PyAutoLabs · Jammy2211 · May 4, 2026 · Apr 30, 2026 · May 4, 2026
diff --git a/docs/conf.py b/docs/conf.py
@@ -74,7 +74,7 @@
 
 # -- Options for Markdown files ----------------------------------------------
 
-myst_enable_extensions = ["colon_fence", "deflist"]
+myst_enable_extensions = ["colon_fence", "deflist", "substitution"]
 myst_heading_anchors = 3
 
 autosummary_generate = True

diff --git a/docs/general/citations.md b/docs/general/citations.md
@@ -0,0 +1,44 @@
+(references)=
+
+# Citations & References
+
+The bibtex entries for **PyAutoGalaxy** and its affiliated software packages can be found
+[here](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/files/citations.bib), with example text for citing **PyAutoGalaxy**
+in [.tex format here](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/files/citations.tex) format here and
+[.md format here](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/files/citations.md).
+
+**PyAutoGalaxy** is published in the [Journal of Open Source Software](https://joss.theoj.org/papers/10.21105/joss.04475#) and its
+entry in the above .bib file is under the citation key `pyautogalaxy`.
+
+As shown in the examples, we would greatly appreciate it if you mention **PyAutoGalaxy** by name and include a link to
+our GitHub page!
+
+You should also specify the non-linear search(es) you use in your analysis (e.g. Dynesty, Emcee, PySwarms, etc) in
+the main body of text, and delete as appropriate any packages your analysis did not use. The citations.bib file includes
+the citation key for all of these projects.
+
+## Jax-Zero-Contour
+
+If you use the zero-contour method for critical curve and caustic computation (the default in
+`visualize/general.yaml` via `critical_curves_method: zero_contour`), please cite the
+`Jax-Zero-Contour` package by Coleman Krawczyk:
+
+```bibtex
+@software{coleman_krawczyk_2025_15730415,
+  author       = {Coleman Krawczyk},
+  title        = {CKrawczyk/Jax-Zero-Contour: Version 2.0.0},
+  month        = jun,
+  year         = 2025,
+  publisher    = {Zenodo},
+  version      = {v2.0.0},
+  doi          = {10.5281/zenodo.15730415},
+  url          = {https://doi.org/10.5281/zenodo.15730415},
+}
+```
+
+The package is available at <https://github.com/CKrawczyk/Jax-Zero-Contour> and archived at
+<https://doi.org/10.5281/zenodo.15730415>.
+
+## Dynesty
+
+If you used the nested sampling algorithm Dynesty, please follow the citation instructions [on the dynesty readthedocs](https://dynesty.readthedocs.io/en/latest/references.html).
diff --git a/docs/general/citations.rst b/docs/general/citations.rst
diff --git a/docs/general/configs.md b/docs/general/configs.md
@@ -0,0 +1,24 @@
+# Configs
+
+**PyAutoGalaxy** uses a number of configuration files that customize the default behaviour of the non-linear searches,
+visualization and other aspects of **PyAutoGalaxy**.
+
+Descriptions of every configuration file and their input parameters are provided in the `README.rst` in
+the [config directory of the workspace](https://github.com/Jammy2211/autogalaxy_workspace/tree/release/config)
+
+## Setup
+
+By default, **PyAutoGalaxy** looks for the config files in a `config` folder in the current working directory, which is
+why we run autogalaxy scripts from the `autogalaxy_workspace` directory.
+
+The configuration path can also be set manually in a script using the project **PyAutoConf** and the following
+command (the path to the `output` folder where the results of a non-linear search are stored is also set below):
+
+```bash
+from autoconf import conf
+
+conf.instance.push(
+    config_path="path/to/config",
+    output_path=f"path/to/output"
+)
+```
diff --git a/docs/general/configs.rst b/docs/general/configs.rst
diff --git a/docs/general/credits.md b/docs/general/credits.md
@@ -0,0 +1,33 @@
+(credits)=
+
+# Credits
+
+**Developers**:
+
+[James Nightingale](https://github.com/Jammy2211): Lead developer & PyAutoGalaxy guru.
+
+[Richard Hayes](https://github.com/rhayes777): Lead developer & [PyAutoFit](https://github.com/rhayes777/PyAutoFit) guru.
+
+[Aristeidis Amvrosiadis](https://github.com/Sketos): Interferometer Analysis.
+
+[Amy Etherington](https://github.com/amyetherington) : Magnification, Critical Curves and Caustic Calculations.
+
+Qiuhan He: NFW Profile Lensing Calculations.
+
+[Johnathan Frawley](https://github.com/jonathanfrawley): Profiling, optimization and build server tools.
+
+[Ashley Kelly](https://github.com/AshKelly): Developer of [pyquad](https://github.com/AshKelly/pyquad) for fast deflections computations.
+
+[Xiaoyue Cao](https://github.com/caoxiaoyue): Analytic Ellipitcal Power-Law Deflection Angle Calculations.
+
+[Nan Li](https://github.com/linan7788626): Docker integration & support.
+
+**Code Donors**:
+
+[Andrew Robertson](https://github.com/Andrew-Robertson): Critical curve & caustic calculations.
+
+Mattia Negrello: Visibility models in the uv-plane via direct Fourier transforms.
+
+[Andrea Enia](https://github.com/AndreaEnia): Voronoi source-plane plotting tools.
+
+Conor O'Riordan : Broken Power-Law mass profile.
diff --git a/docs/general/credits.rst b/docs/general/credits.rst
diff --git a/docs/general/likelihood_function.rst → docs/general/likelihood_function.md b/docs/general/likelihood_function.rst → docs/general/likelihood_function.md
@@ -1,21 +1,20 @@
-.. _likelihood_function:
-
-Likelihood Function
-===================
-
-The ``autogalaxy_workspace`` contains Jupyter notebooks describing the (log) likelihood functions used by **PyAutoGalaxy**.
-
-The notebooks provide a step-by-step guide of how **PyAutoGalaxy** fits galaxy data, with the aim to make
-the analysis clear to readers without background experience in galaxy modeling and make the modeling less
-of a "black box".
-
-We recommend that when writing a paper using **PyAutoGalaxy** the author links to this GitHub repository when describing
-their likelihood function.
-
-Links to every notebook are provided at the GitHub repository linked to below. We recommend authors link to this
-GitHub repository (as opposed to direct links to each) because the URLs to notebooks on the ``autogalaxy_workspace``
-may change after papers are published.
-
-By linking to this repository a permanent URL is provided.
-
-https://github.com/Jammy2211/autogalaxy_likelihood_function
+(likelihood-function)=
+
+# Likelihood Function
+
+The `autogalaxy_workspace` contains Jupyter notebooks describing the (log) likelihood functions used by **PyAutoGalaxy**.
+
+The notebooks provide a step-by-step guide of how **PyAutoGalaxy** fits galaxy data, with the aim to make
+the analysis clear to readers without background experience in galaxy modeling and make the modeling less
+of a "black box".
+
+We recommend that when writing a paper using **PyAutoGalaxy** the author links to this GitHub repository when describing
+their likelihood function.
+
+Links to every notebook are provided at the GitHub repository linked to below. We recommend authors link to this
+GitHub repository (as opposed to direct links to each) because the URLs to notebooks on the `autogalaxy_workspace`
+may change after papers are published.
+
+By linking to this repository a permanent URL is provided.
+
+<https://github.com/Jammy2211/autogalaxy_likelihood_function>