Move from setup.py to pyproject.toml

.github/workflows/testing.yml

@@ -5,9 +5,9 @@ on:
 
   pull_request:
 
-  # everyday at 3 am UTC
-  #  schedule:
-  #   - cron:  '0 3 * * *'
+  # weekly
+  schedule:
+   - cron:  '3 7 * * 4'
 
 jobs:
   testing:
@@ -42,8 +42,9 @@ jobs:
 
     - name: Install python dependencies
       run: |
-        python -m pip install --upgrade setuptools wheel pip 
-        pip install .
+        python -m pip install uv
+        uv pip install --system . 
+        uv pip install --system numpy wheel setuptools
 
     - name: Install S4 in Linux
       if: matrix.os == 'ubuntu-latest'
@@ -64,25 +65,25 @@ jobs:
         cd ..
         rm -rf S4
 
-    - name: Install on Linux and MacOS
-      if: matrix.os != 'windows-latest'
-      run: pip install .
+#    - name: Install on Linux and MacOS
+#      if: matrix.os != 'windows-latest'
+#      run: pip install .
 
-    - name: Install on Windows
-      if: matrix.os == 'windows-latest'
-      run: |
-        pip install .
-      shell: powershell
+#    - name: Install on Windows
+#      if: matrix.os == 'windows-latest'
+#      run: |
+#        pip install .
+#      shell: powershell
 
     - name: Test with pytest
       run: |
-        pip install pytest-cov pytest-rerunfailures
+        uv pip install --system pytest-cov pytest-rerunfailures
         pytest --cov-report= --cov=rayflare tests/ --reruns 5
 
     - name: Codecov
       if: matrix.os == 'ubuntu-latest'
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       run: |
-        pip install codecov
+        uv pip install --system codecov
         codecov

docs/requirements.txt

@@ -8,4 +8,5 @@ matplotlib==3.7.2
 scipy==1.11.2
 solcore==5.10.0
 nbsphinx==0.9.3
-inkstone==0.3.12
+inkstone==0.3.12
+numba==0.58.1

examples/analytical_rt_comparison.py

@@ -13,8 +13,8 @@
 
 options.wavelength = wl
 
-options.nx = 50
-options.ny = 50
+options.nx = 100
+options.ny = 100
 options.n_rays = 1 * options.nx ** 2
 # options.x_limits = [2.5, 7.5]
 # options.y_limits = [2.5, 7.5]
@@ -51,7 +51,7 @@
     overwrite=True,
 )
 
-angle_in = np.linspace(0, 70, 10)
+angle_in = np.linspace(0, 70, 6)
 
 n_int_R_a = np.zeros((len(angle_in), len(wl)))
 n_int_T_a = np.zeros((len(angle_in), len(wl)))

examples/phong_scattering.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from rayflare.ray_tracing.rt import rt_structure
+from rayflare.ray_tracing import rt_structure
 from rayflare.textures import regular_pyramids, planar_surface
 from rayflare.options import default_options
 
@@ -15,7 +15,6 @@
 # setting up some colours for plotting
 pal = sns.color_palette("husl", 4)
 
-
 # setting up Solcore materials
 Air = material("Air")()
 
@@ -146,15 +145,17 @@
 scaled_intensity = n/np.sin(mean_theta_bin)
 
 fig, ax1 = plt.subplots()
-plt.plot(mean_theta_bin, scaled_intensity/np.max(scaled_intensity))
-plt.plot(x, power_law)
+plt.bar(mean_theta_bin*180/np.pi, scaled_intensity/np.max(scaled_intensity), width=180*np.diff(bins)[0]/np.pi,
+        alpha=0.5, label='probability density/area')
+plt.plot(x*180/np.pi, power_law, '-k', label=r'cos$^\alpha(\theta)$')
+plt.legend()
 plt.show()
 
-fig, ax1 = plt.subplots()
-n, _, _ = ax1.hist(thetas, color=pal[2], alpha=0.5, label="Phong 100 % transmission",
-         bins=70, density=True)
-plt.plot((x+1), power_law)
-plt.show()
+# fig, ax1 = plt.subplots()
+# n, _, _ = ax1.hist(thetas, color=pal[2], alpha=0.5, label="Phong 100 % transmission",
+#          bins=70, density=True)
+# plt.plot((x+1), power_law)
+# plt.show()
 
 x2 = np.linspace(0, 1, 100)
 

examples/phong_scattering_2.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from rayflare.ray_tracing.rt import rt_structure
+from rayflare.ray_tracing import rt_structure
 from rayflare.textures import regular_pyramids, planar_surface
 from rayflare.options import default_options
 
@@ -27,7 +27,7 @@
 SiN = material("Si3N4")()
 
 # number of x and y points to scan across
-nxy = 30
+nxy = 50
 
 # setting options
 options = default_options()
@@ -36,10 +36,12 @@
 options.ny = nxy
 options.n_rays = 2 * nxy**2
 options.depth_spacing = si("0.1um")
-options.parallel = False
+options.parallel = True
 options.analytical_ray_tracing = 0
 options.I_thresh = 0.005
 options.randomize_surface = True
+options.project_name = "phong_scattering"
+options.lookuptable_angles = 200
 
 # analytical: phong and regular pyramids 15 degree rear look the same
 front_opening_deg = 50
@@ -58,7 +60,10 @@
 args_same = { "materials": [Si],
                 "widths": [d],
                 "incidence": Air,
-                "transmission": Air}
+                "transmission": Air,
+              "use_TMM": False,
+              "options": options,
+              "overwrite": True}
 
 # set up ray-tracing options
 rtstr_planar = rt_structure(
@@ -79,44 +84,44 @@
 result_list_phong = []
 
 start = time()
-#
-# for alpha in alpha_values:
-#     flat_phong[0].phong_options[0] = alpha
-#     rtstr_phong = rt_structure(
-#         textures=[triangle_surf, flat_phong],
-#         **args_same
-#     )
-#     result_list_phong.append(rtstr_phong.calculate(options))
 
-# result_planar = rtstr_planar.calculate(options)
+for alpha in alpha_values:
+    flat_phong[0].phong_options[0] = alpha
+    rtstr_phong = rt_structure(
+        textures=[triangle_surf, flat_phong],
+        **args_same
+    )
+    result_list_phong.append(rtstr_phong.calculate(options))
+
+result_planar = rtstr_planar.calculate(options)
 
 result_flat_tri = rtstr_flat_tri.calculate(options)
-#
-# result_same_tri = rtstr_same_tri.calculate(options)
-#
+
+result_same_tri = rtstr_same_tri.calculate(options)
+
 print("total time:", time() - start)
-#
-# R0 = result_planar['R0']
-# A_lambertian = (1-R0)*4*Si.n(options.wavelength)**2*Si.alpha(options.wavelength)*d/(1+4*Si.n(options.wavelength)**2*Si.alpha(options.wavelength)*d)
-#
-#
-# plt.figure()
-#
-# for i1, alpha in enumerate(alpha_values):
-#     plt.plot(options.wavelength*1e9, result_list_phong[i1]["A_per_layer"], '-', color=pal[i1],
-#              label=r"phong, $\alpha$ = " + str(alpha))
-#
-#
-# plt.plot(options.wavelength * 1e9, result_planar["A_per_layer"], '-.k',
-#          label="planar", alpha=0.6)
-# plt.plot(options.wavelength * 1e9, result_flat_tri["A_per_layer"], '-k',
-#          label="15 degree pyramid", alpha=0.6)
-# plt.plot(options.wavelength * 1e9, result_same_tri["A_per_layer"], '--k',
-#          label="same angle pyramid", alpha=0.6)
-#
-# plt.ylim(0, 1)
-# plt.xlim(np.min(options.wavelength * 1e9), np.max(options.wavelength * 1e9))
-# plt.legend(title='Rear surface:')
-# plt.xlabel("Wavelength (nm)")
-# plt.ylabel("Absorption")
-# plt.show()
+
+R0 = result_planar['R0']
+A_lambertian = (1-R0)*4*Si.n(options.wavelength)**2*Si.alpha(options.wavelength)*d/(1+4*Si.n(options.wavelength)**2*Si.alpha(options.wavelength)*d)
+
+
+plt.figure()
+
+for i1, alpha in enumerate(alpha_values):
+    plt.plot(options.wavelength*1e9, result_list_phong[i1]["A_per_layer"], '-', color=pal[i1],
+             label=r"phong, $\alpha$ = " + str(alpha))
+
+
+plt.plot(options.wavelength * 1e9, result_planar["A_per_layer"], '-.k',
+         label="planar", alpha=0.6)
+plt.plot(options.wavelength * 1e9, result_flat_tri["A_per_layer"], '-k',
+         label="15 degree pyramid", alpha=0.6)
+plt.plot(options.wavelength * 1e9, result_same_tri["A_per_layer"], '--k',
+         label="same angle pyramid", alpha=0.6)
+
+plt.ylim(0, 1)
+plt.xlim(np.min(options.wavelength * 1e9), np.max(options.wavelength * 1e9))
+plt.legend(title='Rear surface:')
+plt.xlabel("Wavelength (nm)")
+plt.ylabel("Absorption")
+plt.show()

pyproject.toml

@@ -0,0 +1,68 @@
+[build-system]
+requires = ["hatchling>=1.24.2", "hatch-vcs>=0.3.0"]
+build-backend = "hatchling.build"
+
+[project]
+name = "rayflare"
+version = "1.3.0"
+description = "Python-based integrated optical modelling"
+readme = "README.md"
+requires-python = ">=3.7"
+# "LICENSE" is name of the license file, which must be in root of project folder
+license = {file = "LICENSE.txt"}
+authors = [
+    {name = "Phoebe Pearce", email = "p.m.pearce@gmail.com"},
+]
+keywords = [
+    "photovoltaics", "physics", "optics", "ray tracing", " ray optics",
+    "wave optics", "transfer matrix", "rcwa", "tmm", "rigorous coupled wave analysis",
+    "thin film", "thin film optics", "scattering", "light scattering", "light trapping",
+    "ellipsometry", "diffraction", "lens", "lens design", "lens simulation",
+]
+
+# https://pypi.org/classifiers/
+# Add PyPI classifiers here
+classifiers = [
+"Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved",
+        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+        "Natural Language :: English",
+        "Operating System :: OS Independent",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        "Topic :: Scientific/Engineering",
+        "Topic :: Scientific/Engineering :: Physics",
+]
+
+# Required dependencies for install/usage of your package or application
+# If you don't have any dependencies, leave this section empty
+# Format for dependency strings: https://peps.python.org/pep-0508/
+dependencies = [
+    "matplotlib",
+    "scipy",
+    "numpy<2.0.0",
+    "solcore",
+    "xarray",
+    "sparse",
+    "joblib",
+    "seaborn",
+    "inkstone",
+    "numba",
+]
+
+test = [
+    "pytest",
+    "pytest-cov",
+]
+
+[project.urls]
+Homepage = "https://github.com/qpv-research-group/rayflare"
+Documentation = "https://rayflare.readthedocs.io"
+Changelog = "https://rayflare.readthedocs.io/en/latest/news.html"
+
+[tool.hatch.build.targets.sdist]
+include = ["/rayflare"]
+
+[tool.pytest.ini_options]
+testpaths = "tests"  # directory containing your tests

rayflare/matrix_formalism/multiply_matrices.py

@@ -6,7 +6,7 @@
 # Contact: p.pearce@unsw.edu.au
 
 import numpy as np
-from sparse import load_npz, dot, COO, stack, einsum
+from sparse import load_npz, COO, stack, einsum
 from rayflare.angles import make_angle_vector, fold_phi, overall_bin
 import os
 import xarray as xr
@@ -161,18 +161,20 @@ def make_D(alphas, thick, thetas):
 # faster than the previous for loop implementation. Thanks to Johnson Wong
 # (GitHub: arsonwong)
 def dot_wl(mat, vec):
-
+    # note: sometimes get nans here in result, even when there are no nans
+    # in mat or vec.
     if len(mat.shape) == 3:
-        result = einsum('ijk,ik->ij', mat, vec).todense()
+        result = einsum('ijk,ik->ij', mat, COO(vec)).todense()
 
     if len(mat.shape) == 2:
-        result = einsum('jk,ik->ij', mat, vec).todense()
+        result = einsum('jk,ik->ij', mat, COO(vec)).todense()
 
     return result
 
 
 def dot_wl_u2d(mat, vec):
-    result = einsum('jk,ik->ij', mat, vec).todense()
+
+    result = einsum('jk,ik->ij', mat, COO(vec)).todense()
     return result
 
 

rayflare/options.py

@@ -62,6 +62,6 @@ def __init__(self):
         self.analytical_threshold = 0.99
 
         # TMM options
-        self.lookuptable_angles = 300
+        self.lookuptable_angles = 100
         self.coherent = True
         self.coherency_list = None

rayflare/ray_tracing/__init__.py

@@ -1 +1,2 @@
-from .rt import RT, rt_structure
+from .rt_matrix import RT
+from .rt_structure import rt_structure