Merge branch 'dev' into wb-dev

Author: WieraB

.github/workflows/install_and_lint.yml

@@ -0,0 +1,33 @@
+name: Check Linting with pylint
+
+on:
+  push:
+    branches: [ main, dev ]
+  pull_request:
+    branches: [ main, dev ]
+  workflow_dispatch:
+
+jobs:
+  check-lint:
+    name: Lint Code
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          sudo apt update
+          sudo apt install libegl1
+          sudo apt install libgl1 libxext6 libx11-6
+          python -m pip install --upgrade pip
+          pip install pylint
+          pip install -e .
+
+      - name: Lint with pylint
+        run: |
+          pylint src/pyvale --fail-under=7.0

.github/workflows/lint.yml

@@ -2,26 +2,39 @@ name: Run tests
 
 on:
   push:
-    branches: [main]
+    branches: [main, dev]
   pull_request:
-    branches: [main]
+    branches: [main, dev]
   workflow_dispatch:
 
 jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-latest] 
-
+        os: [ubuntu-latest, windows-latest, macos-14, macos-15-intel, macos-latest]
+        include:
+          - os: macos-14
+            llvm: llvm@15
+          - os: macos-15-intel
+            llvm: llvm@18
+          - os: macos-latest
+            llvm: llvm@18
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
 
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'  # or another version you need
+          python-version: '3.11'
+
+      - name: set default compiler on macOS to GCC
+        if: startsWith(matrix.os, 'macos')
+        run: |
+          echo "CC=gcc-15" >> $GITHUB_ENV
+          echo "CXX=g++-15" >> $GITHUB_ENV
 
       - name: Install dependencies for ubuntu-latest
         if: matrix.os == 'ubuntu-latest'
@@ -32,13 +45,19 @@ jobs:
       - name: Upgrade pip and install package
         run: |
           python -m pip install --upgrade pip
-          pip install -e .
+          pip install -e . -v
 
       - name: Smoke test
         run: |
           python -c "import pyvale"
 
-      - name: Run pytests
+      - name: Run sensorsim and DIC tests
+        run: |
+          pip install pytest pytest-mock
+          pytest -v tests/dic/. tests/sensorsim/.
+
+      - name: Run blender tests (skip macOS ARM)
+        if: ${{ !startsWith(matrix.os, 'macos') || contains(matrix.os, 'intel') }}
         run: |
-          pip install pytest
-          pytest -v tests/blender/. tests/dic/. tests/sensorsim
+          pip install pytest pytest-mock
+          pytest -v tests/blender/.

.github/workflows/tests.yml

@@ -1,10 +1,11 @@
-name: Build and Upload Wheels to PyPI
+name: Build Wheels and upload (if new release) to PyPI
 
 on:
   workflow_dispatch:
   push:
-    branches:
-      - main
+    branches: [main, dev]
+  pull_request:
+    branches: [main, dev]
   release:
     types:
       - published
@@ -14,29 +15,28 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # macos13 is intel macos14 is arm
-        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-13, macos-14]
-
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-14, macos-15-intel, macos-latest]
+        include:
+          - os: macos-14
+            llvm: llvm@15
+            macos_deployment_target: "14.0"
+          - os: macos-15-intel
+            llvm: llvm@18
+            macos_deployment_target: "15.0"
+          - os: macos-latest
+            llvm: llvm@18
+            macos_deployment_target: "15.0"
     steps:
       - uses: actions/checkout@v4
-    
-      # Set GCC and Deployment Target for macOS 13
-      - name: Set GCC and MACOSX_DEPLOYMENT_TARGET for macOS 13
-        if: matrix.os == 'macos-13'
-        run: |
-          echo "MACOSX_DEPLOYMENT_TARGET=13.6" >> $GITHUB_ENV
 
-      # Set GCC and Deployment Target for macOS 14
-      - name: Set GCC and MACOSX_DEPLOYMENT_TARGET for macOS 14
-        if: matrix.os == 'macos-14'
-        run: |
-          echo "MACOSX_DEPLOYMENT_TARGET=14.0" >> $GITHUB_ENV
-
-      - name: Install libomp for clang (macOS only)
+      - name: Set compiler on macOS to GCC
         if: startsWith(matrix.os, 'macos')
         run: |
           brew install libomp
-      
+          echo "MACOSX_DEPLOYMENT_TARGET=${{ matrix.macos_deployment_target }}" >> $GITHUB_ENV
+          echo "CC=gcc-15" >> $GITHUB_ENV
+          echo "CXX=g++-15" >> $GITHUB_ENV
+
       - name: Build wheels
         uses: pypa/cibuildwheel@v2.23.3
         with:
@@ -45,11 +45,6 @@ jobs:
           config-file: "{package}/pyproject.toml"
         env:
           CIBW_SKIP: "pp*"
-          CIBW_ENVIRONMENT_MACOS: >
-            CC=$(brew --prefix llvm@15)/bin/clang
-            CXX=$(brew --prefix llvm@15)/bin/clang++
-            LDFLAGS="-L$(brew --prefix libomp)/lib"
-            CPPFLAGS="-I$(brew --prefix libomp)/include"
       - uses: actions/upload-artifact@v4
         with:
           name: pyvale-wheels-${{ matrix.os }}-${{ strategy.job-index }}

.github/workflows/wheels.yml

@@ -9,24 +9,17 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # macos13 is intel macos14 is arm
-        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-13, macos-14]
-
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-14, macos-15-intel, macos-latest]
+        include:
+        - os: macos-14
+          llvm: llvm@15
+        - os: macos-15-intel
+          llvm: llvm@18
+        - os: macos-15-latest
+          llvm: llvm@18
     steps:
       - uses: actions/checkout@v4
 
-      # Set GCC and Deployment Target for macOS 13
-      - name: Set GCC and MACOSX_DEPLOYMENT_TARGET for macOS 13
-        if: matrix.os == 'macos-13'
-        run: |
-          echo "MACOSX_DEPLOYMENT_TARGET=13.6" >> $GITHUB_ENV
-
-      # Set GCC and Deployment Target for macOS 14
-      - name: Set GCC and MACOSX_DEPLOYMENT_TARGET for macOS 14
-        if: matrix.os == 'macos-14'
-        run: |
-          echo "MACOSX_DEPLOYMENT_TARGET=14.0" >> $GITHUB_ENV
-
       - name: Install libomp for clang (macOS only)
         if: startsWith(matrix.os, 'macos')
         run: |
@@ -41,10 +34,8 @@ jobs:
         env:
           CIBW_SKIP: "pp*"
           CIBW_ENVIRONMENT_MACOS: >
-            CC=$(brew --prefix llvm@15)/bin/clang
-            CXX=$(brew --prefix llvm@15)/bin/clang++
-            LDFLAGS="-L$(brew --prefix libomp)/lib"
-            CPPFLAGS="-I$(brew --prefix libomp)/include"
+            CC=gcc-15
+            CXX=g++-15
       - uses: actions/upload-artifact@v4
         with:
           name: pyvale-wheels-${{ matrix.os }}-${{ strategy.job-index }}

.github/workflows/wheels_testpypi.yml

@@ -1,5 +1,7 @@
 #-------------------------------------------------------------------------------
-# vscode / venv
+# pyvale specific ignores
+
+# Environments and VS Code
 .vscode/
 .pyvale-env/
 pyvale-env/
@@ -17,10 +19,10 @@ pyvale-env/
 *.blend
 *.csv
 *.json
-testoutput/
-exampleoutput/
 pyvale-output/
-blender*/
+pyvale-input/
+test-output/
+test-input/
 
 # MOOSE / gmsh
 *-opt
@@ -42,6 +44,8 @@ blender*/
 !tests/mooseherder/output_gold/*.csv
 !tests/mooseherder/output_gold/sim-workdir-*/*.e
 !tests/mooseherder/output_gold/sim-workdir-*/*.json
+!tests/mooseherder/txt_gold/*.csv
+!tests/mooseherder/txt_gold/*.npy
 
 # Image deformation test cases
 *.pkl
@@ -58,6 +62,25 @@ src/pyvale/cython/*.html
 *.a
 *.o
 
+# restructured text files for API documentation.
+pyvale.rst
+pyvale.*.rst
+
+# files generated by sphinx-gallery extension
+docs/source/examples/*/
+# keep the gallery layouts
+!docs/source/examples/examples_*.rst
+
+# doxygen folder generated when compiling docs
+docs/source/doxygen
+
+# rastercyth generated files
+src/pyvale/cython/rastercyth.c
+src/pyvale/cython/rastercyth.html
+
+# Ruff linting cache
+.ruff_cache/
+
 #-------------------------------------------------------------------------------
 # Python Standard Ignore
 
@@ -230,16 +253,9 @@ cpp/Makefile
 #.idea/
 
 
-# restructured text files for API documentation.
-pyvale.rst
-pyvale.*.rst
-
 # files generated by sphinx-gallery extension
 docs/source/examples/
 
 # doxygen folder generated when compiling docs
 docs/source/doxygen
 
-# rastercyth generated files
-src/pyvale/cython/rastercyth.c
-src/pyvale/cython/rastercyth.html