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34 changes: 26 additions & 8 deletions README.md
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Expand Up @@ -27,21 +27,39 @@

## Getting Started

### Human-Readable Documentation and Examples
### Natural Language or Python

The following human-readable documentation and examples are useful for new starters:
You can use **PyAutoGalaxy** by describing what you want in natural language, through the
[**PyAutoGalaxy AI Assistant**](https://github.com/PyAutoLabs/autogalaxy_assistant), or by writing Python yourself. Both
routes use the same software. To start in natural language, paste this prompt into Claude Code, Codex or another AI
coding agent:

<sub><b>Starting prompt for Claude Code, Codex or other AI coding agent</b></sub>

```text
I want to study galaxy structure and morphology with PyAutoGalaxy (https://github.com/PyAutoLabs/PyAutoGalaxy)
and the autogalaxy_assistant (https://github.com/PyAutoLabs/autogalaxy_assistant). First clone that
repository, cd into it and follow its AGENTS.md.

Begin the "start here" guide for a new user.
```

The assistant takes you through the [Start Here](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_1_start_here.html) page as a conversation (grids, light profiles and bulge-plus-disk galaxies, then simulating and fitting a galaxy image), one step at a time, then
helps you get started on your own galaxies. Claude Code and Codex are recommended, and sustained scientific use
normally needs paid access to one of them. Free options are listed on the
[AI Options](https://github.com/PyAutoLabs/PyAutoScientist/blob/main/AI_OPTIONS.md) page.
[Start Here](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_1_start_here.html#natural-language-or-python) explains why **PyAutoGalaxy** is designed to be used in natural
language, and why its Python API is not going anywhere.

### Documentation and Examples

All of the documentation and examples are written for people to read:

- [The PyAutoGalaxy readthedocs](https://pyautogalaxy.readthedocs.io/en/latest), which includes [an overview of PyAutoGalaxy's core features](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_1_start_here.html), [a new user starting guide](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_2_new_user_guide.html) and [an installation guide](https://pyautogalaxy.readthedocs.io/en/latest/installation/overview.html).
- [The introduction Jupyter Notebook on Google Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.10.29.1/start_here.ipynb), where you can try **PyAutoGalaxy** in a web browser (without installation).
- [The autogalaxy_workspace GitHub repository](https://github.com/PyAutoLabs/autogalaxy_workspace): example scripts covering every **PyAutoGalaxy** use case.
- [The HowToGalaxy GitHub repository](https://github.com/PyAutoLabs/HowToGalaxy): a Jupyter notebook lecture series teaching galaxy modeling from the ground up.

### PyAutoGalaxy AI Assistant

The [**PyAutoGalaxy AI Assistant**](https://github.com/PyAutoLabs/autogalaxy_assistant) lets you do galaxy structure and morphology science in natural language from inside an AI coding agent. You can get started simply by asking it a question about galaxy structure or describing the task you would like to perform with **PyAutoGalaxy**. See the assistant for its full scope and instructions.

**The assistant runs inside an AI coding agent: Claude Code or Codex are recommended. Sustained scientific use normally needs paid access to one of them (a personal subscription, institutional access or API billing). OpenCode is an experimental alternative whose client is free but whose model access, cost and capability depend on the provider. Browser chat routes (ChatGPT or Claude with a GitHub connector) are no longer supported.**

## Core Aims

**PyAutoGalaxy** has three core aims:
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59 changes: 59 additions & 0 deletions docs/_static/pyautogalaxy.css
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@@ -0,0 +1,59 @@
/* PyAutoGalaxy-only docs layer. The shared brand file `pyauto.css` is byte-identical
across PyAutoFit / PyAutoGalaxy / PyAutoLens, so repo-specific rules live here
instead of diverging it. The natural-language prompt block below is copied
from PyAutoFit's `pyautofit.css` so prompts look the same in all three docs. */

/* Natural-language prompt blocks. A prompt is written as a blockquote wrapped in
`:::{container} nl-prompt`, which gives it two things a plain blockquote has
not got: a label saying what the block is, and a copy button so the prompt can
be pasted straight into an AI coding agent. The label text lives here in
`content:` so every prompt on every overview page picks it up simply by being
wrapped in the same container — nothing is repeated in the Markdown.

The container is the positioning context for the copy button, which
sphinx-copybutton inserts as a sibling of the blockquote (see
`copybutton_selector` in conf.py). */
.nl-prompt {
position: relative;
margin: 1.2rem 0;
}

.nl-prompt::before {
content: "Example Natural Language Prompt for Claude Code, Codex or other AI coding agent";
display: block;
/* Keeps the label clear of the copy button when it wraps on narrow screens. */
padding-right: 2.5rem;
margin-bottom: 0.35rem;
font-size: 0.7rem;
font-weight: 600;
letter-spacing: 0.06em;
text-transform: uppercase;
line-height: 1.4;
color: var(--color-foreground-muted);
}

/* sphinx-copybutton's own stylesheet positions the button against `.highlight`
code blocks and hard-codes GitHub's light-mode colours; both are re-stated
here in Furo's theme variables so the button sits in the prompt container and
follows light/dark mode. Idle at low opacity (like a code block's button),
full opacity on hover or after a successful copy. */
.nl-prompt button.copybtn {
position: absolute;
top: 0;
right: 0;
opacity: 0.35;
border: 1px solid var(--color-background-border);
background-color: var(--color-background-secondary);
color: var(--color-foreground-muted);
}

.nl-prompt:hover button.copybtn,
.nl-prompt button.copybtn:focus-visible,
.nl-prompt button.copybtn.success {
opacity: 1;
}

.nl-prompt button.copybtn:hover {
background-color: var(--color-background-hover);
color: var(--color-brand-content);
}
12 changes: 11 additions & 1 deletion docs/conf.py
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todo_include_todos = True

# -- Options for copybutton --------------------------------------------------

# The default selector is "div.highlight pre" (code blocks only). The second
# entry adds the natural-language prompt blocks: any blockquote wrapped in a
# `:::{container} nl-prompt` aside gets its own copy button, so a reader can
# lift the prompt straight into an AI coding agent. The button is inserted as a
# sibling of the blockquote, inside the container, and copies the blockquote's
# innerText (the plain prompt, without the Markdown "> " markers).
copybutton_selector = "div.highlight pre, .nl-prompt blockquote"

# -- Options for Markdown files ----------------------------------------------

myst_enable_extensions = ["colon_fence", "deflist", "substitution"]
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language = "en"

html_static_path = ["_static"]
html_css_files = ["pyauto.css"]
html_css_files = ["pyauto.css", "pyautogalaxy.css"]

html_theme_options = {
"light_css_variables": {
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32 changes: 24 additions & 8 deletions docs/index.md
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# Getting Started

## Human-Readable Documentation and Examples
## Natural Language or Python

The following human-readable documentation and examples are useful for new starters:
You can use **PyAutoGalaxy** by describing what you want in natural language, through the
[**PyAutoGalaxy AI Assistant**](https://github.com/PyAutoLabs/autogalaxy_assistant), or by writing Python yourself. Both
routes use the same software. To start in natural language, paste this prompt into Claude Code, Codex or another AI
coding agent:

:::{container} nl-prompt
> I want to study galaxy structure and morphology with PyAutoGalaxy (https://github.com/PyAutoLabs/PyAutoGalaxy)
> and the autogalaxy_assistant (https://github.com/PyAutoLabs/autogalaxy_assistant). First clone that
> repository, cd into it and follow its AGENTS.md.
>
> Begin the "start here" guide for a new user.
:::

The assistant takes you through the [Start Here](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_1_start_here.html) page as a conversation (grids, light profiles and bulge-plus-disk galaxies, then simulating and fitting a galaxy image), one step at a time, then
helps you get started on your own galaxies. Claude Code and Codex are recommended, and sustained scientific use
normally needs paid access to one of them. Free options are listed on the
[AI Options](https://github.com/PyAutoLabs/PyAutoScientist/blob/main/AI_OPTIONS.md) page.
[Start Here](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_1_start_here.html#natural-language-or-python) explains why **PyAutoGalaxy** is designed to be used in natural
language, and why its Python API is not going anywhere.

## Documentation and Examples

All of the documentation and examples are written for people to read:

- [The PyAutoGalaxy readthedocs](https://pyautogalaxy.readthedocs.io/en/latest/), which includes [an overview of PyAutoGalaxy's core features](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_1_start_here.html), [a new user starting guide](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_2_new_user_guide.html) and [an installation guide](https://pyautogalaxy.readthedocs.io/en/latest/installation/overview.html).
- [The introduction Jupyter Notebook on Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.10.29.1/start_here.ipynb), where you can try **PyAutoGalaxy** in a web browser (without installation).
- [The autogalaxy_workspace GitHub repository](https://github.com/PyAutoLabs/autogalaxy_workspace): example scripts covering every **PyAutoGalaxy** use case.
- [The HowToGalaxy GitHub repository](https://github.com/PyAutoLabs/HowToGalaxy): a Jupyter notebook lecture series teaching galaxy modeling from the ground up.

## PyAutoGalaxy AI Assistant

The [**PyAutoGalaxy AI Assistant**](https://github.com/PyAutoLabs/autogalaxy_assistant) lets you do galaxy structure and morphology science in natural language from inside an AI coding agent. You can get started simply by asking it a question about galaxy structure or describing the task you would like to perform with **PyAutoGalaxy**. See the assistant for its full scope and instructions.

**The assistant runs inside an AI coding agent: Claude Code or Codex are recommended. Sustained scientific use normally needs paid access to one of them (a personal subscription, institutional access or API billing). OpenCode is an experimental alternative whose client is free but whose model access, cost and capability depend on the provider. Browser chat routes (ChatGPT or Claude with a GitHub connector) are no longer supported.**

# Core Aims

**PyAutoGalaxy** has three core aims:
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47 changes: 38 additions & 9 deletions docs/overview/overview_1_start_here.md
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# Start Here

## Human-Readable Overview

**PyAutoGalaxy** is software for analysing the morphologies and structures of galaxies:

```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/paper/hstcombined.png
Expand All @@ -17,13 +15,44 @@
- **Model Complexity**: Fitting complex galaxy morphology models (e.g. Multi Gaussian Expansion, Shapelets, Ellipse Fitting, Irregular Meshes) that go beyond just simple Sérsic fitting.
- **Data Variety**: Support for many data types (e.g. CCD imaging, interferometry, multi-band imaging) which can be fitted independently or simultaneously.

This overview gives an overview of **PyAutoGalaxy**'s API, core features and details of the autogalaxy_workspace.

## PyAutoGalaxy AI Assistant

The [**PyAutoGalaxy AI Assistant**](https://github.com/PyAutoLabs/autogalaxy_assistant) lets you do galaxy structure and morphology science in natural language from inside an AI coding agent. You can get started simply by asking it a question about galaxy structure or describing the task you would like to perform with **PyAutoGalaxy**. See the assistant for its full scope and instructions.

**The assistant runs inside an AI coding agent: Claude Code or Codex are recommended. Sustained scientific use normally needs paid access to one of them (a personal subscription, institutional access or API billing). OpenCode is an experimental alternative whose client is free but whose model access, cost and capability depend on the provider. Browser chat routes (ChatGPT or Claude with a GitHub connector) are no longer supported.**
This page gives an overview of **PyAutoGalaxy**'s API, core features and details of the autogalaxy_workspace.

## Natural Language or Python

You can use **PyAutoGalaxy** by describing what you want in **natural language**, or by writing **Python** yourself.
Both routes use the same software and everything on this page can be done either way.

To use natural language, open Claude Code, Codex or another AI coding agent and paste in the prompt below. The
[PyAutoGalaxy AI Assistant](https://github.com/PyAutoLabs/autogalaxy_assistant) then takes you through this page as a
conversation (grids, light profiles and bulge-plus-disk galaxies, then simulating and fitting a galaxy image), with you
typing each request in plain English. Afterwards it helps you get started on your own galaxies:

:::{container} nl-prompt
> I want to study galaxy structure and morphology with PyAutoGalaxy (https://github.com/PyAutoLabs/PyAutoGalaxy)
> and the autogalaxy_assistant (https://github.com/PyAutoLabs/autogalaxy_assistant). First clone that
> repository, cd into it and follow its AGENTS.md.
>
> Begin the "start here" guide for a new user.
:::

The assistant runs inside an AI coding agent. Claude Code and Codex are recommended, and sustained scientific use
normally needs paid access to one of them. Free options are listed on the
[AI Options](https://github.com/PyAutoLabs/PyAutoScientist/blob/main/AI_OPTIONS.md) page.

**Why natural language?** Turning a scientific idea into an analysis has always meant expressing it through the syntax
of a programming language. That syntax was never the science: it is the interface between your ideas and the
computer. **PyAutoGalaxy** is designed so you can describe a galaxy analysis in the language you use to think and
write about it, while you supply the understanding, direction and judgement. The
[PyAuto AI Policy](https://github.com/PyAutoLabs/PyAutoScientist/blob/main/AI_POLICY.md) explains this approach in
more detail.

**Python is not going anywhere.** Every **PyAutoGalaxy** feature remains available through its Python API, and the
assistant writes ordinary **PyAutoGalaxy** code that you can read, run and change. All the documentation is written
for people to read. The rest of this page is the Python overview, the
[autogalaxy_workspace](https://github.com/PyAutoLabs/autogalaxy_workspace) holds runnable examples for every use case,
and the [HowToGalaxy](https://github.com/PyAutoLabs/HowToGalaxy) lectures teach galaxy structure and galaxy modeling
from first principles. That understanding is what lets you direct an analysis with expertise, whether you do it in
natural language or in Python.

## Imports

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# New User Guide

## Human-Readable Guide

**PyAutoGalaxy** can analyse galaxies for different types of data (e.g. CCD imaging and interferometer observations)
and across a range of system scales (a single galaxy, blended multi-galaxy systems, and cluster fields).
Depending on the data you use and the scale of your system, the analysis you perform may differ significantly.

The autogalaxy_workspace contains a suite of example Jupyter Notebooks, organised by dataset type and system scale.
To help you find the most appropriate starting point, answer two simple questions:

## PyAutoGalaxy AI Assistant

The [**PyAutoGalaxy AI Assistant**](https://github.com/PyAutoLabs/autogalaxy_assistant) lets you do galaxy structure and morphology science in natural language from inside an AI coding agent. You can get started simply by asking it a question about galaxy structure or describing the task you would like to perform with **PyAutoGalaxy**. See the assistant for its full scope and instructions.
To help you find the most appropriate starting point, answer two simple questions.

**The assistant runs inside an AI coding agent: Claude Code or Codex are recommended. Sustained scientific use normally needs paid access to one of them (a personal subscription, institutional access or API billing). OpenCode is an experimental alternative whose client is free but whose model access, cost and capability depend on the provider. Browser chat routes (ChatGPT or Claude with a GitHub connector) are no longer supported.**
**In natural language:** if you are using the [PyAutoGalaxy AI Assistant](https://github.com/PyAutoLabs/autogalaxy_assistant), you can skip
the questions below: describe your galaxies and your data type to the assistant and it will pick the matching
example and work through it with you. The examples below are what the assistant uses, and they remain the best place
to see the Python.

## What Scale System?

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