Merge pull request #2808 from SasView/main_release_branch_merged

merged release_6.0.0 branch as agreed at call.

.github/workflows/ci.yml

@@ -180,17 +180,13 @@ jobs:
 
       ### Build documentation (if enabled)
 
-      - name: Install doc-building dependencies
-        if: ${{ matrix.docs }}
-        run: |
-          python -m pip install sphinx
-
-      - name: Build sasmodels and bumps docs
+      - name: Build sasmodels, sasdata, and bumps docs
         if: ${{ matrix.docs }}
         run: |
           make -C ../bumps/doc html || true
           mkdir -p ~/.sasmodels/compiled_models
           make -j4 -C ../sasmodels/doc html || true
+          make -C ../sasdata/docs html || true
 
       - name: Build sasview docs
         if: ${{ matrix.docs }}
@@ -226,25 +222,11 @@ jobs:
           iscc installers/installer.iss
           mv installers/Output/setupSasView.exe installers/dist
 
-      - name: Sign executable and create dmg (OSX)
+      - name: Build sasview installer dmg file (OSX)
         if: ${{ matrix.installer && startsWith(matrix.os, 'macos') }}
-        env:
-          MACOS_CERTIFICATE: ${{ secrets.MACOS_CERTIFICATE }}
-          MACOS_CERTIFICATE_PWD: ${{ secrets.MACOS_CERTIFICATE_PWD }}
         run: |
-          echo $MACOS_CERTIFICATE | base64 --decode > certificate.p12
-          security create-keychain -p DloaAcYP build.keychain
-          security default-keychain -s build.keychain
-          security unlock-keychain -p DloaAcYP build.keychain
-          security import certificate.p12 -k build.keychain -P $MACOS_CERTIFICATE_PWD -T /usr/bin/codesign
-          security set-key-partition-list -S apple-tool:,apple:,codesign: -s -k DloaAcYP build.keychain
-
           cd installers/dist
-          python ../../build_tools/fix_qt_folder_names_for_codesign.py SasView6.app
-          python ../../build_tools/code_sign_osx.py
-          codesign --verify --options=runtime --entitlements ../../build_tools/entitlements.plist --timestamp --deep --verbose=4 --force --sign "Developer ID Application: European Spallation Source Eric (W2AG9MPZ43)" SasView6.app
           hdiutil create SasView6.dmg -srcfolder SasView6.app -ov -format UDZO
-          codesign -s "Developer ID Application: European Spallation Source Eric (W2AG9MPZ43)" SasView6.dmg
 
       - name: Build sasview installer tarball (Linux)
         if: ${{ matrix.installer && startsWith(matrix.os, 'ubuntu') }}
@@ -261,6 +243,26 @@ jobs:
             installers/dist/sasview-pyinstaller-dist.tar.gz
           if-no-files-found: ignore
 
+      - name: Sign executable and create dmg (OSX)
+        if: ${{ matrix.installer && startsWith(matrix.os, 'macos') }}
+        env:
+          MACOS_CERTIFICATE: ${{ secrets.MACOS_CERTIFICATE }}
+          MACOS_CERTIFICATE_PWD: ${{ secrets.MACOS_CERTIFICATE_PWD }}
+        run: |
+          echo $MACOS_CERTIFICATE | base64 --decode > certificate.p12
+          security create-keychain -p DloaAcYP build.keychain
+          security default-keychain -s build.keychain
+          security unlock-keychain -p DloaAcYP build.keychain
+          security import certificate.p12 -k build.keychain -P $MACOS_CERTIFICATE_PWD -T /usr/bin/codesign
+          security set-key-partition-list -S apple-tool:,apple:,codesign: -s -k DloaAcYP build.keychain
+
+          cd installers/dist
+          python ../../build_tools/fix_qt_folder_names_for_codesign.py SasView6.app
+          python  ../../build_tools/code_sign_osx.py
+          codesign --verify --options=runtime --entitlements ../../build_tools/entitlements.plist --timestamp --deep --verbose=4 --force --sign "Developer ID Application: European Spallation Source Eric (W2AG9MPZ43)" SasView6.app
+          hdiutil create SasView6.dmg -srcfolder SasView6.app -ov -format UDZO
+          codesign -s "Developer ID Application: European Spallation Source Eric (W2AG9MPZ43)" SasView6.dmg
+
       - name: Publish installer package
         if: ${{ matrix.installer }}
         uses: actions/upload-artifact@v3
@@ -272,7 +274,6 @@ jobs:
             installers/dist/sasview6.tar.gz
           if-no-files-found: error
 
-
   test-installer:
     needs: [ build-matrix ]
 

INSTALL.txt

@@ -1,7 +1,8 @@
 Quick Intro for Building Sasview
 ================================
 
-Note - at the current time sasview will only run in gui form under Python 3.
+Note - at the current time sasview will only run in gui form under Python 3.11
+and later.
 
 Before trying to install and run sasview you'll need to check what
 dependencies are required:

build_tools/code_sign_osx.py

@@ -15,13 +15,44 @@
     "SasView*.app/Contents/Resources/zmq/.dylibs/*.dylib", recursive=True
 )
 
+pyside_QtWebEngineProcessApp = glob.glob(
+    "SasView*.app/Contents/Resources/PySide6/Qt/lib/QtWebEngineCore.framework/Versions/A/Helpers/QtWebEngineProcess.app", recursive=True
+)
+
+pyside_QtWebEngineCore = glob.glob(
+    "SasView*.app/Contents/Resources/PySide6/Qt/lib/QtWebEngineCore.framework/Versions/A/QtWebEngineCore", recursive=True
+)
+
+pyside_QtWebEngineProcess_Helpers = glob.glob(
+    "SasView*.app/Contents/Resources/PySide6/Qt/lib/QtWebEngineCore.framework/Helpers/QtWebEngineProcess.app/Contents/MacOS/QtWebEngineProcess", recursive=True
+)
+
+pyside_Qtlibs = glob.glob(
+    "SasView*.app/Contents/Resources/PySide6/Qt/lib/Qt*.framework/Versions/A/Qt*", recursive=True
+)
+
+#pyside_libs = pyside_QtWebEngineCore + pyside_QtWebEngineProcess
+
 sign_command = ['codesign', '--timestamp', '--options=runtime', '--verify', '--verbose=4', '--force',
-                '--sign', 'Developer ID Application: European Spallation Source Eric (W2AG9MPZ43)']
+                '--sign',  'Developer ID Application: European Spallation Source Eric (W2AG9MPZ43)']
 
+sign_deep_command = ['codesign', '--timestamp', '--deep', '--options=runtime', '--verify', '--verbose=4', '--force',
+                 '--sign',  'Developer ID Application: European Spallation Source Eric (W2AG9MPZ43)']
 
-#TODO: Check if it is necesarry to do it per file (one long list maybe enough)
-for sfile in itertools.chain(so_list, dylib_list, dylib_list_resources,
-                             zmq_dylib_list_resources):
+#Signing QtWebEngineProcess.app first as it is a helper app
+for sfile in itertools.chain(pyside_QtWebEngineProcessApp):
+    sign_deep_command.append(sfile)
+    subprocess.check_call(sign_deep_command)
+    sign_deep_command.pop()
+
+for sfile in itertools.chain(so_list, dylib_list,
+                             dylib_list_resources,
+                             zmq_dylib_list_resources,
+                             pyside_QtWebEngineCore,
+                             pyside_QtWebEngineProcess_Helpers,
+                             pyside_Qtlibs):
     sign_command.append(sfile)
     subprocess.check_call(sign_command)
     sign_command.pop()
+
+

build_tools/release_notes/6.0.0_notes.txt

@@ -0,0 +1,101 @@
+## New features
+- Orientation viewer
+- Corfunc refactored
+- Simultaneous fitting allows for weighting scheme
+- Preferences panel with display and plotting options (polydispersity and residuals plots can be hidden).
+- Improved label handling on plots
+- Residuals plots refactored
+- PDB reader refactored
+- Wedge slicer added
+- Sasdata package separated
+- Move to PySide6
+- Python 3.11 support
+- Required documentation (https://github.com/SasView/sasview/issues/2641)
+- Improved documentation
+- New Tutorials
+
+## Major bug fixes:
+- Handling of constraints for polydisperse parameters
+- Binning and FitPage plotting of SESANS data 
+- Fixed 1D slit-smearing function
+- Start-up speed improved
+- Magnetic SLD? 
+- Multiplicity model?
+
+## New models
+- New broad peak model
+
+## Anticipated for beta version
+- PDB-based model saved to custom model (for S(q) calculations)?
+- Batch Processing and 2D data slicing and processing for P(r)
+- Local documentation generator
+- Log explorer
+- Send To button with replacement options
+
+
+## What's Changed (This section has to be improved)
+* Fix wrong number of parameters on restore in slicer module by @butlerpd in https://github.com/SasView/sasview/pull/2462
+* Update README.md by @lucas-wilkins in https://github.com/SasView/sasview/pull/2466
+* More changes to corfunc by @lucas-wilkins in https://github.com/SasView/sasview/pull/2463
+* Modify the way perspectives are closed by @rozyczko in https://github.com/SasView/sasview/pull/2469
+* Testing nightly build by @wpotrzebowski in https://github.com/SasView/sasview/pull/2465
+* Add argument to convertUI that forces full UI rebuild by @krzywon in https://github.com/SasView/sasview/pull/2483
+* Pyside6 merge by @rozyczko in https://github.com/SasView/sasview/pull/2478
+* Remove UI conversion from run.py by @krzywon in https://github.com/SasView/sasview/pull/2511
+* Reinstate math import to Plotter.py by @krzywon in https://github.com/SasView/sasview/pull/2517
+* 2111 name changes in corfunc by @lucas-wilkins in https://github.com/SasView/sasview/pull/2485
+* Import pytest in density calculator GUI tests by @krzywon in https://github.com/SasView/sasview/pull/2523
+* 2389: Validate text/int/float inputs within the preferences panel by @krzywon in https://github.com/SasView/sasview/pull/2476
+* C&S fitting widget fixes for PySide6 by @rozyczko in https://github.com/SasView/sasview/pull/2528
+* Reparent QAction from QtWidget to QtGui (PySide6) by @rozyczko in https://github.com/SasView/sasview/pull/2532
+* Fix for save dataset error #2533 by @rozyczko in https://github.com/SasView/sasview/pull/2534
+* Rog and beta q by @smalex-z in https://github.com/SasView/sasview/pull/2535
+* Lowercase PySide6 executables for Linux compatability #2542 by @ehewins in https://github.com/SasView/sasview/pull/2543
+* 2541 nightly build artifact doesnt start on mac by @wpotrzebowski in https://github.com/SasView/sasview/pull/2544
+* Polydisperse parameter check on model load by @rozyczko in https://github.com/SasView/sasview/pull/2553
+* Log explorer fix by @smalex-z in https://github.com/SasView/sasview/pull/2545
+* Syntax highlighting in Pyside6 by @rozyczko in https://github.com/SasView/sasview/pull/2562
+* Avoid parenting mess by calling the widget directly by @rozyczko in https://github.com/SasView/sasview/pull/2559
+* Added model reload signal on data swap by @rozyczko in https://github.com/SasView/sasview/pull/2567
+* Two options to disable residuals and polydispersity distribution plots by @lozanodorian in https://github.com/SasView/sasview/pull/2558
+* 2550 wedge slicer by @ehewins in https://github.com/SasView/sasview/pull/2566
+* Post-v5.0.6 Release Update by @krzywon in https://github.com/SasView/sasview/pull/2536
+* Use a regex for version validity check rather than integer coercion by @krzywon in https://github.com/SasView/sasview/pull/2572
+* Wedge slicer minor upgrages by @ehewins in https://github.com/SasView/sasview/pull/2570
+* Strip debug messages from production version of Qt console by @pkienzle in https://github.com/SasView/sasview/pull/2557
+* unit conversion for gui is missing by @rozyczko in https://github.com/SasView/sasview/pull/2568
+* Adjusts scale and angular range in 1D plots from WedgeSlicer by @butlerpd in https://github.com/SasView/sasview/pull/2580
+* Bump scipy from 1.7.3 to 1.10.0 in /build_tools by @dependabot in https://github.com/SasView/sasview/pull/2547
+* Plot2D instances are now of `Plotter2DWidget` type. Fixes #2586 by @rozyczko in https://github.com/SasView/sasview/pull/2587
+* fix dialog sizes for some calculators. #2437 by @rozyczko in https://github.com/SasView/sasview/pull/2581
+* Fix for getting directory name by @rozyczko in https://github.com/SasView/sasview/pull/2596
+* Remove Unused Dependency: h5py by @gdrosos in https://github.com/SasView/sasview/pull/2585
+* 2577 orientation viewer doesnt work from nigthly build on mac by @lucas-wilkins in https://github.com/SasView/sasview/pull/2600
+* Fixed unmatched method signatures in Box&Wedge Interactor child classes by @ehewins in https://github.com/SasView/sasview/pull/2589
+* Particle editor by @lucas-wilkins in https://github.com/SasView/sasview/pull/2520
+* Pass the Data1D/2D object, not its `data` attribute by @rozyczko in https://github.com/SasView/sasview/pull/2592
+* Bump reportlab from 3.6.6 to 3.6.13 in /build_tools by @dependabot in https://github.com/SasView/sasview/pull/2597
+* Added 3.11, removed 3.8 by @rozyczko in https://github.com/SasView/sasview/pull/2582
+* Fix doc build errors by @smk78 in https://github.com/SasView/sasview/pull/2607
+* Doc toctree fixes by @smk78 in https://github.com/SasView/sasview/pull/2609
+* 2603: Numeric coercion in preferences by @krzywon in https://github.com/SasView/sasview/pull/2605
+* What's new dialog by @lucas-wilkins in https://github.com/SasView/sasview/pull/2608
+* created submenu for slicers being part of #2604 by @astellhorn in https://github.com/SasView/sasview/pull/2610
+* Squish squashed by @lucas-wilkins in https://github.com/SasView/sasview/pull/2616
+* Update sas_gen.py by @timsnow in https://github.com/SasView/sasview/pull/2617
+* Killed Zombie Python Test by @lucas-wilkins in https://github.com/SasView/sasview/pull/2627
+* Remove model.png by @lucas-wilkins in https://github.com/SasView/sasview/pull/2629
+* Populate whats new with last version by @smk78 in https://github.com/SasView/sasview/pull/2625
+* Fix errors while running convertUI by @krzywon in https://github.com/SasView/sasview/pull/2623
+* 2618: Fix GPU and Optimizer Preferences by @krzywon in https://github.com/SasView/sasview/pull/2622
+* Moving OSX signing to nightly by @wpotrzebowski in https://github.com/SasView/sasview/pull/2631
+* Empty lines in data explorer by @rozyczko in https://github.com/SasView/sasview/pull/2643
+
+## New Contributors
+* @smalex-z made their first contribution in https://github.com/SasView/sasview/pull/2535
+* @ehewins made their first contribution in https://github.com/SasView/sasview/pull/2543
+* @lozanodorian made their first contribution in https://github.com/SasView/sasview/pull/2558
+* @gdrosos made their first contribution in https://github.com/SasView/sasview/pull/2585
+* @astellhorn made their first contribution in https://github.com/SasView/sasview/pull/2610
+
+**Full Changelog**: https://github.com/SasView/sasview/compare/nightly-build...v6.0.0-alpha

build_tools/requirements.txt

@@ -33,3 +33,4 @@ zope
 superqt
 pyopengl
 pyopengl_accelerate
+sphinx

docs/sphinx-docs/build_sphinx.py

@@ -19,8 +19,7 @@
 from distutils.util import get_platform
 from distutils.spawn import find_executable
 
-from shutil import copy
-from os import listdir
+from sas.system.user import get_user_dir
 
 platform = '.%s-%s'%(get_platform(),sys.version[:3])
 
@@ -39,6 +38,8 @@
 SASVIEW_BUILD = joinpath(SASVIEW_ROOT, "build", "lib")
 SASVIEW_MEDIA_SOURCE = joinpath(SASVIEW_ROOT, "src", "sas")
 SASVIEW_DOC_TARGET = joinpath(SASVIEW_BUILD, "doc")
+SASVIEW_DOC_SOURCE = joinpath(SASVIEW_DOC_TARGET, "source-temp")
+SASVIEW_DOC_BUILD = joinpath(SASVIEW_DOC_TARGET, "build")
 SASVIEW_API_TARGET = joinpath(SPHINX_SOURCE, "dev", "sasview-api")
 
 # sasmodels paths
@@ -57,6 +58,15 @@
     "index.rst", "install.rst", "intro.rst",
 ]
 
+# sasdata paths
+SASDATA_ROOT = joinpath(SASVIEW_ROOT, "..", "sasdata")
+SASDATA_DOCS = joinpath(SASDATA_ROOT, "docs")
+SASDATA_BUILD = joinpath(SASDATA_ROOT, "build", "lib")
+SASDATA_DEV_SOURCE = joinpath(SASDATA_DOCS, "source", "dev")
+SASDATA_DEV_TARGET = joinpath(SPHINX_SOURCE, "dev", "sasdata-dev")
+SASDATA_GUIDE_SOURCE = joinpath(SASDATA_DOCS, "source", "user")
+SASDATA_GUIDE_TARGET = joinpath(SPHINX_SOURCE, "user", "data")
+
 # bumps paths
 BUMPS_DOCS = joinpath(SASVIEW_ROOT, "..", "bumps", "doc")
 BUMPS_SOURCE = joinpath(BUMPS_DOCS, "guide")
@@ -154,6 +164,15 @@ def retrieve_user_docs():
         inplace_change(joinpath(catdir, filename), "../../model/", "/user/models/")
 
 
+def retrieve_sasdata_docs():
+    """
+        Copies select files from the bumps documentation into fitting perspective
+    """
+    print("=== Sasdata Docs ===")
+    copy_tree(SASDATA_DEV_SOURCE, SASDATA_DEV_TARGET)
+    copy_tree(SASDATA_GUIDE_SOURCE, SASDATA_GUIDE_TARGET)
+
+
 def retrieve_bumps_docs():
     """
     Copies select files from the bumps documentation into fitting perspective
@@ -247,27 +266,31 @@ def build():
     """
     Runs sphinx-build.  Reads in all .rst files and spits out the final html.
     """
+    copy_tree(SPHINX_SOURCE, SASVIEW_DOC_SOURCE)
     print("=== Build HTML Docs from ReST Files ===")
-    subprocess.check_call([
-        "sphinx-build",
-        "-v",
-        "-b", "html", # Builder name. TODO: accept as arg to setup.py.
-        "-d", joinpath(SPHINX_BUILD, "doctrees"),
-        "-W", "--keep-going",
-        SPHINX_SOURCE,
-        joinpath(SPHINX_BUILD, "html")
-    ])
+    try:
+        subprocess.check_call([
+            "sphinx-build",
+            "-v",
+            "-b", "html", # Builder name. TODO: accept as arg to setup.py.
+            "-d", joinpath(SPHINX_BUILD, "doctrees"),
+            "-W", "--keep-going",
+            SPHINX_SOURCE,
+            joinpath(SPHINX_BUILD, "html")
+        ])
+    except Exception as e:
+        print(e)
 
     print("=== Copy HTML Docs to Build Directory ===")
     html = joinpath(SPHINX_BUILD, "html")
-    copy_tree(html, SASVIEW_DOC_TARGET)
-
+    copy_tree(html, SASVIEW_DOC_BUILD)
 
 def rebuild():
     clean()
     setup_source_temp()
     retrieve_user_docs()
     retrieve_bumps_docs()
+    retrieve_sasdata_docs()
     apidoc()
     build()
     if find_executable('latex'):

docs/sphinx-docs/source/conf.py

@@ -37,7 +37,12 @@
               'sphinx.ext.mathjax',
               #'mathjax',  # replacement mathjax that allows a list of paths
               'dollarmath',
-              'sphinx.ext.viewcode']
+              #'sphinx.ext.viewcode',
+              ]
+
+no_highlight = os.environ.get('SAS_NO_HIGHLIGHT', '0') # Check if sphinx highlighting is disabled in this environment
+if no_highlight == '1':
+    extensions.append('sphinx.ext.viewcode')
 
 mathjax_path = (
     'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?'

docs/sphinx-docs/source/dev/dev.rst

@@ -12,6 +12,7 @@ Contents
    SasView API <sasview-api/modules>
    sasmodels overview <sasmodels-dev/index>
    sasmodels API <sasmodels-api/modules>
+   sasdata overview <sasdata-dev/dev>
    OpenGL subsystem <gl/opengl.rst>
 
 Indices and Search

docs/sphinx-docs/source/user/working.rst

@@ -6,13 +6,13 @@ Working with SasView
 .. toctree::
    :maxdepth: 1
 
-   Data Formats <qtgui/MainWindow/data_formats_help>
+   Data Formats <data/data/data_formats_help>
 
    Loading Data <qtgui/MainWindow/data_explorer_help>
 
    Plotting Data/Models <qtgui/MainWindow/graph_help>
 
-   Test Data <example_data/testdata_help>
+   Example Data <example_data/testdata_help>
 
    Tutorials <tutorial>
 

installers/sasview.spec

@@ -18,12 +18,14 @@ datas = [
     ('../src/sas/qtgui/Utilities/WhatsNew/messages', 'sas/qtgui/Utilities/WhatsNew/messages'),
     ('../src/sas/system/log.ini', 'sas/system/'),
     ('../../sasmodels/sasmodels','sasmodels'),
-    ('../docs/sphinx-docs/build/html','doc')
+    ('../docs/sphinx-docs/build','doc/build'),
+    ('../docs/sphinx-docs/source-temp','doc/source')
 ]
 #TODO: Hopefully we can get away from version specific packages
 datas.append((os.path.join(PYTHON_PACKAGES, 'debugpy'), 'debugpy'))
 datas.append((os.path.join(PYTHON_PACKAGES, 'jedi'), 'jedi'))
 datas.append((os.path.join(PYTHON_PACKAGES, 'zmq'), 'zmq'))
+# datas.append((os.path.join(PYTHON_PACKAGES, 'freetype'), 'freetype'))
 
 def add_data(data):
     for component in data: