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Merge pull request #7 from Arcadia-Science/ek/full-codebase-review
Full codebase review
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‎.github/workflows/publish.yml‎

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# This workflow is taken from
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# https://quarto.org/docs/publishing/github-pages.html#github-action, which
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# contains other useful information.
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on:
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workflow_dispatch:
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push:
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branches: publish
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name: Quarto Publish
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jobs:
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build-deploy:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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- name: Render and Publish
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uses: quarto-dev/quarto-actions/publish@v2
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with:
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target: gh-pages
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.gitignore‎

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# Claude Code
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CLAUDE.md
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# UV
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# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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#uv.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/latest/usage/project/#working-with-version-control
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.pdm.toml
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.pdm-python
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.pdm-build/
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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# PyPI configuration file
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.pypirc
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.DS_Store
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# Quarto
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/.quarto/
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/_site/
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/*_files/

‎.pre-commit-config.yaml‎

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exclude: (_extensions/|_freeze/|input/|output/)
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.1.0
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hooks:
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- id: check-yaml
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- id: check-toml
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- id: check-json
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- id: check-case-conflict
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- id: check-merge-conflict
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- id: check-symlinks
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- id: debug-statements
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- id: trailing-whitespace
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- id: mixed-line-ending
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- id: end-of-file-fixer
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- repo: local
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hooks:
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- id: format
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name: Format
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entry: make format
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language: system
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pass_filenames: false
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- id: lint
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name: Lint
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entry: make lint
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language: system
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pass_filenames: false

‎LICENSE‎

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MIT License
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Copyright (c) 2024 Arcadia Science
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎Makefile‎

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.PHONY: lint
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lint:
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ruff check --exit-zero .
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ruff format --check .
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.PHONY: format
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format:
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ruff check --fix .
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ruff format .
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.PHONY: pre-commit
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pre-commit:
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pre-commit run --all-files
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.PHONY: test
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test:
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pytest -v .
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.PHONY: execute
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execute:
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# Project-wide render without executing code cells. Instead, rely on
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# pre-computed results present in _freeze/
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quarto render
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# Now, render `index.ipynb`, with code execution. This will populate
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# _freeze/index/ with pre-computed results.
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quarto render index.ipynb --execute
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.PHONY: preview
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preview:
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quarto preview
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.PHONY: bump-version
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bump-version:
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python _bump_version.py

‎README.md‎

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# Notebook Publication Template
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This repo is a template for Jupyter notebook publications. The template produces a publication rendered and hosted by Quarto, which can be viewed at [this demo URL](https://arcadia-science.github.io/notebook-pub-template/).
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## Template Documentation
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All the learning resources for this template can be found in `developer-docs/`.
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- [Quickstart Guide](developer-docs/QUICKSTART.md) - **The most efficient way to get started** is to follow this guide (the rest can wait)
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- [Environment Setup Guide](developer-docs/ENVIRONMENT_SETUP.md) - How to set up your development environment
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- [Publishing Guide](developer-docs/PUBLISHING_GUIDE.md) - How to publish your notebook publication
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- [Template Architecture](developer-docs/TEMPLATE_ARCHITECTURE.md) - Understanding the template's structure
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---
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**NOTE: When ready to publish, fill in the information below, then delete this line and everything above it.**
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# [PUB-TITLE]
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This code repository contains or points to all materials required for creating and hosting the publication entitled, *"[PUB-TITLE]"*.
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The publication is hosted at [this URL]([PUB-URL]).
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## Data Description
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[DESCRIPTION OF THE DATA]
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## Reproduce
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Please see [SETUP.qmd](SETUP.qmd).
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## Contribute
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Please see [CONTRIBUTING.qmd](CONTRIBUTING.qmd).

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