added the option to write the content of the MINUIT2.OUTPUT ascii file as yaml. This extends the previous commit from Ryan M.L. McFadden.

ignore all files generated from an in-repo build

Approved-by: Andreas Suter

.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 1.9.0 LANGUAGES C CXX)
+project(musrfit VERSION 1.9.5 LANGUAGES C CXX)
 
 #--- musrfit specific options -------------------------------------------------
 option(nexus "build optional NeXus support. Needed for ISIS" OFF)
@@ -109,13 +109,13 @@ find_package(FFTW3 REQUIRED)
 find_package(LibXml2 REQUIRED)
 
 #--- check for OpenMP ---------------------------------------------------------
-if (try_OpenMP AND NOT APPLE)
+if (try_OpenMP)
   find_package(OpenMP)
-  if (OpenMP_FOUND)
+  if (OpenMP_CXX_FOUND)
     add_definitions(-DHAVE_GOMP)
     set(HAVE_GOMP 1 CACHE INTERNAL "Have GOMP")
-  endif (OpenMP_FOUND)
-endif (try_OpenMP AND NOT APPLE)
+  endif (OpenMP_CXX_FOUND)
+endif (try_OpenMP)
 
 #--- check for Qt -------------------------------------------------------------
 if (qt_based_tools)
@@ -222,10 +222,35 @@ else ()
   set(IS_GIT_REPO 0)
 endif ()
 
+#--- rpath related things -----------------------------------------------------
+# use, i.e. don't skip the full RPATH for the build tree
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+
+# add the automatically determined parts of the RPATH
+# which point to directories outside the build tree to the install RPATH
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+# the RPATH to be used when installing, but only if it's not a system directory
+list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
+if("${isSystemDir}" STREQUAL "-1")
+    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+endif("${isSystemDir}" STREQUAL "-1")
+set(rpath ${CMAKE_INSTALL_RPATH})
+string(APPEND rpath ";/usr/local/lib")
+set(CMAKE_INSTALL_RPATH "${rpath}")
+
 #--- propagate to the sub-directories -----------------------------------------
 add_subdirectory(src)
 
 #--- write summary of the installation
+cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+
 message("")
 message("|-----------------------------------------------------------------------|")
 message("|                                                                       |")
@@ -233,8 +258,9 @@ 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(" ----------------")

ChangeLog

@@ -12,6 +12,23 @@ or
 
 https://bitbucket.org/muonspin/musrfit/commits/all
 
+Release of V1.9.3, 2024/04/19
+=============================
+
+fix of function string generation from AST.
+
+Release of V1.9.2, 2023/10/25
+=============================
+
+switch over to smart pointers wherever possible.
+
+Release of V1.9.1, 2023/05/16
+=============================
+
+add option [-c, --count] to dump_header which will dump the number of counts
+per detector and the total number of counts. Currently for MusrRoot data format
+only. For the other data formats it will be implement asap
+
 Release of V1.9.0, 2023/02/17
 =============================
 

README.md

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

cmake/FindFFTW3.cmake

@@ -75,7 +75,7 @@ endfunction()
 #as35 endif()
 
 find_path(FFTW3_INCLUDE NAMES fftw3.h
-  HINTS "/usr/include" "/opt/local/include"
+  HINTS "/usr/include" "/opt/local/include" "/app/include"
 )
 
 find_library(FFTW3_LIBRARY fftw3)

doc/examples/DepthProfiles/1300Ar/depth_profile_startup.xml

@@ -1,35 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<nonlocal xmlns="http://nemu.web.psi.ch/musrfit/nonlocal">
+<depthProf xmlns="http://nemu.web.psi.ch/musrfit/depthProf">
     <comment>
         TrimSp information
     </comment>
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>SiC_1300x_52nm_48nm_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
     </trim_sp>
-</nonlocal>
+</depthProf>

doc/examples/DepthProfiles/1300x/depth_profile_startup.xml

@@ -1,35 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<nonlocal xmlns="http://nemu.web.psi.ch/musrfit/nonlocal">
+<depthProf xmlns="http://nemu.web.psi.ch/musrfit/depthProf">
     <comment>
         TrimSp information
     </comment>
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>SiC_1300x_52nm_48nm_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
     </trim_sp>
-</nonlocal>
+</depthProf>

doc/examples/DepthProfiles/PECVD_Si/depth_profile_startup.xml

@@ -1,35 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<nonlocal xmlns="http://nemu.web.psi.ch/musrfit/nonlocal">
+<depthProf xmlns="http://nemu.web.psi.ch/musrfit/depthProf">
     <comment>
         TrimSp information
     </comment>
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>Si10_2.0_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
     </trim_sp>
-</nonlocal>
+</depthProf>

doc/examples/DepthProfiles/PECVD_thermal_SiC/depth_profile_startup.xml

@@ -1,35 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<nonlocal xmlns="http://nemu.web.psi.ch/musrfit/nonlocal">
+<depthProf xmlns="http://nemu.web.psi.ch/musrfit/depthProf">
     <comment>
         TrimSp information
     </comment>
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>SiO2_70nm2.0_30nm2.2_SiC_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
     </trim_sp>
-</nonlocal>
+</depthProf>

doc/examples/UserFcn/PUserFcn.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

doc/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 429dcaf60d751fc64b55c07d7174ea6f
+config: 81576a0588e1a44f70c715e85985d5a5
 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: '1.8.2',
+    VERSION: '1.9.4',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

doc/html/_static/haiku.css

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

doc/html/_static/style.css

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