initial commit

.github/workflows/deploy.yml

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+name: deploy
+
+on:
+  # Trigger the workflow on push to main branch
+  push:
+    branches:
+      - main
+
+# This job installs dependencies, build the book, and pushes it to `gh-pages`
+jobs:
+  build-and-deploy-book:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.9]
+    steps:
+    - uses: actions/checkout@v2
+
+    # Install dependencies
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: apt install system packages
+      run: |
+        sudo apt install -y graphviz ffmpeg
+    - name: Install dependencies
+      run: |
+        pip install pip --upgrade
+        pip install uv
+        uv pip install -r requirements.txt --system
+
+    # Build the book
+    - name: Build the book
+      run: |
+        jupyter-book build doc
+
+    # Deploy the book's HTML to gh-pages branch
+    - name: GitHub Pages action
+      uses: peaceiris/actions-gh-pages@v3.6.1
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: doc/_build/html

.gitignore

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+# 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/
+.DS_Store
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# builds
+**/_build/**

CODE_OF_CONDUCT.md

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+We adopt a code of conduct that ensures a productive, respectful environment for all open source contributors and participants. We are committed to providing a strong and enforced code of conduct and expect everyone in our community to follow these guidelines when interacting with others in all forums. Our goal is to keep ours a positive, inclusive, thriving, and growing community. The community of participants in open source Astronomy projects such as this present work includes members from around the globe with diverse skills, personalities, and experiences. It is through these differences that our community experiences success and continued growth.
+
+We expect all contributors to adhere to the following principles:
+
+We treat each other with respect and do not tolerate any form of discrimination based on ethnicity, gender, disability, religion or belief, age or sexual orientation or identity. We believe that science is a diverse endeavor: diversity provides new impulses, new ideas, new perspectives, and innovation.
+
+We conduct our research and support the research of others with integrity and according to the highest scientific standards. We are committed to scientific integrity and abiding by the guidelines of good scientific practice. We value scientific quality over quantity.
+
+We discuss problems and implement solutions openly and respectfully; we communicate the principles and processes that underlie our actions and decisions.
+
+We recognize the achievements of others, give credit where it is due, and offer constructive feedback when necessary. Science and innovation depend on an open and constructive discourse in which new ideas can be freely exchanged and old wisdom challenged.
+
+We support each other in achieving our goals by nurturing trust and cooperation and respecting individual capabilities and needs. We know that research is often highly competitive, and people can feel under pressure to produce results. Because of these circumstances, we are committed to being mindful of personal boundaries and contributing to a nurturing work environment based on trust and mutual respect.
+
+Any violations of this Code of Conduct should be reported to any of the core authors of this project.

CONTRIBUTING.md

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+Please open a new issue or new pull request for bugs, feedback, or new features you would like to see. If there is an issue you would like to work on, please leave a comment, and we will be happy to assist. New contributions and contributors are very welcome!

doc/_config.yml

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+#######################################################################################
+# A default configuration that will be loaded for all jupyter books
+# See the documentation for help and more options:
+# https://jupyterbook.org/customize/config.html
+
+#######################################################################################
+# Book settings
+title: jax-astro-guide # The title of the book. Will be placed in the left navbar.
+author: Jaxstronomy # The author of the book
+copyright: "2024" # Copyright year to be placed in the footer
+logo: assets/logo.png # A path to the book logo
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: auto
+  timeout: -1
+
+# 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/JAXtronomy/jax-astro-guide # Online location of your book
+  path_to_book: docs # Optional path to your book, relative to the repository root
+  branch: main # 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

doc/_toc.yml

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+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: intro
+
+parts:
+  - caption: Introduction
+    chapters:
+      - file: chapters/preface
+      - file: chapters/requirements
+
+  - caption: jax
+    chapters:
+      - file: chapters/jax/introduction
+
+  - caption: numpyro
+    chapters:
+      - file: chapters/numpyro/introduction

doc/chapters/jax/introduction.md

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+# Jax

doc/chapters/numpyro/introduction.md

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+# Numpyro

doc/chapters/preface.md

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+# Preface

doc/chapters/requirements.md

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+# Prerequisites
+
+This repo uses the Python 3 programming language, along with a standard set of numerical and data visualization tools in astronomy, scientific experiments, and open-source projects. According to regular surveys, Python is the primary programming language of about 80% of astronomers today. By learning the Python language, you will join a community of millions of software developers and data scientists.
+
+## Getting Started.
+
+A Python program can be executed by any computer, regardless of manufacturer or operating system, provided that support for the language is installed. If you wish to install the version of Python and the libraries that will match this book, we recommend the Python 3 language interpreter. You can also use web-based environments such as [Google Colab](https://colab.research.google.com/), [Deepnote](https://deepnote.com), etc.
+
+This text includes a complete introduction to all of these computational tools. You will learn to write programs, generate figures and files from data, and work with public real-world data sets.

doc/intro.md

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+# A primer on Data Science in Astronomy
+
+This repository is a tentative book on the basics of varied tools using Astronomy language.
+
+This book uses Python as the default programming language.
+
+:::{note}
+Python occupies a large fraction of software development in astronomy today.
+But other languages are as valid for data science.
+:::
+
+:::{warning}
+This page is not updated from the template
+:::
+
+Check out the content pages bundled with this sample book to see more.
+
+
+# Acknowledgements
+
+Jupyter Book is supported by an [open community of contributors](https://github.com/executablebooks/jupyter-book/graphs/contributors), many of whom come from [the Executable Books Community](https://executablebooks.org) and [the Jupyter community](https://jupyter.org/community).
+
+::::{grid} 2 2 2 2
+
+:::{grid-item}
+:columns: 4
+
+```{image} https://sloan.org/storage/app/media/uploaded-files/Logo-1B-SMALL-Gold-Blue.png
+:class: m-auto
+:width: 200px
+```
+
+:::
+
+:::{grid-item}
+:columns: 7
+Many thanks to the Sloan Foundation, which [provides support for the Executable Books Project](https://sloan.org/grant-detail/9231).
+:::

requirements.txt

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+Cython
+astropy
+dask
+distributed
+flax
+ghp-import
+graphviz
+jax
+jaxlib
+jupyter-book
+jupytext
+matplotlib
+numpy
+pandas
+plotly
+pytest
+scikit-learn
+snakemake
+tensorflow
+torch
+numpyro