Merge branch 'main' into backmari_pixi_dev_env

backmari · web-flow · commit 8975d95d5330 · 2026-01-20T13:30:02.000-05:00
diff --git a/.github/dependabot.yaml b/.github/dependabot.yaml
@@ -6,4 +6,8 @@ updates:
     directory: "/"
     schedule:
       # Check for updates to GitHub Actions every week
-      interval: "weekly"
+      interval: "weekly"
+    groups:
+      all-dependencies:
+        patterns:
+          - "*"  # include all actions in a single PR to ensure tied updates are able to work together.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -445,21 +445,21 @@ jobs:
           codesign -s "Developer ID Application: The International Scattering Alliance (8CX8K63BQM)" $MACOS_DMG_NAME
 
       - name: Notarize Release Build (OSX)
-        if: ${{ matrix.os == 'macos-latest' && env.SIGN_INSTALLER }}
+        if: ${{ startsWith(matrix.os, 'macos') && env.SIGN_INSTALLER }}
         uses: lando/notarize-action@v2
         with:
-          product-path: installers/dist/SasView6-macos-latest.dmg
+          product-path: installers/dist/SasView6-${{ matrix.os }}.dmg
           primary-bundle-id: "org.sasview.SasView6"
           appstore-connect-username: ${{ secrets.NOTARIZATION_USERNAME }}
           appstore-connect-password: ${{ secrets.NOTARIZATION_PASSWORD }}
           appstore-connect-team-id: 8CX8K63BQM
           verbose: True
 
       - name: Staple Release Build (OSX)
-        if: ${{ matrix.os == 'macos-latest' && env.SIGN_INSTALLER }}
+        if: ${{ startsWith(matrix.os, 'macos') && env.SIGN_INSTALLER }}
         uses: BoundfoxStudios/action-xcode-staple@v1
         with:
-          product-path: installers/dist/SasView6-macos-latest.dmg
+          product-path: installers/dist/SasView6-${{ matrix.os }}.dmg
 
       - name: Install DigiCert Client tools from Github Custom Actions marketplace
         if: ${{ startsWith(matrix.os, 'windows') && env.SIGN_INSTALLER }}
@@ -495,6 +495,7 @@ jobs:
           path: |
             installers/dist/setupSasView.exe
             installers/dist/SasView6-macos-latest.dmg
+            installers/dist/SasView6-macos-15-intel.dmg
             installers/dist/SasView6.tar.gz
           if-no-files-found: ignore
 
@@ -507,7 +508,7 @@ jobs:
       matrix:
         include: ${{ fromJson(needs.matrix.outputs.installer-matrix-json) }}
 
-    name: Test installer
+    name: "Test ${{ matrix.job_name }}"
 
     runs-on: ${{ matrix.os }}
 
@@ -556,7 +557,7 @@ jobs:
       - name: Retrieve installer (old image)
         if: ${{ env.INSTALLER_USE_OLD_IMAGE == 'true' }}
         id: download-old-installer
-        uses: dawidd6/action-download-artifact@v11
+        uses: dawidd6/action-download-artifact@v12
         with:
           # Select a specific installer image based on the GitHub Actions run id
           run_id: ${{ env.INSTALLER_OLD_RUNID }}
@@ -670,7 +671,7 @@ jobs:
       - name: Retrieve installer debug tarball
         if: ${{ env.INSTALLER_USE_DEBUG == 'true' }}
         id: download-old-debug
-        uses: dawidd6/action-download-artifact@v11
+        uses: dawidd6/action-download-artifact@v12
         with:
           # Select a specific installer image based on the GitHub Actions run id
           run_id: ${{ env.INSTALLER_OLD_RUNID }}
diff --git a/build_tools/contributors.tsv b/build_tools/contributors.tsv
@@ -18,7 +18,7 @@ Name	Affiliation	Creator	Producer	RelatedPerson	ReleaseManager	ORCID	Notes
 "Cooper-Benun, Torin"	ISIS Neutron and Muon Source	x					None
 "Cortes Hernandez, R"	"University of Tennessee, Knoxville"	x					None
 "Corona, Patrick"	"University of California, Santa Barbara"			x			None
-"Crake-Merani, James Akbar"	ISIS Neutron and Muon Source	x			x	0009-0003-1736-5567	None
+"Crake-Merani, James Akbar"	ISIS Neutron and Muon Source	x				0009-0003-1736-5567	None
 "Detiste, Alexandre"	The Debian Project	x					None
 "Doucet, Mathieu"	Oak Ridge National Laboratory	x				0000-0002-5560-6478	None
 "Doutch, James"	ISIS Neutron and Muon Source     	x					None
@@ -51,7 +51,7 @@ Name	Affiliation	Creator	Producer	RelatedPerson	ReleaseManager	ORCID	Notes
 "Kline, Steve"	National Institute of Standards and Technology	x					None
 "Knudsen, Mikkel"	University of Copenhagen			x			Who is this person? What is the connection?
 "Krueger, Susan"	National Institute of Standards and Technology			x			None
-"Krzywon, Jeff"	National Institute of Standards and Technology	x				0000-0002-2380-4090	None 
+"Krzywon, Jeff"	National Institute of Standards and Technology	x			x	0000-0002-2380-4090	None
 "Larsen, Andreas Haahr"	University of Copenhagen		x			0000-0002-2230-2654	None
 "Lee, Sangjoon Bob"	Columbia University		x			0000-0002-2367-3932	None
 "Lin, Jiao"	California Institute of Technology	x					None
@@ -95,6 +95,7 @@ Name	Affiliation	Creator	Producer	RelatedPerson	ReleaseManager	ORCID	Notes
 "Sharp, Paul"	ISIS Neutron and Muon Source	x				0000-0003-3072-6155	None
 "Shan, Xael"	National Institute of Standards and Technology	x					None
 "Shang, Yingrui"	Oak Ridge National Laboratory			x			None
+"Shrestha, Sujaya"	ISIS Neutron and Muon Source	x					None
 "Snow, Tim"	Diamond Light Source	x				0000-0001-7146-6885	None
 "Stellhorn, Annika"	European Spallation Source	x					None
 "Taylor, Jonathan"	European Spallation Source		x				None
diff --git a/build_tools/release_automation.py b/build_tools/release_automation.py
@@ -38,8 +38,8 @@
 # Should import release notes from git repo, for now will need to cut and paste
 sasview_data = {
 'metadata': {
-    'title': 'SasView version 6.1.1',
-    'description': '6.1.1 release',
+    'title': 'SasView version 6.1.2',
+    'description': '6.1.2 release',
     'related_identifiers': [{'identifier': 'https://github.com/SasView/sasview/releases/tag/v6.1.1',
                         'relation': 'isAlternateIdentifier', 'scheme': 'url'}],
     'contributors': [
diff --git a/docs/sphinx-docs/source/conf.py b/docs/sphinx-docs/source/conf.py
@@ -88,7 +88,7 @@
 # The short X.Y version.
 version = '6.1'
 # The full version, including e.g. alpha tags (a1).
-release = '6.1.1'
+release = '6.1.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/docs/sphinx-docs/source/user/RELEASE.rst b/docs/sphinx-docs/source/user/RELEASE.rst
@@ -13,6 +13,63 @@ Release Notes
 Features
 ========
 
+New in Version 6.1.2
+--------------------
+
+This is a minor bug fix release of SasView. It is built with Sasmodels v1.0.12, Sasdata v0.11.0, and Bumps v1.0.2.
+
+This release fixes two major issues introduced in v6.1.1:
+
+- Plugin models now work correctly
+- The 2-Yukawa structure factor is available and does not throw an error.
+
+Bug fixes
+^^^^^^^^^
+
+* Fix for plugin models not being found by @DrPaulSharp in https://github.com/SasView/sasview/pull/3659
+* Fix for Wedge and Sector Slicers in Q using the same plot by @jellybean2004 in https://github.com/SasView/sasview/pull/3597
+* Replaces 'magic numbers' with enum by @jellybean2004 in https://github.com/SasView/sasview/pull/3598
+* Adds plotUpdateSignal to BoxSlicer by @DrPaulSharp in https://github.com/SasView/sasview/pull/3600
+* Fix for Chi2 calculation in Inversion perspective by @jellybean2004 in https://github.com/SasView/sasview/pull/3607
+* Invariant bugfixes and 'TODO' tasks by @jellybean2004 in https://github.com/SasView/sasview/pull/3627
+* Removes redundant param by @jellybean2004 in https://github.com/SasView/sasview/pull/3633
+* Invariant reformat by @jellybean2004 in https://github.com/SasView/sasview/pull/3631
+* Adds module level logging to all files by @jellybean2004 in https://github.com/SasView/sasview/pull/3637
+* Adds function for close by @jellybean2004 in https://github.com/SasView/sasview/pull/3635
+
+Documentation fixes
+^^^^^^^^^^^^^^^^^^^
+
+* Various fixes to try to get sasview sphinx docs to build cleanly. by @pkienzle in https://github.com/SasView/sasview/pull/3504
+* Include API docs from sasmodels in sasview sphinx output by @llimeht in https://github.com/SasView/sasview/pull/3661
+* Update plugin model location in docs by @DrPaulSharp in https://github.com/SasView/sasview/pull/3665
+
+Linting changes
+^^^^^^^^^^^^^^^
+
+* Converts type comments to type hints by @DrPaulSharp in https://github.com/SasView/sasview/pull/3578
+* Explicitly specifies latest version of ruff in CI by @DrPaulSharp in https://github.com/SasView/sasview/pull/3608
+* Adds local pre-commit hook for ruff linting auto fixes by @DrPaulSharp in https://github.com/SasView/sasview/pull/3573
+
+Infrastructure Changes
+^^^^^^^^^^^^^^^^^^^^^^
+
+* Add dependabot for github actions by @krzywon in https://github.com/SasView/sasview/pull/3571
+* Limit windows signing action by @rozyczko in https://github.com/SasView/sasview/pull/3617
+* Install innosetup in windows installer CI runs by @llimeht in https://github.com/SasView/sasview/pull/3606
+* Bump actions/download-artifact from 4 to 5 by @dependabot[bot] in https://github.com/SasView/sasview/pull/3592
+* Bump dawidd6/action-download-artifact from 6 to 11 by @dependabot[bot] in https://github.com/SasView/sasview/pull/3591
+* Bump actions/checkout from 4 to 5 by @dependabot[bot] in https://github.com/SasView/sasview/pull/3590
+* Bump actions/setup-python from 5 to 6 by @dependabot[bot] in https://github.com/SasView/sasview/pull/3588
+* Bump digicert/ssm-code-signing from 1.0.1 to 1.1.1 by @dependabot[bot] in https://github.com/SasView/sasview/pull/3589
+* move qt gui build to cli.py and remove run.py by @pkienzle in https://github.com/SasView/sasview/pull/3596
+* Change remaining mentions of appdirs to platformdirs by @llimeht in https://github.com/SasView/sasview/pull/3640
+* Removes macos-13 from CI by @DrPaulSharp in https://github.com/SasView/sasview/pull/3629
+* Replace direct AUSAXS library integration with the pyAUSAXS wrapper by @klytje in https://github.com/SasView/sasview/pull/3634
+
+
+**Full Changelog**: https://github.com/SasView/sasview/compare/v6.1.1...v6.1.2rc1
+
 New in Version 6.1.1
 --------------------
 
@@ -1729,12 +1786,14 @@ System Requirements
   on the system. We currently use Python 2.7
 * For SasView 5.x: A Python version > 3.0 should be running on the system. We 
   currently use Python 3.6
+* For SasView 6.x: A python version >= 3.10 should be running on the systems. We
+  currently use Python 3.11
 
 Package Dependencies
 --------------------
 * Ensure the required dependencies are installed
-* For the latest list of dependencies see the appropriate yml file in
-  the SasView repo at sasview/build_tools/conda/ymls
+* For the latest list of dependencies, use the requirements.txt file
+  in the /build_tools/ directory.
 
 Installing from Source
 ----------------------
@@ -1750,24 +1809,24 @@ Installing from Source
 * To get a SPECIFIC RELEASE VERSION from source control go to
   https://github.com/SasView/sasview/releases
   and download the required zip or tar.gz file. Unzip/untar it
-  to the source code folder.
+  to the source code folder. Alternately, checkout a specific tag
+  using 'git checkout <tag>` after running `git fetch --all`.
 
 Building and Installing
 -----------------------
-* To build and install the code
-  use 'pip install .'
+* To build and install the code use 'pip install -e .'. The optional
+  '-e' flag will install the project files in editable mode allowing
+  a developer to make changes and test without having to pip install
+  the project every time a change is made.
 * To build a wheel for installation elsewhere
   use 'hatchling build --wheel'
 * To build the documentation
   use 'hatchling build --hooks-only'
 
 Running SasView
 ---------------
-* use 'python run.py'; this runs from the source directories, so you
-  don't have to rebuild every time you make a change, unless you are
-  changing the C model files.
-* if using Conda the above command will also build SasView, but you 
-  must issue 'activate sasview' first.
+* Assuming the python or conda environment that sasview was installed into
+  is active, use 'python -m sas' to launch the app directly from the source.
 
 Known Issues
 ============
@@ -1779,6 +1838,8 @@ users may wish to be aware of can be viewed at the following links:
 
 `[sasmodels] <https://github.com/SasView/sasmodels/milestones>`_
 
+`[sasdata] <https://github.com/SasView/sasdata/milestones>`_
+
 All 5.0.x versions / 4.2.2 - All systems
 ----------------------------------------
 A problem has been identified in Version 4.2.2 which also affects all 5.0.x
diff --git a/installers/installer.iss b/installers/installer.iss
@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "SasView"
-#define MyAppVersion "6.1.1"
+#define MyAppVersion "6.1.2"
 #define MyAppPublisher "(c) 2009 - 2025, UTK, UMD, NIST, ORNL, ISIS, ESS, ILL, ANSTO, TU Delft and DLS"
 #define MyAppURL "http://www.sasview.org"
 #define MyAppExeName "sasview.exe"
diff --git a/src/sas/qtgui/Calculators/DataOperationUtilityPanel.py b/src/sas/qtgui/Calculators/DataOperationUtilityPanel.py
@@ -373,19 +373,17 @@ def onCheckOutputName(self):
     # ########
     # Modification of inputs
     # ########
-    def _findId(self, name):
-        """ find id of name in list of filenames """
-        isinstance(name, str)
-
-        for key_id in list(self.filenames.keys()):
-            # data with title
-            if self.filenames[key_id].name:
-                input = self.filenames[key_id].name
-            # data without title
-            else:
-                input = str(key_id)
-            if name in input:
-                return key_id
+    def _findId(self, name: str) -> str | None:
+        """Verify the displayed name matches a name in the data explorer"""
+        name_list = [str(self.filenames[key_id].name) for key_id in self.filenames.keys()]
+        key_list = [str(key_id) for key_id in self.filenames.keys()]
+        # The name must completely match the key or name to ensure 'non-alphabetic-data_name'
+        # does not match 'M1[non-alphabetic-data_name]'
+        # See https://github.com/SasView/sasview/issues/3796 for reference.
+        if name in name_list or name in key_list:
+            return str(name)
+        else:
+            return None
 
     def _extractData(self, key_id):
         """ Extract data from file with id contained in list of filenames """
diff --git a/src/sas/qtgui/MainWindow/Acknowledgements.py b/src/sas/qtgui/MainWindow/Acknowledgements.py
@@ -32,5 +32,5 @@ def addText(self):
                                  " from the EU Horizon 2020 programme under the SINE2020 project Grant No 654000."
 
         self.textBrowser.setText(acknowledgement_text_1)
-        acknowledgement_text_2 = 'M. Doucet et al. SasView Version ' + str(version) + ', ' + str(doi)
+        acknowledgement_text_2 = 'J. Krzywon, et al. SasView Version ' + str(version) + ', ' + str(doi)
         self.textBrowser_2.setText(acknowledgement_text_2)
diff --git a/src/sas/qtgui/MainWindow/media/preferences_help.rst b/src/sas/qtgui/MainWindow/media/preferences_help.rst
@@ -1,7 +1,7 @@
 .. preferences_help.rst
 
 .. Initial Draft: J Krzywon, August 2022
-.. Last Updated: J Krzywon, Nov. 22, 2023
+.. Last Updated: S Shrestha, January 2026
 
 .. _Preferences:
 
@@ -42,6 +42,9 @@ are completed. The plots can still be accessed in the data explorer under the da
 from Matplotlib. Note: The toolbar can be enabled and disabled in each individual plot by opening the context menu with
 a right click and selecting 'Toggle Navigation Menu'
 
+**Stack plots when using slicers**: When selected, multiple plots generated using slicers will be added to the same plot
+window, each with its own legend entry. When not selected, each plot will open in its own window. *persistent*
+
 .. _Display_Preferences:
 
 Display Preferences
diff --git a/src/sas/qtgui/Plotting/Plotter2D.py b/src/sas/qtgui/Plotting/Plotter2D.py
@@ -20,6 +20,7 @@
 from sas.qtgui.Plotting.Slicers.BoxSum import BoxSumCalculator
 from sas.qtgui.Plotting.Slicers.SectorSlicer import SectorInteractor
 from sas.qtgui.Plotting.Slicers.WedgeSlicer import WedgeInteractorPhi, WedgeInteractorQ
+from sas.system import config
 
 logger = logging.getLogger(__name__)
 
@@ -65,7 +66,7 @@ def __init__(self, parent=None, manager=None, quickplot=False, dimension=2):
         self.slicer = None
         self.slicers = {}
         self.slicer_widget = None
-        self.stackplots = True  # whether to stack multiple slicer plots
+        self.stackplots = config.STACK_PLOTS  # whether to stack multiple slicer plots
         self.slicer_plots_dict = {}  # keep track of slicer plots
         self.vmin = None
         self.vmax = None
diff --git a/src/sas/qtgui/Utilities/Preferences/PlottingPreferencesWidget.py b/src/sas/qtgui/Utilities/Preferences/PlottingPreferencesWidget.py
@@ -11,7 +11,8 @@ def __init__(self):
                               'FITTING_PLOT_LEGEND_MAX_LINE_LENGTH',
                               'DISABLE_RESIDUAL_PLOT',
                               'DISABLE_POLYDISPERSITY_PLOT',
-                              'USE_MATPLOTLIB_TOOLBAR']
+                              'USE_MATPLOTLIB_TOOLBAR',
+                              'STACK_PLOTS']
 
     def _addAllWidgets(self):
         self.legendFullWidth = self.addCheckBox(
@@ -44,6 +45,11 @@ def _addAllWidgets(self):
             checked=config.USE_MATPLOTLIB_TOOLBAR)
         self.useMatplotlibToolbar.clicked.connect(
             lambda: self._stageChange('USE_MATPLOTLIB_TOOLBAR', self.useMatplotlibToolbar.isChecked()))
+        self.stackplots = self.addCheckBox(
+            title="Stack plots when using slicers",
+            checked=config.STACK_PLOTS)
+        self.stackplots.clicked.connect(
+            lambda: self._stageChange('STACK_PLOTS', self.stackplots.isChecked()))
 
     def _toggleBlockAllSignaling(self, toggle):
         self.legendFullWidth.blockSignals(toggle)
@@ -52,6 +58,7 @@ def _toggleBlockAllSignaling(self, toggle):
         self.disableResidualPlot.blockSignals(toggle)
         self.disablePolydispersityPlot.blockSignals(toggle)
         self.useMatplotlibToolbar.blockSignals(toggle)
+        self.stackplots.blockSignals(toggle)
 
     def _restoreFromConfig(self):
         self.legendFullWidth.setChecked(bool(config.FITTING_PLOT_FULL_WIDTH_LEGENDS))
@@ -61,3 +68,4 @@ def _restoreFromConfig(self):
         self.disableResidualPlot.setChecked(config.DISABLE_RESIDUAL_PLOT)
         self.disablePolydispersityPlot.setChecked(config.DISABLE_POLYDISPERSITY_PLOT)
         self.useMatplotlibToolbar.setChecked(config.USE_MATPLOTLIB_TOOLBAR)
+        self.stackplots.setChecked(config.STACK_PLOTS)
diff --git a/src/sas/system/config/config.py b/src/sas/system/config/config.py
@@ -213,6 +213,10 @@ def __init__(self):
         # Last version that the update prompt was dismissed for
         self.LAST_UPDATE_DISMISSED_VERSION = "5.0.0"
 
+        # Stack plots when using slicers
+        # If true, plots generated when using slicers will be on the same canvas
+        self.STACK_PLOTS = True
+
         #
         # Lock the class down, this is necessary both for
         # securing the class, and for setting up reading/writing files
diff --git a/src/sas/system/version.py b/src/sas/system/version.py
@@ -1,7 +1,7 @@
 try:
     from ._version import __version__
 except ImportError:
-    __version__ = "6.1.1"
+    __version__ = "6.1.2"
 
 __release_date__ = "2025"
 __build__ = "GIT_COMMIT"
diff --git a/src/sas/system/zenodo.py b/src/sas/system/zenodo.py
@@ -1 +1 @@
-__DOI__ = "10.5281/zenodo.17237394"
+__DOI__ = "10.5281/zenodo.17795298"
