Deprecates physicsnemo.utils.mesh.py (#1487)

* Adds DeprecationWarning on module.

* Changelog update for deprecations

Author: peterdsharpe

CHANGELOG.md

@@ -25,6 +25,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
+- `physicsnemo.utils.mesh` is deprecated and will be removed in v2.2.0. For
+  isosurface extraction, use `physicsnemo.mesh.generate.marching_cubes` instead
+  of `sdf_to_stl`. For VTP/OBJ/STL file conversion (`combine_vtp_files`,
+  `convert_tesselated_files_in_directory`), use VTK or PyVista directly.
+
 ### Removed
 
 ### Fixed

physicsnemo/core/version_check.py

@@ -193,10 +193,6 @@ def _format_install_hint(
         "scikit-learn",
         direct_install="scikit-learn",
     ),
-    "scikit-image": _format_install_hint(  # To be removed with utils/mesh/
-        "scikit-image",
-        direct_install="scikit-image",
-    ),
     # Data format packages
     "xarray": _format_install_hint(
         "xarray",

physicsnemo/utils/mesh/combine_vtp_files.py

@@ -15,6 +15,7 @@
 # limitations under the License.
 
 import importlib
+import warnings
 from typing import List
 
 from physicsnemo.core.version_check import check_version_spec
@@ -36,6 +37,13 @@ def combine_vtp_files(input_files: List[str], output_file: str) -> None:
         - input_files (list[str]): List of paths to the input VTP files to be combined.
         - output_file (str): Path to save the combined VTP file.
         """
+        warnings.warn(
+            "combine_vtp_files is deprecated and will be removed in v2.2.0. "
+            "Use PyVista instead: "
+            "pyvista.merge([pyvista.read(f) for f in files]).save(output_file)",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         reader = vtkXMLPolyDataReader()
         append = vtkAppendPolyData()
 
@@ -56,6 +64,13 @@ def combine_vtp_files(input_files: List[str], output_file: str) -> None:
 else:
 
     def combine_vtp_files(*args, **kwargs):
+        warnings.warn(
+            "combine_vtp_files is deprecated and will be removed in v2.2.0. "
+            "Use PyVista instead: "
+            "pyvista.merge([pyvista.read(f) for f in files]).save(output_file)",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         raise RuntimeError(
             "combine_vtp_files: VTK is not available, please install vtk with `pip install vtk`"
         )

physicsnemo/utils/mesh/convert_file_formats.py

@@ -16,6 +16,7 @@
 
 import importlib
 import os
+import warnings
 
 from physicsnemo.core.version_check import check_version_spec
 
@@ -74,6 +75,14 @@ def convert_tesselated_files_in_directory(conversion_type, input_dir, output_dir
         - input_dir (str): Path to the directory containing input files.
         - output_dir (str): Path to the directory to save the converted files.
         """
+        warnings.warn(
+            "convert_tesselated_files_in_directory is deprecated and will be "
+            "removed in v2.2.0. Use PyVista for format conversion: "
+            "pyvista.read(input_file).save(output_file) supports OBJ, VTP, "
+            "and STL formats.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
 
         if conversion_type == "obj2vtp":
             src_ext = ".obj"
@@ -113,4 +122,12 @@ def convert_vtp_to_stl(*args, **kwargs):
         raise_vtk_not_available()
 
     def convert_tesselated_files_in_directory(*args, **kwargs):
+        warnings.warn(
+            "convert_tesselated_files_in_directory is deprecated and will be "
+            "removed in v2.2.0. Use PyVista for format conversion: "
+            "pyvista.read(input_file).save(output_file) supports OBJ, VTP, "
+            "and STL formats.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         raise_vtk_not_available()

physicsnemo/utils/mesh/generate_stl.py

@@ -17,6 +17,7 @@
 # ruff: noqa: F401
 
 import importlib
+import warnings
 
 import numpy as np
 import warp as wp
@@ -52,6 +53,14 @@ def sdf_to_stl(
         filename : str, optional
             Filename for output stl file, by default "output_stl.stl"
         """
+        warnings.warn(
+            "sdf_to_stl is deprecated and will be removed in v2.2.0. "
+            "Use physicsnemo.mesh.generate.marching_cubes instead, which "
+            "returns a Mesh object. To save as STL: "
+            "marching_cubes(field).to_pyvista().save('output.stl')",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         if backend == "warp":
             # Warp MarchingCubes.surface() requires wp.float32; coerce if caller passed float64
             field = np.asarray(field, dtype=np.float32)
@@ -98,6 +107,14 @@ def sdf_to_stl(
 else:
 
     def sdf_to_stl(*args, **kwargs):
+        warnings.warn(
+            "sdf_to_stl is deprecated and will be removed in v2.2.0. "
+            "Use physicsnemo.mesh.generate.marching_cubes instead, which "
+            "returns a Mesh object. To save as STL: "
+            "marching_cubes(field).to_pyvista().save('output.stl')",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         raise RuntimeError(
             "STL is not available, please install stl with `pip install stl`"
         )

test/utils/test_mesh_utils.py

@@ -49,6 +49,7 @@ def sphere_stl(tmp_path):
 
 
 @requires_module(["vtk", "warp", "stl"])
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_mesh_utils(tmp_path, pytestconfig):
     """Tests the utility for combining VTP files and converting tesselated files."""
 
@@ -184,6 +185,7 @@ def _create_random_obj_mesh(num_vertices: int, num_faces: int, dir: str) -> None
 
 @requires_module(["warp", "skimage", "stl", "pyvista"])
 @pytest.mark.parametrize("backend", ["warp", "skimage"])
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_stl_gen(pytestconfig, backend, sphere_stl, tmp_path):
     from stl import mesh