fullwave25 1.2.6.dev2__tar.gz → 1.2.6.dev3__tar.gz

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "1.2.6-dev2"
+current_version = "1.2.6-dev3"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
         args: ["--maxkb=10000"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.11.0
+    rev: v0.15.2
     hooks:
       # Run the linter.
       - id: ruff

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fullwave25
-Version: 1.2.6.dev2
+Version: 1.2.6.dev3
 Summary: Fullwave 2.5: Ultrasound wave propagation simulation with heterogeneous power law attenuation modelling capabilities
 Author: Masashi Sode, Gianmarco Pinton
 Maintainer: Masashi Sode

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/__init__.py

@@ -60,7 +60,7 @@ try:
     __version__ = version("fullwave")
 except PackageNotFoundError:
     # Update via bump-my-version, not manually
-    __version__ = "1.2.6-dev2"
+    __version__ = "1.2.6-dev3"
 
 VERSION = __version__  # for convenience
 logger.info("Fullwave version: %s", __version__)

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/beamformer/beamformer.py

@@ -14,7 +14,8 @@ class Beamformer:
     For faster implementations, consider using libraries such as
     mach beamformer: https://github.com/Forest-Neurotech/mach
 
-    References:
+    References
+    ----------
     - Fullwave2 BMME890 implementation
     - https://github.com/gfpinton/fullwave_bmme890/blob/master/fullwave2_launcher_imaging_planewave.m
 

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/medium.py

@@ -231,7 +231,8 @@ class MediumRelaxationMaps:
     ) -> None:
         """Check if the relaxation parameter updates have valid keys and matching shapes.
 
-        Raises:
+        Raises
+        ------
             ValueError: If the keys do not match the desired keys or
             if the shapes of the values do not match the domain shape.
 
@@ -1147,11 +1148,13 @@ class Medium:
         it uses the relaxation parameters look up table
         to generate the relaxation parameters.
 
-        Returns:
+        Returns
+        -------
             MediumRelaxationMaps: An instance of MediumRelaxationMaps
             built from the retrieved relaxation parameters.
 
-        Raises:
+        Raises
+        ------
             ValueError: If an unknown attenuation_builder is specified.
 
         """
@@ -1216,7 +1219,8 @@ class Medium:
     def build_exponential(self) -> MediumExponentialAttenuation:
         """Build MediumExponentialAttenuation from alpha and power maps.
 
-        Returns:
+        Returns
+        -------
             MediumExponentialAttenuation: An instance of MediumExponentialAttenuation
             built from the alpha and power maps.
 

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/sensor.py

@@ -21,7 +21,7 @@ class Sensor:
     outcoords: NDArray[np.int64]
     sampling_modulus_time: int = 1
 
-    def __init__(  # noqa: PLR0915
+    def __init__(
         self,
         mask: NDArray[np.bool] | None = None,
         sampling_modulus_time: int = 1,
@@ -189,7 +189,8 @@ class Sensor:
     ) -> None:
         """Plot the transducer mask, optionally exporting and displaying the figure.
 
-        Raises:
+        Raises
+        ------
             ValueError: If the sensor is 3D because plotting is not supported.
 
         """

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/solver/cuda_utils.py

@@ -113,7 +113,8 @@ def cuda_api_call(func: Callable) -> Callable:
     Decorator for CUDA API calls
     Raises RuntimeError if the CUDA call does not return CUDA_SUCCESS.
 
-    Returns:
+    Returns
+    -------
         Callable: The wrapped function that checks CUDA API call results.
 
     """
@@ -138,7 +139,8 @@ def cuda_api_call_warn(func: Callable) -> Callable:
 
     Prints a warning message if the CUDA call does not return CUDA_SUCCESS.
 
-    Returns:
+    Returns
+    -------
         Callable: The wrapped function that checks CUDA API call results.
 
     """
@@ -230,7 +232,8 @@ def get_cuda_device_specs() -> list[dict[str, Any]]:
         'cuda_cores': int
     }
 
-    Returns:
+    Returns
+    -------
         A list of dictionaries containing specifications for each CUDA device.
 
     """
@@ -325,7 +328,8 @@ def get_cuda_architecture() -> list[dict[str, Any]]:
         'architecture': str,
     }
 
-    Returns:
+    Returns
+    -------
         A list of dictionaries containing architecture information for each CUDA device.
 
     """
@@ -363,7 +367,8 @@ def get_cuda_architecture() -> list[dict[str, Any]]:
 def retrieve_cuda_version() -> float:
     """Retrieve the CUDA driver version.
 
-    Returns:
+    Returns
+    -------
         str: CUDA version in the format "major.minor" or "unknown" if retrieval fails.
 
     """

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/solver/pml_builder.py

@@ -115,7 +115,7 @@ class PMLBuilder:
     pml_mask_x: NDArray[np.float64] = field(init=False)
     pml_mask_y: NDArray[np.float64] = field(init=False)
 
-    def __init__(  # noqa: PLR0915
+    def __init__(
         self,
         grid: fullwave.Grid,
         medium: fullwave.Medium,
@@ -898,7 +898,7 @@ class PMLBuilder:
 
         return extended_medium
 
-    def _apply_pml_3d(  # noqa: PLR0915
+    def _apply_pml_3d(
         self,
         extended_medium: fullwave.MediumRelaxationMaps,
         theoritical_reflection_coefficient: float,
@@ -1184,7 +1184,7 @@ class PMLBuilder:
 
         return extended_medium
 
-    def _apply_transition_and_pml(  # noqa: C901, PLR0912, PLR0915
+    def _apply_transition_and_pml(  # noqa: PLR0912
         self,
         input_array: NDArray[np.float64],
         value_target: float,
@@ -1465,7 +1465,7 @@ class PMLBuilder:
 class PMLBuilderExponentialAttenuation(PMLBuilder):
     """A class to set up PML for exponential attenuation media."""
 
-    def __init__(  # noqa: PLR0915
+    def __init__(
         self,
         grid: fullwave.Grid,
         medium: fullwave.Medium,

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/solver/solver.py

@@ -309,7 +309,7 @@ class Solver:
     generates the required input files, and runs the simulation executable.
     """
 
-    def __init__(  # noqa: PLR0912, PLR0915, C901
+    def __init__(  # noqa: PLR0912
         self,
         work_dir: Path,
         grid: fullwave.Grid,

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/solver/utils.py

@@ -17,10 +17,12 @@ def load_dat_data(dat_file_path: Path, dtype: DTypeLike = np.float32) -> NDArray
         dat_file_path (Path): Path to the .dat file.
         dtype: Data type to use when reading the file.
 
-    Raises:
+    Raises
+    ------
         ValueError: if dat_file_path does not exist.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.float64]: Array of data read from the file.
 
     """
@@ -58,7 +60,8 @@ def load_dat_and_reshape(
         n_sensors: Number of sensors
         dtype: Data type to use when reading the file.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.float64]: Array of data read from the file.
 
     """
@@ -88,7 +91,8 @@ def initialize_relaxation_param_dict(
 ) -> dict[str, NDArray[np.float64]]:
     """Initialize a dictionary with relaxation parameters.
 
-    Returns:
+    Returns
+    -------
         dict[str, NDArray[np.float64]]: Dictionary of relaxation parameters.
 
     """
@@ -125,10 +129,12 @@ def load_data_with_time_step(
         dtype: Data type to use when reading the file.
         time_step: Time step index to load.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.float64]: Array of data read from the file.
 
-    Raises:
+    Raises
+    ------
         ValueError: if file_path does not exist.
 
     """
@@ -159,10 +165,12 @@ def load_data_with_sensor_index(
         sensor_index: Sensor index to load.
         dtype: Data type to use when reading the file.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.float64]: Array of data read from the file.
 
-    Raises:
+    Raises
+    ------
         ValueError: if file_path does not exist.
 
     """

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/source.py

@@ -30,7 +30,7 @@ class Source:
     w0: NDArray[np.float64] | None = None
     incoords_w: NDArray[np.int64] | None = None
 
-    def __init__(  # noqa: C901 PLR0912 PLR0915
+    def __init__(  # noqa: PLR0912
         self,
         p0: NDArray[np.float64] | None = None,
         mask: NDArray[np.bool] | None = None,

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/transducer.py

@@ -22,7 +22,8 @@ logger = logging.getLogger("__main__." + __name__)
 def _make_pos_int(val: float | tuple[float] | tuple[int]) -> NDArray[np.int64]:
     """Force value to be a positive integer.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.int64]: Array with positive integers.
 
     """
@@ -202,7 +203,7 @@ class TransducerGeometry:
         ) = self._create_element_coords()
         logger.debug("TransducerGeometry instance created.")
 
-    def _init_dimensions(  # noqa: C901, PLR0912
+    def _init_dimensions(  # noqa: PLR0912
         self,
         grid: Grid,
         element_width_px: int | None,
@@ -313,7 +314,7 @@ class TransducerGeometry:
             assert len(position_m) == 3, "position_m must have 3 elements for 3D transducer"
         return position_px, position_m
 
-    def _create_element_coords(  # noqa: PLR0912, PLR0915
+    def _create_element_coords(  # noqa: PLR0912
         self,
     ) -> tuple[NDArray[np.int64], NDArray[np.int64], NDArray[np.int64], NDArray[np.int64]]:
         """Build flat coordinate arrays for source and sensor pixels.
@@ -813,15 +814,15 @@ class Transducer:
     def source_coords(self) -> NDArray[np.int64]:
         """Coordinates of active source pixels; shape [N_src, ndim]."""
         active_ids = np.where(self.active_source_elements)[0] + 1
-        mask = np.isin(self.transducer_geometry._source_ids, active_ids)  # noqa: SLF001
-        return self.transducer_geometry._source_coords[mask]  # noqa: SLF001
+        mask = np.isin(self.transducer_geometry._source_ids, active_ids)
+        return self.transducer_geometry._source_coords[mask]
 
     @property
     def sensor_coords(self) -> NDArray[np.int64]:
         """Coordinates of active sensor pixels; shape [N_snsr, ndim]."""
         active_ids = np.where(self.active_sensor_elements)[0] + 1
-        mask = np.isin(self.transducer_geometry._sensor_ids, active_ids)  # noqa: SLF001
-        return self.transducer_geometry._sensor_coords[mask]  # noqa: SLF001
+        mask = np.isin(self.transducer_geometry._sensor_ids, active_ids)
+        return self.transducer_geometry._sensor_coords[mask]
 
     @property
     def element_id_to_element_surface(self) -> dict[int, NDArray[np.int64]]:
@@ -986,8 +987,8 @@ class Transducer:
     @property
     def element_id_to_element_center(self) -> dict[int, NDArray[np.int64]]:
         """Return the dictionary mapping element IDs to their center coordinates."""
-        coords = self.transducer_geometry._source_coords  # noqa: SLF001
-        ids = self.transducer_geometry._source_ids  # noqa: SLF001
+        coords = self.transducer_geometry._source_coords
+        ids = self.transducer_geometry._source_ids
         n = self.transducer_geometry.number_elements
         ndim = coords.shape[1] if len(coords) else (3 if self.is_3d else 2)
         out: dict[int, NDArray[np.int64]] = {}
@@ -1049,7 +1050,7 @@ class Transducer:
 
         it plots whole transducer geometry including the inactive/active source and sensor elements.
         """
-        import matplotlib.pyplot as plt
+        import matplotlib.pyplot as plt  # noqa: PLC0415
 
         fig, ax = plt.subplots(1, 1, figsize=(10, 10))
         plot_mask = np.zeros(self.transducer_geometry.stored_grid_size)
@@ -1089,7 +1090,7 @@ class Transducer:
 
         it plots whole transducer geometry including the inactive/active source and sensor elements.
         """
-        import matplotlib.pyplot as plt
+        import matplotlib.pyplot as plt  # noqa: PLC0415
 
         fig, ax = plt.subplots(1, 1, figsize=(10, 10))
         plot_mask = np.zeros(self.transducer_geometry.stored_grid_size)

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/utils/check_functions.py

@@ -7,7 +7,8 @@ from typing import Any
 def check_instance(target_var: Any, instances: list[Any] | Any) -> None:  # noqa: ANN401
     """Check whether target_var is an instance of the specified type.
 
-    Raises:
+    Raises
+    ------
         TypeError: If target_var is not an instance of instance.
 
     """
@@ -21,7 +22,8 @@ def check_instance(target_var: Any, instances: list[Any] | Any) -> None:  # noqa
 def check_path_exists(target_path: Path) -> None:
     """Check whether the provided target_path exists.
 
-    Raises:
+    Raises
+    ------
         ValueError: If target_path does not exist.
 
     """
@@ -37,7 +39,8 @@ def check_compatible_value(
 ) -> None:
     """Check whether the provided value is in the list of compatible values.
 
-    Raises:
+    Raises
+    ------
         ValueError: If value is not in compatible_values.
 
     """

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/utils/coordinates.py

@@ -16,7 +16,8 @@ def make_circle_idx(
         cen: The center of the circle.
         rad: The radius of the circle.
 
-    Returns:
+    Returns
+    -------
         mask: The mask of the circle.
 
     """
@@ -32,7 +33,8 @@ def map_to_coords(
 ) -> NDArray[np.int64]:
     """Map the mask map to coordinates.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.int64]: An array of coordinates corresponding to non-zero elements in the mask.
 
     """
@@ -103,7 +105,8 @@ def map_to_coords_with_sort(map_data: NDArray[np.int64]) -> NDArray[np.int64]:
     Args:
         map_data: The mask map.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.int64]: An array of coordinates corresponding to non-zero elements in the mask.
 
     """
@@ -124,7 +127,8 @@ def map_to_coordinates(
         is_3d: Whether the grid is 3D or not.
         sort: Whether to sort the coordinates by the first dimension.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.int64]: An array of coordinates corresponding to non-zero elements in the mask.
 
     """

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/utils/memory_tempfile.py

@@ -31,7 +31,7 @@ class MemoryTempfile:
     and create temporary files and directories.
     """
 
-    def __init__(  # noqa: C901, PLR0912
+    def __init__(  # noqa: PLR0912
         self,
         *,
         preferred_paths: list | None = None,
@@ -182,7 +182,7 @@ class MemoryTempfile:
         self,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
     ) -> str:
         """Create a temporary directory.
 
@@ -207,7 +207,7 @@ class MemoryTempfile:
         self,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
         *,
         text: bool = False,
     ) -> tuple[int, str]:
@@ -241,7 +241,7 @@ class MemoryTempfile:
         self,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
     ) -> tempfile.TemporaryDirectory[str]:
         """Create a temporary directory and return a TemporaryDirectory object.
 
@@ -275,7 +275,7 @@ class MemoryTempfile:
         newline: str | None = None,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
     ) -> tempfile.SpooledTemporaryFile:
         """Create a spooled temporary file.
 
@@ -329,7 +329,7 @@ class MemoryTempfile:
         newline: str | None = None,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
         *,
         delete: bool = True,
     ) -> tempfile.NamedTemporaryFile:
@@ -379,7 +379,7 @@ class MemoryTempfile:
         newline: str | None = None,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
     ) -> tempfile.TemporaryFile:
         """Create and return a temporary file.
 

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/utils/plot_utils.py

@@ -13,7 +13,7 @@ from numpy.typing import NDArray
 from tqdm import tqdm
 
 
-def plot_array(  # noqa: C901, D417, PLR0912
+def plot_array(  # noqa: PLR0912
     x: NDArray[np.float64 | np.int64 | np.bool],
     aspect: float | None = None,
     vmin: float | None = None,
@@ -553,7 +553,7 @@ def plot_wave_propagation_animation(
     animation_data.save(export_name, writer="ffmpeg", dpi=dpi)
 
 
-def plot_wave_propagation_with_map(  # noqa: PLR0915, C901
+def plot_wave_propagation_with_map(
     propagation_map: NDArray[np.float64],
     c_map: NDArray[np.float64],
     rho_map: NDArray[np.float64],
@@ -868,7 +868,7 @@ def plot_wave_propagation_with_map(  # noqa: PLR0915, C901
     plt.close("all")
 
 
-def plot_wave_propagation_snapshot(  # noqa: PLR0915
+def plot_wave_propagation_snapshot(
     propagation_map: NDArray[np.float64],
     c_map: NDArray[np.float64],
     rho_map: NDArray[np.float64],

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/fullwave/utils/signal_filter.py

@@ -25,7 +25,7 @@ def _check_cupy() -> bool:
     global _CUPY_AVAILABLE  # noqa: PLW0603
     if _CUPY_AVAILABLE is None:
         try:
-            import cupy  # noqa: F401
+            import cupy  # noqa: F401, PLC0415
 
             _CUPY_AVAILABLE = True
         except ImportError:
@@ -145,7 +145,7 @@ def apply_filter(
     )
 
     if use_gpu and _check_cupy():
-        import cupy as cp
+        import cupy as cp  # noqa: PLC0415
 
         logger.debug("apply_filter: using CuPy GPU backend")
         data_gpu = cp.asarray(data, dtype=cp.float64)

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fullwave25"
-version = "1.2.6-dev2" # Update via bump-my-version, not manually
+version = "1.2.6-dev3" # Update via bump-my-version, not manually
 description = "Fullwave 2.5: Ultrasound wave propagation simulation with heterogeneous power law attenuation modelling capabilities"
 readme = "README.md"
 requires-python = ">=3.10"