Merge branch 'release_6.0.0' into 2663-update-nomenclature-for-sesans…

…-plots
SasView · Mar 12, 2024 · 4153f65 · 4153f65
2 parents b4eba95 + b4bc808
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -109,7 +109,7 @@ jobs:
 
       - name: Fetch sources for sibling projects
         run: |
-          git clone --depth=50 --branch=master https://github.com/SasView/sasdata.git ../sasdata
+          git clone --depth=50 --branch=release_0.9.0 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
 
@@ -120,6 +120,7 @@ jobs:
           rm -rf dist
           python setup.py clean
           python setup.py build
+          mv build/lib/sasdata/example_data/* ../sasview/src/sas/example_data/
           python -m pip install --no-deps .
 
       - name: Build and install sasmodels
@@ -180,17 +181,13 @@ 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 }}
@@ -240,11 +237,7 @@ jobs:
           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 +254,43 @@ 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: Notarize Release Build (OSX)
+        if: ${{ matrix.installer && startsWith(matrix.os, 'macos') }}
+        uses: lando/notarize-action@v2
+        with:
+          product-path: "installers/dist/SasView6.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: ${{ matrix.installer && startsWith(matrix.os, 'macos') }}
+        uses: BoundfoxStudios/action-xcode-staple@v1
+        with:
+          product-path: "installers/dist/SasView6.dmg"
+
       - name: Publish installer package
         if: ${{ matrix.installer }}
         uses: actions/upload-artifact@v3
@@ -272,6 +302,33 @@ jobs:
             installers/dist/sasview6.tar.gz
           if-no-files-found: error
 
+      - name: Rename artifacts (Windows)
+        if: ${{ matrix.installer && startsWith(matrix.os, 'windows') }}
+        run: |
+          mv installers/dist/setupSasView.exe installers/dist/setupSasView-6.0.0-alpha-Win64.exe
+
+      - name: Rename artifacts (MacOS)
+        if: ${{ matrix.installer && startsWith(matrix.os, 'macos') }}
+        run: |    
+          mv installers/dist/SasView6.dmg  installers/dist/SasView-6.0.0-alpha-MacOSX.dmg
+
+      - name: Rename artifacts (Linux)
+        if: ${{ matrix.installer && startsWith(matrix.os, 'ubuntu') }}
+        run: |    
+          mv installers/dist/sasview6.tar.gz installers/dist/SasView-6.0.0-alpha-Linux.tar.gz
+
+      - name: Upload Release Installer to GitHub
+        uses: ncipollo/release-action@v1
+        with:
+          draft: false
+          prerelease: true
+          allowUpdates: true
+          replacesArtifacts: true
+          token: ${{ secrets.GITHUB_TOKEN }}
+          artifacts: "installers/dist/setupSasView-6.0.0-alpha-Win64.exe, installers/dist/SasView-6.0.0-alpha-MacOSX.dmg, installers/dist/SasView-6.0.0-alpha-Linux.tar.gz"
+          name: "Release 6.0.0-alpha"
+          bodyFile: "build_tools/release_notes/6.0.0_notes.txt"
+          tag: "v6.0.0-alpha"
 
   test-installer:
     needs: [ build-matrix ]

diff --git a/INSTALL.txt b/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:

diff --git a/build_tools/code_sign_osx.py b/build_tools/code_sign_osx.py
@@ -15,13 +15,42 @@
     "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)']
 
+#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()
 
-#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):
+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()
diff --git a/build_tools/release_notes/6.0.0_notes.txt b/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
diff --git a/build_tools/requirements.txt b/build_tools/requirements.txt
@@ -33,3 +33,4 @@ zope
 superqt
 pyopengl
 pyopengl_accelerate
+sphinx
-Original file line number
+Diff line change
@@ Expand Up / @@ -33,3 +33,4 @@ zope @@
     superqt
     pyopengl
     pyopengl_accelerate
+    sphinx