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8 changes: 5 additions & 3 deletions README.rst
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Expand Up @@ -34,7 +34,7 @@ PyAutoFit: Classy Probabilistic Programming
`Installation Guide <https://pyautofit.readthedocs.io/en/latest/installation/overview.html>`_ |
`readthedocs <https://pyautofit.readthedocs.io/en/latest/index.html>`_ |
`Introduction on Colab <https://colab.research.google.com/github/PyAutoLabs/autofit_workspace/blob/2026.4.13.6/notebooks/overview/overview_1_the_basics.ipynb>`_ |
`HowToFit <https://pyautofit.readthedocs.io/en/latest/howtofit/howtofit.html>`_
`HowToFit <https://github.com/PyAutoLabs/HowToFit>`_

**PyAutoFit** is a Python based probabilistic programming language for model fitting and Bayesian inference
of large datasets.
Expand All @@ -57,7 +57,9 @@ The following links are useful for new starters:

- `The introduction Jupyter Notebook on Colab <https://colab.research.google.com/github/PyAutoLabs/autofit_workspace/blob/2026.4.13.6/notebooks/overview/overview_1_the_basics.ipynb>`_, where you can try **PyAutoFit** in a web browser (without installation).

- `The autofit_workspace GitHub repository <https://github.com/Jammy2211/autofit_workspace>`_, which includes example scripts and the `HowToFit Jupyter notebook lectures <https://github.com/Jammy2211/autofit_workspace/tree/main/notebooks/howtofit>`_ which give new users a step-by-step introduction to **PyAutoFit**.
- `The autofit_workspace GitHub repository <https://github.com/Jammy2211/autofit_workspace>`_, which includes example scripts demonstrating **PyAutoFit**'s features.

- `The standalone HowToFit repository <https://github.com/PyAutoLabs/HowToFit>`_, a series of Jupyter notebook lectures which give new users a step-by-step introduction to **PyAutoFit**.

Support
-------
Expand All @@ -76,7 +78,7 @@ For users less familiar with Bayesian inference and scientific analysis you may
the **HowToFits** lectures. These teach you the basic principles of Bayesian inference, with the
content pitched at undergraduate level and above.

A complete overview of the lectures `is provided on the HowToFit readthedocs page <https://pyautofit.readthedocs.io/en/latest/howtofit/howtofit.htmll>`_
The lectures are available in the `standalone HowToFit repository <https://github.com/PyAutoLabs/HowToFit>`_.

API Overview
------------
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2 changes: 1 addition & 1 deletion docs/api/analysis.rst
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Expand Up @@ -11,7 +11,7 @@ It acts as an interface between the data, model and the non-linear search.
- `readthedocs: example using Analysis object <https://pyautofit.readthedocs.io/en/latest/overview/model_fit.html>`_.
- `autofit_workspace: simple tutorial <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/overview/simple/fit.ipynb>`_
- `autofit_workspace: complex tutorial <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/overview/complex/fit.ipynb>`_
- `HowToFit: introduction chapter (detailed step-by-step examples) <https://pyautofit.readthedocs.io/en/latest/howtofit/chapter_1_introduction.html>`_
- `HowToFit: tutorial lectures (detailed step-by-step examples) <https://github.com/PyAutoLabs/HowToFit>`_

--------
Analysis
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2 changes: 1 addition & 1 deletion docs/api/database.rst
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Expand Up @@ -10,7 +10,7 @@ inspection, analysis and interpretation.

- `readthedocs: example using database functionality <https://pyautofit.readthedocs.io/en/latest/features/database.html>`_
- `autofit_workspace: tutorial using database <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/database.ipynb>`_
- `HowToFit: database chapter (detailed step-by-step examples) <https://pyautofit.readthedocs.io/en/latest/howtofit/chapter_database.html>`_
- `HowToFit: tutorial lectures (detailed step-by-step examples) <https://github.com/PyAutoLabs/HowToFit>`_

----------
Aggregator
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2 changes: 1 addition & 1 deletion docs/api/model.rst
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Expand Up @@ -14,7 +14,7 @@ It is recommended the `model API cookbooks <https://pyautofit.readthedocs.io/en/
- `readthedocs: example using Collection object <https://pyautofit.readthedocs.io/en/latest/overview/model_complex.html>`_.
- `autofit_workspace: simple tutorial <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/overview/simple/fit.ipynb>`_
- `autofit_workspace: complex tutorial <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/overview/complex/fit.ipynb>`_
- `HowToFit: introduction chapter (detailed step-by-step examples) <https://pyautofit.readthedocs.io/en/latest/howtofit/chapter_1_introduction.html>`_
- `HowToFit: tutorial lectures (detailed step-by-step examples) <https://github.com/PyAutoLabs/HowToFit>`_

------
Models
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2 changes: 1 addition & 1 deletion docs/api/plot.rst
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Expand Up @@ -9,7 +9,7 @@ by **PyAutoFit**.

- `readthedocs: non-linear search example <https://pyautofit.readthedocs.io/en/latest/overview/non_linear_search.html>`_
- `autofit_workspace: plot tutorials <https://github.com/Jammy2211/autofit_workspace/tree/release/notebooks/plot>`_
- `HowToFit: introduction chapter (detailed step-by-step examples) <https://pyautofit.readthedocs.io/en/latest/howtofit/chapter_1_introduction.html>`_
- `HowToFit: tutorial lectures (detailed step-by-step examples) <https://github.com/PyAutoLabs/HowToFit>`_

--------
Plotters
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2 changes: 1 addition & 1 deletion docs/api/priors.rst
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Expand Up @@ -12,7 +12,7 @@ The priors of parameters of every component of a mdoel, which is fitted to data,
- `readthedocs: example using Collection object <https://pyautofit.readthedocs.io/en/latest/overview/model_complex.html>`_.
- `autofit_workspace: simple tutorial <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/overview/simple/fit.ipynb>`_
- `autofit_workspace: complex tutorial <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/overview/complex/fit.ipynb>`_
- `HowToFit: introduction chapter (detailed step-by-step examples) <https://pyautofit.readthedocs.io/en/latest/howtofit/chapter_1_introduction.html>`_
- `HowToFit: tutorial lectures (detailed step-by-step examples) <https://github.com/PyAutoLabs/HowToFit>`_

Priors
------
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2 changes: 1 addition & 1 deletion docs/api/samples.rst
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Expand Up @@ -12,7 +12,7 @@ For example, for an MCMC model-fit, the ``Samples`` objects contains every sampl
- `readthedocs: example on using results <https://pyautofit.readthedocs.io/en/latest/overview/result.html>`_.
- `autofit_workspace: simple results tutorial <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/overview/simple/result.ipynb>`_
- `autofit_workspace: complex result tutorial <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/overview/complex/result.ipynb>`_
- `HowToFit: introduction chapter (detailed step-by-step examples) <https://pyautofit.readthedocs.io/en/latest/howtofit/chapter_1_introduction.html>`_
- `HowToFit: tutorial lectures (detailed step-by-step examples) <https://github.com/PyAutoLabs/HowToFit>`_

Samples
-------
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2 changes: 1 addition & 1 deletion docs/api/searches.rst
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Expand Up @@ -12,7 +12,7 @@ Markov Chain Monte Carlo (MCMC) and Maximum Likelihood Estimators (MLE).
- `readthedocs: example using non-linear searches <https://pyautofit.readthedocs.io/en/latest/overview/non_linear_search.html>`_.
- `autofit_workspace: simple tutorial <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/overview/simple/fit.ipynb>`_
- `autofit_workspace: complex tutorial <https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/overview/complex/fit.ipynb>`_
- `HowToFit: introduction chapter (detailed step-by-step examples) <https://pyautofit.readthedocs.io/en/latest/howtofit/chapter_1_introduction.html>`_
- `HowToFit: tutorial lectures (detailed step-by-step examples) <https://github.com/PyAutoLabs/HowToFit>`_

Nested Samplers
---------------
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2 changes: 1 addition & 1 deletion docs/cookbooks/multiple_datasets.rst
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Expand Up @@ -605,7 +605,7 @@ from large datasets.

**PyAutoFit** has a dedicated feature set for fitting hierarchical and graphical models and interested readers should
checkout the hierarchical and graphical modeling
chapter of **HowToFit** (https://pyautofit.readthedocs.io/en/latest/howtofit/chapter_graphical_models.html)
chapter of **HowToFit** (https://github.com/PyAutoLabs/HowToFit/blob/main/notebooks/chapter_3_graphical_models)

Interpolation
-------------
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10 changes: 6 additions & 4 deletions docs/features/graphical.rst
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Expand Up @@ -67,7 +67,8 @@ This is what our three Gaussians look like:
:alt: Alternative text

They are much lower signal-to-noise than the Gaussian's in other examples. Graphical models extract a lot more information
from lower quantity datasets, something we demonstrate explic in the **HowToFit** lectures on graphical models.
from lower quantity datasets, something we demonstrate explic in the `HowToFit lectures on graphical models
<https://github.com/PyAutoLabs/HowToFit/blob/main/notebooks/chapter_3_graphical_models>`_.

For each dataset we now create a corresponding ``Analysis`` class. By associating each dataset with an ``Analysis``
class we are therefore associating it with a unique ``log_likelihood_function``. If our dataset had many different
Expand Down Expand Up @@ -164,9 +165,10 @@ We can now choose a non-linear search and fit the factor graph.

This will fit the N=7 dimension parameter space where every Gaussian has a shared centre!

This is all expanded upon in the **HowToFit** chapter on graphical models, where we will give a more detailed
description of why this approach to model-fitting extracts a lot more information than fitting each dataset
one-by-one.
This is all expanded upon in the `HowToFit chapter on graphical models
<https://github.com/PyAutoLabs/HowToFit/blob/main/notebooks/chapter_3_graphical_models>`_, where we will give a
more detailed description of why this approach to model-fitting extracts a lot more information than fitting each
dataset one-by-one.

Expectation Propagation
-----------------------
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9 changes: 4 additions & 5 deletions docs/general/workspace.rst
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Expand Up @@ -16,12 +16,11 @@ New users should begin by checking out the following parts of the workspace.
HowToFit
--------

The **HowToFit** lecture series are a collection of Jupyter notebooks describing how to build a **PyAutoFit** model
fitting project and giving illustrations of different statistical methods and techniiques.
The **HowToFit** lecture series is a collection of Jupyter notebooks describing how to build a **PyAutoFit** model
fitting project and giving illustrations of different statistical methods and techniques.

Checkout the
`tutorials section <https://pyautofit.readthedocs.io/en/latest/howtofit/howtofit.html>`_ for a
full description of the lectures and online examples of every notebook.
HowToFit now lives in its own standalone repository at `PyAutoLabs/HowToFit <https://github.com/PyAutoLabs/HowToFit>`_.
Clone or browse the repo for a full description of the lectures and the notebooks for every chapter.

Scripts / Notebooks
-------------------
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