pstdElastic3D

.github/workflows/codespell.yml

@@ -0,0 +1,25 @@
+name: Spell Check
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  spellcheck:
+    name: Spell Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install codespell
+        run: pip install codespell
+
+      - name: Run codespell
+        run: codespell --config .codespellrc 

.github/workflows/pytest.yml

@@ -58,23 +58,22 @@ jobs:
           files: |
             ./collectedValues
           outPath: collectedValues.tar.gz
-      - name: upload reference values artifact
+      - name: Upload reference values artifact
         id: artifact-upload-step
-        if: ${{ steps.matlab-refs-cache.outputs.cache-hit != 'true' }}
         uses: actions/upload-artifact@v4
         with:
           name: matlab_reference_test_values
           path: collectedValues.tar.gz
           # overwrite: true
+
       - name: Output artifact URL
-        if: ${{ steps.matlab-refs-cache.outputs.cache-hit != 'true' }}
         run:  echo 'Artifact URL is ${{ steps.artifact-upload-step.outputs.artifact-url }}'
   test:
     needs: collect_references
     strategy:
       matrix:
         os: [ "windows-latest", "ubuntu-latest" , "macos-latest"]
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
     runs-on: ${{matrix.os}}
     steps:
       - uses: actions/checkout@v4

.github/workflows/run-examples.yml

@@ -0,0 +1,56 @@
+name: Run K-Wave Examples
+
+on:
+  schedule:
+    - cron: '0 0 * * 1'  # Every Monday at 00:00 UTC
+  workflow_dispatch:      # Manual trigger
+
+jobs:
+  discover-examples:
+    runs-on: ubuntu-latest
+    outputs:
+      example_paths: ${{ steps.find-examples.outputs.examples }}
+    steps:
+      - uses: actions/checkout@v4
+      - id: find-examples
+        run: |
+          # Find all Python files in examples subdirectories
+          EXAMPLES=$(find examples -name "*.py" -not -path "*/\.*" | jq -R -s -c 'split("\n")[:-1]')
+          echo "examples=$EXAMPLES" >> "$GITHUB_OUTPUT"
+
+  run-examples:
+    needs: discover-examples
+    runs-on: ubuntu-latest
+    timeout-minutes: 60  # 1 hour timeout per example
+    strategy:
+      fail-fast: false  # Continue running other examples even if one fails
+      matrix:
+        example: ${{ fromJson(needs.discover-examples.outputs.example_paths) }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y ffmpeg
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'  # Matches requires-python from pyproject.toml
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # Install the package with example dependencies
+          pip install -e ".[example]"
+
+      - name: Run example
+        env:
+          KWAVE_FORCE_CPU: 1
+        run: |
+          echo "Running example: ${{ matrix.example }}"
+          python "${{ matrix.example }}" 

.github/workflows/test_example.yml

@@ -7,7 +7,7 @@ jobs:
     strategy:
       matrix:
         os: [ "windows-latest", "ubuntu-latest" , "macos-latest"]
-        python-version: [ "3.9", "3.10", "3.11", "3.12"]
+        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
     runs-on: ${{matrix.os}}
     steps:
       - uses: actions/checkout@v4
@@ -23,7 +23,7 @@ jobs:
         run: |
           python3 examples/us_bmode_linear_transducer/us_bmode_linear_transducer.py
       - name: Upload example results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: example_bmode_reconstruction_results_${{ matrix.os }}_${{ matrix.python-version }}
           path: ${{ github.workspace }}/example_bmode.png

.github/workflows/test_optional_dependencies.yml

@@ -13,7 +13,7 @@ jobs:
         strategy:
             matrix:
                 os: [ "windows-latest", "ubuntu-latest" , "macos-latest"]
-                python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+                python-version: [ "3.10", "3.11", "3.12", "3.13" ]
                 extra_requirements: [ "test", "examples", "docs", "dev", "all" ]
         runs-on: ${{matrix.os}}
         steps:
@@ -26,4 +26,4 @@ jobs:
                   cache: 'pip'
             - name: Install dependencies
               run: |
-                  pip install '.[${{ matrix.extra_requirements }}]'
+                  pip install '.[${{ matrix.extra_requirements }}]'

.github/workflows/test_pages.yml

@@ -10,9 +10,9 @@ jobs:
         fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.10'
         cache: 'pip'
     - name: Build and Commit
       uses: waltsims/[email protected]
       with:
-        pyproject_toml_deps: ".[docs]"
+        pyproject_toml_deps: ".[docs]"

.gitignore

@@ -44,3 +44,8 @@ tests/reference_outputs
 kspaceFirstOrder-*_metadata.json
 
 
+*.nii
+*.vtk
+*.vtk
+examples/benchmarks/8/runner.log
+*.vtk

examples/at_focused_annular_array_3D/at_focused_annular_array_3D.py

@@ -161,7 +161,7 @@
 amp_on_axis = amp[:, Ny // 2]
 
 # define axis vectors for plotting
-x_vec = kgrid.x_vec[source_x_offset + 1 :, :] - kgrid.x_vec[source_x_offset]
+x_vec = kgrid.x_vec[source_x_offset + 1: -1, :] - kgrid.x_vec[source_x_offset]
 y_vec = kgrid.y_vec
 
 # =========================================================================