purposes like default working- and executable directories etc.
   std::unique_ptr<QFileSystemWatcher> fFileSystemWatcher; ///< checks if msr-files are changing on the disk while being open in musredit.
   bool fFileSystemWatcherActive; ///< flag to enable/disable the file system watcher
   QTimer fFileSystemWatcherTimeout; ///< timer used to re-enable file system watcher. Needed to delay the re-enabling
-  QString fLastDirInUse; ///< string holding the path from where the last file was loaded.
+  QString fLastDirInUse{QString("")}; ///< string holding the path from where the last file was loaded.
   QStringList fMusrFTPrevCmd;
-  int fEditW, fEditH;
+  int fEditW{900}, fEditH{800};
 
   QMap<QString, QAction*> fActions;
   std::unique_ptr<QAction> fMusrT0Action;
@@ -186,7 +189,8 @@ private:
 
   std::unique_ptr<QComboBox> fComboFont; ///< combo box for the font selector
   std::unique_ptr<QComboBox> fComboSize; ///< combo box for the font size
-  bool fFontChanging; ///< flag needed to prevent some textChanged feature to occure when only the font changed
+  bool fFontChanging{false}; ///< flag needed to prevent some textChanged feature to occure when only the font changed
+  std::unique_ptr<QComboBox> fJumpToBlock; ///< combo box used to jump to the msr-file blocks
 
   std::unique_ptr<QTabWidget> fTabWidget; ///< tab widget in which the text editor(s) are placed
   QMap<PSubTextEdit*, QString> fFilenames; ///< mapper between tab widget object and filename

src/musredit_qt5/musredit/forms/PMsr2DataDialog.ui

@@ -338,7 +338,7 @@
       <x>6</x>
       <y>20</y>
       <width>560</width>
-      <height>131</height>
+      <height>135</height>
      </rect>
     </property>
     <layout class="QHBoxLayout" name="horizontalLayout_9">
@@ -456,6 +456,13 @@
          </property>
         </widget>
        </item>
+       <item>
+        <widget class="QCheckBox" name="fYamlOut_checkBox">
+         <property name="text">
+          <string>yaml out</string>
+         </property>
+        </widget>
+       </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_8">
          <item>

src/musredit_qt5/musredit/forms/PPrefsDialog.ui

@@ -9,8 +9,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>452</width>
+    <width>460</width>
-    <height>180</height>
+    <height>200</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -20,279 +20,293 @@
    <iconset>
     <normaloff>:/images/musrfit.xpm</normaloff>:/images/musrfit.xpm</iconset>
   </property>
-  <widget class="QWidget" name="layoutWidget_0">
+  <layout class="QHBoxLayout" name="horizontalLayout_3">
-   <property name="geometry">
+   <item>
-    <rect>
+    <layout class="QVBoxLayout" name="verticalLayout">
-     <x>0</x>
+     <item>
-     <y>5</y>
+      <widget class="QTabWidget" name="fTabWidget">
-     <width>451</width>
+       <property name="currentIndex">
-     <height>171</height>
+        <number>0</number>
-    </rect>
+       </property>
-   </property>
+       <widget class="QWidget" name="fGeneral_tab">
-   <layout class="QVBoxLayout" name="verticalLayout">
+        <attribute name="title">
-    <item>
+         <string>general</string>
-     <widget class="QTabWidget" name="fTabWidget">
+        </attribute>
-      <property name="currentIndex">
+        <widget class="QPushButton" name="fDefaultPath_pushButton">
-       <number>2</number>
+         <property name="geometry">
-      </property>
+          <rect>
-      <widget class="QWidget" name="fGeneral_tab">
+           <x>10</x>
-       <attribute name="title">
+           <y>80</y>
-        <string>general</string>
+           <width>421</width>
-       </attribute>
+           <height>31</height>
-       <widget class="QPushButton" name="fDefaultPath_pushButton">
+          </rect>
-        <property name="geometry">
+         </property>
-         <rect>
+         <property name="text">
-          <x>10</x>
+          <string>Change Default Search Paths</string>
-          <y>70</y>
+         </property>
-          <width>421</width>
+        </widget>
-          <height>31</height>
+        <widget class="QWidget" name="">
-         </rect>
+         <property name="geometry">
-        </property>
+          <rect>
-        <property name="text">
+           <x>10</x>
-         <string>Change Default Search Paths</string>
+           <y>10</y>
-        </property>
+           <width>416</width>
+           <height>61</height>
+          </rect>
+         </property>
+         <layout class="QHBoxLayout" name="horizontalLayout_2">
+          <item>
+           <widget class="QLineEdit" name="fTimeout_lineEdit"/>
+          </item>
+          <item>
+           <widget class="QLabel" name="fTimeout_label">
+            <property name="text">
+             <string>timeout</string>
+            </property>
+           </widget>
+          </item>
+          <item>
+           <spacer name="horizontalSpacer_2">
+            <property name="orientation">
+             <enum>Qt::Horizontal</enum>
+            </property>
+            <property name="sizeHint" stdset="0">
+             <size>
+              <width>38</width>
+              <height>30</height>
+             </size>
+            </property>
+           </spacer>
+          </item>
+          <item>
+           <layout class="QVBoxLayout" name="verticalLayout_2">
+            <item>
+             <widget class="QCheckBox" name="fIgnoreThemeAutoDetection_checkBox">
+              <property name="text">
+               <string>Ignore Theme Auto Detect</string>
+              </property>
+             </widget>
+            </item>
+            <item>
+             <widget class="QCheckBox" name="fDarkThemeIconsMenu_checkBox">
+              <property name="text">
+               <string>Dark Theme Icons Menu</string>
+              </property>
+             </widget>
+            </item>
+            <item>
+             <widget class="QCheckBox" name="fDarkThemeIconsToolbar_checkBox">
+              <property name="text">
+               <string>Dark Theme Icons Toolbar</string>
+              </property>
+             </widget>
+            </item>
+           </layout>
+          </item>
+         </layout>
+        </widget>
        </widget>
-       <widget class="QWidget" name="layoutWidget">
+       <widget class="QWidget" name="fMusrfit_tab">
-        <property name="geometry">
+        <attribute name="title">
-         <rect>
+         <string>musrfit</string>
-          <x>12</x>
+        </attribute>
-          <y>10</y>
+        <widget class="QCheckBox" name="fKeepMn2Output_checkBox">
-          <width>415</width>
+         <property name="geometry">
-          <height>62</height>
+          <rect>
-         </rect>
+           <x>10</x>
-        </property>
+           <y>10</y>
-        <layout class="QHBoxLayout" name="horizontalLayout_2">
+           <width>161</width>
-         <item>
+           <height>23</height>
-          <widget class="QLineEdit" name="fTimeout_lineEdit"/>
+          </rect>
-         </item>
+         </property>
-         <item>
+         <property name="text">
-          <widget class="QLabel" name="fTimeout_label">
+          <string>keep minuit2 output</string>
-           <property name="text">
+         </property>
-            <string>timeout</string>
+        </widget>
-           </property>
+        <widget class="QCheckBox" name="fDumpAscii_checkBox">
-          </widget>
+         <property name="geometry">
-         </item>
+          <rect>
-         <item>
+           <x>10</x>
-          <spacer name="horizontalSpacer_2">
+           <y>35</y>
-           <property name="orientation">
+           <width>151</width>
-            <enum>Qt::Horizontal</enum>
+           <height>23</height>
-           </property>
+          </rect>
-           <property name="sizeHint" stdset="0">
+         </property>
-            <size>
+         <property name="text">
-             <width>38</width>
+          <string>dump ascii</string>
-             <height>30</height>
+         </property>
-            </size>
+        </widget>
-           </property>
+        <widget class="QCheckBox" name="fDumpRoot_checkBox">
-          </spacer>
+         <property name="geometry">
-         </item>
+          <rect>
-         <item>
+           <x>10</x>
-          <layout class="QVBoxLayout" name="verticalLayout_2">
+           <y>60</y>
-           <item>
+           <width>131</width>
-            <widget class="QCheckBox" name="fDarkThemeIconsMenu_checkBox">
+           <height>23</height>
-             <property name="text">
+          </rect>
-              <string>Dark Theme Icons Menu</string>
+         </property>
-             </property>
+         <property name="text">
-            </widget>
+          <string>dump root</string>
-           </item>
+         </property>
-           <item>
+        </widget>
-            <widget class="QCheckBox" name="fDarkThemeIconsToolbar_checkBox">
+        <widget class="QCheckBox" name="fTitleFromData_checkBox">
-             <property name="text">
+         <property name="geometry">
-              <string>Dark Theme Icons Toolbar</string>
+          <rect>
-             </property>
+           <x>170</x>
-            </widget>
+           <y>10</y>
-           </item>
+           <width>161</width>
-          </layout>
+           <height>23</height>
-         </item>
+          </rect>
-        </layout>
+         </property>
+         <property name="text">
+          <string>take title from data file</string>
+         </property>
+        </widget>
+        <widget class="QCheckBox" name="fPerRunBlockChisq_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>170</x>
+           <y>35</y>
+           <width>181</width>
+           <height>22</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>keep per run block chisq</string>
+         </property>
+        </widget>
+        <widget class="QCheckBox" name="fEstimateN0_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>170</x>
+           <y>60</y>
+           <width>171</width>
+           <height>22</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>estimate N0</string>
+         </property>
+        </widget>
+        <widget class="QCheckBox" name="fYamlOut_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>350</x>
+           <y>10</y>
+           <width>85</width>
+           <height>21</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>yaml out</string>
+         </property>
+        </widget>
+       </widget>
+       <widget class="QWidget" name="fMusrview_tab">
+        <attribute name="title">
+         <string>musrview</string>
+        </attribute>
+        <widget class="QCheckBox" name="fFourier_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>10</x>
+           <y>10</y>
+           <width>421</width>
+           <height>22</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>start with Fourier</string>
+         </property>
+        </widget>
+        <widget class="QCheckBox" name="fAvg_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>10</x>
+           <y>40</y>
+           <width>421</width>
+           <height>21</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>start with averaged data/Fourier</string>
+         </property>
+        </widget>
+        <widget class="QCheckBox" name="fOneToOne_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>260</x>
+           <y>10</y>
+           <width>181</width>
+           <height>26</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>theo at data points only</string>
+         </property>
+        </widget>
+       </widget>
+       <widget class="QWidget" name="fMusrt0_tab">
+        <attribute name="title">
+         <string>musrt0</string>
+        </attribute>
+        <widget class="QCheckBox" name="fEnableMusrT0_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>10</x>
+           <y>10</y>
+           <width>131</width>
+           <height>23</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>enable it</string>
+         </property>
+        </widget>
        </widget>
       </widget>
-      <widget class="QWidget" name="fMusrfit_tab">
+     </item>
-       <attribute name="title">
+     <item>
-        <string>musrfit</string>
+      <layout class="QHBoxLayout" name="horizontalLayout">
-       </attribute>
+       <item>
-       <widget class="QCheckBox" name="fKeepMn2Output_checkBox">
+        <widget class="QPushButton" name="fHelp_pushButton">
-        <property name="geometry">
+         <property name="text">
-         <rect>
+          <string>&amp;Help</string>
-          <x>10</x>
+         </property>
-          <y>10</y>
+        </widget>
-          <width>161</width>
+       </item>
-          <height>23</height>
+       <item>
-         </rect>
+        <spacer name="horizontalSpacer">
-        </property>
+         <property name="orientation">
-        <property name="text">
+          <enum>Qt::Horizontal</enum>
-         <string>keep minuit2 output</string>
+         </property>
-        </property>
+         <property name="sizeHint" stdset="0">
-       </widget>
+          <size>
-       <widget class="QCheckBox" name="fDumpAscii_checkBox">
+           <width>88</width>
-        <property name="geometry">
+           <height>20</height>
-         <rect>
+          </size>
-          <x>10</x>
+         </property>
-          <y>35</y>
+        </spacer>
-          <width>151</width>
+       </item>
-          <height>23</height>
+       <item>
-         </rect>
+        <widget class="QPushButton" name="fOk_pushButton">
-        </property>
+         <property name="text">
-        <property name="text">
+          <string>&amp;OK</string>
-         <string>dump ascii</string>
+         </property>
-        </property>
+        </widget>
-       </widget>
+       </item>
-       <widget class="QCheckBox" name="fDumpRoot_checkBox">
+       <item>
-        <property name="geometry">
+        <widget class="QPushButton" name="fCancel_pushButton">
-         <rect>
+         <property name="text">
-          <x>10</x>
+          <string>&amp;Cancel</string>
-          <y>60</y>
+         </property>
-          <width>131</width>
+        </widget>
-          <height>23</height>
+       </item>
-         </rect>
+      </layout>
-        </property>
+     </item>
-        <property name="text">
+    </layout>
-         <string>dump root</string>
+   </item>
-        </property>
+  </layout>
-       </widget>
-       <widget class="QCheckBox" name="fTitleFromData_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>190</x>
-          <y>10</y>
-          <width>241</width>
-          <height>23</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>take title from data file</string>
-        </property>
-       </widget>
-       <widget class="QCheckBox" name="fPerRunBlockChisq_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>190</x>
-          <y>35</y>
-          <width>241</width>
-          <height>22</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>keep per run block chisq</string>
-        </property>
-       </widget>
-       <widget class="QCheckBox" name="fEstimateN0_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>190</x>
-          <y>60</y>
-          <width>241</width>
-          <height>22</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>estimate N0</string>
-        </property>
-       </widget>
-      </widget>
-      <widget class="QWidget" name="fMusrview_tab">
-       <attribute name="title">
-        <string>musrview</string>
-       </attribute>
-       <widget class="QCheckBox" name="fFourier_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>10</x>
-          <y>10</y>
-          <width>421</width>
-          <height>22</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>start with Fourier</string>
-        </property>
-       </widget>
-       <widget class="QCheckBox" name="fAvg_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>10</x>
-          <y>40</y>
-          <width>421</width>
-          <height>21</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>start with averaged data/Fourier</string>
-        </property>
-       </widget>
-       <widget class="QCheckBox" name="fOneToOne_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>260</x>
-          <y>10</y>
-          <width>181</width>
-          <height>26</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>theo at data points only</string>
-        </property>
-       </widget>
-      </widget>
-      <widget class="QWidget" name="fMusrt0_tab">
-       <attribute name="title">
-        <string>musrt0</string>
-       </attribute>
-       <widget class="QCheckBox" name="fEnableMusrT0_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>10</x>
-          <y>10</y>
-          <width>131</width>
-          <height>23</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>enable it</string>
-        </property>
-       </widget>
-      </widget>
-     </widget>
-    </item>
-    <item>
-     <layout class="QHBoxLayout" name="horizontalLayout">
-      <item>
-       <widget class="QPushButton" name="fHelp_pushButton">
-        <property name="text">
-         <string>&amp;Help</string>
-        </property>
-       </widget>
-      </item>
-      <item>
-       <spacer name="horizontalSpacer">
-        <property name="orientation">
-         <enum>Qt::Horizontal</enum>
-        </property>
-        <property name="sizeHint" stdset="0">
-         <size>
-          <width>88</width>
-          <height>20</height>
-         </size>
-        </property>
-       </spacer>
-      </item>
-      <item>
-       <widget class="QPushButton" name="fOk_pushButton">
-        <property name="text">
-         <string>&amp;OK</string>
-        </property>
-       </widget>
-      </item>
-      <item>
-       <widget class="QPushButton" name="fCancel_pushButton">
-        <property name="text">
-         <string>&amp;Cancel</string>
-        </property>
-       </widget>
-      </item>
-     </layout>
-    </item>
-   </layout>
-  </widget>
  </widget>
  <tabstops>
   <tabstop>fTabWidget</tabstop>

src/musredit_qt5/musredit/musredit.h

@@ -56,6 +56,7 @@ struct PMsr2DataParam {
   bool openFilesAfterFitting;  ///< flag: true = open msr-file after fit in musredit. false = do not open msr-file after fit.
   bool titleFromDataFile;      ///< flag indicating if the title for the msr-file shall be extracted from the data-file ('-t' in msr2data)
   bool estimateN0;             ///< flag indicating if the N0 shall be estimated for single histogram fitting
+  bool yamlOut;                ///< flag indicating if the MINUIT2.OUTPUT content should be written to <msr-file>.yaml
   bool perRunBlockChisq;       ///< flag indicating if per-run-block-chisq shall be dumped into the msr-file
   bool createMsrFileOnly;      ///< flag: true = just create the msr-files without any fitting ('msr-<template>' in msr2data)
   bool fitOnly;                ///< flag: true = just perform the fits wihtout generating any msr-files ('fit' in msr2data).

src/musredit_qt5/musredit/musredit_startup.xml.in

@@ -14,10 +14,12 @@
     <title_from_data_file>y</title_from_data_file>
     <chisq_per_run_block>n</chisq_per_run_block>
     <estimate_n0>y</estimate_n0>
+    <yaml_out>n</yaml_out>
     <musrview_show_fourier>n</musrview_show_fourier>
     <musrview_show_avg>n</musrview_show_avg>
     <musrview_show_one_to_one>n</musrview_show_one_to_one>
     <enable_musrt0>y</enable_musrt0>
+    <ignore_theme_auto_detection>n</ignore_theme_auto_detection>
     <dark_theme_icons_menu>n</dark_theme_icons_menu>
     <dark_theme_icons_toolbar>n</dark_theme_icons_toolbar>
     <edit_w>900</edit_w>

src/musredit_qt6/mupp/Pmupp.cpp

@@ -645,12 +645,17 @@ PmuppCollection PParamDataHandler::ReadColumnParamFile(const QString fln, bool &
         param.SetName(headerInfo[i]);
         param.SetValue(dval);
         if (i+1 < token.size()) {
-          if (headerCode[i+1] == PMUPP_VALUE) {
+          if ((headerCode[i+1] == PMUPP_VALUE) || (headerCode[i+1] == PMUPP_RUN)) {
             param.SetNegErr(0.0);
             param.SetPosErr(0.0);
             run.AddParam(param);
             param.ResetParam();
           }
+        } else { // last token
+          param.SetNegErr(0.0);
+          param.SetPosErr(0.0);
+          run.AddParam(param);
+          param.ResetParam();
         }
       } else if (headerCode[i] == PMUPP_POSNEGERR) {
         param.SetPosErr(dval);

src/musredit_qt6/mupp/PmuppGui.cpp

@@ -637,7 +637,7 @@ void PmuppGui::fileOpen()
          this,
          "muSR Parameter Files",
          "./",
-         "db-files (*.db);; All Params (*.msr *.db *.dat);; Msr-Files (*.msr);; dat-Files (*.dat);; All (*)");
+        "dat-files (*.dat);; db-Files (*.db);; All Params (*.msr *.db *.dat);; Msr-Files (*.msr);; All (*)");
 
   if (list.count() == 0)
     return;
@@ -973,7 +973,8 @@ void PmuppGui::refresh()
 
   for (int i=0; i<fParamDataHandler->GetNoOfCollections(); i++) {
     if (fParamDataHandler->GetCollection(i)->GetName() == label) { // found collection
-      pathName = fParamDataHandler->GetCollection(i)->GetPathName();
+      QDir dir(QDir::currentPath());
+      pathName = dir.path() + "/" + fParamDataHandler->GetCollection(i)->GetName();
       collIdx = i;
       break;
     }

src/musredit_qt6/musredit/PAdmin.cpp

@@ -150,6 +150,8 @@ bool PAdminXMLParser::startElement()
     fKeyWord = eMusrviewShowOneToOne;
   } else if (qName == "enable_musrt0") {
     fKeyWord = eEnableMusrT0;
+  } else if (qName == "ignore_theme_auto_detection") {
+    fKeyWord = eIgnoreThemeAutoDetection;
   } else if (qName == "dark_theme_icons_menu") {
     fKeyWord = eDarkThemeIconsMenu;
   } else if (qName == "dark_theme_icons_toolbar") {
@@ -158,14 +160,16 @@ bool PAdminXMLParser::startElement()
     fKeyWord = eEditW;
   } else if (qName == "edit_h") {
     fKeyWord = eEditH;
-  } else if (qName =="keep_minuit2_output") {
+  } else if (qName == "keep_minuit2_output") {
     fKeyWord = eKeepMinuit2Output;
   } else if (qName == "dump_ascii") {
     fKeyWord = eDumpAscii;
-  } else if (qName =="dump_root") {
+  } else if (qName == "dump_root") {
     fKeyWord = eDumpRoot;
   } else if (qName == "estimate_n0") {
     fKeyWord = eEstimateN0;
+  } else if (qName == "yaml_out") {
+    fKeyWord = eYamlOut;
   } else if (qName == "chisq_per_run_block") {
     fKeyWord = eChisqPreRunBlock;
   } else if (qName == "path_file_name") {
@@ -279,7 +283,6 @@ bool PAdminXMLParser::endElement()
 bool PAdminXMLParser::characters()
 {
   QString str = fXml.text().toString();
-
   if (str.isEmpty())
     return true;
 
@@ -342,6 +345,13 @@ bool PAdminXMLParser::characters()
         flag = false;
       fAdmin->setEnableMusrT0Flag(flag);
       break;
+    case eIgnoreThemeAutoDetection:
+      if (str == "y")
+        flag = true;
+      else
+        flag = false;
+      fAdmin->setIgnoreThemeAutoDetection(flag);
+      break;
     case eDarkThemeIconsMenu:
       if (str == "y")
         flag = true;
@@ -396,6 +406,14 @@ bool PAdminXMLParser::characters()
       fAdmin->fMsr2DataParam.estimateN0 = flag;
       fAdmin->setEstimateN0Flag(flag);
       break;
+    case eYamlOut:
+      if (str == "y")
+        flag = true;
+      else
+        flag = false;
+      fAdmin->fMsr2DataParam.yamlOut = flag;
+      fAdmin->setYamlOutFlag(flag);
+      break;
     case eChisqPreRunBlock:
       if (str == "y")
         flag = true;
@@ -615,9 +633,11 @@ void PAdminXMLParser::dump()
   std::cout << "debug> title_from_data_file : " << fAdmin->getTitleFromDataFileFlag() << std::endl;
   std::cout << "debug> chisq_per_run_block : " << fAdmin->getChisqPerRunBlockFlag() << std::endl;
   std::cout << "debug> estimate_n0 : " << fAdmin->getEstimateN0Flag() << std::endl;
+  std::cout << "debug> yaml_out : " << fAdmin->getYamlOutFlag() << std::endl;
   std::cout << "debug> musrview_show_fourier : " << fAdmin->getMusrviewShowFourierFlag() << std::endl;
   std::cout << "debug> musrview_show_avg : " << fAdmin->getMusrviewShowAvgFlag() << std::endl;
   std::cout << "debug> enable_musrt0 : " << fAdmin->getEnableMusrT0Flag() << std::endl;
+  std::cout << "debug> ignore_theme_auto_detection : " << fAdmin->getIgnoreThemeAutoDetection() << std::endl;
   std::cout << "debug> dark_theme_icons_menu : " << fAdmin->getDarkThemeIconsMenuFlag() << std::endl;
   std::cout << "debug> dark_theme_icons_toolbar : " << fAdmin->getDarkThemeIconsToolbarFlag() << std::endl;
   std::cout << "debug> edit_w : " << fAdmin->getEditWidth() << std::endl;
@@ -732,29 +752,6 @@ QString PAdminXMLParser::expandPath(const QString &str)
  */
 PAdmin::PAdmin() : QObject()
 {
-  fTimeout = 3600;
-
-  fFontName = QString("Courier"); // default font
-  fFontSize = 11; // default font size
-
-  fPrefPathName = QString("");
-  fExecPath = QString("");
-  fDefaultSavePath = QString("");
-  fTheoFuncPixmapPath = QString("");
-
-  fBeamline   = QString("");
-  fInstitute  = QString("");
-  fFileFormat = QString("");
-
-  fMusrviewShowFourier = false;
-  fMusrviewShowAvg = false;
-
-  fTitleFromDataFile  = false;
-  fEnableMusrT0       = false;
-  fLifetimeCorrection = true;
-  fEstimateN0         = true;
-  fChisqPreRunBlock   = false;
-
   fMsr2DataParam.runList  = QString("");
   fMsr2DataParam.runListFileName = QString("");
   fMsr2DataParam.msrFileExtension = QString("");
@@ -764,6 +761,7 @@ PAdmin::PAdmin() : QObject()
   fMsr2DataParam.ignoreDataHeaderInfo = false;
   fMsr2DataParam.keepMinuit2Output = false;
   fMsr2DataParam.estimateN0 = fEstimateN0;
+  fMsr2DataParam.yamlOut = false;
   fMsr2DataParam.writeColumnData = false;
   fMsr2DataParam.recreateDbFile = false;
   fMsr2DataParam.chainFit = true;
@@ -995,6 +993,12 @@ int PAdmin::savePrefs(QString pref_fln)
         else
           data[i] = "    <estimate_n0>n</estimate_n0>";
       }
+      if (data[i].contains("<yaml_out>") && data[i].contains("</yaml_out>")) {
+        if (fYamlOut)
+          data[i] = "    <yaml_out>y</yaml_out>";
+        else
+          data[i] = "    <yaml_out>n</yaml_out>";
+      }
       if (data[i].contains("<musrview_show_fourier>") && data[i].contains("</musrview_show_fourier>")) {
         if (fMusrviewShowFourier)
           data[i] = "    <musrview_show_fourier>y</musrview_show_fourier>";
@@ -1013,17 +1017,23 @@ int PAdmin::savePrefs(QString pref_fln)
         else
           data[i] = "    <enable_musrt0>n</enable_musrt0>";
       }
+      if (data[i].contains("<ignore_theme_auto_detection>")) {
+        if (fIgnoreThemeAutoDetection)
+          data[i] = "    <ignore_theme_auto_detection>y</ignore_theme_auto_detection>";
+        else
+          data[i] = "    <ignore_theme_auto_detection>n</ignore_theme_auto_detection>";
+      }
       if (data[i].contains("<dark_theme_icons_menu>") && data[i].contains("</dark_theme_icons_menu>")) {
         if (fDarkThemeIconsMenu)
-          data[i] = "     <dark_theme_icons_menu>y</dark_theme_icons_menu>";
+          data[i] = "    <dark_theme_icons_menu>y</dark_theme_icons_menu>";
         else
-          data[i] = "     <dark_theme_icons_menu>n</dark_theme_icons_menu>";
+          data[i] = "    <dark_theme_icons_menu>n</dark_theme_icons_menu>";
       }
       if (data[i].contains("<dark_theme_icons_toolbar>") && data[i].contains("</dark_theme_icons_toolbar>")) {
         if (fDarkThemeIconsToolbar)
-          data[i] = "     <dark_theme_icons_toolbar>y</dark_theme_icons_toolbar>";
+          data[i] = "    <dark_theme_icons_toolbar>y</dark_theme_icons_toolbar>";
         else
-          data[i] = "     <dark_theme_icons_toolbar>n</dark_theme_icons_toolbar>";
+          data[i] = "    <dark_theme_icons_toolbar>n</dark_theme_icons_toolbar>";
       }
       if (data[i].contains("<font_name>") && data[i].contains("</font_name>")) {
         data[i] = QString("    <font_name>%1</font_name>").arg(fFontName);

src/musredit_qt6/musredit/PAdmin.h

@@ -71,9 +71,9 @@ class PAdminXMLParser
 
   private:
     enum EAdminKeyWords {eEmpty, eTimeout, eKeepMinuit2Output, eDumpAscii, eDumpRoot,
-                         eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0,
+                         eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0, eYamlOut,
                          eMusrviewShowFourier, eMusrviewShowAvg, eMusrviewShowOneToOne, eEnableMusrT0,
-                         eDarkThemeIconsMenu, eDarkThemeIconsToolbar, eEditW, eEditH,
+                         eIgnoreThemeAutoDetection, eDarkThemeIconsMenu, eDarkThemeIconsToolbar, eEditW, eEditH,
                          eFontName, eFontSize, eExecPath, eDefaultSavePath,
                          eRecentFile, eBeamline, eInstitute, eFileFormat, eLifetimeCorrection,
                          eTheoFuncPixmapPath, eFunc, eFuncName, eFuncComment, eFuncLabel,
@@ -125,11 +125,13 @@ class PAdmin : public QObject
     bool    getMusrviewShowAvgFlag() { return fMusrviewShowAvg; }
     bool    getMusrviewShowOneToOneFlag() { return fMusrviewShowOneToOne; }
     bool    getEnableMusrT0Flag() { return fEnableMusrT0; }
+    bool    getYamlOutFlag() { return fYamlOut; }
     bool    getKeepMinuit2OutputFlag() { return fKeepMinuit2Output; }
     bool    getDumpAsciiFlag() { return fDumpAscii; }
     bool    getDumpRootFlag() { return fDumpRoot; }
     bool    getEstimateN0Flag() { return fEstimateN0; }
     bool    getChisqPerRunBlockFlag() { return fChisqPreRunBlock; }
+    bool    getIgnoreThemeAutoDetection() { return fIgnoreThemeAutoDetection; }
     bool    getDarkThemeIconsMenuFlag() { return fDarkThemeIconsMenu; }
     bool    getDarkThemeIconsToolbarFlag() { return fDarkThemeIconsToolbar; }
     int     getEditWidth() { return fEditWidth; }
@@ -157,7 +159,9 @@ class PAdmin : public QObject
     void setDumpAsciiFlag(const bool flag) { fDumpAscii = flag; }
     void setDumpRootFlag(const bool flag) { fDumpRoot = flag; }
     void setEstimateN0Flag(const bool flag) { fEstimateN0 = flag; }
+    void setYamlOutFlag(const bool flag) { fYamlOut = flag; }
     void setChisqPerRunBlockFlag(const bool flag) { fChisqPreRunBlock = flag; }
+    void setIgnoreThemeAutoDetection(const bool flag) { fIgnoreThemeAutoDetection = flag; }
     void setDarkThemeIconsMenuFlag(const bool flag) { fDarkThemeIconsMenu = flag; }
     void setDarkThemeIconsToolbarFlag(const bool flag) { fDarkThemeIconsToolbar = flag; }
     void setEditWidth(const int width) { fEditWidth = width; }
@@ -184,30 +188,32 @@ class PAdmin : public QObject
   private:
     friend class PAdminXMLParser;
 
-    int fTimeout;       ///< timeout in seconds
+    int fTimeout{3600};       ///< timeout in seconds
 
-    QString fFontName;  ///< default font name
+    QString fFontName{QString("Monospace")};  ///< default font name
-    int fFontSize;      ///< default font size
+    int fFontSize{11};      ///< default font size
 
-    QString fPrefPathName;       ///< path-name of the musredit_startup.xml
+    QString fPrefPathName{QString("")};       ///< path-name of the musredit_startup.xml
-    QString fExecPath;           ///< system path to the musrfit executables
+    QString fExecPath{QString("")};           ///< system path to the musrfit executables
-    QString fDefaultSavePath;    ///< default path where the msr-file should be saved
+    QString fDefaultSavePath{QString("")};    ///< default path where the msr-file should be saved
-    QString fTheoFuncPixmapPath; ///< path where the default pixmaps can be found
+    QString fTheoFuncPixmapPath{QString("")}; ///< path where the default pixmaps can be found
 
     QVector<QString> fRecentFile; ///< keep vector of recent path-file names
 
-    bool fMusrviewShowFourier;  ///< flag indicating if musrview should show at startup data (=false) or Fourier of data (=true).
+    bool fMusrviewShowFourier{false};  ///< flag indicating if musrview should show at startup data (=false) or Fourier of data (=true).
-    bool fMusrviewShowAvg;      ///< flag indicating if musrview should show at startup averaged (=true) or original (=false) data/Fourier.
+    bool fMusrviewShowAvg{false};      ///< flag indicating if musrview should show at startup averaged (=true) or original (=false) data/Fourier.
-    bool fMusrviewShowOneToOne; ///< flag indicating if theory points are calculate only at the data points (=true) or a higher density theory points is calculated
+    bool fMusrviewShowOneToOne{false}; ///< flag indicating if theory points are calculate only at the data points (=true) or a higher density theory points is calculated
-    bool fKeepMinuit2Output;    ///< flag indicating if the Minuit2 output shall be kept (default: no)
+    bool fKeepMinuit2Output{false};    ///< flag indicating if the Minuit2 output shall be kept (default: no)
-    bool fDumpAscii;            ///< flag indicating if musrfit shall make an ascii-dump file (for debugging purposes, default: no).
+    bool fDumpAscii{false};            ///< flag indicating if musrfit shall make an ascii-dump file (for debugging purposes, default: no).
-    bool fDumpRoot;             ///< flag indicating if musrfit shall make an root-dump file (for debugging purposes, default: no).
+    bool fDumpRoot{false};             ///< flag indicating if musrfit shall make an root-dump file (for debugging purposes, default: no).
-    bool fTitleFromDataFile;    ///< flag indicating if the title should be extracted from the data file (default: yes).
+    bool fTitleFromDataFile{true};     ///< flag indicating if the title should be extracted from the data file (default: yes).
-    bool fChisqPreRunBlock;     ///< flag indicating if musrfit shall write 'per run block' chisq to the msr-file (default: no).
+    bool fChisqPreRunBlock{false};     ///< flag indicating if musrfit shall write 'per run block' chisq to the msr-file (default: no).
-    bool fEstimateN0;           ///< flag indicating if musrfit shall estimate N0 for single histogram fits (default: yes).
+    bool fEstimateN0{true};            ///< flag indicating if musrfit shall estimate N0 for single histogram fits (default: yes).
-    bool fEnableMusrT0;         ///< flag indicating if musrT0 shall be enabled at startup from within musredit (default: yes).
+    bool fYamlOut{false};              ///< flag indicating if the MINUIT2.OUTPUT file should also be written as <msr-file>.yaml output. (default: no).
-    bool fDarkThemeIconsMenu;   ///< flag indicating if dark theme icons shall be used in the menu (default: no)
+    bool fEnableMusrT0{true};          ///< flag indicating if musrT0 shall be enabled at startup from within musredit (default: yes).
-    bool fDarkThemeIconsToolbar; ///< flag indicating if dark theme icons shall be used in the toolbar (default: no)
+    bool fIgnoreThemeAutoDetection{false}; ///< flag indicating that the theme autodetection shall be ignored. (default: no)
+    bool fDarkThemeIconsMenu{false};   ///< flag indicating if dark theme icons shall be used in the menu (default: no)
+    bool fDarkThemeIconsToolbar{false}; ///< flag indicating if dark theme icons shall be used in the toolbar (default: no)
     int  fEditWidth{900};       ///< startup edit width
     int  fEditHeight{800};      ///< startup edit height
 

src/musredit_qt6/musredit/PMsr2DataDialog.cpp

@@ -84,6 +84,7 @@ PMsr2DataDialog::PMsr2DataDialog(PMsr2DataParam *msr2DataParam, const QString he
   fIgnoreDataHeaderInfo_checkBox->setChecked(fMsr2DataParam->ignoreDataHeaderInfo);
   fKeepMinuit2Output_checkBox->setChecked(fMsr2DataParam->keepMinuit2Output);
   fEstimateN0_checkBox->setChecked(fMsr2DataParam->estimateN0);
+  fYamlOut_checkBox->setChecked(fMsr2DataParam->yamlOut);
   fWriteColumnData_checkBox->setChecked(fMsr2DataParam->writeColumnData);
   fRecreateDataFile_checkBox->setChecked(fMsr2DataParam->recreateDbFile);
   fChainFit_checkBox->setChecked(fMsr2DataParam->chainFit);
@@ -121,6 +122,7 @@ PMsr2DataParam* PMsr2DataDialog::getMsr2DataParam()
   fMsr2DataParam->ignoreDataHeaderInfo = fIgnoreDataHeaderInfo_checkBox->isChecked();
   fMsr2DataParam->keepMinuit2Output = fKeepMinuit2Output_checkBox->isChecked();
   fMsr2DataParam->estimateN0 = fEstimateN0_checkBox->isChecked();
+  fMsr2DataParam->yamlOut = fYamlOut_checkBox->isChecked();
   fMsr2DataParam->writeColumnData = fWriteColumnData_checkBox->isChecked();
   fMsr2DataParam->recreateDbFile = fRecreateDataFile_checkBox->isChecked();
   fMsr2DataParam->chainFit = fChainFit_checkBox->isChecked();

src/musredit_qt6/musredit/PPrefsDialog.cpp

@@ -59,6 +59,12 @@ PPrefsDialog::PPrefsDialog(PAdmin *admin) : fAdmin(admin)
     fDarkThemeIconsToolbar_checkBox->setCheckState(Qt::Unchecked);
   }
 
+  if (fAdmin->getIgnoreThemeAutoDetection()) {
+    fIgnoreThemeAutoDetection_checkBox->setCheckState(Qt::Checked);
+  } else {
+    fIgnoreThemeAutoDetection_checkBox->setCheckState(Qt::Unchecked);
+  }
+
   fKeepMn2Output_checkBox->setChecked(fAdmin->getKeepMinuit2OutputFlag());
 
   if (fAdmin->getDumpAsciiFlag() && !fAdmin->getDumpRootFlag()) {
@@ -76,6 +82,7 @@ PPrefsDialog::PPrefsDialog(PAdmin *admin) : fAdmin(admin)
   fEnableMusrT0_checkBox->setChecked(fAdmin->getEnableMusrT0Flag());
   fPerRunBlockChisq_checkBox->setChecked(fAdmin->getChisqPerRunBlockFlag());
   fEstimateN0_checkBox->setChecked(fAdmin->getEstimateN0Flag());
+  fYamlOut_checkBox->setChecked(fAdmin->getYamlOutFlag());
   fFourier_checkBox->setChecked(fAdmin->getMusrviewShowFourierFlag());
   fAvg_checkBox->setChecked(fAdmin->getMusrviewShowAvgFlag());
   fOneToOne_checkBox->setChecked(fAdmin->getMusrviewShowOneToOneFlag());

src/musredit_qt6/musredit/PPrefsDialog.h

@@ -54,6 +54,8 @@ class PPrefsDialog : public QDialog, private Ui::PPrefsDialog
     bool getEnableMusrT0Flag()      { return fEnableMusrT0_checkBox->isChecked(); }
     bool getKeepRunPerBlockChisqFlag() { return fPerRunBlockChisq_checkBox->isChecked(); }
     bool getEstimateN0Flag()        { return fEstimateN0_checkBox->isChecked(); }
+    bool getYamlOutFlag()           { return fYamlOut_checkBox->isChecked(); }
+    bool getIgnoreThemeAutoDetection() { return fIgnoreThemeAutoDetection_checkBox->isChecked(); }
     bool getDarkThemeIconsMenuFlag()    { return fDarkThemeIconsMenu_checkBox->isChecked(); }
     bool getDarkThemeIconsToolbarFlag()    { return fDarkThemeIconsToolbar_checkBox->isChecked(); }
     bool getOneToOneFlag() { return fOneToOne_checkBox->isChecked(); }

src/musredit_qt6/musredit/PTextEdit.cpp

@@ -88,11 +88,11 @@
 PTextEdit::PTextEdit( QWidget *parent )
     : QMainWindow( parent )
 {
-  bool gotTheme = getTheme();
-
   // reads and manages the conents of the xml-startup (musredit_startup.xml) file
   fAdmin = std::make_unique<PAdmin>();
 
+  bool gotTheme = getTheme();
+
   // set default setting of the fDarkMenuIconIcons only if a theme has been recognized, otherwise take the
   // one from the xml startup file.
   if (gotTheme) {
@@ -117,8 +117,6 @@ PTextEdit::PTextEdit( QWidget *parent )
   }
 
   // initialize stuff
-//as35  fMusrT0Action = nullptr;
-
   fMsr2DataParam = nullptr;
   fFindReplaceData = nullptr;
 
@@ -127,6 +125,7 @@ PTextEdit::PTextEdit( QWidget *parent )
   setupEditActions();
   setupTextActions();
   setupMusrActions();
+  setupJumpToBlock();
   setupHelpActions();
 
   fTabWidget = std::make_unique<QTabWidget>( this );
@@ -135,7 +134,6 @@ PTextEdit::PTextEdit( QWidget *parent )
 
   textFamily(fAdmin->getFontName());
   textSize(QString("%1").arg(fAdmin->getFontSize()));
-  fFontChanging = false;
 
   QString iconName("");
   if (fDarkMenuIcon)
@@ -164,12 +162,6 @@ PTextEdit::PTextEdit( QWidget *parent )
  */
 void PTextEdit::aboutToQuit()
 {
-/* //as35
-  if (fMusrT0Action) {
-    delete fMusrT0Action;
-    fMusrT0Action = nullptr;
-  }
-*/ //as35
   if (fMsr2DataParam) {
     delete fMsr2DataParam;
     fMsr2DataParam = nullptr;
@@ -965,6 +957,31 @@ void PTextEdit::setupHelpActions()
   menu->addAction(a);
 }
 
+//----------------------------------------------------------------------------------------------------
+/**
+ * <p>Setup the JumpToBlock actions.
+ */
+void PTextEdit::setupJumpToBlock()
+{
+  QToolBar *tb = new QToolBar( this );
+  tb->setWindowTitle( "JumpToBlock Actions" );
+  addToolBar( tb );
+
+  QStringList jumpToBlockStr = {"FITPARAMETER", "THEORY", "FUNCTIONS", "GLOBAL", "RUN", "COMMANDS", "PLOT", "FOURIER", "STATISTIC"};
+  fJumpToBlock = std::make_unique<QComboBox>();
+  if (fJumpToBlock == nullptr)
+    return;
+  fJumpToBlock->addItems(jumpToBlockStr);
+  fJumpToBlock->setEditable(false);
+
+  connect( fJumpToBlock.get(), SIGNAL( activated(int) ), this, SLOT( jumpToBlock(int) ));
+
+  QLabel *jstr = new QLabel("  Jump to block: ");
+
+  tb->addWidget(jstr);
+  tb->addWidget(fJumpToBlock.get());
+}
+
 //----------------------------------------------------------------------------------------------------
 /**
  * <p>load a msr-file.
@@ -981,6 +998,7 @@ void PTextEdit::load( const QString &f, const int index )
   // create a new text edit object
   PSubTextEdit *edit = new PSubTextEdit( fAdmin.get() );
   edit->setFont(QFont(fAdmin->getFontName(), fAdmin->getFontSize()));
+  edit->setCenterOnScroll(true);
 
   // place the text edit object at the appropriate tab position
   if (index == -1)
@@ -1165,6 +1183,7 @@ void PTextEdit::fileNew()
 {
   PSubTextEdit *edit = new PSubTextEdit( fAdmin.get() );
   edit->setFont(QFont(fAdmin->getFontName(), fAdmin->getFontSize()));
+  edit->setCenterOnScroll(true);
   doConnections( edit );
   fTabWidget->addTab( edit, tr( "noname" ) );
   fTabWidget->setCurrentIndex(fTabWidget->indexOf(edit));
@@ -1398,18 +1417,18 @@ void PTextEdit::fileSavePrefs()
   QString msg("");
   QMessageBox msgBox;
   msgBox.setText("Which Preferences do you want to open?");
-  msgBox.addButton("Default", QMessageBox::AcceptRole);
+  QAbstractButton *def = msgBox.addButton("Default", QMessageBox::AcceptRole);
-  msgBox.addButton("Custom", QMessageBox::AcceptRole);
+  QAbstractButton *cust = msgBox.addButton("Custom", QMessageBox::AcceptRole);
   msgBox.setStandardButtons(QMessageBox::Cancel);
   int result = msgBox.exec();
   if (result == QMessageBox::Cancel) {
     return;
-  } else if (result == 0) { // default dir
+  } else if (msgBox.clickedButton() == def) { // default dir
     fln = fAdmin->getDefaultPrefPathName();
     msg = QString("Current Default Preferences Path-Name:\n") + fln;
     if (QMessageBox::information(this, "INFO", msg, QMessageBox::Ok, QMessageBox::Cancel) == QMessageBox::Cancel)
       return;
-  } else if (result == 1) { // custom dir
+  } else if (msgBox.clickedButton() == cust) { // custom dir
     fln = QFileDialog::getSaveFileName( this,
                     tr( "Save Prefs As" ), "musredit_startup.xml",
                     tr( "xml-Files (*.xml);;All Files (*)" ) );
@@ -2108,6 +2127,11 @@ void PTextEdit::musrFit()
     cmd.append("--estimateN0");
   }
 
+  // check yamlOut flag
+  if (fAdmin->getYamlOutFlag()) {
+    cmd.append("--yaml");
+  }
+
   // check per-run-block-chisq flag
   if (fAdmin->getChisqPerRunBlockFlag()) {
     cmd.append("--per-run-block-chisq");
@@ -2184,6 +2208,7 @@ void PTextEdit::musrMsr2Data()
   fMsr2DataParam->keepMinuit2Output = fAdmin->getKeepMinuit2OutputFlag();
   fMsr2DataParam->titleFromDataFile = fAdmin->getTitleFromDataFileFlag();
   fMsr2DataParam->estimateN0 = fAdmin->getEstimateN0Flag();
+  fMsr2DataParam->yamlOut = fAdmin->getYamlOutFlag();
   fMsr2DataParam->perRunBlockChisq = fAdmin->getChisqPerRunBlockFlag();
 
   PMsr2DataDialog *dlg = new PMsr2DataDialog(fMsr2DataParam, fAdmin->getHelpUrl("msr2data"));
@@ -2206,6 +2231,7 @@ void PTextEdit::musrMsr2Data()
     fAdmin->setKeepMinuit2OutputFlag(fMsr2DataParam->keepMinuit2Output);
     fAdmin->setTitleFromDataFileFlag(fMsr2DataParam->titleFromDataFile);
     fAdmin->setEstimateN0Flag(fMsr2DataParam->estimateN0);
+    fAdmin->setYamlOutFlag(fMsr2DataParam->yamlOut);
     fAdmin->setChisqPerRunBlockFlag(fMsr2DataParam->perRunBlockChisq);
 
     // analyze parameters
@@ -2336,6 +2362,11 @@ void PTextEdit::musrMsr2Data()
       cmd.append("-e");
     }
 
+    // yaml out. Add flag only if a fit is done
+    if (fMsr2DataParam->yamlOut && (fMsr2DataParam->fitOnly || fMsr2DataParam->templateRunNo != -1)) {
+      cmd.append("-y");
+    }
+
     // write per-run-block chisq. Add flag only if a fit is done
     if (fMsr2DataParam->perRunBlockChisq && (fMsr2DataParam->fitOnly || fMsr2DataParam->templateRunNo != -1)) {
       cmd.append("-p");
@@ -2691,6 +2722,7 @@ void PTextEdit::musrPrefs()
   }
 
   if (dlg->exec() == QDialog::Accepted) {
+    fAdmin->setIgnoreThemeAutoDetection(dlg->getIgnoreThemeAutoDetection());
     fAdmin->setDarkThemeIconsMenuFlag(dlg->getDarkThemeIconsMenuFlag());
     fAdmin->setDarkThemeIconsToolbarFlag(dlg->getDarkThemeIconsToolbarFlag());
     fAdmin->setMusrviewShowFourierFlag(dlg->getMusrviewShowFourierFlag());
@@ -2713,6 +2745,7 @@ void PTextEdit::musrPrefs()
     fAdmin->setTimeout(dlg->getTimeout());
     fAdmin->setChisqPerRunBlockFlag(dlg->getKeepRunPerBlockChisqFlag());
     fAdmin->setEstimateN0Flag(dlg->getEstimateN0Flag());
+    fAdmin->setYamlOutFlag(dlg->getYamlOutFlag());
   }
 
   delete dlg;
@@ -3278,12 +3311,35 @@ void PTextEdit::setFileSystemWatcherActive()
   fFileSystemWatcherActive = true;
 }
 
+//----------------------------------------------------------------------------------------------------
+/**
+ * <p>slot called when jumpToBlock combobox is selected
+ * @param idx
+ */
+void PTextEdit::jumpToBlock(int idx)
+{
+  QString str = fJumpToBlock->itemText(idx);
+
+  QTextDocument::FindFlags flags= QTextDocument::FindCaseSensitively | QTextDocument::FindWholeWords;
+
+  bool found = currentEditor()->find(str, flags);
+  if (found)
+    return;
+
+  // set cursor to start
+  currentEditor()->moveCursor(QTextCursor::Start);
+  currentEditor()->find(str, flags);
+}
+
 //----------------------------------------------------------------------------------------------------
 /**
  * @brief PTextEdit::getTheme
  */
 bool PTextEdit::getTheme()
 {
+  if (fAdmin->getIgnoreThemeAutoDetection())
+    return false;
+
   fDarkMenuIcon = false; // true if theme is dark
   fDarkToolBarIcon = false; // needed for ubuntu dark since there the menu icons are dark, however the toolbar icons are plain!
 
@@ -3315,10 +3371,9 @@ bool PTextEdit::getTheme()
 
   if (str.contains("dark", Qt::CaseInsensitive)) {
     fDarkMenuIcon = true;
-    if (str.contains("ubuntu", Qt::CaseInsensitive)) {
+    if (str.contains("ubuntu", Qt::CaseInsensitive) ||
-      fDarkMenuIcon = false;
+        str.contains("xfce", Qt::CaseInsensitive) ||
-      fDarkToolBarIcon = false;
+        str.contains("mx", Qt::CaseInsensitive)) {
-    } else if (str.contains("xfce", Qt::CaseInsensitive)) {
       fDarkMenuIcon = false;
       fDarkToolBarIcon = false;
     } else {

src/musredit_qt6/musredit/PTextEdit.h

@@ -30,6 +30,8 @@
 #ifndef _PTEXTEDIT_H_
 #define _PTEXTEDIT_H_
 
+#include <memory>
+
 #include <QAction>
 #include <QMainWindow>
 #include <QString>
@@ -46,8 +48,6 @@
 
 #include <QtDebug>
 
-#include <memory>
-
 #include "PAdmin.h"
 #include "musredit.h"
 
@@ -86,6 +86,7 @@ private:
   void setupTextActions();
   void setupMusrActions();
   void setupHelpActions();
+  void setupJumpToBlock();
   void load( const QString &f, const int index=-1 );
   PSubTextEdit *currentEditor() const;
   void doConnections( PSubTextEdit *e );
@@ -167,16 +168,18 @@ private slots:
   void fileChanged(const QString &fileName);
   void setFileSystemWatcherActive();
 
+  void jumpToBlock(int idx);
+
 private:
-  bool fDarkMenuIcon; ///< flag indicating if a dark or plain icon shall be used in the menu pull-downs
+  bool fDarkMenuIcon{false}; ///< flag indicating if a dark or plain icon shall be used in the menu pull-downs
-  bool fDarkToolBarIcon; ///< flag indicating if a dark or plain icon shall be used in the toolbar
+  bool fDarkToolBarIcon{false}; ///< flag indicating if a dark or plain icon shall be used in the toolbar
   std::unique_ptr<PAdmin> fAdmin; ///< pointer to the xml-startup file informations. Needed for different purposes like default working- and executable directories etc.
   std::unique_ptr<QFileSystemWatcher> fFileSystemWatcher; ///< checks if msr-files are changing on the disk while being open in musredit.
   bool fFileSystemWatcherActive; ///< flag to enable/disable the file system watcher
   QTimer fFileSystemWatcherTimeout; ///< timer used to re-enable file system watcher. Needed to delay the re-enabling
-  QString fLastDirInUse; ///< string holding the path from where the last file was loaded.
+  QString fLastDirInUse{QString("")}; ///< string holding the path from where the last file was loaded.
   QStringList fMusrFTPrevCmd;
-  int fEditW, fEditH;
+  int fEditW{900}, fEditH{800};
 
   QMap<QString, QAction*> fActions;
   std::unique_ptr<QAction> fMusrT0Action;
@@ -186,7 +189,8 @@ private:
 
   std::unique_ptr<QComboBox> fComboFont; ///< combo box for the font selector
   std::unique_ptr<QComboBox> fComboSize; ///< combo box for the font size
-  bool fFontChanging; ///< flag needed to prevent some textChanged feature to occure when only the font changed
+  bool fFontChanging{false}; ///< flag needed to prevent some textChanged feature to occure when only the font changed
+  std::unique_ptr<QComboBox> fJumpToBlock; ///< combo box used to jump to the msr-file blocks
 
   std::unique_ptr<QTabWidget> fTabWidget; ///< tab widget in which the text editor(s) are placed
   QMap<PSubTextEdit*, QString> fFilenames; ///< mapper between tab widget object and filename

src/musredit_qt6/musredit/forms/PMsr2DataDialog.ui

@@ -338,7 +338,7 @@
       <x>6</x>
       <y>20</y>
       <width>560</width>
-      <height>131</height>
+      <height>135</height>
      </rect>
     </property>
     <layout class="QHBoxLayout" name="horizontalLayout_9">
@@ -456,6 +456,13 @@
          </property>
         </widget>
        </item>
+       <item>
+        <widget class="QCheckBox" name="fYamlOut_checkBox">
+         <property name="text">
+          <string>yaml out</string>
+         </property>
+        </widget>
+       </item>
        <item>
         <layout class="QHBoxLayout" name="horizontalLayout_8">
          <item>

src/musredit_qt6/musredit/forms/PPrefsDialog.ui

@@ -9,8 +9,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>452</width>
+    <width>460</width>
-    <height>180</height>
+    <height>200</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -20,279 +20,293 @@
    <iconset>
     <normaloff>:/images/musrfit.xpm</normaloff>:/images/musrfit.xpm</iconset>
   </property>
-  <widget class="QWidget" name="layoutWidget_0">
+  <layout class="QHBoxLayout" name="horizontalLayout_3">
-   <property name="geometry">
+   <item>
-    <rect>
+    <layout class="QVBoxLayout" name="verticalLayout">
-     <x>0</x>
+     <item>
-     <y>5</y>
+      <widget class="QTabWidget" name="fTabWidget">
-     <width>451</width>
+       <property name="currentIndex">
-     <height>171</height>
+        <number>0</number>
-    </rect>
+       </property>
-   </property>
+       <widget class="QWidget" name="fGeneral_tab">
-   <layout class="QVBoxLayout" name="verticalLayout">
+        <attribute name="title">
-    <item>
+         <string>general</string>
-     <widget class="QTabWidget" name="fTabWidget">
+        </attribute>
-      <property name="currentIndex">
+        <widget class="QPushButton" name="fDefaultPath_pushButton">
-       <number>2</number>
+         <property name="geometry">
-      </property>
+          <rect>
-      <widget class="QWidget" name="fGeneral_tab">
+           <x>10</x>
-       <attribute name="title">
+           <y>80</y>
-        <string>general</string>
+           <width>421</width>
-       </attribute>
+           <height>31</height>
-       <widget class="QPushButton" name="fDefaultPath_pushButton">
+          </rect>
-        <property name="geometry">
+         </property>
-         <rect>
+         <property name="text">
-          <x>10</x>
+          <string>Change Default Search Paths</string>
-          <y>70</y>
+         </property>
-          <width>421</width>
+        </widget>
-          <height>31</height>
+        <widget class="QWidget" name="">
-         </rect>
+         <property name="geometry">
-        </property>
+          <rect>
-        <property name="text">
+           <x>10</x>
-         <string>Change Default Search Paths</string>
+           <y>10</y>
-        </property>
+           <width>416</width>
+           <height>61</height>
+          </rect>
+         </property>
+         <layout class="QHBoxLayout" name="horizontalLayout_2">
+          <item>
+           <widget class="QLineEdit" name="fTimeout_lineEdit"/>
+          </item>
+          <item>
+           <widget class="QLabel" name="fTimeout_label">
+            <property name="text">
+             <string>timeout</string>
+            </property>
+           </widget>
+          </item>
+          <item>
+           <spacer name="horizontalSpacer_2">
+            <property name="orientation">
+             <enum>Qt::Horizontal</enum>
+            </property>
+            <property name="sizeHint" stdset="0">
+             <size>
+              <width>38</width>
+              <height>30</height>
+             </size>
+            </property>
+           </spacer>
+          </item>
+          <item>
+           <layout class="QVBoxLayout" name="verticalLayout_2">
+            <item>
+             <widget class="QCheckBox" name="fIgnoreThemeAutoDetection_checkBox">
+              <property name="text">
+               <string>Ignore Theme Auto Detect</string>
+              </property>
+             </widget>
+            </item>
+            <item>
+             <widget class="QCheckBox" name="fDarkThemeIconsMenu_checkBox">
+              <property name="text">
+               <string>Dark Theme Icons Menu</string>
+              </property>
+             </widget>
+            </item>
+            <item>
+             <widget class="QCheckBox" name="fDarkThemeIconsToolbar_checkBox">
+              <property name="text">
+               <string>Dark Theme Icons Toolbar</string>
+              </property>
+             </widget>
+            </item>
+           </layout>
+          </item>
+         </layout>
+        </widget>
        </widget>
-       <widget class="QWidget" name="layoutWidget">
+       <widget class="QWidget" name="fMusrfit_tab">
-        <property name="geometry">
+        <attribute name="title">
-         <rect>
+         <string>musrfit</string>
-          <x>12</x>
+        </attribute>
-          <y>10</y>
+        <widget class="QCheckBox" name="fKeepMn2Output_checkBox">
-          <width>415</width>
+         <property name="geometry">
-          <height>62</height>
+          <rect>
-         </rect>
+           <x>10</x>
-        </property>
+           <y>10</y>
-        <layout class="QHBoxLayout" name="horizontalLayout_2">
+           <width>161</width>
-         <item>
+           <height>23</height>
-          <widget class="QLineEdit" name="fTimeout_lineEdit"/>
+          </rect>
-         </item>
+         </property>
-         <item>
+         <property name="text">
-          <widget class="QLabel" name="fTimeout_label">
+          <string>keep minuit2 output</string>
-           <property name="text">
+         </property>
-            <string>timeout</string>
+        </widget>
-           </property>
+        <widget class="QCheckBox" name="fDumpAscii_checkBox">
-          </widget>
+         <property name="geometry">
-         </item>
+          <rect>
-         <item>
+           <x>10</x>
-          <spacer name="horizontalSpacer_2">
+           <y>35</y>
-           <property name="orientation">
+           <width>151</width>
-            <enum>Qt::Horizontal</enum>
+           <height>23</height>
-           </property>
+          </rect>
-           <property name="sizeHint" stdset="0">
+         </property>
-            <size>
+         <property name="text">
-             <width>38</width>
+          <string>dump ascii</string>
-             <height>30</height>
+         </property>
-            </size>
+        </widget>
-           </property>
+        <widget class="QCheckBox" name="fDumpRoot_checkBox">
-          </spacer>
+         <property name="geometry">
-         </item>
+          <rect>
-         <item>
+           <x>10</x>
-          <layout class="QVBoxLayout" name="verticalLayout_2">
+           <y>60</y>
-           <item>
+           <width>131</width>
-            <widget class="QCheckBox" name="fDarkThemeIconsMenu_checkBox">
+           <height>23</height>
-             <property name="text">
+          </rect>
-              <string>Dark Theme Icons Menu</string>
+         </property>
-             </property>
+         <property name="text">
-            </widget>
+          <string>dump root</string>
-           </item>
+         </property>
-           <item>
+        </widget>
-            <widget class="QCheckBox" name="fDarkThemeIconsToolbar_checkBox">
+        <widget class="QCheckBox" name="fTitleFromData_checkBox">
-             <property name="text">
+         <property name="geometry">
-              <string>Dark Theme Icons Toolbar</string>
+          <rect>
-             </property>
+           <x>170</x>
-            </widget>
+           <y>10</y>
-           </item>
+           <width>161</width>
-          </layout>
+           <height>23</height>
-         </item>
+          </rect>
-        </layout>
+         </property>
+         <property name="text">
+          <string>take title from data file</string>
+         </property>
+        </widget>
+        <widget class="QCheckBox" name="fPerRunBlockChisq_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>170</x>
+           <y>35</y>
+           <width>181</width>
+           <height>22</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>keep per run block chisq</string>
+         </property>
+        </widget>
+        <widget class="QCheckBox" name="fEstimateN0_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>170</x>
+           <y>60</y>
+           <width>171</width>
+           <height>22</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>estimate N0</string>
+         </property>
+        </widget>
+        <widget class="QCheckBox" name="fYamlOut_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>350</x>
+           <y>10</y>
+           <width>85</width>
+           <height>21</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>yaml out</string>
+         </property>
+        </widget>
+       </widget>
+       <widget class="QWidget" name="fMusrview_tab">
+        <attribute name="title">
+         <string>musrview</string>
+        </attribute>
+        <widget class="QCheckBox" name="fFourier_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>10</x>
+           <y>10</y>
+           <width>421</width>
+           <height>22</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>start with Fourier</string>
+         </property>
+        </widget>
+        <widget class="QCheckBox" name="fAvg_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>10</x>
+           <y>40</y>
+           <width>421</width>
+           <height>21</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>start with averaged data/Fourier</string>
+         </property>
+        </widget>
+        <widget class="QCheckBox" name="fOneToOne_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>260</x>
+           <y>10</y>
+           <width>181</width>
+           <height>26</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>theo at data points only</string>
+         </property>
+        </widget>
+       </widget>
+       <widget class="QWidget" name="fMusrt0_tab">
+        <attribute name="title">
+         <string>musrt0</string>
+        </attribute>
+        <widget class="QCheckBox" name="fEnableMusrT0_checkBox">
+         <property name="geometry">
+          <rect>
+           <x>10</x>
+           <y>10</y>
+           <width>131</width>
+           <height>23</height>
+          </rect>
+         </property>
+         <property name="text">
+          <string>enable it</string>
+         </property>
+        </widget>
        </widget>
       </widget>
-      <widget class="QWidget" name="fMusrfit_tab">
+     </item>
-       <attribute name="title">
+     <item>
-        <string>musrfit</string>
+      <layout class="QHBoxLayout" name="horizontalLayout">
-       </attribute>
+       <item>
-       <widget class="QCheckBox" name="fKeepMn2Output_checkBox">
+        <widget class="QPushButton" name="fHelp_pushButton">
-        <property name="geometry">
+         <property name="text">
-         <rect>
+          <string>&amp;Help</string>
-          <x>10</x>
+         </property>
-          <y>10</y>
+        </widget>
-          <width>161</width>
+       </item>
-          <height>23</height>
+       <item>
-         </rect>
+        <spacer name="horizontalSpacer">
-        </property>
+         <property name="orientation">
-        <property name="text">
+          <enum>Qt::Horizontal</enum>
-         <string>keep minuit2 output</string>
+         </property>
-        </property>
+         <property name="sizeHint" stdset="0">
-       </widget>
+          <size>
-       <widget class="QCheckBox" name="fDumpAscii_checkBox">
+           <width>88</width>
-        <property name="geometry">
+           <height>20</height>
-         <rect>
+          </size>
-          <x>10</x>
+         </property>
-          <y>35</y>
+        </spacer>
-          <width>151</width>
+       </item>
-          <height>23</height>
+       <item>
-         </rect>
+        <widget class="QPushButton" name="fOk_pushButton">
-        </property>
+         <property name="text">
-        <property name="text">
+          <string>&amp;OK</string>
-         <string>dump ascii</string>
+         </property>
-        </property>
+        </widget>
-       </widget>
+       </item>
-       <widget class="QCheckBox" name="fDumpRoot_checkBox">
+       <item>
-        <property name="geometry">
+        <widget class="QPushButton" name="fCancel_pushButton">
-         <rect>
+         <property name="text">
-          <x>10</x>
+          <string>&amp;Cancel</string>
-          <y>60</y>
+         </property>
-          <width>131</width>
+        </widget>
-          <height>23</height>
+       </item>
-         </rect>
+      </layout>
-        </property>
+     </item>
-        <property name="text">
+    </layout>
-         <string>dump root</string>
+   </item>
-        </property>
+  </layout>
-       </widget>
-       <widget class="QCheckBox" name="fTitleFromData_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>190</x>
-          <y>10</y>
-          <width>241</width>
-          <height>23</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>take title from data file</string>
-        </property>
-       </widget>
-       <widget class="QCheckBox" name="fPerRunBlockChisq_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>190</x>
-          <y>35</y>
-          <width>241</width>
-          <height>22</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>keep per run block chisq</string>
-        </property>
-       </widget>
-       <widget class="QCheckBox" name="fEstimateN0_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>190</x>
-          <y>60</y>
-          <width>241</width>
-          <height>22</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>estimate N0</string>
-        </property>
-       </widget>
-      </widget>
-      <widget class="QWidget" name="fMusrview_tab">
-       <attribute name="title">
-        <string>musrview</string>
-       </attribute>
-       <widget class="QCheckBox" name="fFourier_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>10</x>
-          <y>10</y>
-          <width>421</width>
-          <height>22</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>start with Fourier</string>
-        </property>
-       </widget>
-       <widget class="QCheckBox" name="fAvg_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>10</x>
-          <y>40</y>
-          <width>421</width>
-          <height>21</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>start with averaged data/Fourier</string>
-        </property>
-       </widget>
-       <widget class="QCheckBox" name="fOneToOne_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>260</x>
-          <y>10</y>
-          <width>181</width>
-          <height>26</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>theo at data points only</string>
-        </property>
-       </widget>
-      </widget>
-      <widget class="QWidget" name="fMusrt0_tab">
-       <attribute name="title">
-        <string>musrt0</string>
-       </attribute>
-       <widget class="QCheckBox" name="fEnableMusrT0_checkBox">
-        <property name="geometry">
-         <rect>
-          <x>10</x>
-          <y>10</y>
-          <width>131</width>
-          <height>23</height>
-         </rect>
-        </property>
-        <property name="text">
-         <string>enable it</string>
-        </property>
-       </widget>
-      </widget>
-     </widget>
-    </item>
-    <item>
-     <layout class="QHBoxLayout" name="horizontalLayout">
-      <item>
-       <widget class="QPushButton" name="fHelp_pushButton">
-        <property name="text">
-         <string>&amp;Help</string>
-        </property>
-       </widget>
-      </item>
-      <item>
-       <spacer name="horizontalSpacer">
-        <property name="orientation">
-         <enum>Qt::Horizontal</enum>
-        </property>
-        <property name="sizeHint" stdset="0">
-         <size>
-          <width>88</width>
-          <height>20</height>
-         </size>
-        </property>
-       </spacer>
-      </item>
-      <item>
-       <widget class="QPushButton" name="fOk_pushButton">
-        <property name="text">
-         <string>&amp;OK</string>
-        </property>
-       </widget>
-      </item>
-      <item>
-       <widget class="QPushButton" name="fCancel_pushButton">
-        <property name="text">
-         <string>&amp;Cancel</string>
-        </property>
-       </widget>
-      </item>
-     </layout>
-    </item>
-   </layout>
-  </widget>
  </widget>
  <tabstops>
   <tabstop>fTabWidget</tabstop>

src/musredit_qt6/musredit/musredit.h

@@ -56,6 +56,7 @@ struct PMsr2DataParam {
   bool openFilesAfterFitting;  ///< flag: true = open msr-file after fit in musredit. false = do not open msr-file after fit.
   bool titleFromDataFile;      ///< flag indicating if the title for the msr-file shall be extracted from the data-file ('-t' in msr2data)
   bool estimateN0;             ///< flag indicating if the N0 shall be estimated for single histogram fitting
+  bool yamlOut;                ///< flag indicating if the MINUIT2.OUTPUT content should be written to <msr-file>.yaml
   bool perRunBlockChisq;       ///< flag indicating if per-run-block-chisq shall be dumped into the msr-file
   bool createMsrFileOnly;      ///< flag: true = just create the msr-files without any fitting ('msr-<template>' in msr2data)
   bool fitOnly;                ///< flag: true = just perform the fits wihtout generating any msr-files ('fit' in msr2data).

src/musredit_qt6/musredit/musredit_startup.xml.in

@@ -14,10 +14,12 @@
     <title_from_data_file>y</title_from_data_file>
     <chisq_per_run_block>n</chisq_per_run_block>
     <estimate_n0>y</estimate_n0>
+    <yaml_out>n</yaml_out>
     <musrview_show_fourier>n</musrview_show_fourier>
     <musrview_show_avg>n</musrview_show_avg>
     <musrview_show_one_to_one>n</musrview_show_one_to_one>
     <enable_musrt0>y</enable_musrt0>
+    <ignore_theme_auto_detection>n</ignore_theme_auto_detection>
     <dark_theme_icons_menu>n</dark_theme_icons_menu>
     <dark_theme_icons_toolbar>n</dark_theme_icons_toolbar>
     <edit_w>900</edit_w>

src/musrfit.cpp

@@ -127,6 +127,7 @@ void musrfit_syntax()
   std::cout << std::endl << "                       (ii)  if present under $HOME/.musrfit/";
   std::cout << std::endl << "                       (iii) if present under $MUSRFITPATH/";
   std::cout << std::endl << "                       (iv)  if present under $ROOTSYS/";
+  std::cout << std::endl << "       -y, --yaml: write fit results (MINUIT2.OUTPUT) into a yaml-file. Output <msr-file>.yaml";
   std::cout << std::endl << "       --dump <type> is writing a data file with the fit data and the theory";
   std::cout << std::endl << "              <type> can be 'ascii', 'root'";
   std::cout << std::endl << "       --timeout <timeout_tag>: overwrites to predefined timeout of " << timeout << " (sec).";
@@ -446,6 +447,7 @@ int main(int argc, char *argv[])
   int  status;
   bool keep_mn2_output = false;
   bool chisq_only = false;
+  bool yaml_out = false;
   bool title_from_data_file = false;
   bool timeout_enabled = true;
   bool reset_startup_file = false;
@@ -532,6 +534,8 @@ int main(int argc, char *argv[])
       startup_options.estimateN0 = true;
     } else if (!strcmp(argv[i], "-p") || !strcmp(argv[i], "--per-run-block-chisq")) {
       startup_options.writeExpectedChisq = true;
+    } else if (!strcmp(argv[i], "-y") || !strcmp(argv[i], "--yaml")) {
+      yaml_out = true;
     } else if (!strcmp(argv[i], "-n") || !strcmp(argv[i], "--no-of-cores-avail")) {
 #ifdef HAVE_GOMP
         std::cout << std::endl;
@@ -724,7 +728,7 @@ int main(int argc, char *argv[])
   // do fitting
   std::unique_ptr<PFitter> fitter;
   if (success) {
-    fitter = std::make_unique<PFitter>(msrHandler.get(), runListCollection.get(), chisq_only);
+    fitter = std::make_unique<PFitter>(msrHandler.get(), runListCollection.get(), chisq_only, yaml_out);
     if (fitter->IsValid()) {
       fitter->DoFit();
       if (!fitter->IsScanOnly())

src/musrview.cpp

@@ -37,6 +37,7 @@
 
 #include <iostream>
 #include <memory>
+#include <vector>
 
 #include <TApplication.h>
 #include <TSAXParser.h>
@@ -301,15 +302,15 @@ int main(int argc, char *argv[])
   }
 
   if (result == PMUSR_SUCCESS) {
-    // generate Root application needed for PMusrCanvas
+    // create the ROOT application needed for PMusrCanvas
-    int cc=0;
+    // and pass it only essential arguments
-    char **arg;
+    std::vector<char*> args;
+    args.push_back(argv[0]); // program name
     if (graphicsOutput || asciiOutput) {
-      arg[cc] = (char*)malloc(16*sizeof(char));
+      args.push_back((char*)"-b"); // batch mode flag
-      strcpy(arg[cc], "-b");
-      cc++;
     }
-    TApplication app("App", &cc, arg);
+    int cc = args.size();
+    TApplication app("App", &cc, args.data());
 
     std::vector<PMusrCanvas*> canvasVector;
     PMusrCanvas *musrCanvas;