adopted from AFS to NFS.

switch Qt docu from Qt5 to Qt6

.gitea/workflows/deploy-pages.yml

@@ -0,0 +1,45 @@
+name: Build and Deploy Documentation
+
+on:
+  push:
+    branches:
+      - root6
+  workflow_dispatch:
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    container:
+      image: gitea.psi.ch/images/alpine-jupyterbook
+    steps:
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install system dependencies
+        run: |
+          apk add doxygen graphviz
+
+      - name: Build musrfit-tech-docu
+        run: |
+          cd doc
+          mkdir technical 
+          doxygen musrfit_dox.cfg
+          doxygen musredit_qt6_dox.cfg
+          doxygen mupp_qt6_dox.cfg
+          doxygen musrStep_qt6_dox.cfg
+          doxygen musrWiz_qt6_dox.cfg
+
+      - name: Configure Git
+        run: |
+          git config --global user.name "Gitea Actions"
+          git config --global user.email "actions@gitea.local"
+
+      - name: Push to gitea-pages branch
+        run: |
+          git checkout --orphan gitea-pages
+          git reset --hard
+          cp -r ./doc/technical/html/* .
+          git add .
+          git commit -m "Deploy site"
+          git push --verbose -f https://${{secrets.GITHUB_TOKEN}}@gitea.psi.ch/${{ github.repository }}.git gitea-pages

.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 1.9.9 LANGUAGES C CXX)
 
 #--- musrfit specific options -------------------------------------------------
 option(nexus "build optional NeXus support. Needed for ISIS" OFF)
@@ -92,11 +92,19 @@ endif ()
 set(ROOT_GRTEQ_24 ${ROOT_GRTEQ_24} CACHE INTERNAL "ROOT Version check")
 
 #--- check for boost ----------------------------------------------------------
-find_package(Boost REQUIRED
-  COMPONENTS
-    system
-    filesystem
-)
+find_package(Boost QUIET)
+if (Boost_VERSION VERSION_GREATER_EQUAL "1.89")
+  find_package(Boost REQUIRED
+    COMPONENTS
+      filesystem
+  )
+else (Boost_VERSION VERSION_GREATER_EQUAL "1.89")
+  find_package(Boost REQUIRED
+    COMPONENTS
+      system
+      filesystem
+  )
+endif (Boost_VERSION VERSION_GREATER_EQUAL "1.89")
 message(STATUS "Boost libs: ${Boost_LIBRARIES}")
 
 #--- check for gsl ------------------------------------------------------------
@@ -109,13 +117,13 @@ find_package(FFTW3 REQUIRED)
 find_package(LibXml2 REQUIRED)
 
 #--- check for OpenMP ---------------------------------------------------------
-if (try_OpenMP AND NOT APPLE)
+if (try_OpenMP)
   find_package(OpenMP)
-  if (OpenMP_FOUND)
+  if (OpenMP_CXX_FOUND)
     add_definitions(-DHAVE_GOMP)
     set(HAVE_GOMP 1 CACHE INTERNAL "Have GOMP")
-  endif (OpenMP_FOUND)
-endif (try_OpenMP AND NOT APPLE)
+  endif (OpenMP_CXX_FOUND)
+endif (try_OpenMP)
 
 #--- check for Qt -------------------------------------------------------------
 if (qt_based_tools)
@@ -200,8 +208,10 @@ endif (qt_based_tools)
 
 #--- if NeXus check also for HDF4, HDF5, and MXML -----------------------------
 if (nexus)
-  find_package(HDF5 COMPONENTS CXX REQUIRED )
-  find_package(HDF4 REQUIRED)
+  find_package(HDF5 COMPONENTS CXX REQUIRED)
+  if (HAVE_HDF4)
+    find_package(HDF4 REQUIRED)
+  endif (HAVE_HDF4)  
   find_package(NEXUS REQUIRED)
   add_definitions(-DPNEXUS_ENABLED)
 endif (nexus)
@@ -222,6 +232,19 @@ else ()
   set(IS_GIT_REPO 0)
 endif ()
 
+#--- start create git-revision.h ----------------------------------------------
+if (IS_GIT_REPO)
+  execute_process(COMMAND sh ${CMAKE_SOURCE_DIR}/src/git_revision.sh)
+
+  set(HAVE_GIT_REV_H "-DHAVE_GIT_REV_H")  
+  set(GIT_REV_H "git-revision.h")
+else (IS_GIT_REPO)
+  set(HAVE_GIT_REV_H "")  
+  set(GIT_REV_H "")
+endif (IS_GIT_REPO)
+
+#--- end create git-revision.h ------------------------------------------------
+
 #--- rpath related things -----------------------------------------------------
 # use, i.e. don't skip the full RPATH for the build tree
 set(CMAKE_SKIP_BUILD_RPATH FALSE)
@@ -249,6 +272,8 @@ set(CMAKE_INSTALL_RPATH "${rpath}")
 add_subdirectory(src)
 
 #--- write summary of the installation
+cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+
 message("")
 message("|-----------------------------------------------------------------------|")
 message("|                                                                       |")
@@ -256,8 +281,9 @@ message("|                            Summary
 message("|                                                                       |")
 message("|-----------------------------------------------------------------------|")
 message("")
-message(" System: ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
-message(" -------")
+message(" System:    ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
+message(" Processor: ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})")
+message(" ----------")
 message("")
 message(" musrfit Version: ${musrfit_VERSION}")
 message(" ----------------")
@@ -283,7 +309,11 @@ endif (OpenMP_FOUND)
 
 if (nexus)
   message("")
-  message(" HDF4    found in ${HDF4_INCLUDE_DIRS}")
+  if (HAVE_HDF4)
+    message(" HDF4    found in ${HDF4_INCLUDE_DIRS}")
+  else (HAVE_HDF4)
+    message(" HDF4    not present.")	  
+  endif (HAVE_HDF4)	  
   message(" HDF5    found in ${HDF5_INCLUDE_DIRS}, Version: ${HDF5_VERSION}")
   message(" NeXus   found in ${NEXUS_INCLUDE_DIR}, Version: ${NEXUS_VERSION_STRING}")
 endif (nexus)

ChangeLog

@@ -6,11 +6,47 @@ The ChangeLog will describe feature changes rather than coding detail changes.
 
 For detailed information about changes have a look here:
 
-https://gitlab.psi.ch/nemu/musrfit/activity
+https://gitea.psi.ch/LMU/musrfit
 
 or 
 
-https://bitbucket.org/muonspin/musrfit/commits/all
+https://bitbucket.org/muonspin/musrfit
+
+Release of V1.9.9, 2025/06/08
+=============================
+
+add THEORY functions for local Gaussian / global Lorentzian, and a simple F-mu-F function.
+
+Release of V1.9.8, 2025/03/24
+=============================
+
+add a user interface option to export data from a msr-file view (single- or multiple files).
+
+Release of V1.9.7, 2025/01/18
+=============================
+
+allow spaces in RUN block path-filename
+
+Release of V1.9.6, 2024/12/02
+=============================
+
+added jump to block feature in musredit.
+
+
+Release of V1.9.5, 2024/06/24
+=============================
+
+yaml export of ALL fit-parameters, as initiated by R.M.L. McFadden.
+
+Release of V1.9.4, 2024/06/08
+=============================
+
+enable OpenMP for macOS.
+
+Release of V1.9.3, 2024/04/19
+=============================
+
+fix of function string generation from AST.
 
 Release of V1.9.2, 2023/10/25
 =============================

INSTALL

@@ -18,7 +18,7 @@ directory and
    cd build 
    cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS (or where ever musrfit should be installed)
    cmake --build ./ --clean-first
-   make install                              (as superuser -- maybe)
+   cmake --install ./                           (as superuser -- maybe)
    /sbin/ldconfig                            (as superuser)
     
 cmake configuration allows a couple of switches.  For details check the documentation at 
@@ -31,7 +31,7 @@ An example with NeXus support and BMWlibs needed would look like this
    cd build
    cmake ../ -Dnexus=1 -DBMWlibs=1 -DCMAKE_INSTALL_PREFIX=$ROOTSYS 
    cmake --build ./ --clean-first
-   make install                              (as superuser -- maybe)
+   cmake --install ./                        (as superuser -- maybe)
    /sbin/ldconfig                            (as superuser)
 
 In the optimal case everything is ready to be used ;-)
@@ -43,7 +43,7 @@ In the optimal case everything is ready to be used ;-)
 More information regarding software requirements and the installation process 
 can be found here:
 
-   http://lmu.web.psi.ch/musrfit/user/MUSR/MusrFitSetup.html
+   https://lmu.pages.psi.ch/musrfit-docu/setup-standard.html
 
 #---------------------------------------------------------------------
 # this is the end ...

README

@@ -32,7 +32,7 @@ Documentation
 
 For a more exhaustive user documentation see:
 
-  http://lmu.web.psi.ch/musrfit/user/html/index.html
+  https://lmu.pages.psi.ch/musrfit-docu/index.html
 
 Contacts
 

README.md

@@ -1,37 +1,37 @@
-# musrfit - muSR and beta-NMR data analysis package #
-
-### Contents ###
-
-This is a data analysis package to analyze time differential muSR and beta-NMR data.
-Currently it allows the following:
-
-* set up most commonly used fitting functions for muSR and beta-NMR
-* fit data, including global fits
-* show the fit results and the residuals
-* show the Fourier transform of the data
-* easily extract the fit parameters and import in other programs (gnuplot, qtiplot/origin, ...)
-* generate input fitting files for follow-up runs
-* generate global input fitting files based on a single run template
-* implement more sophisticated user functions
-  (e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
-
-### Currently supported platforms: ###
-
-* Linux
-* Mac OS X
-* Windows 10 1809 or newer - current state is for the commited ones
-* Web based implementation - http://musruser.psi.ch/cgi-bin/musrfit.cgi
-
-### Documentation ####
-
-For a more exhaustive user documentation see:
-
-  http://lmu.web.psi.ch/musrfit/user/html/index.html
-
-### Contacts ###
-
-<andreas.suter@psi.ch>
-
-For the beta-NMR related parts, please contact Zaher Salman
-<zaher.salman@psi.ch>
-
+# musrfit - muSR and beta-NMR data analysis package #
+
+### Contents ###
+
+This is a data analysis package to analyze time differential muSR and beta-NMR data.
+Currently it allows the following:
+
+* set up most commonly used fitting functions for muSR and beta-NMR
+* fit data, including global fits
+* show the fit results and the residuals
+* show the Fourier transform of the data
+* easily extract the fit parameters and import in other programs (gnuplot, qtiplot/origin, ...)
+* generate input fitting files for follow-up runs
+* generate global input fitting files based on a single run template
+* implement more sophisticated user functions
+  (e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles)
+
+### Currently supported platforms: ###
+
+* Linux
+* Mac OS X
+* Windows 10 1809 or newer - current state is for the commited ones
+* Web based implementation - http://musruser.psi.ch/cgi-bin/musrfit.cgi
+
+### Documentation ####
+
+For a more exhaustive user documentation see:
+
+  https://lmu.pages.psi.ch/musrfit-docu/index.html
+
+### Contacts ###
+
+<andreas.suter@psi.ch>
+
+For the beta-NMR related parts, please contact Zaher Salman
+<zaher.salman@psi.ch>
+

cmake/configure_musrfit_version_file.cmake.in

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

doc/examples/UserFcn/PUserFcn.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2024 by Andreas Suter                              *
+ *   Copyright (C) 2007-2025 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

doc/examples/UserFcn/PUserFcn.h

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

doc/examples/test-histo-ROOT-NPP.msr

@@ -15,9 +15,6 @@ asymmetry      3
 simplExpo      4          (rate)
 TFieldCos      1     2       (phase frequency)
 
-###############################################################
-#FUNCTIONS
-
 ###############################################################
 RUN data/lem08_his_2279 MUE4 PSI ROOT-NPP   (name beamline institute data-file-format)
 fittype         0         (single histogram fit)
@@ -39,6 +36,14 @@ MINIMIZE
 MINOS
 SAVE
 
+###############################################################
+FOURIER
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    10
+apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
+dc-corrected     true
+
 ###############################################################
 PLOT 0   (single histo plot)
 runs     1   

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: b18a215470778ea2da02b3cad4d0e07c
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: a49a5e0b750ed752f738f66d3ddeadd4
 tags: 645f666f9bcd5a90fca523b33c5a78b7

doc/html/_images/musrview2dat.svg

@@ -0,0 +1,259 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   width="22"
+   height="22"
+   viewBox="0 0 22.000001 22"
+   id="svg2"
+   version="1.1"
+   inkscape:version="1.0.2 (e86c870879, 2021-01-15)"
+   sodipodi:docname="musrview2dat-plain.svg">
+  <defs
+     id="defs4">
+    <marker
+       inkscape:stockid="Arrow1Sstart"
+       orient="auto"
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+    </g>
+    <path
+       style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.935414;stroke-linecap:round;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
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doc/html/_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,123 @@
+/* Compatability shim for jQuery and underscores.js.
+ *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}