Merge branch 'main' into SlicerExtension_1344

SasView · Jan 18, 2024 · 36d0918 · 36d0918
2 parents f29ef5c + cc09ed0
commit 36d0918
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,7 +1,11 @@
 name: CI
 
 on:
-  [push, pull_request]
+  workflow_call:
+  pull_request:
+  push:
+    branches: [main]
+    tags: ['v*']
 
 defaults:
   run:
@@ -25,14 +29,19 @@ jobs:
 
     runs-on: ubuntu-latest
 
+    # Stop existing workflows for matching branches and pull requests
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+      cancel-in-progress: true
+
     outputs:
       matrix-json: ${{ steps.set-matrix.outputs.matrix }}
 
     steps:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - uses: actions/checkout@v3
       - id: set-matrix
@@ -72,7 +81,7 @@ jobs:
       - name: Install X11 libraries (Linux)
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
         run: |
-          sudo apt install libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 x11-utils xvfb
+          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
         run: |
@@ -158,16 +167,16 @@ jobs:
         run: |
           python -m pytest -v -s test
 
-      - name: Test GUI (Linux)
-        if: ${{ matrix.tests && matrix.os == 'ubuntu-latest' }}
-        env:
-          PYOPENCL_COMPILER_OUTPUT: 1
-        run: |
-          # Suppress SIGSEGV from the tests until they can be fixed
-          retval=0
-          xvfb-run -a --server-args="-screen 0 1600x900x24" python -m pytest -rsx -v src/sas/qtgui/ || retval=$?
-          if [ $retval -eq 139 ]; then echo "WARNING: Python interpreter exited with Segmentation Fault. This normally indicates that Qt objects were not correctly deleted. This error is currently suppressed in SasView's test suite."; retval=0; fi
-          exit $retval
+      # - name: Test GUI (Linux)
+      #   if: ${{ matrix.tests && matrix.os == 'ubuntu-latest' }}
+      #   env:
+      #     PYOPENCL_COMPILER_OUTPUT: 1
+      #   run: |
+      #     # Suppress SIGSEGV from the tests until they can be fixed
+      #     retval=0
+      #     xvfb-run -a --server-args="-screen 0 1600x900x24" python -m pytest -rsx -v src/sas/qtgui/ || retval=$?
+      #     if [ $retval -eq 139 ]; then echo "WARNING: Python interpreter exited with Segmentation Fault. This normally indicates that Qt objects were not correctly deleted. This error is currently suppressed in SasView's test suite."; retval=0; fi
+      #     exit $retval
 
       ### Build documentation (if enabled)
 
@@ -195,7 +204,7 @@ jobs:
       - name: Install utilities to build installer
         if: ${{ matrix.installer }}
         run: |
-          python -m pip install pyinstaller==5.7.0
+          python -m pip install pyinstaller==5.13.2
 
       - name: Build sasview with pyinstaller
         if: ${{ matrix.installer }}
@@ -217,17 +226,31 @@ jobs:
           iscc installers/installer.iss
           mv installers/Output/setupSasView.exe installers/dist
 
-      - name: Build sasview installer dmg file (OSX)
+      - 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
-          hdiutil create SasView5.dmg -srcfolder SasView5.app -ov -format UDZO
+          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') }}
         run: |
           cd installers/dist
-          tar zcf sasview5.tar.gz sasview
+          tar zcf sasview6.tar.gz sasview
 
       - name: Collect a debug tarball of the installer package
         if: ${{ matrix.installer }}
@@ -238,84 +261,25 @@ 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 SasView5.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)" SasView5.app
-          hdiutil create SasView5.dmg -srcfolder SasView5.app -ov -format UDZO
-          codesign -s "Developer ID Application: European Spallation Source Eric (W2AG9MPZ43)" SasView5.dmg
-          
       - name: Publish installer package
         if: ${{ matrix.installer }}
         uses: actions/upload-artifact@v3
         with:
           name: SasView-Installer-${{ matrix.os }}-${{ matrix.python-version }}
           path: |
             installers/dist/setupSasView.exe
-            installers/dist/SasView5.dmg
-            installers/dist/sasview5.tar.gz
+            installers/dist/SasView6.dmg
+            installers/dist/sasview6.tar.gz
           if-no-files-found: error
 
 
-  #     - name: Notarize Release Build (OSX)
-  #       if: ${{ env.RELEASE == 'true' && matrix.installer && startsWith(matrix.os, 'macos') }}
-  #       uses: devbotsxyz/xcode-notarize@v1
-  #       with:
-  #           product-path: "installers/dist/SasView5.dmg"
-  #           primary-bundle-id: "org.sasview.SasView5"
-  #           appstore-connect-username: ${{ secrets.NOTARIZATION_USERNAME }}
-  #           appstore-connect-password: ${{ secrets.NOTARIZATION_PASSWORD }}
-
-  #     - name: Staple Release Build (OSX)
-  #       if: ${{ startsWith(matrix.os, 'macos') }}
-  #       uses: devbotsxyz/xcode-staple@v1
-  #       with:
-  #           product-path: "installers/dist/SasView5.dmg"
-
-      - name: Declare env variables on push only
-        if: ${{ env.RELEASE == 'true' && matrix.installer && github.event_name == 'push' }}
-        shell: bash
-        run: echo "BRANCH_NAME=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
-
-      - name: Declare env variables on pull_request only
-        if: ${{ env.RELEASE == 'true' && matrix.installer && github.event_name == 'pull_request' }}
-        shell: bash
-        run: echo "BRANCH_NAME=$GITHUB_HEAD_REF" >> $GITHUB_ENV
-
-      - name: Upload installer to GitHub releases
-        if: ${{ env.RELEASE == 'true' && matrix.installer }}
-        uses: ncipollo/release-action@v1
-        with:
-          draft: true
-          prerelease: true
-          allowUpdates: true
-          replacesArtifacts: true
-          token: ${{ secrets.GITHUB_TOKEN }}
-          artifacts: "installers/dist/SasView5.dmg, installers/Output/setupSasView.exe"
-          name: ${{ env.BRANCH_NAME }}
-          tag: ${{ env.BRANCH_NAME }}
-
-
   test-installer:
     needs: [ build-matrix ]
 
     strategy:
       matrix:
         os: [ windows-latest, ubuntu-20.04 ]
-        python-version: [ 3.8 ]
+        python-version: [ 3.11 ]
       fail-fast: false
 
     name: Test installer
@@ -415,7 +379,7 @@ jobs:
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
         run: |
           # $INSTALL_PATH is already the base directory
-          tar xf "$DL_PATH/sasview5.tar.gz"
+          tar xf "$DL_PATH/sasview6.tar.gz"
 
       - name: Check installation files
         run: |

diff --git a/.github/workflows/matrix.py b/.github/workflows/matrix.py
@@ -38,7 +38,7 @@
 
 # List of python versions to use for release builds
 python_release_list = [
-    '3.8',
+    '3.11',
 ]
 
 # List of python versions to use for tests

diff --git a/.github/workflows/nightly-build.yml b/.github/workflows/nightly-build.yml
@@ -0,0 +1,69 @@
+name: Nightly Build
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+
+  #Reuse ci.yml workflow on main branch and upload artifacts to release page
+  reuse_main_ci:
+    uses: ./.github/workflows/ci.yml
+    secrets: inherit
+
+  upload_nighly_builds:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ macos-latest]
+        python-version: [ 3.11 ]
+    needs: reuse_main_ci
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Retrieve saved artifacts
+        uses: actions/download-artifact@v3
+        with:
+          path: installers/dist
+
+      - name: Display structure of downloaded files
+        run: ls -R
+        working-directory: installers/dist
+
+      - name: Rename remaining artifacts artifacts
+        run: |
+          mv installers/dist/SasView-Installer-windows-*/setupSasView.exe installers/dist/setupSasView-nightly-Win64.exe
+          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: lando/notarize-action@v2
+        with:
+            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)
+        uses: BoundfoxStudios/action-xcode-staple@v1
+        with:
+          product-path: "installers/dist/SasView-nightly-MacOSX.dmg"
+
+      - name: Upload Nightly Build Installer to GitHub releases
+        uses: ncipollo/release-action@v1
+        with:
+          draft: false
+          prerelease: true
+          allowUpdates: true
+          replacesArtifacts: true
+          token: ${{ secrets.GITHUB_TOKEN }}
+          artifacts: "installers/dist/setupSasView-nightly-Win64.exe, installers/dist/SasView-nightly-MacOSX.dmg, installers/dist/SasView-nightly-Linux.tar.gz"
+          body: "Nightly build of main SasView branch"
+          name: "nightly-build"
+          tag: "nightly-build"
diff --git a/.gitignore b/.gitignore
@@ -39,6 +39,7 @@ default_categories.json
 **/UI/*.py
 !**/UI/__init__.py
 config.json
+**/db.sqlite3
 
 # doc build
 /docs/sphinx-docs/build

diff --git a/LICENSE.TXT b/LICENSE.TXT
@@ -1,4 +1,4 @@
-Copyright (c) 2009-2022, SasView Developers
+Copyright (c) 2009-2023, SasView Developers
 
 
 All rights reserved.

diff --git a/build_tools/code_sign_osx.py b/build_tools/code_sign_osx.py
@@ -6,19 +6,22 @@
 import subprocess
 import itertools
 
-so_list = glob.glob("SasView5.app/Contents/MacOS/**/*.so", recursive=True)
-dylib_list = glob.glob("SasView5.app/Contents/MacOS/**/*.dylib", recursive=True)
+so_list = glob.glob("SasView*.app/Contents/MacOS/**/*.so", recursive=True)
+dylib_list = glob.glob("SasView*.app/Contents/MacOS/**/*.dylib", recursive=True)
 dylib_list_resources = glob.glob(
-    "SasView5.app/Contents/Resources/.dylibs/*.dylib", recursive=True
+    "SasView*.app/Contents/Resources/.dylibs/*.dylib", recursive=True
+)
+zmq_dylib_list_resources = glob.glob(
+    "SasView*.app/Contents/Resources/zmq/.dylibs/*.dylib", recursive=True
 )
 
 sign_command = ['codesign', '--timestamp', '--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):
+for sfile in itertools.chain(so_list, dylib_list, dylib_list_resources,
+                             zmq_dylib_list_resources):
     sign_command.append(sfile)
     subprocess.check_call(sign_command)
     sign_command.pop()
-
diff --git a/build_tools/release_automation.py b/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',
-Original file line number
+Diff line change
@@ Expand Up / @@ -38,7 +38,7 @@ @@
     # List of python versions to use for release builds
     python_release_list = [
-        '3.8',
+        '3.11',
     ]
     # List of python versions to use for tests
@@ Expand Down @@