Py: Fix tests, fix bugs

Author: w1th0utnam3

pysplashsurf/README.md

@@ -48,6 +48,7 @@ import pysplashsurf
 # Load particles from mesh file
 mesh = meshio.read("input.vtk")
 particles = np.array(mesh.points, dtype=np.float64)
+
 # Reconstruct the points/particles with some post-processing
 mesh_with_data, reconstruction = pysplashsurf.reconstruction_pipeline(
     particles,
@@ -66,7 +67,8 @@ mesh_with_data, reconstruction = pysplashsurf.reconstruction_pipeline(
     subdomain_num_cubes_per_dim=64,
     output_mesh_smoothing_weights=True
 )
-# Write the mesh with attributes to a file using meshio
+
+# Write the mesh with attributes to file using meshio
 mesh_with_data.write_to_file("surface.vtk")
 ```
 The `reconstruction_pipeline` method provides (mostly) the same arguments as the splashsurf binary CLI.

pysplashsurf/pysplashsurf/pysplashsurf.pyi

@@ -6,6 +6,8 @@ from __future__ import annotations
 import builtins
 import numpy
 import numpy.typing
+import os
+import pathlib
 import typing
 from enum import Enum
 
@@ -112,9 +114,9 @@ class MeshWithData:
         
         There has to be exactly one attribute value per vertex in the mesh.
         As attribute data, the following numpy array types are supported:
-         - 1D array with shape (N,) of `np.uint64`
-         - 1D array with shape (N,) of the mesh scalar type (`np.float32` or `np.float64`)
-         - 2D array with shape (N,3) of the mesh scalar type (`np.float32` or `np.float64`)
+         - 1D array with shape (N,) of ``np.uint64``
+         - 1D array with shape (N,) of the mesh scalar type (``np.float32`` or ``np.float64``)
+         - 2D array with shape (N,3) of the mesh scalar type (``np.float32`` or ``np.float64``)
         The data is copied into the mesh object.
         """
     def add_cell_attribute(self, name:builtins.str, attribute:numpy.typing.NDArray[typing.Any]) -> None:
@@ -123,12 +125,12 @@ class MeshWithData:
         
         There has to be exactly one attribute value per cell in the mesh.
         As attribute data, the following numpy array types are supported:
-         - 1D array with shape (N,) of `np.uint64`
-         - 1D array with shape (N,) of the mesh scalar type (`np.float32` or `np.float64`)
-         - 2D array with shape (N,3) of the mesh scalar type (`np.float32` or `np.float64`)
+         - 1D array with shape (N,) of ``np.uint64``
+         - 1D array with shape (N,) of the mesh scalar type (``np.float32`` or ``np.float64``)
+         - 2D array with shape (N,3) of the mesh scalar type (``np.float32`` or ``np.float64``)
         The data is copied into the mesh object.
         """
-    def write_to_file(self, path:builtins.str, *, file_format:typing.Optional[builtins.str]='vtk42') -> None:
+    def write_to_file(self, path:builtins.str | os.PathLike | pathlib.Path, *, file_format:typing.Optional[builtins.str]='vtk42') -> None:
         r"""
         Writes the mesh and its attributes to a file using `meshio.write_points_cells`
         """
@@ -159,7 +161,7 @@ class MixedTriQuadMesh3d:
         r"""
         Returns a copy of all quad cells of the mesh as an `Nx4` array of vertex indices
         """
-    def write_to_file(self, path:builtins.str, *, file_format:typing.Optional[builtins.str]='vtk42') -> None:
+    def write_to_file(self, path:builtins.str | os.PathLike | pathlib.Path, *, file_format:typing.Optional[builtins.str]='vtk42') -> None:
         r"""
         Writes the mesh to a file using `meshio.write_points_cells`
         """
@@ -259,7 +261,7 @@ class TriMesh3d:
         r"""
         Computes the vertex-vertex connectivity of the mesh
         """
-    def write_to_file(self, path:builtins.str, *, file_format:typing.Optional[builtins.str]='vtk42') -> None:
+    def write_to_file(self, path:builtins.str | os.PathLike | pathlib.Path, *, file_format:typing.Optional[builtins.str]='vtk42') -> None:
         r"""
         Writes the mesh to a file using `meshio.write_points_cells`
         """

pysplashsurf/src/aabb.rs

@@ -38,7 +38,7 @@ impl PyAabb3d {
         points: &Bound<'py, PyArray2<R>>,
     ) -> PyResult<Self> {
         let points = points.try_readonly()?;
-        let points_vec: &[Vector3<f32>] = bytemuck::cast_slice(points.as_slice()?);
+        let points_vec: &[Vector3<R>] = bytemuck::cast_slice(points.as_slice()?);
         Ok(Self::from(Aabb3d::par_from_points(points_vec)))
     }
 }

pysplashsurf/src/mesh.rs

@@ -1,3 +1,6 @@
+use crate::NumpyUsize;
+use crate::utils;
+use crate::utils::{enum_impl_from, enum_wrapper_impl_from};
 use bytemuck::{NoUninit, Pod};
 use ndarray::Array2;
 use numpy as np;
@@ -6,7 +9,7 @@ use numpy::{Element, PyArray, PyArray1, PyArray2, PyArrayDescr, PyUntypedArray};
 use pyo3::IntoPyObjectExt;
 use pyo3::exceptions::{PyTypeError, PyValueError};
 use pyo3::prelude::*;
-use pyo3::types::{IntoPyDict, PyDict, PyTuple};
+use pyo3::types::{IntoPyDict, PyDict};
 use pyo3_stub_gen::derive::*;
 use splashsurf_lib::mesh::TriangleCell;
 use splashsurf_lib::{
@@ -18,10 +21,7 @@ use splashsurf_lib::{
     nalgebra::{Unit, Vector3},
 };
 use std::ops::Deref;
-
-use crate::NumpyUsize;
-use crate::utils;
-use crate::utils::{enum_impl_from, enum_wrapper_impl_from};
+use std::path::PathBuf;
 
 fn view_triangles_generic<'py>(
     triangles: &[TriangleCell],
@@ -209,7 +209,7 @@ impl PyTriMesh3d {
     #[pyo3(signature = (path, *, file_format = Some("vtk42")))]
     pub fn write_to_file<'py>(
         this: Bound<'py, Self>,
-        path: &str,
+        path: PathBuf,
         file_format: Option<&str>,
     ) -> PyResult<()> {
         let py = this.py();
@@ -308,7 +308,7 @@ impl PyMixedTriQuadMesh3d {
     #[pyo3(signature = (path, *, file_format = Some("vtk42")))]
     pub fn write_to_file<'py>(
         this: Bound<'py, Self>,
-        path: &str,
+        path: PathBuf,
         file_format: Option<&str>,
     ) -> PyResult<()> {
         let py = this.py();
@@ -727,9 +727,9 @@ impl PyMeshWithData {
     ///
     /// There has to be exactly one attribute value per vertex in the mesh.
     /// As attribute data, the following numpy array types are supported:
-    ///  - 1D array with shape (N,) of `np.uint64`
-    ///  - 1D array with shape (N,) of the mesh scalar type (`np.float32` or `np.float64`)
-    ///  - 2D array with shape (N,3) of the mesh scalar type (`np.float32` or `np.float64`)
+    ///  - 1D array with shape (N,) of ``np.uint64``
+    ///  - 1D array with shape (N,) of the mesh scalar type (``np.float32`` or ``np.float64``)
+    ///  - 2D array with shape (N,3) of the mesh scalar type (``np.float32`` or ``np.float64``)
     /// The data is copied into the mesh object.
     pub fn add_point_attribute<'py>(
         &mut self,
@@ -763,9 +763,9 @@ impl PyMeshWithData {
     ///
     /// There has to be exactly one attribute value per cell in the mesh.
     /// As attribute data, the following numpy array types are supported:
-    ///  - 1D array with shape (N,) of `np.uint64`
-    ///  - 1D array with shape (N,) of the mesh scalar type (`np.float32` or `np.float64`)
-    ///  - 2D array with shape (N,3) of the mesh scalar type (`np.float32` or `np.float64`)
+    ///  - 1D array with shape (N,) of ``np.uint64``
+    ///  - 1D array with shape (N,) of the mesh scalar type (``np.float32`` or ``np.float64``)
+    ///  - 2D array with shape (N,3) of the mesh scalar type (``np.float32`` or ``np.float64``)
     /// The data is copied into the mesh object.
     pub fn add_cell_attribute<'py>(
         &mut self,
@@ -799,7 +799,7 @@ impl PyMeshWithData {
     #[pyo3(signature = (path, *, file_format = Some("vtk42")))]
     pub fn write_to_file<'py>(
         this: Bound<'py, Self>,
-        path: &str,
+        path: PathBuf,
         file_format: Option<&str>,
     ) -> PyResult<()> {
         let py = this.py();