Merge pull request #30 from BYUCamachoLab/Version-2.0.0

Bump Version 1.4.0 -> 2.0.0
BYUCamachoLab · Jul 7, 2022 · 27dfe52 · 27dfe52
2 parents 1e37e48 + a5971b3
commit 27dfe52
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.0
+current_version = 2.0.0
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)?

diff --git a/.github/workflows/continuous-integration-pip-master.yml b/.github/workflows/continuous-integration-pip-master.yml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.6, 3.7]
+        python-version: ['3.7', '3.8', '3.9', '3.10']
 
     steps:
     - uses: actions/checkout@v2

diff --git a/.github/workflows/continuous-integration-pip.yml b/.github/workflows/continuous-integration-pip.yml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.6, 3.7]
+        python-version: ['3.7', '3.8', '3.9', '3.10']
 
     steps:
       - uses: actions/checkout@v2

diff --git a/README.rst b/README.rst
@@ -1,5 +1,5 @@
 **************************
-SiPANN 1.4.0
+SiPANN 2.0.0
 **************************
 .. image:: https://img.shields.io/pypi/v/SiPANN.svg
    :target: https://pypi.python.org/pypi/SiPANN

diff --git a/SiPANN/LR/regress.py b/SiPANN/LR/regress.py
@@ -28,7 +28,10 @@
 print("Multivariate linear regression MSE: {:e}".format(MSE_REGRESION))
 
 # Save so our ImportLR can use it
-d = {"coef_": model.named_steps["linear"].coef_, "degree_": model.named_steps["poly"].degree}
+d = {
+    "coef_": model.named_steps["linear"].coef_,
+    "degree_": model.named_steps["poly"].degree,
+}
 
 n_features = model.named_steps["poly"].n_input_features_
 n_out = 1 if len(d["coef_"].shape) == 1 else d["coef_"].shape[0]

diff --git a/SiPANN/__init__.py b/SiPANN/__init__.py
@@ -5,6 +5,6 @@
 photonic device circuits.
 """
 
-__version__ = "1.4.0"
+__version__ = "2.0.0"
 __author__ = "Easton Potokar, Alec Hammond, R Scott Collings <[email protected]>"
 __all__ = []
diff --git a/SiPANN/comp.py b/SiPANN/comp.py
@@ -1,6 +1,5 @@
 import warnings
-from abc import ABC
-from abc import abstractmethod
+from abc import ABC, abstractmethod
 
 import gdspy
 import numpy as np
@@ -9,12 +8,8 @@
 import scipy.special as special
 
 from SiPANN.import_nn import ImportLR
-from SiPANN.nn import bentWaveguide
-from SiPANN.nn import straightWaveguide
-from SiPANN.scee import clean_inputs
-from SiPANN.scee import get_coeffs
-from SiPANN.scee import HalfRacetrack
-
+from SiPANN.nn import bentWaveguide, straightWaveguide
+from SiPANN.scee import HalfRacetrack, clean_inputs, get_coeffs
 
 """
 Similarly to before, we initialize all ANN's and regressions as global objects to speed things up.

diff --git a/SiPANN/import_nn.py b/SiPANN/import_nn.py
@@ -131,13 +131,18 @@ def __init__(self, directory):
         self.sess = tf.compat.v1.Session(graph=self.graph)
         with self.graph.as_default():
             # Import graph
-            imported_meta = tf.compat.v1.train.import_meta_graph(f"{directory}/model.meta")
+            imported_meta = tf.compat.v1.train.import_meta_graph(
+                f"{directory}/model.meta"
+            )
             imported_meta.restore(self.sess, f"{directory}/model")
 
             # get all tensor names
             self.output_tf = self.graph.get_tensor_by_name("OUTPUT:0")
             self.input_tf = self.graph.get_tensor_by_name("INPUT:0")
-            self.input_tf_parts = [self.graph.get_tensor_by_name(f"INPUT_{i}:0") for i in range(self.s_data[0])]
+            self.input_tf_parts = [
+                self.graph.get_tensor_by_name(f"INPUT_{i}:0")
+                for i in range(self.s_data[0])
+            ]
 
             self.keep_prob = self.graph.get_tensor_by_name("KEEP_PROB:0")
         tf.compat.v1.disable_eager_execution()

diff --git a/SiPANN/nn.py b/SiPANN/nn.py
@@ -21,8 +21,7 @@
 import pkg_resources
 import skrf as rf
 from scipy.interpolate import UnivariateSpline
-from scipy.signal import find_peaks
-from scipy.signal import peak_widths
+from scipy.signal import find_peaks, peak_widths
 
 from SiPANN import import_nn
 

diff --git a/SiPANN/scee.py b/SiPANN/scee.py
@@ -1,6 +1,5 @@
 import warnings
-from abc import ABC
-from abc import abstractmethod
+from abc import ABC, abstractmethod
 
 import gdspy
 import numpy as np
@@ -32,7 +31,7 @@ def get_neff(wavelength, width, thickness, sw_angle=90):
             wavelength (Valid for 1450nm-1650nm)
         width:    float or ndarray
             width (Valid for 400nm-600nm)
-        thickness:    float or ndarray 
+        thickness:    float or ndarray
             thickness (Valid for 180nm-240nm)
         sw_angle:    float or ndarray
             sw_angle (Valid for 80-90 degrees)
@@ -812,7 +811,13 @@ def predict(self, ports, wavelength):
         # determine z distance
         if 1 in ports and 3 in ports:
             z_dist = 2 * (radius + width / 2)
-        elif 1 in ports and 4 in ports or (2 not in ports or 4 not in ports) and 2 in ports and 3 in ports:
+        elif (
+            1 in ports
+            and 4 in ports
+            or (2 not in ports or 4 not in ports)
+            and 2 in ports
+            and 3 in ports
+        ):
             z_dist = np.pi * radius / 2 + radius + width / 2
         elif 2 in ports and 4 in ports:
             z_dist = np.pi * radius
@@ -997,7 +1002,13 @@ def predict(self, ports, wavelength):
         # determine z distance
         if 1 in ports and 3 in ports:
             z_dist = 2 * (radius + width / 2) + length
-        elif 1 in ports and 4 in ports or (2 not in ports or 4 not in ports) and 2 in ports and 3 in ports:
+        elif (
+            1 in ports
+            and 4 in ports
+            or (2 not in ports or 4 not in ports)
+            and 2 in ports
+            and 3 in ports
+        ):
             z_dist = np.pi * radius / 2 + radius + width / 2 + length
         elif 2 in ports and 4 in ports:
             z_dist = np.pi * radius + length
@@ -1171,7 +1182,16 @@ def predict(self, ports, wavelength):
             offset = np.pi / 2
 
         # determine z distance
-        if 1 in ports and 3 in ports or 1 in ports and 4 in ports or 2 in ports and 4 in ports or 2 in ports and 3 in ports:
+        if (
+            1 in ports
+            and 3 in ports
+            or 1 in ports
+            and 4 in ports
+            or 2 in ports
+            and 4 in ports
+            or 2 in ports
+            and 3 in ports
+        ):
             z_dist = length
         else:
             return np.zeros(len(wavelength))
@@ -1363,7 +1383,16 @@ def predict(self, ports, wavelength):
         z_dist = length + 2 * np.sqrt(
             H ** 2 + (V * np.pi / 2) ** 2
         ) / np.pi * special.ellipeinc(np.pi, m)
-        if 1 in ports and 3 in ports or 1 in ports and 4 in ports or 2 in ports and 4 in ports or 2 in ports and 3 in ports:
+        if (
+            1 in ports
+            and 3 in ports
+            or 1 in ports
+            and 4 in ports
+            or 2 in ports
+            and 4 in ports
+            or 2 in ports
+            and 3 in ports
+        ):
             z_dist = z_dist
         else:
             return np.zeros(len(wavelength))
@@ -1555,7 +1584,16 @@ def predict(self, ports, wavelength):
             offset = np.pi / 2
 
         # determine z distance
-        if 1 in ports and 3 in ports or 1 in ports and 4 in ports or 2 in ports and 4 in ports or 2 in ports and 3 in ports:
+        if (
+            1 in ports
+            and 3 in ports
+            or 1 in ports
+            and 4 in ports
+            or 2 in ports
+            and 4 in ports
+            or 2 in ports
+            and 3 in ports
+        ):
             z_dist = np.pi * radius
         else:
             return np.zeros(len(wavelength))
@@ -1699,7 +1737,13 @@ def predict(self, ports, wavelength):
         # determine z distance
         if 1 in ports and 3 in ports:
             z_dist = np.pi * (radius + width + gap)
-        elif 1 in ports and 4 in ports or (2 not in ports or 4 not in ports) and 2 in ports and 3 in ports:
+        elif (
+            1 in ports
+            and 4 in ports
+            or (2 not in ports or 4 not in ports)
+            and 2 in ports
+            and 3 in ports
+        ):
             z_dist = np.pi * (radius + width + gap) / 2 + np.pi * radius / 2
         elif 2 in ports and 4 in ports:
             z_dist = np.pi * radius

diff --git a/SiPANN/scee_int.py b/SiPANN/scee_int.py
@@ -2,8 +2,7 @@
 from simphony import Model
 from simphony.layout import Circuit
 from simphony.pins import Pin, PinList
-from simphony.tools import freq2wl
-from simphony.tools import wl2freq
+from simphony.tools import freq2wl, wl2freq
 
 ########################################################################
 ####### This file contains integration of SCEE into various other ######
@@ -41,7 +40,9 @@ def export_interconnect(sparams, wavelength, filename, clear=True):
                 temp = np.vstack((freq, np.abs(sp), np.unwrap(np.angle(sp)))).T
 
                 # Save header
-                header = f'("port {out+1}", "TE", 1, "port {in_+1}", 1, "transmission")\n'
+                header = (
+                    f'("port {out+1}", "TE", 1, "port {in_+1}", 1, "transmission")\n'
+                )
                 header += f"{temp.shape}"
 
                 # save data
@@ -67,7 +68,14 @@ class SimphonyWrapper(Model):
     def __init__(self, model, sigmas=dict()):
         self.model = model
         self.sigmas = sigmas
-        self.pins = PinList([Pin(self.model, "n1"), Pin(self.model, "n2"), Pin(self.model, "n3"), Pin(self.model, "n4")])  #: The default pin names of the device
+        self.pins = PinList(
+            [
+                Pin(self.model, "n1"),
+                Pin(self.model, "n2"),
+                Pin(self.model, "n3"),
+                Pin(self.model, "n4"),
+            ]
+        )  #: The default pin names of the device
         self.model.pins = self.pins
         self.model.circuit = Circuit(self.model)
 
@@ -78,7 +86,9 @@ def __init__(self, model, sigmas=dict()):
 
         self.model.s_parameters = self.s_parameters
         self.model.monte_carlo_s_parameters = self.monte_carlo_s_parameters
-        self.model.regenerate_monte_carlo_parameters = self.regenerate_monte_carlo_parameters
+        self.model.regenerate_monte_carlo_parameters = (
+            self.regenerate_monte_carlo_parameters
+        )
 
         # save actual parameters for switching back from monte_carlo
         self.og_params = self.model.__dict__.copy()

diff --git a/SiPANN/scee_opt.py b/SiPANN/scee_opt.py
@@ -3,14 +3,10 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
-from numba import njit
-from numba import vectorize
+from numba import njit, vectorize
 from numba.extending import get_cython_function_address
 from scipy import special
-from tables import ComplexCol
-from tables import Float64Col
-from tables import IsDescription
-from tables import open_file
+from tables import ComplexCol, Float64Col, IsDescription, open_file
 from tqdm import tqdm
 
 from SiPANN import scee
@@ -44,7 +40,7 @@ def bernstein_quick(n, j, t):
     test : float
         Result of computing the jth berstein polynomial at t
     """
-    return binom_fn(n, j) * t**j * (1 - t) ** (n - j)
+    return binom_fn(n, j) * t ** j * (1 - t) ** (n - j)
 
 
 def bezier_quick(g, length):
@@ -104,7 +100,7 @@ def bezier_quick(g, length):
             ),
             axis=0,
         )
-        / length**2,
+        / length ** 2,
     }
 
 

diff --git a/docs/changelog/2.0.0-changelog.md b/docs/changelog/2.0.0-changelog.md
@@ -0,0 +1,14 @@
+## 2.0.0 - 2022-07-06
+
+Maintenance update and drop support for Python 3.6.
+
+### Added
+- None
+
+### Changed
+- Bug fix for `SimphonyWrapper` class in `scee_int.py`. Changed tuple of `str` to `PinList`. [Check this PR for more details.](https://github.com/BYUCamachoLab/SiPANN/pull/24)
+- Bug fix in `nn.py` [See here for more info.](https://github.com/BYUCamachoLab/SiPANN/pull/29)
+- Code cleanup [See here for more info.](https://github.com/BYUCamachoLab/SiPANN/pull/27)
+
+### Removed
+- Support for Python 3.6
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -21,7 +21,7 @@
 author = "Easton Potokar, R Scott Collings, Alec Hammond"
 
 # The full version, including alpha/beta/rc tags
-release = "1.4.0"
+release = "2.0.0"
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/examples/Tutorials/export_to_rst.py b/examples/Tutorials/export_to_rst.py
@@ -16,7 +16,7 @@ def convert_jupyter(file):
 
     # remove previous and move data to static
     filename = file.split(".")[0]
-    files = fr"{filename}_files"
+    files = rf"{filename}_files"
     os.system(f"rm -rf ../../docs/source/tutorials/{files}")
     os.system(f"cp -r {files} ../../docs/source/tutorials")
     os.system(f"rm {files}/**_**_**.png")

diff --git a/examples/racetrack.py b/examples/racetrack.py
@@ -1,8 +1,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from SiPANN import comp
-from SiPANN import dc
+from SiPANN import comp, dc
 
 # units in nanometers
 r = 12e3

diff --git a/setup.py b/setup.py
@@ -2,8 +2,7 @@
 from io import open
 from os import path
 
-from setuptools import find_packages
-from setuptools import setup
+from setuptools import find_packages, setup
 
 # io.open is needed for projects that support Python 2.7
 # It ensures open() defaults to text mode with universal newlines,
@@ -38,7 +37,7 @@
     # For a discussion on single-sourcing the version across setup.py and the
     # project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version="1.4.0",  # Required
+    version="2.0.0",  # Required
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field:
     # https://packaging.python.org/specifications/core-metadata/#summary
@@ -91,8 +90,10 @@
         # Specify the Python versions you support here. In particular, ensure
         # that you indicate whether you support Python 2, Python 3 or both.
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
     ],
     # This field adds keywords for your project which will appear on the
     # project page. What does your project relate to?
@@ -131,12 +132,10 @@
         "gdspy >= 1.5.2",
         "scikit-rf",
         "numba",
-        "numpy<1.22",
+        "numpy>=1.22;python_version>='3.8'",
+        "numpy<1.22;python_version=='3.7'",
         "simphony",
-        "nlopt<=2.7.1;python_version=='3.7'",
-        "nlopt<=2.7.0;python_version=='3.8'",
-        "nlopt==2.7.0;python_version=='3.9'",
-        "nlopt<2.7.0;python_version=='3.10'",
+        "nlopt==2.7.1",
         "matplotlib",
         "tables",
         "tqdm",