Merge pull request #55 from zasexton/main

fixing reported telemetry issues and [accel] extra uploads

Author: zasexton

.github/workflows/test-upload.yml

@@ -106,15 +106,15 @@ jobs:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD_SVV }}
       - name: Validate TestPyPI token (svv-accelerated)
-        if: ${{ hashFiles('dist/svv-accelerated-*.whl') != '' }}
+        if: ${{ hashFiles('dist/svv_accelerated-*.whl') != '' }}
         run: |
           if [ -z "${{ secrets.TEST_PYPI_PASSWORD_ACCEL }}" ]; then
             echo "::error title=Missing secret::The repository secret 'TEST_PYPI_PASSWORD_ACCEL' is not configured. Set it to a TestPyPI API token with access to the 'svv-accelerated' project.";
             exit 1;
           fi
       - name: Upload accelerated wheels (svv-accelerated) to TestPyPI
-        if: ${{ hashFiles('dist/svv-accelerated-*.whl') != '' }}
-        run: twine upload --non-interactive --skip-existing --verbose --repository testpypi dist/svv-accelerated-*.whl
+        if: ${{ hashFiles('dist/svv_accelerated-*.whl') != '' }}
+        run: twine upload --non-interactive --skip-existing --verbose --repository testpypi dist/svv_accelerated-*.whl
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD_ACCEL }}

.github/workflows/upload.yml

@@ -117,7 +117,8 @@ jobs:
       - name: Upload accelerated wheels (svv-accelerated) to PyPI
         run: |
           set -euo pipefail
-          files=$(ls dist/svv-accelerated-*.whl 2>/dev/null || true)
+          # Wheel filenames normalize '-' to '_' (PEP 427), e.g. svv_accelerated-0.0.42-...
+          files=$(ls dist/svv[-_]accelerated-*.whl 2>/dev/null || true)
           if [ -z "$files" ]; then
             echo "No svv-accelerated artifacts found; skipping upload."
             exit 0
@@ -159,4 +160,5 @@ jobs:
           files: |
             dist/svv-*.whl
             dist/svv-*.tar.gz
+            dist/svv_accelerated-*.whl
             dist/svv-accelerated-*.whl

MANIFEST.in

@@ -5,6 +5,7 @@ include README.md
 recursive-include svv/utils/spatial *.pyx
 recursive-include svv/tree/utils *.pyx
 recursive-include svv/domain/routines *.pyx
+recursive-include svv/simulation/utils *.pyx
 
 # Include all remesher executables
 include svv/utils/remeshing/Linux/mmg2d_O3
@@ -20,5 +21,8 @@ include svv/utils/remeshing/Windows/mmg2d_O3.exe
 include svv/utils/remeshing/Windows/mmg3d_O3.exe
 include svv/utils/remeshing/Windows/mmgs_O3.exe
 
+# Include GUI assets (theme tokens, icons, etc.)
+recursive-include svv/visualize/gui *.json *.qss *.png *.svg
+
 # Exclude any compiled extension artifacts from source distribution
 global-exclude *.so *.pyd *.dylib *.dll

pyproject.toml

@@ -1,7 +1,7 @@
 [build-system]
 requires = [
   "setuptools>=45.0",
-  "wheel>=0.36; python_version < '3.12' ",
+  "wheel>=0.36",
   # Ensure PEP 517 build environments have the headers/tools needed to compile extensions
   "Cython>=3.0.7",
   "numpy>=1.24; python_version < '3.12'",

setup.py

@@ -612,7 +612,19 @@ def parse_requirements(path="requirements.txt"):
     long_description=DESCRIPTION,
     long_description_content_type="text/markdown",
     ext_modules=cythonize(extensions) if (extensions and HAS_CYTHON) else [],
-    package_data=( {'svv.bin': ['*']} if not ACCEL_COMPANION else {} ),
+    package_data=(
+        {
+            'svv.bin': ['*'],
+            'svv.visualize.gui': [
+                'design_tokens.json',
+                'theme.qss',
+                'svIcon.png',
+                'icons/*.svg',
+            ],
+        }
+        if not ACCEL_COMPANION
+        else {}
+    ),
     exclude_package_data=(
         {"svv": ["*.so", "*.pyd", "*.dylib", "*.dll"]} if not ACCEL_COMPANION else {}
     ),

svv/domain/domain.py

@@ -92,10 +92,20 @@ def save(self, path, include_boundary=False, include_mesh=False, include_patch_n
           boundary/mesh. Ensure `create()`, `solve()`, and `build()` have run so
           these arrays exist; otherwise save() will raise an error.
         - Boundary and mesh persistence are optional to keep files compact.
+
+        Returns
+        -------
+        str
+            The path written to (with the ``.dmn`` extension enforced).
         """
         from svv.domain.io.dmn import write_dmn
-        write_dmn(self, path, include_boundary=include_boundary, include_mesh=include_mesh,
-                  include_patch_normals=include_patch_normals)
+        return write_dmn(
+            self,
+            path,
+            include_boundary=include_boundary,
+            include_mesh=include_mesh,
+            include_patch_normals=include_patch_normals,
+        )
 
     @classmethod
     def load(cls, path):

svv/domain/io/dmn.py

@@ -1,6 +1,6 @@
 import os
 import json
-from typing import Optional
+from typing import Optional, Union
 
 import numpy as np
 from scipy.spatial import cKDTree
@@ -14,10 +14,30 @@
 DMN_FORMAT = "svv.domain/1.0"
 
 
-def _ensure_ext(path: str) -> str:
-    if not path.lower().endswith(".dmn"):
-        return path + ".dmn"
-    return path
+def ensure_dmn_path(path: Union[str, os.PathLike]) -> str:
+    """
+    Normalize an output path for .dmn persistence.
+
+    - Accepts ``str`` or ``PathLike`` objects.
+    - Ensures the returned path ends with a lowercase ``.dmn`` extension.
+    - Collapses legacy ``.dmn.npz`` filenames (from NumPy ``savez`` behavior)
+      to ``.dmn``.
+    """
+    path_str = os.fsdecode(os.fspath(path))
+    lower = path_str.lower()
+
+    # Legacy: np.savez_compressed("name.dmn", ...) writes "name.dmn.npz"
+    if lower.endswith(".npz") and lower[:-4].endswith(".dmn"):
+        path_str = path_str[:-4]
+        lower = lower[:-4]
+
+    if lower.endswith(".dmn"):
+        return path_str[:-4] + ".dmn"
+    return path_str + ".dmn"
+
+
+def _ensure_ext(path: Union[str, os.PathLike]) -> str:
+    return ensure_dmn_path(path)
 
 
 def _compute_firsts_from_pts(PTS: np.ndarray) -> np.ndarray:
@@ -39,8 +59,8 @@ def _compute_firsts_from_pts(PTS: np.ndarray) -> np.ndarray:
     return firsts
 
 
-def write_dmn(domain, path: str, include_boundary: bool = False, include_mesh: bool = False,
-              include_patch_normals: bool = True) -> None:
+def write_dmn(domain, path: Union[str, os.PathLike], include_boundary: bool = False, include_mesh: bool = False,
+              include_patch_normals: bool = True) -> str:
     """
     Serialize a Domain instance into a .dmn file.
 
@@ -188,9 +208,33 @@ def write_dmn(domain, path: str, include_boundary: bool = False, include_mesh: b
     # Use a file handle to avoid NumPy forcing a .npz extension
     with open(out_path, "wb") as fh:
         np.savez_compressed(fh, **arrays)
+    return out_path
+
+
+def resolve_dmn_read_path(path: Union[str, os.PathLike]) -> str:
+    """
+    Resolve a path for reading a Domain from disk.
+
+    Accepts filenames both with and without the ``.dmn`` suffix. Also attempts
+    to load legacy ``.dmn.npz`` files created by passing a ``.dmn`` filename
+    directly to NumPy ``savez`` routines.
+    """
+    path_str = os.fsdecode(os.fspath(path))
+    if os.path.isfile(path_str):
+        return path_str
+
+    candidate = ensure_dmn_path(path_str)
+    if os.path.isfile(candidate):
+        return candidate
+
+    legacy_candidate = candidate + ".npz"
+    if os.path.isfile(legacy_candidate):
+        return legacy_candidate
+
+    return candidate
 
 
-def read_dmn(path: str):
+def read_dmn(path: Union[str, os.PathLike]):
     """
     Deserialize a Domain from a .dmn file.
 
@@ -213,7 +257,7 @@ def read_dmn(path: str):
     from svv.domain.domain import Domain
     from svv.domain.patch import Patch
 
-    file_path = _ensure_ext(path)
+    file_path = resolve_dmn_read_path(path)
     data = np.load(file_path, allow_pickle=False)
 
     # Parse metadata

svv/domain/io/read.py

@@ -7,8 +7,9 @@ def read(data, **kwargs):
     Read and process mesh data. Supports PyVista objects and file paths to mesh files.
 
     Parameters:
-        data: pyvista.PolyData or str
+        data: pyvista.PolyData, pyvista.UnstructuredGrid, or str
             Input mesh data as a PyVista object or a file path to a supported mesh file.
+            For UnstructuredGrid objects (e.g., from .vtu files), the surface is extracted.
         **kwargs:
             feature_angle: float
                 Angle used to determine sharp edges for normal computation.
@@ -29,8 +30,12 @@ def read(data, **kwargs):
     if isinstance(data, str):
         data = pyvista.read(data)
 
+    # Handle UnstructuredGrid by extracting surface (e.g., from .vtu files)
+    if isinstance(data, pyvista.UnstructuredGrid):
+        data = data.extract_surface()
+
     if not isinstance(data, pyvista.PolyData):
-        raise TypeError("Input data must be a PyVista PolyData object or a valid file path.")
+        raise TypeError("Input data must be a PyVista PolyData, UnstructuredGrid, or a valid file path.")
 
     data = data.compute_normals(split_vertices=True, feature_angle=feature_angle)
 

svv/tree/branch/root.py

@@ -139,18 +139,30 @@ def set_root(tree, **kwargs):
                         lower = set(tree.domain.mesh_tree.query_ball_point(_start, threshold)[0])
                         cells = list(upper.difference(lower))
                         if tree.domain.points.shape[1] == 2:
-                            cells = tree.domain.random_generator.choice(cells, min(attempts, len(cells)),
-                                                                        p=(tree.domain.mesh['Area'][cells] /
-                                                                           tree.domain.mesh['Area'][cells].sum()),
+                            areas = tree.domain.mesh['Area'][cells]
+                            valid_mask = areas > 0
+                            if not numpy.any(valid_mask):
+                                count += 1
+                                continue
+                            valid_indices = numpy.array(cells)[valid_mask]
+                            valid_areas = areas[valid_mask]
+                            p = valid_areas / valid_areas.sum()
+                            p = p / p.sum()  # Ensure exact sum of 1.0 for numerical stability
+                            cells = tree.domain.random_generator.choice(valid_indices, min(attempts, len(valid_indices)),
+                                                                        p=p,
                                                                         replace=False)
                         elif tree.domain.points.shape[1] == 3:
-                            print("Cells: ", cells)
-                            print("Mesh Volume: ", tree.domain.mesh['Volume'][cells])
-                            print("Mesh Volume Sum: ", tree.domain.mesh['Volume'][cells].sum())
-                            print("Mesh Volume Fraction: ", tree.domain.mesh['Volume'][cells] / tree.domain.mesh['Volume'][cells].sum())
-                            cells = tree.domain.random_generator.choice(cells, min(attempts, len(cells)),
-                                                                        p=(tree.domain.mesh['Volume'][cells] /
-                                                                           tree.domain.mesh['Volume'][cells].sum()),
+                            volumes = tree.domain.mesh['Volume'][cells]
+                            valid_mask = volumes > 0
+                            if not numpy.any(valid_mask):
+                                count += 1
+                                continue
+                            valid_indices = numpy.array(cells)[valid_mask]
+                            valid_volumes = volumes[valid_mask]
+                            p = valid_volumes / valid_volumes.sum()
+                            p = p / p.sum()  # Ensure exact sum of 1.0 for numerical stability
+                            cells = tree.domain.random_generator.choice(valid_indices, min(attempts, len(valid_indices)),
+                                                                        p=p,
                                                                         replace=False)
                         else:
                             raise ValueError("Only 2D and 3D domains are supported.")