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58 changes: 58 additions & 0 deletions docs/general/citations.md
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(references)=

# Citations & References

The bibtex entries for **PyAutoLens** and its affiliated software packages can be found
[here](https://github.com/Jammy2211/PyAutoLens/blob/main/files/citations.bib), with example text for citing **PyAutoLens**
in [.tex format here](https://github.com/Jammy2211/PyAutoLens/blob/main/files/citations.tex) format here and
[.md format here](https://github.com/Jammy2211/PyAutoLens/blob/main/files/citations.md). As shown in the examples, we
would greatly appreciate it if you mention **PyAutoLens** by name and include a link to our GitHub page!

**PyAutoLens** is published in the [Journal of Open Source Software](https://joss.theoj.org/papers/10.21105/joss.02825#) and its
entry in the above .bib file is under the citation key `pyautolens`. Please also cite the MNRAS AutoLens
papers (<https://academic.oup.com/mnras/article/452/3/2940/1749640> and <https://academic.oup.com/mnras/article-abstract/478/4/4738/5001434?redirectedFrom=fulltext>) which are included
under the citation keys `Nightingale2015` and `Nightingale2018`.

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).

## Mass Models

If you use decomposed mass models (e.g. stellar mass models like an `Sersic` or dark matter models like
an `NFW`) please cite the following paper <https://arxiv.org/abs/2106.11464> under
citation key `Oguri2021`. Our deflection angle calculations are based on this method.

If you specifically use a decomposed mass model with the `gNFW` please cite the following paper <https://academic.oup.com/mnras/article/488/1/1387/5526256> under
citation key `Anowar2019`.

## Science Papers

The citations.bib file above also includes my work on [using strong lensing to study galaxy structure](https://ui.adsabs.harvard.edu/abs/2019MNRAS.489.2049N/abstract). If you're feeling kind, please go ahead and stick
a citation in your introduction using citep\{Nightingale2019} or [@Nightingale2019] ;).
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# Configs

**PyAutoLens** uses a number of configuration files that customize the default behaviour of the non-linear searches,
visualization and other aspects of **PyAutoLens**.

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/autolens_workspace/tree/release/config)

## Setup

By default, **PyAutoLens** looks for the config files in a `config` folder in the current working directory, which is
why we run autolens scripts from the `autolens_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"
)
```
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# Credits

**Developers**:

[James Nightingale](https://github.com/Jammy2211): Lead developer & PyAutoLens 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.
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