📝 Add docstrings to fix-test-syntax-bug-600

kwave/kWaveSimulation.py

@@ -36,6 +36,25 @@ class kWaveSimulation(object):
     def __init__(
         self, kgrid: kWaveGrid, source: kSource, sensor: NotATransducer, medium: kWaveMedium, simulation_options: SimulationOptions
     ):
+        """
+        Initialize kWaveSimulation and prepare internal state for simulation validation and preparation.
+
+        Creates and stores copies of the provided grid, source, sensor, medium, and options; initializes flags, defaults, and internal placeholders used throughout the input-checking and preparation pipeline. If sensor.time_reversal_boundary_data is provided, the constructor converts inputs into a Dirichlet-style source and a minimal sensor for deprecated time-reversal mode, warns about deprecation, and configures the Recorder accordingly.
+
+        Parameters:
+            kgrid (kWaveGrid): Spatial grid definition for the simulation.
+            source (kSource): User-provided source definition (a deep copy is stored internally; the original is preserved on original_source).
+            sensor (NotATransducer): User-provided sensor definition (a deep copy is stored internally; the original is preserved on original_sensor).
+            medium (kWaveMedium): Medium properties (sound speed, density, absorption, etc.).
+            simulation_options (SimulationOptions): Simulation-wide options and flags.
+
+        Side effects:
+            - Stores deep copies as self.source and self.sensor and preserves originals in self.original_source and self.original_sensor.
+            - Sets many internal flags and default values (mask type, time-reversal flag, PML/simulation defaults, source/sensor indexing placeholders, absorption operator placeholders, recorder and logging setup).
+            - May replace source and sensor with a Dirichlet-style source/sensor when time-reversal boundary data is present.
+
+        No return value.
+        """
         self.precision = None
         self.kgrid = kgrid
         self.medium = medium
@@ -1500,14 +1519,9 @@ def check_time_reversal(self) -> bool:
 
     def _is_binary_sensor_mask(self, kgrid_dim: int) -> bool:
         """
-        Check if the sensor mask is a binary grid matching the kgrid dimensions.
-        Takes into account that the PML may have been added to the sensor mask.
-
-        Args:
-            kgrid_dim: Dimensionality of the kWaveGrid
-
-        Returns:
-            bool: True if the sensor mask is a binary grid matching kgrid dimensions
+        Return True if the sensor mask is a binary grid matching the simulation grid (kgrid), accounting for optional PML padding.
+
+        Checks whether sensor.mask has the same shape as kgrid.k or—when a PML size is configured in self.options.pml_size—matches the grid shape extended by 2*pml in each dimension. Supports 1D, 2D, and 3D grids and accepts a scalar or per-axis PML size representation.
         """
         # Get the grid shape without PML
         grid_shape = self.kgrid.k.shape

tests/test_kspaceFirstOrder3D_state.py

@@ -19,6 +19,30 @@
 
 def make_simulation_parameters(directory: Path):
     # create the computational grid
+    """
+    Create a minimal 3D k-Wave simulation configuration used for testing.
+
+    Parameters:
+        directory (Path): Directory used to construct input/output/checkpoint filenames;
+            no files are created by this function.
+
+    Returns:
+        tuple: (kgrid, medium, source, sensor, simulation_options, execution_options)
+            - kgrid (kWaveGrid): 3D computational grid with PML applied.
+            - medium (kWaveMedium): Homogeneous medium with sound_speed=1500 m/s.
+            - source (kSource): Contains a smoothed spherical initial pressure field (`p0`).
+            - sensor (kSensor): Binary planar sensor mask (plane at the first x-index).
+            - simulation_options (SimulationOptions): Options configured for disk I/O,
+              PML, data casting, and filenames pointing into `directory`.
+            - execution_options (SimulationExecutionOptions): CPU execution settings
+              with checkpointing configured.
+
+    Notes:
+        - The initial pressure (`source.p0`) is generated as a smoothed ball and
+          smoothing at runtime is disabled (`smooth_p0=False`).
+        - Filenames for input, output, and checkpoint are set to `{directory}/kwave_input.h5`,
+          `{directory}/kwave_output.h5`, and `{directory}/kwave_checkpoint.h5` respectively.
+    """
     PML_size = 10  # size of the PML in grid points
     N = Vector([32, 64, 64]) - 2 * PML_size  # number of grid points
     d = Vector([0.2e-3, 0.2e-3, 0.2e-3])  # grid point spacing [m]