Merge branch 'main' into face_props_mass_matrices

Author: dccowan

.ci/azure/run_tests.sh

@@ -10,23 +10,19 @@ test_args=""
 
 source activate discretize-test
 
-if ${do_doc}
-then
-  if ${is_azure}
-  then
+if [[ "$is_azure" == "true" ]]; then
+  if [[ "$do_doc" == "true" ]]; then
     .ci/setup_headless_display.sh
   fi
 fi
-if ${do_cov}
-then
+if [[ "do_cov" == "true" ]]; then
   echo "Testing with coverage"
   test_args="--cov --cov-config=pyproject.toml $test_args"
 fi
 
 pytest -vv $test_args
 
-if ${do_cov}
-then
+if [[ "do_cov" == "true" ]]; then
   coverage xml
 fi
 

.ci/azure/setup_env.sh

@@ -4,23 +4,31 @@ set -ex #echo on and exit if any line fails
 # TF_BUILD is set to True on azure pipelines.
 is_azure=$(echo "${TF_BUILD:-false}" | tr '[:upper:]' '[:lower:]')
 do_doc=$(echo "${DOC_BUILD:-false}" | tr '[:upper:]' '[:lower:]')
+is_free_threaded=$(echo "${PYTHON_FREETHREADING:-false}" | tr '[:upper:]' '[:lower:]')
+is_rc=$(echo "${PYTHON_RELEASE_CANDIDATE:-false}" | tr '[:upper:]' '[:lower:]')
+is_bare=$(echo "${ENVIRON_BARE:-false}" | tr '[:upper:]' '[:lower:]')
 
-if ${is_azure}
-then
-  if ${do_doc}
-  then
+if [[ "$is_azure" == "true" ]]; then
+  if [[ "$do_doc" == "true" ]]; then
     .ci/setup_headless_display.sh
   fi
 fi
 
-cp .ci/environment_test.yml environment_test_with_pyversion.yml
-echo "  - python="$PYTHON_VERSION >> environment_test_with_pyversion.yml
+if [[ "$is_free_threaded" == "true" || "$is_bare" == "true" ]]; then
+  cp .ci/environment_test_bare.yml environment_test_with_pyversion.yml
+  echo "  - python-freethreading="$PYTHON_VERSION >> environment_test_with_pyversion.yml
+else
+  cp .ci/environment_test.yml environment_test_with_pyversion.yml
+  echo "  - python="$PYTHON_VERSION >> environment_test_with_pyversion.yml
+fi
 
+if [[ "$is_rc" == "true" ]]; then
+  sed -i '/^channels:/a\  - conda-forge/label/python_rc' environment_test_with_pyversion.yml
+fi
 conda env create --file environment_test_with_pyversion.yml
 rm environment_test_with_pyversion.yml
 
-if ${is_azure}
-then
+if [[ "$is_azure" == "true" ]]; then
   source activate discretize-test
   pip install pytest-azurepipelines
 else

.ci/azure/test.yml

@@ -2,22 +2,31 @@ jobs:
 - job:
   strategy:
     matrix:
-      linux-Python310:
-        image: ubuntu-latest
-        python.version: '3.10'
-        coverage: True
       linux-Python311:
         image: ubuntu-latest
         python.version: '3.11'
+        coverage: True
       linux-Python312:
         image: ubuntu-latest
         python.version: '3.12'
       linux-Python313:
         image: ubuntu-latest
         python.version: '3.13'
-      osx-Python310:
-        image: macOS-latest
-        python.version: '3.10'
+      linux-Python313t:
+        image: ubuntu-latest
+        python.version: '3.13'
+        environ.bare: True
+        python.freethreading: True
+        coverage: True
+      linux-Python314:
+        image: ubuntu-latest
+        environ.bare: True
+        python.version: '3.14'
+      linux-Python314t:
+        image: ubuntu-latest
+        python.version: '3.14'
+        environ.bare: True
+        python.freethreading: True
       osx-Python311:
         image: macOS-latest
         python.version: '3.11'
@@ -27,9 +36,19 @@ jobs:
       osx-Python313:
         image: macOS-latest
         python.version: '3.13'
-      win-Python310:
-        image: windows-latest
-        python.version: '3.10'
+      osx-Python313t:
+        image: macOS-latest
+        python.version: '3.13'
+        python.freethreading: True
+      osx-Python314:
+        image: macOS-latest
+        python.version: '3.14'
+        environ.bare: True
+      osx-Python314t:
+        image: macOS-latest
+        python.version: '3.14'
+        environ.bare: True
+        python.freethreading: True
       win-Python311:
         image: windows-latest
         python.version: '3.11'
@@ -39,6 +58,20 @@ jobs:
       win-Python313:
         image: windows-latest
         python.version: '3.13'
+      win-Python313t:
+        image: windows-latest
+        python.version: '3.13'
+        environ.bare: True
+        python.freethreading: True
+      win-Python314:
+        image: windows-latest
+        environ.bare: True
+        python.version: '3.14'
+      win-Python314t:
+        image: windows-latest
+        python.version: '3.14'
+        environ.bare: True
+        python.freethreading: True
   displayName: "${{ variables.image }} ${{ variables.python.version }}"
   pool:
     vmImage: $(image)

.ci/environment_test.yml

@@ -31,5 +31,5 @@ dependencies:
   - meson-python>=0.14.0
   - meson
   - ninja
-  - cython>=0.29.35
+  - cython>=3.1.0
   - setuptools_scm

.ci/environment_test_bare.yml

@@ -0,0 +1,19 @@
+name: discretize-test
+channels:
+  - conda-forge
+dependencies:
+  - numpy>=1.22.4
+  - scipy>=1.12
+
+  # testing
+  - sympy
+  - pytest
+  - pytest-cov
+
+  # Building
+  - pip
+  - meson-python>=0.14.0
+  - meson
+  - ninja
+  - cython>=3.1.0
+  - setuptools_scm

.github/workflows/build_distributions.yml

@@ -8,16 +8,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # macos-13 is an intel runner, macos-14 is apple silicon
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        # macos-15-intel is an Intel runner, macos-14 is Apple silicon
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15-intel, macos-14]
 
     steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
+      - uses: actions/checkout@v5
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21.3
+        uses: pypa/cibuildwheel@v3.2.0
 
       - uses: actions/upload-artifact@v4
         with:

README.rst

@@ -114,7 +114,7 @@ Code:
 https://github.com/simpeg/discretize
 
 Tests:
-https://travis-ci.org/simpeg/discretize
+https://dev.azure.com/simpeg/discretize/_build
 
 Bugs & Issues:
 https://github.com/simpeg/discretize/issues

discretize/_extensions/interputils_cython.pyx

@@ -1,5 +1,6 @@
 # cython: embedsignature=True, language_level=3
 # cython: linetrace=True
+# cython: freethreading_compatible = True
 import numpy as np
 import cython
 cimport numpy as np

discretize/_extensions/simplex_helpers.pyx

@@ -1,6 +1,7 @@
 # distutils: language=c++
 # cython: embedsignature=True, language_level=3
 # cython: linetrace=True
+# cython: freethreading_compatible = True
 
 from libcpp.pair cimport pair
 from libcpp.unordered_map cimport unordered_map

discretize/_extensions/tree.cpp

@@ -418,6 +418,44 @@ void Cell::refine_func(node_map_t& nodes, function test_func, double *xs, double
     }
 }
 
+void Cell::refine_image(node_map_t& nodes, double* image, int_t *shape_cells, double *xs, double*ys, double *zs, bool diag_balance){
+    // early exit if my level is higher than or equal to target
+    if (level == max_level){
+        return;
+    }
+    int_t start_ix = points[0]->location_ind[0]/2;
+    int_t start_iy = points[0]->location_ind[1]/2;
+    int_t start_iz = n_dim == 2 ? 0 : points[0]->location_ind[2]/2;
+    int_t end_ix = points[3]->location_ind[0]/2;
+    int_t end_iy = points[3]->location_ind[1]/2;
+    int_t end_iz = n_dim == 2? 1 : points[7]->location_ind[2]/2;
+    int_t nx = shape_cells[0];
+    int_t ny = shape_cells[1];
+    int_t nz = shape_cells[2];
+
+    int_t i_image = (nx * ny) * start_iz + nx * start_iy + start_ix;
+    double val_start = image[i_image];
+    bool all_unique = true;
+
+    // if any of the image data contained in the cell are different, subdivide myself
+    for(int_t iz=start_iz; iz<end_iz && all_unique; ++iz)
+        for(int_t iy=start_iy; iy<end_iy && all_unique; ++iy)
+            for(int_t ix=start_ix; ix<end_ix && all_unique; ++ix){
+                i_image = (nx * ny) * iz + nx * iy + ix;
+                all_unique = image[i_image] == val_start;
+            }
+
+    if(!all_unique){
+        if(is_leaf()){
+            divide(nodes, xs, ys, zs, true, diag_balance);
+        }
+        // recurse into children
+        for(int_t i = 0; i < (1<<n_dim); ++i){
+            children[i]->refine_image(nodes, image, shape_cells, xs, ys, zs, diag_balance);
+        }
+    }
+}
+
 void Cell::divide(node_map_t& nodes, double* xs, double* ys, double* zs, bool balance, bool diag_balance){
     // Gaurd against dividing a cell that is already at the max level
     if (level == max_level){
@@ -896,6 +934,18 @@ void Tree::refine_function(function test_func, bool diagonal_balance){
                 roots[iz][iy][ix]->refine_func(nodes, test_func, xs, ys, zs, diagonal_balance);
 };
 
+void Tree::refine_image(double *image, bool diagonal_balance){
+    int_t shape_cells[3];
+    shape_cells[0] = nx/2;
+    shape_cells[1] = ny/2;
+    shape_cells[2] = nz/2;
+    for(int_t iz=0; iz<nz_roots; ++iz)
+        for(int_t iy=0; iy<ny_roots; ++iy)
+            for(int_t ix=0; ix<nx_roots; ++ix)
+                roots[iz][iy][ix]->refine_image(nodes, image, shape_cells, xs, ys, zs, diagonal_balance);
+}
+
+
 void Tree::finalize_lists(){
     for(int_t iz=0; iz<nz_roots; ++iz)
         for(int_t iy=0; iy<ny_roots; ++iy)