Convert to pyproject.toml

.github/workflows/continuous-integration-pip-master.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/continuous-integration-pip.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
       - uses: actions/checkout@v2

.gitignore

@@ -1,6 +1,115 @@
-**/.ipynb_checkpoints
-**/__pycache__
-SiPANN.egg-info/
-**/build
-**/.vscode
-dist/*
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/build/
+docs/_build/
+docs/source/reference/api/
+docs/api/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+nojax/
+py38/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# VSCode
+.vscode
+
+# Mac users
+.DS_Store

CHANGELOG.md

@@ -0,0 +1,64 @@
+# Changelog
+
+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).
+
+---
+
+## [2.0.0](https://github.com/BYUCamachoLab/SiPANN/releases/tag/v2.0.0) - <small>2022-07-06</small>
+
+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
+
+
+---
+
+## [1.4.0](https://github.com/BYUCamachoLab/SiPANN/releases/tag/v1.4.0) - <small>2022-06-13</small>
+
+Maintenance update.
+
+### Added
+- None
+
+### Changed
+- Correct "invalid ports" errors (fixed some conditional statements).
+
+### Removed
+- None
+
+---
+
+## [1.3.2](https://github.com/BYUCamachoLab/SiPANN/releases/tag/v1.3.2) - <small>2022-05-16</small>
+
+Maintenance update.
+
+### Added
+- None
+
+### Changed
+- Code cleanup (changed some syntax to be more Pythonic).
+- Modified some code to work with the latest version of 
+  [Simphony](https://github.com/BYUCamachoLab/simphony).
+
+### Removed
+- None
+
+---
+
+## [1.3.1](https://github.com/BYUCamachoLab/SiPANN/releases/tag/v1.3.1) - <small></small>
+
+This version is mostly a maintenance update. We have added
+
+* Continuous Integration via github actions
+* precommit hooks to keep code maintained
+* Small bug fix in `SiPANN.scee.Waveguide`. It should now work properly with `SiPANN.scee_int.SimphonyWrapper`.

Makefile

@@ -1,10 +1,15 @@
 
 install:
-	pip install -r requirements.txt --upgrade
-	pip install -e .
+	pip install -e .[dev]
 	pip install pre-commit
 	pre-commit install
 
+book:
+	jb build docs
+
+serve:
+	cd docs/_build/html/ && python -m http.server 0
+
 lint:
 	flake8
 

README.md

@@ -0,0 +1,123 @@
+# SiPANN 2.0.0
+
+<div style="text-align: left">
+<a href="https://pypi.python.org/pypi/SiPANN"><img alt="PyPI Version" src="https://img.shields.io/pypi/v/SiPANN.svg"></a>
+<a href="https://github.com/BYUCamachoLab/SiPANN/actions?query=workflow%3A%22build+%28pip%29%22"><img alt="Build Status" src="https://github.com/BYUCamachoLab/SiPANN/workflows/build%20(pip)/badge.svg"></a>
+<a href="https://github.com/pre-commit/pre-commit"><img src="https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white" alt="pre-commit" style="max-width:100%;"></a>
+<a href="https://sipann.readthedocs.io/en/latest/?badge=latest"><img alt="Documentation Status" src="https://readthedocs.org/projects/sipann/badge/?version=latest"></a>
+<a href="https://pypi.python.org/pypi/SiPANN/"><img alt="License" src="https://img.shields.io/pypi/l/SiPANN.svg"></a>
+<a href="https://github.com/BYUCamachoLab/SiPANN/commits/master"><img alt="Latest Commit" src="https://img.shields.io/github/last-commit/BYUCamachoLab/SiPANN.svg"></a>
+</div>
+
+**Si**licon **P**hotonics with **A**rtificial **N**eural **N**etworks. SiPANN aims to implement various silicon photonics simulators based on machine learning techniques found in literature. The majority of these techniques are linear regression or neural networks. As a results SiPANN can return scattering parameters of (but not limited to)
+
+* Half Rings
+* Arbitrarily shaped directional couplers
+* Racetrack Resonators
+* Waveguides
+
+And with the help of [simphony](https://github.com/BYUCamachoLab/simphony) and 
+SiPANN's accompanying simphony wrapper
+
+* Ring Resonators
+* Doubly Coupled Rings
+* Hybrid Devices (ie Green Machine)
+
+## Installation
+
+SiPANN is distributed via [PyPI](https://pypi.org/project/SiPANN/) and can be installed with ``pip``:
+
+```{bash}
+pip install SiPANN
+```
+
+Note that some dependencies (``gdspy``) require building from source. You'll
+need the Python3 dev package:
+
+```{bash}
+sudo apt-get install python3-dev
+```
+
+SiPANN depends on TensorFlow. This is a large package (~500 MB)! Installation 
+may take a while. Additionally, if you're on a machine with a GPU, you'll need
+to install CUDA. Alternatively, you can tell TensorFlow to ignore the GPU
+by first setting the environment variable:
+
+```{bash}
+export CUDA_VISIBLE_DEVICES=0
+```
+
+This package also depends on ``nlopt``, which does not currently provide PyPI
+builds for M-series Macs. If you're on an M-series Mac, you'll need to install
+``nlopt`` manually.
+
+```{bash}
+
+## Developmental Build
+
+If you want a developmental build, it can be had by executing
+
+```{bash}
+git clone https://github.com/contagon/SiPANN.git
+pip install -e SiPANN/
+```
+
+This development version allows you to make changes to this code directly (or pull changes from GitHub) without having to reinstall SiPANN each time.
+
+You should then be able to run the examples and tutorials in the examples folder, and call SiPANN from any other python file.
+
+````{note}
+
+If installing on Windows, one of SiPANN's dependencies, ``gdspy``, requires a C compiler for installation. This can be bypassed by first installing the ``gdspy`` wheel. This is done by downloading the wheel from [gdspy](https://github.com/heitzmann/gdspy/releases), navigating to the location of the wheel, and executing
+
+```{bash}
+pip install gds*.whl
+```
+
+After this simply install SiPANN using your desired method.
+````
+
+## References
+
+SiPANN is based on a variety of methods found in various papers, including:
+
+[1] A. Hammond, E. Potokar, and R. Camacho, "Accelerating silicon photonic parameter extraction using artificial neural networks," OSA Continuum  2, 1964-1973 (2019).
+
+## Bibtex citation
+
+```
+@misc{SiP-ANN_2019,
+   title={SiP-ANN},
+   author={Easton Potokar, Alec M. Hammond, Ryan M. Camacho},
+   year={2019},
+   publisher={GitHub},
+   howpublished={{https://github.com/contagon/SiP-ANN}}
+}
+```
+
+## Releasing
+
+Make sure you have committed a changelog file titled 
+"[major].[minor].[patch]-changelog.md" before bumping version. 
+
+To bump version prior to a release, run one of the following commands:
+
+```{bash}
+bumpversion major
+bumpversion minor
+bumpversion patch
+```
+
+This will automatically create a git tag in the repository with the 
+corrresponding version number and commit the modified files (where version
+numbers were updated). Pushing the tags (a manual process) to the remote will 
+automatically create a new release. Releases are automatically published to 
+PyPI and GitHub when git tags matching the "v*" pattern are created 
+(e.g. "v0.2.1"), as bumpversion does.
+
+To view the tags on the local machine, run ``git tag``. To push the tags to
+the remote server, you can run ``git push origin <tagname>``.
+
+For code quality, please run isort and black before committing (note that the
+latest release of isort may not work through VSCode's integrated terminal, and
+it's safest to run it separately through another terminal).