Merge main into release_6.0.0 branch

.github/pull_request_template.md

@@ -8,13 +8,20 @@ Fixes # (issue/issues)
 
 Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce.
 
-## Review Checklist (please remove items if they don't apply):
-
-- [ ] Code has been reviewed
-- [ ] Functionality has been tested
-- [ ] Windows installer (GH artifact) has been tested (installed and worked) 
-- [ ] MacOSX installer (GH artifact) has been tested (installed and worked) 
-- [ ] User documentation is available and complete (if required)
-- [ ] Developers documentation is available and complete (if required)
-- [ ] The introduced changes comply with SasView license (BSD 3-Clause)
+## Review Checklist:
+
+[if using the editor, use `[x]` in place of `[ ]` to check a box]
+
+**Documentation** (check at least one)
+- [ ] There is **nothing** that needs documenting
+- [ ] Documentation changes are **in this PR**
+- [ ] There is an **issue** open for the documentation (link?)
+
+**Installers**
+- [ ] There is a chance this will affect the **installers**, if so
+  - [ ] **Windows** installer (GH artifact) has been tested (installed and worked) 
+  - [ ] **MacOSX** installer (GH artifact) has been tested (installed and worked) 
+
+**Licencing** (untick if necessary)
+- [x] The introduced changes comply with SasView license (BSD 3-Clause)
 

.github/workflows/ci.yml

@@ -1,7 +1,11 @@
 name: CI
 
 on:
-  [push, pull_request, workflow_call]
+  workflow_call:
+  pull_request:
+  push:
+    branches: [main]
+    tags: ['v*']
 
 defaults:
   run:
@@ -77,6 +81,7 @@ jobs:
       - name: Install X11 libraries (Linux)
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
         run: |
+          sudo apt-get update
           sudo apt install libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 x11-utils xvfb libegl-dev
 
       - name: Install Python dependencies
@@ -105,9 +110,9 @@ jobs:
 
       - name: Fetch sources for sibling projects
         run: |
-          git clone --depth=50 --branch=release_0.9.0 https://github.com/SasView/sasdata.git ../sasdata
-          git clone --depth=50 --branch=release_1.0.8 https://github.com/SasView/sasmodels.git ../sasmodels
-          git clone --depth=50 --branch=v0.9.2 https://github.com/bumps/bumps.git ../bumps
+          git clone --depth=50 --branch=master https://github.com/SasView/sasdata.git ../sasdata
+          git clone --depth=50 --branch=master https://github.com/SasView/sasmodels.git ../sasmodels
+          git clone --depth=50 --branch=master https://github.com/bumps/bumps.git ../bumps
 
       - name: Build and install sasdata
         run: |
@@ -195,6 +200,7 @@ jobs:
       ### Build the installer (if enabled)
 
       - name: Install utilities to build installer
+        if: ${{ matrix.installer }}
         run: |
           python -m pip install pyinstaller
 
@@ -452,6 +458,7 @@ jobs:
       - name: Install X11 libraries (Linux)
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
         run: |
+          sudo apt-get update
           sudo apt install libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 x11-utils xvfb
 
       - name: Try running the installation (Linux)

.github/workflows/nightly-build.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       matrix:
         os: [ macos-latest]
-        python-version: [ 3.8 ]
+        python-version: [ 3.11 ]
     needs: reuse_main_ci
 
     steps:
@@ -62,20 +62,20 @@ jobs:
       - name: Rename artifacts
         run: |
           mv installers/dist/SasView-Installer-windows-*/setupSasView.exe installers/dist/setupSasView-nightly-Win64.exe
-          mv installers/dist/SasView-Installer-macos-*/SasView5.dmg  installers/dist/SasView-nightly-MacOSX.dmg
-          mv installers/dist/SasView-Installer-ubuntu-*/sasview5.tar.gz installers/dist/SasView-nightly-Linux.tar.gz
+          mv installers/dist/SasView-Installer-macos-*/SasView6.dmg installers/dist/SasView-nightly-MacOSX.dmg
+          mv installers/dist/SasView-Installer-ubuntu-*/sasview6.tar.gz installers/dist/SasView-nightly-Linux.tar.gz
 
       - name: Notarize Release Build (OSX)
-        uses: GuillaumeFalourd/xcode-notarize@v1
+        uses: lando/notarize-action@v2
         with:
-          product-path: "installers/dist/SasView-nightly-MacOSX.dmg"
-          primary-bundle-id: "org.sasview.SasView5"
-          appstore-connect-username: ${{ secrets.NOTARIZATION_USERNAME }}
-          appstore-connect-password: ${{ secrets.NOTARIZATION_PASSWORD }}
-          verbose: True
+            product-path: "installers/dist/SasView-nightly-MacOSX.dmg"
+            primary-bundle-id: "org.sasview.SasView6"
+            appstore-connect-username: ${{ secrets.NOTARIZATION_USERNAME }}
+            appstore-connect-password: ${{ secrets.NOTARIZATION_PASSWORD }}
+            appstore-connect-team-id: W2AG9MPZ43
+            verbose: True
 
       - name: Staple Release Build (OSX)
-        if: ${{ startsWith(matrix.os, 'macos') }}
         uses: BoundfoxStudios/action-xcode-staple@v1
         with:
           product-path: "installers/dist/SasView-nightly-MacOSX.dmg"

.gitignore

@@ -39,6 +39,7 @@ default_categories.json
 **/UI/*.py
 !**/UI/__init__.py
 config.json
+**/db.sqlite3
 
 # doc build
 /docs/sphinx-docs/build

src/sas/qtgui/Calculators/SldPanel.py

@@ -116,11 +116,8 @@ def setupUi(self):
         self.ui.setupUi(self)
 
         # set validators
-        # TODO: GuiUtils.FormulaValidator() crashes with Qt5 - fix
-        #self.ui.editMolecularFormula.setValidator(GuiUtils.FormulaValidator(self.ui.editMolecularFormula))
-
-        # No need for recalculate
-        self.ui.recalculateButton.setVisible(False)
+        # Chemical formula is checked via periodictable.formula module.
+        self.ui.editMolecularFormula.setValidator(GuiUtils.FormulaValidator(self.ui.editMolecularFormula))
 
         rx = QtCore.QRegularExpression("[+\-]?(?:0|[1-9]\d*)(?:\.\d*)?(?:[eE][+\-]?\d+)?")
         self.ui.editMassDensity.setValidator(QtGui.QRegularExpressionValidator(rx, self.ui.editMassDensity))
@@ -130,7 +127,7 @@ def setupUi(self):
         # signals
         self.ui.helpButton.clicked.connect(self.displayHelp)
         self.ui.closeButton.clicked.connect(self.closePanel)
-        self.ui.recalculateButton.clicked.connect(self.calculateSLD)
+        self.ui.calculateButton.clicked.connect(self.calculateSLD)
 
     def calculateSLD(self):
         self.recalculateSLD()
@@ -147,11 +144,6 @@ def setupModel(self):
 
         #self.model.dataChanged.connect(self.dataChanged)
 
-        self.ui.editMassDensity.textChanged.connect(self.recalculateSLD)
-        self.ui.editMolecularFormula.textChanged.connect(self.recalculateSLD)
-        self.ui.editNeutronWavelength.textChanged.connect(self.recalculateSLD)
-        self.ui.editXrayWavelength.textChanged.connect(self.recalculateSLD)
-
         self.modelReset()
 
     def setupMapper(self):

src/sas/qtgui/Calculators/UI/SldPanel.ui

@@ -322,7 +322,7 @@
      </property>
      <layout class="QGridLayout" name="gridLayout">
       <item row="0" column="0">
-       <widget class="QPushButton" name="recalculateButton">
+       <widget class="QPushButton" name="calculateButton">
         <property name="enabled">
          <bool>true</bool>
         </property>
@@ -336,7 +336,10 @@
          <enum>Qt::NoFocus</enum>
         </property>
         <property name="text">
-         <string>Recalculate</string>
+         <string>Calculate</string>
+        </property>
+        <property name="autoDefault">
+         <bool>true</bool>
         </property>
        </widget>
       </item>
@@ -364,6 +367,9 @@
         <property name="text">
          <string>Close</string>
         </property>
+        <property name="autoDefault">
+         <bool>false</bool>
+        </property>
        </widget>
       </item>
       <item row="0" column="3">
@@ -377,6 +383,9 @@
         <property name="text">
          <string>Help</string>
         </property>
+        <property name="autoDefault">
+         <bool>false</bool>
+        </property>
        </widget>
       </item>
      </layout>
@@ -398,7 +407,7 @@
   <tabstop>editNeutronLength</tabstop>
   <tabstop>closeButton</tabstop>
   <tabstop>helpButton</tabstop>
-  <tabstop>recalculateButton</tabstop>
+  <tabstop>calculateButton</tabstop>
  </tabstops>
  <resources/>
  <connections/>

src/sas/qtgui/MainWindow/DataExplorer.py

@@ -1883,7 +1883,9 @@ def closeAllPlots(self):
         """
         Close all currently displayed plots
         """
-
+        # results panel
+        self.parent.results_frame.setVisible(False)
+        # plots
         for plot_id in PlotHelper.currentPlotIds():
             try:
                 plotter = PlotHelper.plotById(plot_id)

src/sas/qtgui/Perspectives/Fitting/UI/FittingWidgetUI.ui

@@ -360,7 +360,7 @@
        <item row="0" column="0">
         <widget class="QGroupBox" name="groupBox_3">
          <property name="title">
-          <string>Polydispersity and Orientational Distribution</string>
+          <string>Number-average Polydispersity and Orientational Distribution</string>
          </property>
          <layout class="QGridLayout" name="gridLayout_9">
           <item row="0" column="0">

src/sas/qtgui/Utilities/DocRegenInProgess.py

@@ -14,6 +14,8 @@ def __init__(self, parent=None):
         self.setupUi(self)
         self.parent = parent
 
+        self.setWindowTitle("Documentation Regenerating")
+        self.label.setText("Regeneration In Progress")
         self.textBrowser.setText("Placeholder Text.")
         self.file_watcher = QtCore.QFileSystemWatcher()
         self.addSignals()

src/sas/qtgui/Utilities/GuiUtils.py

@@ -741,16 +741,15 @@ def __init__(self, parent=None):
     def validate(self, input, pos):
 
         self._setStyleSheet("")
-        return QtGui.QValidator.Acceptable, pos
 
-        #try:
-        #    Formula(str(input))
-        #    self._setStyleSheet("")
-        #    return QtGui.QValidator.Acceptable, pos
+        try:
+            Formula(str(input))
+            self._setStyleSheet("")
+            return QtGui.QValidator.Acceptable
 
-        #except Exception as e:
-        #    self._setStyleSheet("background-color:pink;")
-        #    return QtGui.QValidator.Intermediate, pos
+        except Exception as e:
+            self._setStyleSheet("background-color:pink;")
+            return QtGui.QValidator.Intermediate
 
     def _setStyleSheet(self, value):
         try:

src/sas/qtgui/Utilities/TabbedModelEditor.py

@@ -172,6 +172,15 @@ def onLoad(self, at_launch=False):
         self.file_to_regenerate = filename
         self.loadFile(str(filename))
 
+    def allBuiltinModels(self):
+        """
+        create a list of all builtin models
+        """
+        from sas.sascalc.fit.models import ModelManager
+        model_list = ModelManager().cat_model_list()
+        model_names = [model.name for model in model_list]
+        return model_names
+
     def loadFile(self, filename):
         """
         Performs the load operation and updates the view
@@ -491,6 +500,14 @@ def canWriteModel(self, model=None, full_path=""):
                 QtWidgets.QMessageBox.critical(self, "Plugin Error", msg)
                 # Don't accept but return
                 return False
+
+        if model['filename'].casefold() in (model.casefold() for model in self.builtinmodels):
+            # notify the viewer
+            msg = "Built-in model with specified name already exists.\n"
+            msg += "Please specify different filename."
+            QtWidgets.QMessageBox.critical(self, "Plugin Error", msg)
+            # Don't accept but return
+            return False
         # Update model editor if plugin definition changed
         func_str = model['text']
         msg = None

src/sas/webfit/analyze/admin.py

@@ -0,0 +1,3 @@
+from django.contrib import admin
+
+# Register your models here.

src/sas/webfit/analyze/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class DataConfig(AppConfig):
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "analyze"

src/sas/webfit/analyze/fitting/admin.py

@@ -0,0 +1,4 @@
+from django.contrib import admin
+from .models import Fit, FitParameter
+
+# Register your models here.

src/sas/webfit/analyze/fitting/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class FittingConfig(AppConfig):
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "analyze.fitting"

src/sas/webfit/analyze/fitting/migrations/0001_initial.py

@@ -0,0 +1,40 @@
+# Generated by Django 4.2.2 on 2023-08-10 22:02
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('analyze', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Fit',
+            fields=[
+                ('analysisbase_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='analyze.analysisbase')),
+                ('results', models.CharField(blank=True, help_text='the string result', max_length=1000000, null=True)),
+                ('status', models.IntegerField(choices=[(1, 'Queued'), (2, 'Running'), (3, 'Complete')], default=1)),
+                ('q_minimum', models.FloatField(blank=True, default=0.0005, help_text='Minimum Q value for the fit', null=True)),
+                ('q_maximum', models.FloatField(blank=True, default=0.5, help_text='Maximum Q value for the fit', null=True)),
+                ('polydispersity', models.BooleanField(default=False, help_text='Is polydispersity being checked in this model')),
+                ('magnetism', models.BooleanField(default=False, help_text='Is magnetism being checked in this model?')),
+                ('model', models.CharField(help_text='model string', max_length=256)),
+                ('optimizer', models.CharField(blank=True, help_text='optimizer string', max_length=50)),
+            ],
+            bases=('analyze.analysisbase',),
+        ),
+        migrations.CreateModel(
+            name='FitParameter',
+            fields=[
+                ('analysisparameterbase_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='analyze.analysisparameterbase')),
+                ('polydisperse', models.BooleanField(default=False, help_text='Is this a polydisperse parameter?')),
+                ('magnetic', models.BooleanField(default=False, help_text='is this a magnetic parameter?')),
+            ],
+            bases=('analyze.analysisparameterbase',),
+        ),
+    ]