update tests, docs, bump version

.github/workflows/testing.yml

@@ -75,7 +75,7 @@ jobs:
     - name: Test with pytest
       run: |
         pip install pytest-cov pytest-rerunfailures
-        pytest --cov-report= --cov=rayflare tests/ --reruns 3
+        pytest --cov-report= --cov=rayflare tests/ --reruns 5
 
     - name: Codecov
       if: matrix.os == 'ubuntu-latest'

docs/Installation/installation.rst

@@ -97,7 +97,7 @@ To do a normal installation from PyPI (using :literal:`pip`):
     pip install setuptools wheel numba
     pip install rayflare
 
-This will install install the most recent version uploaded to PyPI (currently 1.2.0), which is not necessarily the most
+This will install install the most recent version uploaded to PyPI (currently 1.2.1), which is not necessarily the most
 up to date version.
 
 To install RayFlare from source (GitHub):

docs/Options/user_options.rst

@@ -9,7 +9,7 @@ rule, values with units of distance (wavelength, depth spacing) are in m while a
 General options/options for matrix framework
 ---------------------------------------------
 
-- **wavelengths**: wavelengths at which to carry out calculations (in m)
+- **wavelength**: wavelengths at which to carry out calculations (in m)
 - **theta_in**: polar angle of incident light (in radians)
 - **phi_in**: azimuthal angle of incident light (in radians). If you are using the angular redistribution matrix framework,
   you can also set this to 'all' to spread the incident light evenly over all the azimuthal bins
@@ -34,9 +34,12 @@ Options used only by RCWA (S4)
 ---------------------------------------------
 
 - **A_per_order**: whether or not to calculate absorption per diffraction order (Boolean)
-- **S4_options**: options which are passed to S4. See S4 documentation for details
+- **S4_options**: options which are passed to S4. See S4 documentation for details. Note that these are
+  not used by Inkstone.
 - **orders**: the number of Fourier orders to retain. The actual number of orders used may be different, depending on
   the lattice truncation rule used.
+- **RCWA_method**: 'Inkstone' or 'S4'. If 'Inkstone', the Inkstone RCWA implementation is used. If 'S4', the S4 RCWA implementation is used.
+  The default is S4. Note that this is not case-sensitive.
 
 
 Options used only by the ray-tracer

docs/news.rst

@@ -8,6 +8,18 @@ To update to the latest version of RayFlare, run the following command in your t
 
    pip install rayflare --upgrade
 
+Version 1.2.1 released (2023-11-19)
+------------------------------------
+**Highlights:**
+
+- New RCWA method ([Inkstone](https://github.com/alexysong/inkstone) now intergrated with RayFlare.
+  This is an all-Python program which is therefore easy to install (unlike S4). This means all core u
+  functionality of RayFlare is now available without the need to compile anything on your computer.
+  Users can toggle between S4 and Inkstone by setting the ``RCWA_method`` option.
+- Calculations with unpolarized light using RCWA should be faster now.
+- The ``wavelengths`` user options is now called ``wavelength``, for compatibility with Solcore.
+  ``wavelengths`` still works, but will be deprecated in future.
+
 Version 1.2.0 released (2023-03-21)
 ------------------------------------
 

rayflare/rigorous_coupled_wave_analysis/rcwa.py

@@ -1321,50 +1321,6 @@ def get_fourier_epsilon(
 
         return xs, ys, a_r, a_i
 
-    def get_fourier_epsilon_inkstone(
-        self, layer_index, wavelength, options, extent=None, n_points=200, plot=True
-    ):
-        """
-        Get the Fourier-decomposed epsilon scanning across x-y points for some layer in the structure for the number
-        of order specified in the options for the structure. Can also plot this automatically.
-
-        :param layer_index: index of the layer in which to get epsilon. layer 0 is the incidence medium, layer 1 is the first layer in the stack, etc.
-        :param wavelength: wavelength (in nm) at which to get epsilon
-        :param options: dictionary or State object containing user options
-        :param extent: range of x/y values in format [[x_min, x_max], [y_min, y_max]]. Default is 'None', will choose a reasonable area based \
-        on the unit cell size by default
-        :param n_points: number of points to scan across in the x and y directions
-        :param plot: plot the results (True or False, default True)
-
-        :return: xs, ys, a_r, a_i. The x points, y points, and the real and imaginary parts of the dielectric function.
-        """
-
-        wl_ind = np.argmin(np.abs(self.current_wavelengths * 1e9 - wavelength))
-
-        S = self.make_S(options, wl_ind)
-
-        xs, ys, epsilon, mu = S.ReconstructLayer(f"layer_{layer_index + 1}", n_points, n_points)
-
-        # assume material is isotropic! top left entry of dielectric tensor
-        a_r = np.real(epsilon)[:, :, 0, 0]
-        a_i = np.imag(epsilon)[:, :, 0, 0]
-
-        if plot:
-            fig, axs = plt.subplots(1, 2, figsize=(7, 2.6))
-            im1 = axs[0].pcolormesh(xs, ys, a_r.T, cmap="magma")
-            fig.colorbar(im1, ax=axs[0])
-            axs[0].set_xlabel("x (nm)")
-            axs[0].set_ylabel("y (nm)")
-            axs[0].set_aspect(aspect=1)
-
-            im2 = axs[1].pcolormesh(xs, ys, a_i.T, cmap="magma")
-            fig.colorbar(im2, ax=axs[1])
-            axs[1].set_xlabel("x (nm)")
-            axs[1].set_ylabel("y (nm)")
-            axs[1].set_aspect(aspect=1)
-            plt.show()
-
-        return xs, ys, a_r, a_i
 
     def get_fields(
         self, layer_index, wavelength, options, extent=None, depth=1e-10, n_points=200, plot=True

setup.py

@@ -63,7 +63,7 @@ def gen_data_files(*dirs):
 
 setup(
     name="rayflare",
-    version="1.2.0",
+    version="1.2.1",
     description="Python-based integrated optical modelling",
     long_description=long_description,
     long_description_content_typgie="text/markdown",

tests/test_errors.py

@@ -1,5 +1,5 @@
 import numpy as np
-from pytest import raises, mark
+from pytest import raises
 
 def pol_error():
     from rayflare.rigorous_coupled_wave_analysis.rcwa import process_pol

tests/test_textures.py

@@ -342,8 +342,6 @@ def test_hemisphere_cap_surface():
 
     front, _ = hemisphere_surface(Lx, 101, Lx / 3, offset, 0, 1)
 
-    o_t_array = np.empty((4, 40))
-
     normals = front.N
     # radius of sphere with an offset:
     # radius is Lx/3