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4 changes: 3 additions & 1 deletion CLAUDE.md
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Expand Up @@ -96,9 +96,11 @@ Sub-packages within `scripts/` and `notebooks/`:
- `interferometer/` — ALMA/JVLA uv-plane modeling
- `multi/` — Multi-wavelength simultaneous modeling
- `guides/` — API guides: modeling, results, plotting, over-sampling, HPC
- `howtogalaxy/` — Tutorial lecture series
- `ellipse/` — Ellipse fitting (non-parametric morphology)

The tutorial lecture series now lives in its own repository at
`https://github.com/PyAutoLabs/HowToGalaxy`.

Each data-type package contains: `modeling.py`, `simulator.py`, `fit.py`, `features/`, `data_preparation/`, `likelihood_function.py`.

## Core API Patterns
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19 changes: 5 additions & 14 deletions README.rst
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Expand Up @@ -8,8 +8,8 @@ PyAutoGalaxy Workspace

`Installation Guide <https://pyautogalaxy.readthedocs.io/en/latest/installation/overview.html>`_ |
`readthedocs <https://pyautogalaxy.readthedocs.io/en/latest/index.html>`_ |
`Introduction on Colab <https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.4.13.6/start_here.ipynb>`_
`HowToGalaxy <https://pyautogalaxy.readthedocs.io/en/latest/howtogalaxy/howtogalaxy.html>`_
`Introduction on Colab <https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.4.13.6/start_here.ipynb>`_ |
`HowToGalaxy <https://github.com/PyAutoLabs/HowToGalaxy>`_

Welcome to the **PyAutoGalaxy** Workspace!

Expand Down Expand Up @@ -38,18 +38,10 @@ to navigate the workspace for your science case.
HowToGalaxy
-----------

For experienced scientists, the run through above will have been a breeze. Concepts surrounding galaxy structure and
morphology were already familiar and the statistical techniques used for fitting and modeling already understood.
If you are new to galaxy modeling or the statistical techniques it relies on, the **HowToGalaxy** lecture series
takes you from first principles through to modeling real galaxy imaging data. It now lives in its own repository:

For those less familiar with these concepts (e.g. undergraduate students, new PhD students or interested members of the
public), things may have been less clear and a slower more detailed explanation of each concept would be beneficial.

The **HowToGalaxy** Jupyter Notebook lectures are provide exactly this They are a 3+ chapter guide which thoroughly
take you through the core concepts of galaxy light profiles, teach you the principles ofthe statistical techniques
used in modeling and ultimately will allow you to undertake scientific research like a professional astronomer.

If this sounds like it suits you, checkout the `autogalaxy_workspace/notebooks/howtogalaxy` package now, its it
recommended you go here before anywhere else!
https://github.com/PyAutoLabs/HowToGalaxy

Workspace Structure
-------------------
Expand All @@ -68,7 +60,6 @@ The examples in the ``notebooks`` and ``scripts`` folders are structured as foll
- ``imaging``: Examples for galaxy modeling using CCD imaging (e.g. Hubble, James Webb, Euclid).
- ``interferometer``: Examples for galaxies observed with an interferometer (e.g. ALMA, JVLA).
- ``multi``: Examples for modeling galaxies observed in multiple wavebands.
- ``howtogalaxy``: Conceptual tutorials introducing galaxy modeling and inference with **PyAutoGalaxy**.

The dataset packages (e.g. ``imaging``, ``interferometer`` and ``multi``) include the following types of examples:

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2 changes: 0 additions & 2 deletions config/build/env_vars.yaml
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Expand Up @@ -23,8 +23,6 @@ defaults:
overrides:
# Non-simulator scripts that load committed FITS data need full-size
# datasets to avoid shape mismatch with pre-existing 100x100 data.
- pattern: "howtogalaxy/"
unset: [PYAUTO_SMALL_DATASETS]
- pattern: "guides/"
unset: [PYAUTO_SMALL_DATASETS]
# guides/results/start_here.py must produce real samples so the example
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3 changes: 0 additions & 3 deletions config/build/no_run.yaml
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Expand Up @@ -17,7 +17,6 @@
# banner. Investigate the failure, fix the underlying bug, and remove
# the NEEDS_FIX marker.

- tutorial_searches
- guides/results/start_here # SLOW 2026-04-10 - exceeds 60s test timeout; unsets TEST_MODE to produce real samples for downstream examples
- guides/results/examples/galaxies_fit # SLOW 2026-04-10 - exceeds 60s test timeout; unsets TEST_MODE for downstream examples
- guides/results/examples/samples # SLOW 2026-04-10 - exceeds 60s test timeout; unsets TEST_MODE for downstream examples
Expand All @@ -35,8 +34,6 @@
- ellipse/database # Ellipse model needs refactor and JAX support
- ellipse/modeling # NEEDS_FIX 2026-04-10 - KeyError on 'ellipses.0.centre_0' kwargs after API drift in ellipse model
- guides/advanced/over_sampling # NEEDS_FIX 2026-04-10 - plot_grid() got unexpected kwarg 'plot_grid_lines' after plotter API drift
- howtogalaxy/chapter_4_pixelizations/tutorial_2_mappers # NEEDS_FIX 2026-04-10 - IndexError in mapper tutorial, likely empty mapping array
- howtogalaxy/chapter_4_pixelizations/tutorial_5_model_fit # NEEDS_FIX 2026-04-10 - LinAlgError: matrix not positive definite in pixelization fit
- imaging/data_preparation/manual/mask_irregular # NEEDS_FIX 2026-04-10 - silent failure, needs investigation
- imaging/features/pixelization/modeling # NEEDS_FIX 2026-04-10 - LinAlgError: matrix not positive definite in pixelization modeling
- autogalaxy_workspace/scripts/imaging/modeling # NEEDS_FIX 2026-04-10 - KeyError on ('galaxies','galaxy','bulge','ell_comps'...) kwargs after API drift in top-level imaging/modeling.py
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4 changes: 3 additions & 1 deletion notebooks/README.rst
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Expand Up @@ -15,4 +15,6 @@ Folders
- ``interferometer``: Examples for galaxies observed with an interferometer (e.g. ALMA, JVLA).
- ``ellipse``: Examples for perform ellipse isophote fitting on galaxy images.
- ``multi``: Examples for multiple datasets simultaneously (E.g. multi-wavelength imaging, imaging and interferometry).
- ``howtogalaxy``: The **HowToGalaxy** lectures which teach inexperienced scientists what galaxy fitting is and how to use **PyAutoGalaxy**.

The **HowToGalaxy** lecture series, which teaches inexperienced scientists what galaxy fitting is and how to use
**PyAutoGalaxy**, now lives in its own repository: https://github.com/PyAutoLabs/HowToGalaxy
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