fullwave25 1.2.6.dev2__tar.gz → 1.2.6.dev4__tar.gz

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev4}/.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "1.2.6-dev2"
+current_version = "1.2.6-dev4"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev4}/.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.dev4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fullwave25
-Version: 1.2.6.dev2
+Version: 1.2.6.dev4
 Summary: Fullwave 2.5: Ultrasound wave propagation simulation with heterogeneous power law attenuation modelling capabilities
 Author: Masashi Sode, Gianmarco Pinton
 Maintainer: Masashi Sode
@@ -13,7 +13,6 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.10
-Requires-Dist: joblib>=1.5.3
 Requires-Dist: matplotlib>=3.10.7
 Requires-Dist: numba>=0.63.1
 Requires-Dist: numexpr>=2.14.1

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev4}/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-dev4"
 
 VERSION = __version__  # for convenience
 logger.info("Fullwave version: %s", __version__)

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev4}/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.dev4}/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.dev4}/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.dev4}/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.dev4}/fullwave/solver/launcher.py

@@ -31,6 +31,7 @@ class Launcher:
         use_gpu: bool = True,
         cuda_device_id: str | int | list | None = None,
         save_gpu_memory: bool = False,
+        verify_gpu: bool = True,
     ) -> None:
         """Initialize a FullwaveLauncher instance.
 
@@ -62,6 +63,11 @@ class Launcher:
             depending on the hardware and the simulation settings.
             useful in 3D simulations with large grid sizes
             where GPU memory is a limiting factor.
+        verify_gpu : bool, optional
+            Whether to verify that the specified CUDA devices exist on the system.
+            Defaults to True. Set to False when generating input files only
+            (``generate_input_only=True``) on a machine that may not have
+            the target GPUs available.
 
         """
         self._path_fullwave_simulation_bin = path_fullwave_simulation_bin
@@ -69,7 +75,10 @@ class Launcher:
         assert self._path_fullwave_simulation_bin.exists(), error_msg
         self.is_3d = is_3d
         self.use_gpu = use_gpu
-        self.cuda_device_id = self._configure_cuda_device_id(cuda_device_id)
+        self.cuda_device_id = self._configure_cuda_device_id(
+            cuda_device_id,
+            verify_gpu=verify_gpu,
+        )
         self.save_gpu_memory = save_gpu_memory
         logger.debug("Launcher instance created.")
 
@@ -152,13 +161,20 @@ class Launcher:
                 raise ValueError(message)
 
     @staticmethod
-    def _configure_cuda_device_id(cuda_device_id: str | int | list | None) -> str:
+    def _configure_cuda_device_id(
+        cuda_device_id: str | int | list | None,
+        *,
+        verify_gpu: bool = True,
+    ) -> str:
         """Verify and assign the CUDA device ID.
 
         Parameters
         ----------
         cuda_device_id : str | int | None
             The CUDA device ID to verify and assign.
+        verify_gpu : bool, optional
+            Whether to verify that the specified CUDA devices exist.
+            Defaults to True.
 
         Returns
         -------
@@ -167,7 +183,8 @@ class Launcher:
 
         """
         output = Launcher._parse_cuda_device_id(cuda_device_id)
-        Launcher._verify_cuda_devices_exist(output)
+        if verify_gpu:
+            Launcher._verify_cuda_devices_exist(output)
         return output
 
     def run(

{fullwave25-1.2.6.dev2 → fullwave25-1.2.6.dev4}/fullwave/solver/pml_builder.py

@@ -5,13 +5,11 @@ import logging
 from collections import OrderedDict
 from dataclasses import dataclass, field
 from functools import cached_property
-from itertools import starmap
 from pathlib import Path
 
 import matplotlib.pyplot as plt
 import numexpr as ne
 import numpy as np
-from joblib import Parallel, delayed
 from numpy.typing import NDArray
 
 import fullwave
@@ -115,7 +113,7 @@ 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,
@@ -834,21 +832,24 @@ class PMLBuilder:
 
         items = list(rename_dict.items())
 
-        results = Parallel(n_jobs=self.medium_org.n_jobs, backend="threading")(
-            delayed(_compute_one)(
-                key_fw2,
-                key_py,
-                relaxation_param_dict,
-                alpha_target_higher_nu,
-                d_target_higher_nu,
-                alpha_target_pml,
-                d_target_pml,
-                n_polynomial,
-                self.is_3d,
-                self._apply_transition_and_pml,
-            )
-            for key_fw2, key_py in items
-        )
+        with concurrent.futures.ThreadPoolExecutor() as executor:
+            futures = [
+                executor.submit(
+                    _compute_one,
+                    key_fw2,
+                    key_py,
+                    relaxation_param_dict,
+                    alpha_target_higher_nu,
+                    d_target_higher_nu,
+                    alpha_target_pml,
+                    d_target_pml,
+                    n_polynomial,
+                    self.is_3d,
+                    self._apply_transition_and_pml,
+                )
+                for key_fw2, key_py in items
+            ]
+            results = [f.result() for f in futures]
         out_dict = dict(results)
 
         logger.debug("Calculating PML a and b coefficients...")
@@ -876,13 +877,9 @@ class PMLBuilder:
             # Return keys + values so parent can update dict safely
             return (f"a_pml_{axis}{nu}", a, f"b_pml_{axis}{nu}", b)
 
-        results = Parallel(
-            n_jobs=self.medium_org.n_jobs,  # use all cores
-            backend="loky",  # process-based; safe default for Python code
-            prefer="processes",
-        )(
-            starmap(delayed(_worker), tasks),
-        )
+        with concurrent.futures.ThreadPoolExecutor() as executor:
+            futures = [executor.submit(_worker, nu, axis) for nu, axis in tasks]
+            results = [f.result() for f in futures]
 
         for a_key, a_val, b_key, b_val in results:
             out_dict[a_key] = a_val
@@ -898,7 +895,7 @@ class PMLBuilder:
 
         return extended_medium
 
-    def _apply_pml_3d(  # noqa: PLR0915
+    def _apply_pml_3d(
         self,
         extended_medium: fullwave.MediumRelaxationMaps,
         theoritical_reflection_coefficient: float,
@@ -1119,21 +1116,24 @@ class PMLBuilder:
             raise ValueError(error_msg)
 
         items = list(rename_dict.items())
-        results = Parallel(n_jobs=self.medium_org.n_jobs, backend="threading")(
-            delayed(_compute_one)(
-                key_fw2,
-                key_py,
-                relaxation_param_dict,
-                alpha_target_higher_nu,
-                d_target_higher_nu,
-                alpha_target_pml,
-                d_target_pml,
-                n_polynomial,
-                self.is_3d,
-                self._apply_transition_and_pml,
-            )
-            for key_fw2, key_py in items
-        )
+        with concurrent.futures.ThreadPoolExecutor() as executor:
+            futures = [
+                executor.submit(
+                    _compute_one,
+                    key_fw2,
+                    key_py,
+                    relaxation_param_dict,
+                    alpha_target_higher_nu,
+                    d_target_higher_nu,
+                    alpha_target_pml,
+                    d_target_pml,
+                    n_polynomial,
+                    self.is_3d,
+                    self._apply_transition_and_pml,
+                )
+                for key_fw2, key_py in items
+            ]
+            results = [f.result() for f in futures]
         out_dict = dict(results)
 
         logger.debug("Calculating PML a and b coefficients...")
@@ -1162,13 +1162,9 @@ class PMLBuilder:
             # Return keys + values so parent can update dict safely
             return (f"a_pml_{axis}{nu}", a, f"b_pml_{axis}{nu}", b)
 
-        results = Parallel(
-            n_jobs=self.medium_org.n_jobs,  # use all cores
-            backend="loky",  # process-based; safe default for Python code
-            prefer="processes",
-        )(
-            starmap(delayed(_worker), tasks),
-        )
+        with concurrent.futures.ThreadPoolExecutor() as executor:
+            futures = [executor.submit(_worker, nu, axis) for nu, axis in tasks]
+            results = [f.result() for f in futures]
 
         for a_key, a_val, b_key, b_val in results:
             out_dict[a_key] = a_val
@@ -1184,7 +1180,7 @@ 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 +1461,7 @@ 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,