Api update (#227)

* Revert "Release 0.2.0"
This reverts commit 060647c.
* updated public api
* removed unused second outputs from operators

Author: astanziola

CHANGELOG.md

@@ -4,8 +4,6 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
-
-## [0.2.0] - 2023-12-18
 ### Fixed
 - Fixed arguments error in helmholtz notebook
 
@@ -99,8 +97,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Pml for 1D and 3D simulations.
 - Plotting functions of `jwave.utils` now work with both `Field`s and arrays.
 
-[Unreleased]: https://github.com/ucl-bug/jwave/compare/0.2.0...master
-[0.2.0]: https://github.com/ucl-bug/jwave/compare/0.1.5...0.2.0
+[Unreleased]: https://github.com/ucl-bug/jwave/compare/0.1.5...master
 [0.1.5]: https://github.com/ucl-bug/jwave/compare/0.1.4...0.1.5
 [0.1.4]: https://github.com/ucl-bug/jwave/compare/0.1.3...0.1.4
 [0.1.3]: https://github.com/ucl-bug/jwave/compare/0.1.2...0.1.3
@@ -111,4 +108,3 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 [0.0.3]: https://github.com/ucl-bug/jwave/compare/0.0.2...0.0.3
 [0.0.2]: https://github.com/ucl-bug/jwave/compare/0.0.1...0.0.2
 [0.0.1]: https://github.com/ucl-bug/jwave/releases/tag/0.0.1
-

jwave/__init__.py

@@ -14,9 +14,53 @@
 # License along with j-Wave. If not, see <https://www.gnu.org/licenses/>.
 
 # nopycln: file
-from jaxdf.discretization import *
+from jaxdf import (
+  operator,
+  Continuous,
+  Domain,
+  FiniteDifferences,
+  FourierSeries,
+  Field,
+  Linear,
+  OnGrid
+)
+
+from .acoustics import (
+  angular_spectrum,
+  born_iteration,
+  born_series,
+  db2neper,
+  helmholtz_solver_verbose,
+  helmholtz_solver,
+  helmholtz,
+  homogeneous_helmholtz_green,
+  laplacian_with_pml,
+  mass_conservation_rhs,
+  momentum_conservation_rhs,
+  pml,
+  pressure_from_density,
+  rayleigh_integral,
+  scale_source_helmholtz,
+  scattering_potential,
+  simulate_wave_propagation,
+  spectral,
+  wave_propagation_symplectic_step,
+  wavevector,
+  TimeWavePropagationSettings,
+)
+from .geometry import (
+  BLISensors,
+  DistributedTransducer,
+  Medium,
+  Sensors,
+  Sources,
+  TimeAxis,
+  TimeHarmonicSource,
+)
 
 from jwave import acoustics as ac
 from jwave import geometry as geometry
+from jwave import logger as logger
+from jwave import phantoms as phantoms
 from jwave import signal_processing as signal_processing
 from jwave import utils as utils

jwave/acoustics/__init__.py

@@ -14,6 +14,31 @@
 # License along with j-Wave. If not, see <https://www.gnu.org/licenses/>.
 
 # nopycln: file
-from .operators import *
-from .time_harmonic import *
-from .time_varying import *
+from .conversion import db2neper
+from .operators import (
+  helmholtz,
+  laplacian_with_pml,
+  scale_source_helmholtz,
+  wavevector,
+)
+from .time_harmonic import (
+  angular_spectrum,
+  born_iteration,
+  born_series,
+  helmholtz_solver,
+  helmholtz_solver_verbose,
+  homogeneous_helmholtz_green,
+  rayleigh_integral,
+  scattering_potential
+)
+from .time_varying import (
+  mass_conservation_rhs,
+  momentum_conservation_rhs,
+  pressure_from_density,
+  simulate_wave_propagation,
+  wave_propagation_symplectic_step,
+  TimeWavePropagationSettings,
+)
+
+from . import spectral
+from . import pml

jwave/acoustics/time_harmonic.py

@@ -342,7 +342,7 @@ def body_fun(carry):
 
     out_field = _cbs_unnorm_units(out_field, _conversion)
 
-    return out_field, None
+    return out_field
 
 
 @operator
@@ -377,7 +377,7 @@ def born_iteration(field: Field,
     G = homogeneous_helmholtz_green(V1 + src, k0=k0, epsilon=epsilon)
     V2 = scattering_potential(field - G, k_sq, k0=k0, epsilon=epsilon)
 
-    return field - (1j / epsilon) * V2, params
+    return field - (1j / epsilon) * V2
 
 
 @operator
@@ -401,7 +401,7 @@ def scattering_potential(field: Field,
 
     k = k_sq - k0**2 - 1j * epsilon
     out = field * k
-    return out, params
+    return out
 
 
 @operator
@@ -430,7 +430,7 @@ def homogeneous_helmholtz_green(field: FourierSeries,
     u_fft = jnp.fft.fftn(u)
     Gu_fft = g_fourier * u_fft
     Gu = jnp.fft.ifftn(Gu_fft)
-    return field.replace_params(Gu), params
+    return field.replace_params(Gu)
 
 
 @operator
@@ -500,7 +500,7 @@ def direc_exp_term(x, y, z):
     # Weights of the Rayleigh integral
     weights = jax.vmap(jax.vmap(direc_exp_term, in_axes=(0, 0, 0)),
                        in_axes=(0, 0, 0))(R[..., 0], R[..., 1], R[..., 2])
-    return jnp.sum(weights * pressure.on_grid) * area, None
+    return jnp.sum(weights * pressure.on_grid) * area
 
 
 @operator
@@ -560,7 +560,7 @@ def helm_func(u):
         )[0]
     elif method == "bicgstab":
         out = bicgstab(helm_func, source, guess, tol=tol, maxiter=maxiter)[0]
-    return -1j * omega * out, None
+    return -1j * omega * out
 
 
 def helmholtz_solver_verbose(

jwave/acoustics/time_varying.py

@@ -82,8 +82,6 @@ def __init__(
         self.smooth_initial = smooth_initial
 
 
-default_time_wave_prop_settings = TimeWavePropagationSettings()
-
 
 def _shift_rho(rho0, direction, dx):
     if isinstance(rho0, OnGrid):
@@ -382,7 +380,7 @@ def simulate_wave_propagation(
     medium: Medium[OnGrid],
     time_axis: TimeAxis,
     *,
-    settings: TimeWavePropagationSettings = default_time_wave_prop_settings,
+    settings: TimeWavePropagationSettings = TimeWavePropagationSettings(),
     sources=None,
     sensors=None,
     u0=None,
@@ -533,7 +531,7 @@ def simulate_wave_propagation(
     medium: Medium[FourierSeries],
     time_axis: TimeAxis,
     *,
-    settings: TimeWavePropagationSettings = default_time_wave_prop_settings,
+    settings: TimeWavePropagationSettings = TimeWavePropagationSettings(),
     sources=None,
     sensors=None,
     u0=None,

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "jwave"
-version = "0.2.0"
+version = "0.1.5"
 description = "Fast and differentiable acoustic simulations in JAX."
 authors = [
   "Antonio Stanziola <[email protected]>",
@@ -108,9 +108,12 @@ split_before_logical_operator = true
 
 [tool.pytest.ini_options]
 addopts = """\
-    --doctest-modules \
+    --doctest-modules\
 """
 
+[tool.pytest_env]
+CUDA_VISIBLE_DEVICES = ""
+
 [tool.coverage.report]
 exclude_lines = [
     'if TYPE_CHECKING:',