Merge branch 'main' into customFitModels

.github/workflows/nightly-build.yml

@@ -56,7 +56,7 @@ jobs:
 
       - name: Staple Release Build (OSX)
         if: ${{ startsWith(matrix.os, 'macos') }}
-        uses: devbotsxyz/xcode-staple@v1
+        uses: BoundfoxStudios/action-xcode-staple@v1
         with:
           product-path: "installers/dist/SasView-nightly-MacOSX.dmg"
 

LICENSE.TXT

@@ -1,4 +1,4 @@
-Copyright (c) 2009-2022, SasView Developers
+Copyright (c) 2009-2023, SasView Developers
 
 
 All rights reserved.

build_tools/release_automation.py

@@ -14,9 +14,9 @@
 #Should import release notes from git repo, for now will need to cut and paste
 sasview_data = {
     'metadata': {
-    'title': 'SasView version 5.0.5',
-    'description': '5.0.5 release',
-    'related_identifiers': [{'identifier': 'https://github.com/SasView/sasview/releases/tag/v5.0.5',
+    'title': 'SasView version 5.0.6',
+    'description': '5.0.6 release',
+    'related_identifiers': [{'identifier': 'https://github.com/SasView/sasview/releases/tag/v5.0.6',
                         'relation': 'isAlternateIdentifier', 'scheme': 'url'}],
     'contributors': [
         {'name': 'Anuchitanukul, Atijit', 'affiliation': 'STFC - Rutherford Appleton Laboratory', 'type':'Researcher'},
@@ -49,6 +49,7 @@
         {'name': 'Alina, Gervaise','affiliation': 'University of Tennessee Knoxville'},
         {'name': 'Attala, Ziggy', 'affiliation': 'STFC - Rutherford Appleton Laboratory'},
         {'name': 'Bakker, Jurrian','affiliation': 'Technical Unviersity Delft'},
+        {'name': 'Beaucage, Peter','affiliation': 'National Institute of Standards and Technology', 'orcid': '0000-0002-2147-0728'},
         {'name': 'Bouwman, Wim','affiliation': 'Technical Univeristy Deflt' },
         {'name': 'Bourne, Robert', 'affiliation': 'STFC - Rutherford Appleton Laboratory'},
         {'name': 'Butler, Paul','affiliation': 'National Institute of Standards and Technology', 'orcid': '0000-0002-5978-4714'},
@@ -63,7 +64,7 @@
         {'name': 'Jackson, Andrew','affiliation': 'European Spallation Source ERIC', 'orcid': '0000-0002-6296-0336'},
         {'name': 'King, Stephen','affiliation': 'STFC - Rutherford Appleton Laboratory', 'orcid': '0000-0003-3386-9151'},
         {'name': 'Kienzle, Paul','affiliation': 'National Institute of Standards and Technology'},
-        {'name': 'Krzywon, Jeff','affiliation': 'National Institute of Standards and Technology'},
+        {'name': 'Krzywon, Jeff','affiliation': 'National Institute of Standards and Technology', 'orcid': '0000-0002-2380-4090'},
         {'name': 'Maranville, Brian', 'affiliation': 'National Institute of Standards and Technology', 'orcid': '0000-0002-6105-8789'},
         {'name': 'Martinez, Nicolas','affiliation': 'Institut Laue-Langevin'},
         {'name': 'Murphy, Ryan', 'affiliation': 'National Institute of Standards and Technology', 'orcid': '0000-0002-4080-7525'},
@@ -76,7 +77,7 @@
         {'name': 'Snow, Tim','affiliation': 'Diamond Light Source','orcid': '0000-0001-7146-6885'},
         {'name': 'Washington, Adam','affiliation': 'STFC - Rutherford Appleton Laboratory'},
         {'name': 'Wilkins, Lucas','affiliation': 'STFC - Rutherford Appleton Laboratory'},
-        {'name': 'Wolf, Caitlyn','affiliation': 'National Institute of Standards and Technology'}
+        {'name': 'Wolf, Caitlyn','affiliation': 'National Institute of Standards and Technology', 'orcid': '0000-0002-2956-7049'}
         ],
     'grants': [{'id': '10.13039/501100000780::654000'}],
     'license': 'BSD-3-Clause',

build_tools/requirements.txt

@@ -1,5 +1,5 @@
-numpy 
-scipy==1.7.3 
+numpy<1.24
+scipy==1.10.0 
 docutils 
 pytest
 pytest_qt

docs/sphinx-docs/source/conf.py

@@ -11,7 +11,7 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os, collections
+import sys, os, datetime
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -69,8 +69,9 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'SasView'
-copyright = u'2022, The SasView Project'
+year = datetime.datetime.now().year
+project = 'SasView'
+copyright = f'{year}, The SasView Project'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -79,9 +80,9 @@
 # The version number must follow StrictVersion rules as outlined
 # in http://epydoc.sourceforge.net/stdlib/distutils.version.StrictVersion-class.html
 # The short X.Y version.
-version = '5.0'
+version = '6.0'
 # The full version, including e.g. alpha tags (a1).
-release = '5.0.5'
+release = '6.0.0a1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

src/sas/cli.py

@@ -68,6 +68,8 @@ def parse_cli(argv):
         help="Open console to display output (windows only)")
     parser.add_argument("-q", "--quiet", action='store_true',
         help="Don't print banner when entering interactive mode")
+    parser.add_argument("-l", "--loglevel", type=str,
+        help="Logging level (production or development for now)")
     parser.add_argument("args", nargs="*",
         help="script followed by args")
 
@@ -118,12 +120,18 @@ def main(logging="production"):
     cli = parse_cli(sys.argv)
 
     # Setup logger and sasmodels
-    if logging == "production":
+    if cli.loglevel:
+        logging = cli.loglevel
+    logging = logging.upper()
+    if logging == "PRODUCTION":
         log.production()
-    elif logging == "development":
+    elif logging == "DEVELOPMENT":
         log.development()
+    elif logging.upper() in {'DEBUG', 'INFO', 'WARN', 'ERROR', 'CRITICAL'}:
+        log.setup_logging(logging)
     else:
         raise ValueError(f"Unknown logging mode \"{logging}\"")
+
     lib.setup_sasmodels()
     lib.setup_qt_env() # Note: does not import any gui libraries
 

src/sas/qtgui/Calculators/DensityPanel.py

@@ -57,8 +57,7 @@ def setupUi(self):
         self.ui = Ui_DensityPanel()
         self.ui.setupUi(self)
 
-        #self.setFixedSize(self.minimumSizeHint())
-        self.resize(self.minimumSizeHint())
+        self.setFixedSize(self.minimumSizeHint())
 
         # set validators
         #self.ui.editMolecularFormula.setValidator(FormulaValidator(self.ui.editMolecularFormula))

src/sas/qtgui/Calculators/GenericScatteringCalculator.py

@@ -57,6 +57,7 @@ def __init__(self, parent=None):
         self.setupUi(self)
         # disable the context help icon
         self.setWindowFlags(self.windowFlags() & ~QtCore.Qt.WindowContextHelpButtonHint)
+        self.setFixedSize(self.minimumSizeHint())
 
         self.manager = parent
         self.communicator = self.manager.communicator()

src/sas/qtgui/Calculators/ResolutionCalculatorPanel.py

@@ -42,6 +42,7 @@ def __init__(self, parent=None):
         self.setupUi(self)
         # disable the context help icon
         self.setWindowFlags(self.windowFlags() & ~QtCore.Qt.WindowContextHelpButtonHint)
+        self.setFixedSize(self.minimumSizeHint())
 
         self.manager = parent
 

src/sas/qtgui/Calculators/SldPanel.py

@@ -97,6 +97,7 @@ def __init__(self, parent=None):
         self.setupUi()
         # disable the context help icon
         self.setWindowFlags(self.windowFlags() & ~QtCore.Qt.WindowContextHelpButtonHint)
+        self.setFixedSize(self.minimumSizeHint())
 
         self.setupModel()
         self.setupMapper()

src/sas/qtgui/MainWindow/DataExplorer.py

@@ -22,8 +22,8 @@
 from sas.qtgui.Plotting.PlotterData import Data1D
 from sas.qtgui.Plotting.PlotterData import Data2D
 from sas.qtgui.Plotting.PlotterData import DataRole
-from sas.qtgui.Plotting.Plotter import Plotter
-from sas.qtgui.Plotting.Plotter2D import Plotter2D
+from sas.qtgui.Plotting.Plotter import Plotter, PlotterWidget
+from sas.qtgui.Plotting.Plotter2D import Plotter2D, Plotter2DWidget
 from sas.qtgui.Plotting.MaskEditor import MaskEditor
 
 from sas.qtgui.MainWindow.DataManager import DataManager
@@ -232,7 +232,7 @@ def loadFolder(self, event=None):
         caption = 'Choose a directory'
         options = QtWidgets.QFileDialog.ShowDirsOnly | QtWidgets.QFileDialog.DontUseNativeDialog
         directory = self.default_load_location
-        folder = QtWidgets.QFileDialog.getExistingDirectory(parent, caption, directory, "", options)
+        folder = QtWidgets.QFileDialog.getExistingDirectory(parent, caption, directory, options)
 
         if folder is None:
             return
@@ -1086,11 +1086,17 @@ def displayData(self, data_list, id=None):
 
             plot_name = plot_to_show.name
             role = plot_to_show.plot_role
-            stand_alone_types = [DataRole.ROLE_RESIDUAL, DataRole.ROLE_STAND_ALONE]
+            stand_alone_types = [DataRole.ROLE_RESIDUAL, DataRole.ROLE_STAND_ALONE, DataRole.ROLE_POLYDISPERSITY]
 
             if (role in stand_alone_types and shown) or role == DataRole.ROLE_DELETABLE:
                 # Nothing to do if stand-alone plot already shown or plot to be deleted
                 continue
+            elif role == DataRole.ROLE_RESIDUAL and config.DISABLE_RESIDUAL_PLOT:
+                # Nothing to do if residuals are not plotted
+                continue
+            elif role == DataRole.ROLE_POLYDISPERSITY and config.DISABLE_POLYDISPERSITY_PLOT:
+                # Nothing to do if polydispersity plot is not plotted
+                continue
             elif role in stand_alone_types:
                 # Stand-alone plots should always be separate
                 self.plotData([(plot_item, plot_to_show)])
@@ -1132,7 +1138,7 @@ def addDataPlot2D(self, plot_set, item):
         """
         Create a new 2D plot and add it to the workspace
         """
-        plot2D = Plotter2D(self)
+        plot2D = Plotter2DWidget(parent=self, manager=self)
         plot2D.item = item
         plot2D.plot(plot_set)
         self.addPlot(plot2D)
@@ -1160,7 +1166,7 @@ def plotData(self, plots, transform=True):
         for item, plot_set in plots:
             if isinstance(plot_set, Data1D):
                 if 'new_plot' not in locals():
-                    new_plot = Plotter(self)
+                    new_plot = PlotterWidget(manager=self, parent=self)
                     new_plot.item = item
                 new_plot.plot(plot_set, transform=transform)
                 # active_plots may contain multiple charts
@@ -1245,7 +1251,7 @@ def appendPlot(self):
     @staticmethod
     def appendOrUpdatePlot(self, data, plot):
         name = data.name
-        if isinstance(plot, Plotter2D) or name in plot.plot_dict.keys():
+        if isinstance(plot, Plotter2DWidget) or name in plot.plot_dict.keys():
             plot.replacePlot(name, data)
         else:
             plot.plot(data)

src/sas/qtgui/MainWindow/GuiManager.py

@@ -122,6 +122,9 @@ def __init__(self, parent=None):
         logging.info(f" --- SasView session started, version {SASVIEW_VERSION}, {SASVIEW_RELEASE_DATE} ---")
         # Log the python version
         logging.info("Python: %s" % sys.version)
+        #logging.debug("Debug messages are shown.")
+        #logging.warn("Warnings are shown.")
+        #logging.error("Errors are shown.")
 
         # Set up the status bar
         self.statusBarSetup()

src/sas/qtgui/Perspectives/Fitting/FittingUtilities.py

@@ -643,7 +643,7 @@ def plotPolydispersities(model):
         data1d.symbol = 'Line'
         data1d.name = "{} polydispersity".format(name)
         data1d.id = data1d.name # placeholder, has to be completed later
-        data1d.plot_role = DataRole.ROLE_STAND_ALONE
+        data1d.plot_role = DataRole.ROLE_POLYDISPERSITY
         plots.append(data1d)
     return plots
 

src/sas/qtgui/Perspectives/Fitting/FittingWidget.py

@@ -223,6 +223,8 @@ def data(self, value):
         self.smearing_widget.resetSmearer()
         # Enable/disable UI components
         self.setEnablementOnDataLoad()
+        # Reinitialize model list for constrained/simult fitting
+        self.newModelSignal.emit()
 
     def initializeGlobals(self):
         """

src/sas/qtgui/Plotting/Plotter2D.py

@@ -19,9 +19,10 @@
 from sas.qtgui.Plotting.BoxSum import BoxSum
 from sas.qtgui.Plotting.SlicerParameters import SlicerParameters
 
-# TODO: move to sas.qtgui namespace
 from sas.qtgui.Plotting.Slicers.BoxSlicer import BoxInteractorX
 from sas.qtgui.Plotting.Slicers.BoxSlicer import BoxInteractorY
+from sas.qtgui.Plotting.Slicers.WedgeSlicer import WedgeInteractorQ
+from sas.qtgui.Plotting.Slicers.WedgeSlicer import WedgeInteractorPhi
 from sas.qtgui.Plotting.Slicers.AnnulusSlicer import AnnulusInteractor
 from sas.qtgui.Plotting.Slicers.SectorSlicer import SectorInteractor
 from sas.qtgui.Plotting.Slicers.BoxSum import BoxSumCalculator
@@ -189,6 +190,10 @@ def createContextMenu(self):
         self.actionBoxAveragingX.triggered.connect(self.onBoxAveragingX)
         self.actionBoxAveragingY = self.contextMenu.addAction("&Box Averaging in Qy")
         self.actionBoxAveragingY.triggered.connect(self.onBoxAveragingY)
+        self.actionWedgeAveragingQ = self.contextMenu.addAction("&Wedge Averaging in Q")
+        self.actionWedgeAveragingQ.triggered.connect(self.onWedgeAveragingQ)
+        self.actionWedgeAveragingPhi = self.contextMenu.addAction("&Wedge Averaging in Phi")
+        self.actionWedgeAveragingPhi.triggered.connect(self.onWedgeAveragingPhi)
         # Additional items for slicer interaction
         if self.slicer:
             self.actionClearSlicer = self.contextMenu.addAction("&Clear Slicer")
@@ -456,6 +461,20 @@ def onBoxAveragingY(self):
         """
         self.setSlicer(slicer=BoxInteractorY)
 
+    def onWedgeAveragingQ(self):
+        """
+        Perform 2D data averaging on Q
+        Create a new slicer .
+        """
+        self.setSlicer(slicer=WedgeInteractorQ)
+
+    def onWedgeAveragingPhi(self):
+        """
+        Perform 2D data averaging on Phi
+        Create a new slicer .
+        """
+        self.setSlicer(slicer=WedgeInteractorPhi)
+
     def onColorMap(self):
         """
         Display the color map dialog and modify the plot's map accordingly

src/sas/qtgui/Plotting/PlotterData.py

@@ -27,6 +27,8 @@ class DataRole(Enum):
     ROLE_RESIDUAL = 3
     # Stand alone is for plots that should be plotted separately
     ROLE_STAND_ALONE = 4
+    # Polydispersity is for stand-alone polydispersity plot
+    ROLE_POLYDISPERSITY = 5
 
 
 class Data1D(PlottableData1D, LoadData1D):

src/sas/qtgui/Plotting/SlicerParameters.py

@@ -14,6 +14,8 @@
 from sas.qtgui.Plotting.PlotterData import Data1D
 from sas.qtgui.Plotting.Slicers.BoxSlicer import BoxInteractorX
 from sas.qtgui.Plotting.Slicers.BoxSlicer import BoxInteractorY
+from sas.qtgui.Plotting.Slicers.WedgeSlicer import WedgeInteractorQ
+from sas.qtgui.Plotting.Slicers.WedgeSlicer import WedgeInteractorPhi
 from sas.qtgui.Plotting.Slicers.AnnulusSlicer import AnnulusInteractor
 from sas.qtgui.Plotting.Slicers.SectorSlicer import SectorInteractor
 
@@ -56,7 +58,9 @@ def __init__(self, parent=None,
                           1: SectorInteractor,
                           2: AnnulusInteractor,
                           3: BoxInteractorX,
-                          4: BoxInteractorY}
+                          4: BoxInteractorY,
+                          5: WedgeInteractorQ,
+                          6: WedgeInteractorPhi}
 
         # Define a proxy model so cell enablement can be finegrained.
         self.proxy = ProxyModel(self)
@@ -216,7 +220,7 @@ def onChooseFilesLocation(self):
         caption = 'Save files to:'
         options = QtWidgets.QFileDialog.ShowDirsOnly | QtWidgets.QFileDialog.DontUseNativeDialog
         directory = self.save_location
-        folder = QtWidgets.QFileDialog.getExistingDirectory(parent, caption, directory, "", options)
+        folder = QtWidgets.QFileDialog.getExistingDirectory(parent, caption, directory, options)
 
         if folder is None:
             return