diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml new file mode 100644 index 0000000..8fc01b1 --- /dev/null +++ b/.github/workflows/pages.yml @@ -0,0 +1,41 @@ +name: Sphinx docs to gh-pages + +on: + push: + branches: + - main + workflow_dispatch: + +jobs: + sphinx_docs_to_gh-pages: + runs-on: ubuntu-latest + name: Sphinx docs to gh-pages + steps: + - name: Cancel Workflow Action + uses: styfle/cancel-workflow-action@0.11.0 + - uses: actions/checkout@v3 + - uses: conda-incubator/setup-miniconda@v2 + with: + python-version: "3.10" + mamba-version: "*" + channels: conda-forge,defaults + channel-priority: true + activate-environment: anaconda-client-env + - name: Add conda to system path + run: | + echo $CONDA/bin >> $GITHUB_PATH + - name: Installing the library + shell: bash -l {0} + run: | + pip install -r requirements.txt + sudo wget https://github.com/jgm/pandoc/releases/download/1.16.0.2/pandoc-1.16.0.2-1-amd64.deb + sudo dpkg -i pandoc-1.16.0.2-1-amd64.deb + #sudo apt install pandoc + python3 -m pip install sphinx + pip install myst_parser + - name: Running the Sphinx to gh-pages Action + uses: uibcdf/action-sphinx-docs-to-gh-pages@v1.0-beta.2 + with: + branch: main + dir_docs: bootcamp + sphinxopts: "" diff --git a/.gitignore copy b/.gitignore copy new file mode 100644 index 0000000..b6e4761 --- /dev/null +++ b/.gitignore copy @@ -0,0 +1,129 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-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/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ diff --git a/LICENSE copy b/LICENSE copy new file mode 100644 index 0000000..a6bc4b5 --- /dev/null +++ b/LICENSE copy @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2022 CamachoLab + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README copy.md b/README copy.md new file mode 100644 index 0000000..29f037b --- /dev/null +++ b/README copy.md @@ -0,0 +1,2 @@ +# Photonics-Bootcamp +The CamachoLab Photonics Bootcamp, with support from Google. diff --git a/bootcamp/_config.yml b/bootcamp/_config.yml new file mode 100644 index 0000000..2d7eb45 --- /dev/null +++ b/bootcamp/_config.yml @@ -0,0 +1,32 @@ +# Book settings +# Learn more at https://jupyterbook.org/customize/config.html + +title: Google Photonics Bootcamp +author: CamachoLab and Google +logo: logo.png + +# Force re-execution of notebooks on each build. +# See https://jupyterbook.org/content/execute.html +execute: + execute_notebooks: force + +# Define the name of the latex output file for PDF builds +latex: + latex_documents: + targetname: book.tex + +# Add a bibtex file so that we can create citations +bibtex_bibfiles: + - references.bib + +# Information about where the book exists on the web +repository: + url: https://github.com/BYUCamachoLab/sky130ph # Online location of your book + path_to_book: bootcamp # Optional path to your book, relative to the repository root + branch: master # Which branch of the repository should be used when creating links (optional) + +# Add GitHub buttons to your book +# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository +html: + use_issues_button: true + use_repository_button: true diff --git a/bootcamp/_toc.yml b/bootcamp/_toc.yml new file mode 100644 index 0000000..57d4a0b --- /dev/null +++ b/bootcamp/_toc.yml @@ -0,0 +1,58 @@ +# Table of contents +# Learn more at https://jupyterbook.org/customize/toc.html + +format: jb-book +root: intro +parts: + - caption: Introduction + chapters: + - file: pages/introduction + - caption: PDK + chapters: + - file: pages/what_is_a_pdk + - file: pages/gds + - file: pages/components + - file: common_components + sections: + - file: pages/waveguides + - file: pages/y_junctions + - file: pages/directional_couplers + - file: pages/ring_resonators + - file: pages/tapers + - file: pages/mmis + - file: pages/grating_couplers + - file: pages/edge_couplers + - file: pages/phase_shifters_heaters + - file: pages/voas + - file: pages/subcircuits + - caption: Designing Circuits + chapters: + - file: pages/the_mach_zehnder_interferometer + - file: pages/design_for_testing + - file: pages/layout + - caption: Testing + chapters: + - file: pages/equipment + - file: pages/sweeps + - file: pages/analyzing_circuits + - caption: Software References + chapters: + - file: pages/computer_setup + - file: pages/git_and_github + - file: pages/vs_code + - file: pages/makefiles + - file: pages/cmake + - file: pages/python_environments_and_conda + - file: pages/open_source + - file: pages/git_and_github + - file: pages/klayout + - file: pages/gdsfactory + - file: pages/meep + - file: pages/cookiecutter + - caption: Other References + numbered: false + chapters: + - url: https://github.com/BYUCamachoLab/sky130ph + title: Repository + - url: https://github.com/BYUCamachoLab/sky130ph/docs + title: PDK Documentation diff --git a/bootcamp/intro.md b/bootcamp/intro.md new file mode 100644 index 0000000..6e75304 --- /dev/null +++ b/bootcamp/intro.md @@ -0,0 +1,14 @@ +# Welcome to your the Google Photonics Bootcamp + +This bootcamp is intended for those with experience in electrical engineering +but are interested in learning about designing integrated photonic circuits and +their applications. + +This course was created as a collaboration between +[CamachoLab at Brigham Young University](https://camacholab.byu.edu/) and +[Google's Skywater Project](https://skywater-pdk.readthedocs.io/en/main/). + +## Contents + +```{tableofcontents} +``` diff --git a/bootcamp/logo.png b/bootcamp/logo.png new file mode 100644 index 0000000..06d56f4 Binary files /dev/null and b/bootcamp/logo.png differ diff --git a/bootcamp/markdown.md b/bootcamp/markdown.md new file mode 100644 index 0000000..0ddaab3 --- /dev/null +++ b/bootcamp/markdown.md @@ -0,0 +1,55 @@ +# Markdown Files + +Whether you write your book's content in Jupyter Notebooks (`.ipynb`) or +in regular markdown files (`.md`), you'll write in the same flavor of markdown +called **MyST Markdown**. +This is a simple file to help you get started and show off some syntax. + +## What is MyST? + +MyST stands for "Markedly Structured Text". It +is a slight variation on a flavor of markdown called "CommonMark" markdown, +with small syntax extensions to allow you to write **roles** and **directives** +in the Sphinx ecosystem. + +For more about MyST, see [the MyST Markdown Overview](https://jupyterbook.org/content/myst.html). + +## Sample Roles and Directives + +Roles and directives are two of the most powerful tools in Jupyter Book. They +are kind of like functions, but written in a markup language. They both +serve a similar purpose, but **roles are written in one line**, whereas +**directives span many lines**. They both accept different kinds of inputs, +and what they do with those inputs depends on the specific role or directive +that is being called. + +Here is a "note" directive: + +```{note} +Here is a note +``` + +It will be rendered in a special box when you build your book. + +Here is an inline directive to refer to a document: {doc}`markdown-notebooks`. + + +## Citations + +You can also cite references that are stored in a `bibtex` file. For example, +the following syntax: `` {cite}`holdgraf_evidence_2014` `` will render like +this: {cite}`holdgraf_evidence_2014`. + +Moreover, you can insert a bibliography into your page with this syntax: +The `{bibliography}` directive must be used for all the `{cite}` roles to +render properly. +For example, if the references for your book are stored in `references.bib`, +then the bibliography is inserted with: + +```{bibliography} +``` + +## Learn more + +This is just a simple starter to get you started. +You can learn a lot more at [jupyterbook.org](https://jupyterbook.org). diff --git a/bootcamp/references.bib b/bootcamp/references.bib new file mode 100644 index 0000000..7306e20 --- /dev/null +++ b/bootcamp/references.bib @@ -0,0 +1,56 @@ +--- +--- + +@inproceedings{holdgraf_evidence_2014, + address = {Brisbane, Australia, Australia}, + title = {Evidence for {Predictive} {Coding} in {Human} {Auditory} {Cortex}}, + booktitle = {International {Conference} on {Cognitive} {Neuroscience}}, + publisher = {Frontiers in Neuroscience}, + author = {Holdgraf, Christopher Ramsay and de Heer, Wendy and Pasley, Brian N. and Knight, Robert T.}, + year = {2014} +} + +@article{holdgraf_rapid_2016, + title = {Rapid tuning shifts in human auditory cortex enhance speech intelligibility}, + volume = {7}, + issn = {2041-1723}, + url = {http://www.nature.com/doifinder/10.1038/ncomms13654}, + doi = {10.1038/ncomms13654}, + number = {May}, + journal = {Nature Communications}, + author = {Holdgraf, Christopher Ramsay and de Heer, Wendy and Pasley, Brian N. and Rieger, Jochem W. and Crone, Nathan and Lin, Jack J. and Knight, Robert T. and Theunissen, Frédéric E.}, + year = {2016}, + pages = {13654}, + file = {Holdgraf et al. - 2016 - Rapid tuning shifts in human auditory cortex enhance speech intelligibility.pdf:C\:\\Users\\chold\\Zotero\\storage\\MDQP3JWE\\Holdgraf et al. - 2016 - Rapid tuning shifts in human auditory cortex enhance speech intelligibility.pdf:application/pdf} +} + +@inproceedings{holdgraf_portable_2017, + title = {Portable learning environments for hands-on computational instruction using container-and cloud-based technology to teach data science}, + volume = {Part F1287}, + isbn = {978-1-4503-5272-7}, + doi = {10.1145/3093338.3093370}, + abstract = {© 2017 ACM. There is an increasing interest in learning outside of the traditional classroom setting. This is especially true for topics covering computational tools and data science, as both are challenging to incorporate in the standard curriculum. These atypical learning environments offer new opportunities for teaching, particularly when it comes to combining conceptual knowledge with hands-on experience/expertise with methods and skills. Advances in cloud computing and containerized environments provide an attractive opportunity to improve the efficiency and ease with which students can learn. This manuscript details recent advances towards using commonly-Available cloud computing services and advanced cyberinfrastructure support for improving the learning experience in bootcamp-style events. We cover the benets (and challenges) of using a server hosted remotely instead of relying on student laptops, discuss the technology that was used in order to make this possible, and give suggestions for how others could implement and improve upon this model for pedagogy and reproducibility.}, + booktitle = {{ACM} {International} {Conference} {Proceeding} {Series}}, + author = {Holdgraf, Christopher Ramsay and Culich, A. and Rokem, A. and Deniz, F. and Alegro, M. and Ushizima, D.}, + year = {2017}, + keywords = {Teaching, Bootcamps, Cloud computing, Data science, Docker, Pedagogy} +} + +@article{holdgraf_encoding_2017, + title = {Encoding and decoding models in cognitive electrophysiology}, + volume = {11}, + issn = {16625137}, + doi = {10.3389/fnsys.2017.00061}, + abstract = {© 2017 Holdgraf, Rieger, Micheli, Martin, Knight and Theunissen. Cognitive neuroscience has seen rapid growth in the size and complexity of data recorded from the human brain as well as in the computational tools available to analyze this data. This data explosion has resulted in an increased use of multivariate, model-based methods for asking neuroscience questions, allowing scientists to investigate multiple hypotheses with a single dataset, to use complex, time-varying stimuli, and to study the human brain under more naturalistic conditions. These tools come in the form of “Encoding” models, in which stimulus features are used to model brain activity, and “Decoding” models, in which neural features are used to generated a stimulus output. Here we review the current state of encoding and decoding models in cognitive electrophysiology and provide a practical guide toward conducting experiments and analyses in this emerging field. Our examples focus on using linear models in the study of human language and audition. We show how to calculate auditory receptive fields from natural sounds as well as how to decode neural recordings to predict speech. The paper aims to be a useful tutorial to these approaches, and a practical introduction to using machine learning and applied statistics to build models of neural activity. The data analytic approaches we discuss may also be applied to other sensory modalities, motor systems, and cognitive systems, and we cover some examples in these areas. In addition, a collection of Jupyter notebooks is publicly available as a complement to the material covered in this paper, providing code examples and tutorials for predictive modeling in python. The aimis to provide a practical understanding of predictivemodeling of human brain data and to propose best-practices in conducting these analyses.}, + journal = {Frontiers in Systems Neuroscience}, + author = {Holdgraf, Christopher Ramsay and Rieger, J.W. and Micheli, C. and Martin, S. and Knight, R.T. and Theunissen, F.E.}, + year = {2017}, + keywords = {Decoding models, Encoding models, Electrocorticography (ECoG), Electrophysiology/evoked potentials, Machine learning applied to neuroscience, Natural stimuli, Predictive modeling, Tutorials} +} + +@book{ruby, + title = {The Ruby Programming Language}, + author = {Flanagan, David and Matsumoto, Yukihiro}, + year = {2008}, + publisher = {O'Reilly Media} +} diff --git a/bootcamp/requirements.txt b/bootcamp/requirements.txt new file mode 100644 index 0000000..7e821e4 --- /dev/null +++ b/bootcamp/requirements.txt @@ -0,0 +1,3 @@ +jupyter-book +matplotlib +numpy diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..7e821e4 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,3 @@ +jupyter-book +matplotlib +numpy