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‎.github/workflows/docs.yml‎

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name: Build and deploy Astro docs
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on:
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push:
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branches: [main]
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workflow_dispatch:
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permissions:
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contents: read
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pages: write
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id-token: write
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout your repository using git
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uses: actions/checkout@v6
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- name: Install, build, and upload your site
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uses: withastro/action@v5
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with:
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path: './docs'
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deploy:
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needs: build
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runs-on: ubuntu-latest
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.github/workflows/lint.yml‎

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- uses: actions/checkout@v4
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- uses: chartboost/ruff-action@v1
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with:
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src: "./pyenzyme"
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src: './pyenzyme'
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- uses: chartboost/ruff-action@v1
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with:
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src: "./tests"
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src: './tests'

‎.github/workflows/publish.yaml‎

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: 'Build and publish to PyPi'
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uses: JRubics/poetry-publish@v2.0
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with:
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pypi_token: ${{ secrets.PYPI_API_TOKEN }}
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- name: Checkout
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uses: actions/checkout@v6
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Build
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run: uv build
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- name: Smoke test (wheel)
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run: uv run --isolated --no-project --with dist/*.whl tests/smoke_test.py
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- name: Smoke test (source distribution)
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run: uv run --isolated --no-project --with dist/*.tar.gz tests/smoke_test.py
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- name: Publish to PyPI
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run: uv publish
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env:
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UV_PUBLISH_TOKEN: ${{ secrets.PYPI_API_TOKEN }}

‎.github/workflows/remote-tests.yaml‎

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name: Remote Tests
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on: [push]
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jobs:
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remote-tests:
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runs-on: ubuntu-latest
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strategy:
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max-parallel: 4
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fail-fast: false
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matrix:
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python-version: ['3.10', '3.11', '3.12', '3.13']
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steps:
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- name: Checkout
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uses: actions/checkout@v6
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Install the project
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run: uv sync --locked --all-extras --all-groups
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- name: Run remote tests
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run: uv run pytest -vv -m "remote"

‎.github/workflows/test-publish.yaml‎

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: 'Build and publish to TestPyPi'
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uses: JRubics/poetry-publish@v2.0
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with:
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pypi_token: ${{ secrets.TEST_PYPI_TOKEN }}
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repository_name: 'testpypi'
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repository_url: 'https://test.pypi.org/legacy/'
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- uses: actions/checkout@v6
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Build
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run: uv build
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- name: Smoke test (wheel)
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run: uv run --isolated --no-project --with dist/*.whl tests/smoke_test.py
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- name: Smoke test (source distribution)
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run: uv run --isolated --no-project --with dist/*.tar.gz tests/smoke_test.py
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- name: Publish to TestPyPI
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run: uv publish --publish-url https://test.pypi.org/legacy/
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env:
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UV_PUBLISH_TOKEN: ${{ secrets.TEST_PYPI_API_TOKEN }}

‎.github/workflows/unit-tests.yaml‎

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steps:
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- name: Checkout
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uses: actions/checkout@v4
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uses: actions/checkout@v6
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python3 -m pip install --upgrade pip
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python3 -m pip install pytest-cov openpyxl pytest-httpx pysces copasi-basico lmfit seaborn numexpr python-libcombine deepdiff deprecation
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pip3 install -e .
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- name: Test with pytest
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run: |
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python3 -m pytest -v
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Install the project
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run: uv sync --locked --all-extras --all-groups
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- name: Run tests
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run: uv run pytest -vv -m "not remote"

‎docs/.gitignore‎

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# build output
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dist/
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# generated types
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.astro/
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# dependencies
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node_modules/
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# logs
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npm-debug.log*
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yarn-debug.log*
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yarn-error.log*
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pnpm-debug.log*
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# environment variables
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.env
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.env.production
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# macOS-specific files
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.DS_Store

‎docs/Makefile‎

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‎docs/README.md‎

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# Starlight Starter Kit: Basics
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[![Built with Starlight](https://astro.badg.es/v2/built-with-starlight/tiny.svg)](https://starlight.astro.build)
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```
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npm create astro@latest -- --template starlight
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```
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> 🧑‍🚀 **Seasoned astronaut?** Delete this file. Have fun!
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## 🚀 Project Structure
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Inside of your Astro + Starlight project, you'll see the following folders and files:
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```
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.
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├── public/
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├── src/
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│ ├── assets/
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│ ├── content/
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│ │ └── docs/
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│ └── content.config.ts
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├── astro.config.mjs
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├── package.json
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└── tsconfig.json
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```
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Starlight looks for `.md` or `.mdx` files in the `src/content/docs/` directory. Each file is exposed as a route based on its file name.
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Images can be added to `src/assets/` and embedded in Markdown with a relative link.
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Static assets, like favicons, can be placed in the `public/` directory.
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## 🧞 Commands
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All commands are run from the root of the project, from a terminal:
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| Command | Action |
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| :------------------------ | :----------------------------------------------- |
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| `npm install` | Installs dependencies |
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| `npm run dev` | Starts local dev server at `localhost:4321` |
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| `npm run build` | Build your production site to `./dist/` |
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| `npm run preview` | Preview your build locally, before deploying |
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| `npm run astro ...` | Run CLI commands like `astro add`, `astro check` |
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| `npm run astro -- --help` | Get help using the Astro CLI |
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## 👀 Want to learn more?
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Check out [Starlight’s docs](https://starlight.astro.build/), read [the Astro documentation](https://docs.astro.build), or jump into the [Astro Discord server](https://astro.build/chat).

‎docs/_apiref/modules.rst‎

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