In the main body of the paper:

We use the probabilistic programming language \textt{PyAutoFit}\footnote{https://github.com/rhayes777/PyAutoFit} \citep{pyautofit} to...

At the end of the paper (delete as appropriate, see https://pyautofit.readthedocs.io/en/latest/general/citations.html):

\section*{Software Citations}

This work uses the following software packages:

\begin{itemize}

\item
\href{https://github.com/dfm/corner.py}{\textt{corner.py}}
\citep{corner}

\item
\href{https://github.com/joshspeagle/dynesty}{\textt{dynesty}}
\citep{dynesty}

\item
\href{https://github.com/dfm/emcee}{\textt{emcee}}
\citep{emcee}

\item
\href{https://github.com/matplotlib/matplotlib}{\textt{matplotlib}}
\citep{matplotlib}

\item
\href{https://github.com/numpy/numpy}{\textt{NumPy}}
\citep{numpy}

\item
\href{https://www.python.org/}{\textt{Python}}
\citep{python}

\item
\href{https://github.com/scipy/scipy}{\textt{Scipy}}
\citep{scipy}

\item
\href{https://www.sqlite.org/index.html}
\citep{sqlite}

\item
\href{https://github.com/minaskar/zeus}{\textt{zeus}}
\citep{zeus1, zeus2}

\end{itemize}