diff --git a/CITATIONS.md b/CITATIONS.md new file mode 100644 index 000000000..cb6645ecd --- /dev/null +++ b/CITATIONS.md @@ -0,0 +1,16 @@ +# 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). + +As shown in the examples, we would greatly appreciate it if you mention **PyAutoGalaxy** by name and include a link to +our GitHub page! + +**PyAutoGalaxy** 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 `pyautogalaxy`. + +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. diff --git a/CITATIONS.rst b/CITATIONS.rst deleted file mode 100644 index 26b2b0665..000000000 --- a/CITATIONS.rst +++ /dev/null @@ -1,20 +0,0 @@ -.. _references: - -Citations & References -====================== - -The bibtex entries for **PyAutoGalaxy** and its affiliated software packages can be found -`here `_, with example text for citing **PyAutoGalaxy** -in `.tex format here `_ format here and -`.md format here `_. - -As shown in the examples, we would greatly appreciate it if you mention **PyAutoGalaxy** by name and include a link to -our GitHub page! - -**PyAutoGalaxy** is published in the `Journal of Open Source Software `_ and its -entry in the above .bib file is under the citation key ``pyautogalaxy``. - -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. - diff --git a/MANIFEST.in b/MANIFEST.in index a29c18a7f..fd73f05df 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,8 +1,8 @@ # MANIFEST.in exclude .gitignore -include README.rst +include README.md include setup.cfg -include CITATIONS.rst +include CITATIONS.md include LICENSE include requirements.txt include optional_requirements.txt diff --git a/README.md b/README.md new file mode 100644 index 000000000..0dedf74d7 --- /dev/null +++ b/README.md @@ -0,0 +1,72 @@ +# PyAutoGalaxy: Open-Source Multi Wavelength Galaxy Structure & Morphology + +[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.1.4/start_here.ipynb) +[![Documentation Status](https://readthedocs.org/projects/pyautogalaxy/badge/?version=latest)](https://pyautogalaxy.readthedocs.io/en/latest/?badge=latest) +[![Tests](https://github.com/Jammy2211/PyAutoGalaxy/actions/workflows/main.yml/badge.svg)](https://github.com/Jammy2211/PyAutoGalaxy/actions) +[![Build](https://github.com/Jammy2211/PyAutoBuild/actions/workflows/release.yml/badge.svg)](https://github.com/Jammy2211/PyAutoBuild/actions) +[![Code Style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![JOSS](https://joss.theoj.org/papers/10.21105/joss.04475/status.svg)](https://doi.org/10.21105/joss.04475) +[![pyOpenSci Peer-Reviewed](https://pyopensci.org/badges/peer-reviewed.svg)](https://github.com/pyOpenSci/software-submission/issues/235) +[![Zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7546914.svg)](https://doi.org/10.5281/zenodo.7546914) +[![Project Status: Active](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) +[![Python Versions](https://img.shields.io/pypi/pyversions/autogalaxy)](https://pypi.org/project/autogalaxy/) +[![PyPI Version](https://img.shields.io/pypi/v/autogalaxy.svg)](https://pypi.org/project/autogalaxy/) + +[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/2026.5.1.4/start_here.ipynb) | +[HowToGalaxy](https://pyautogalaxy.readthedocs.io/en/latest/howtogalaxy/howtogalaxy.html) + +**PyAutoGalaxy** is software for analysing the morphologies and structures of galaxies: + +[![HST Combined](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/hstcombined.png?raw=true)](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/hstcombined.png) + +**PyAutoGalaxy** also fits interferometer data from observatories such as ALMA: + +[![ALMA Combined](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/almacombined.png?raw=true)](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/almacombined.png) + +## Getting Started + +The following links are useful for new starters: + +- [The PyAutoGalaxy readthedocs](https://pyautogalaxy.readthedocs.io/en/latest), which includes [an overview of PyAutoGalaxy's core features](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_1_start_here.html), [a new user starting guide](https://pyautogalaxy.readthedocs.io/en/latest/overview/overview_2_new_user_guide.html) and [an installation guide](https://pyautogalaxy.readthedocs.io/en/latest/installation/overview.html). +- [The introduction Jupyter Notebook on Google Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.1.4/start_here.ipynb), where you can try **PyAutoGalaxy** in a web browser (without installation). +- [The autogalaxy_workspace GitHub repository](https://github.com/PyAutoLabs/autogalaxy_workspace): example scripts covering every **PyAutoGalaxy** use case. +- [The HowToGalaxy GitHub repository](https://github.com/PyAutoLabs/HowToGalaxy): a Jupyter notebook lecture series teaching galaxy modeling from the ground up. + +## Core Aims + +**PyAutoGalaxy** has three core aims: + +- **Big Data**: Scaling automated Sérsic fitting to extremely large datasets, *accelerated with JAX on GPUs and using tools like an SQL database to **build a scalable scientific workflow***. +- **Model Complexity**: Fitting complex galaxy morphology models (e.g. Multi Gaussian Expansion, Shapelets, Ellipse Fitting, Irregular Meshes) that go beyond just simple Sérsic fitting. +- **Data Variety**: Support for many data types (e.g. CCD imaging, interferometry, multi-band imaging) which can be fitted independently or simultaneously. + +A complete overview of the software's aims is provided in our [Journal of Open Source Software paper](https://joss.theoj.org/papers/10.21105/joss.04475). + +## Community & Support + +Support for **PyAutoGalaxy** is available via our Slack workspace, where the community shares updates, discusses +galaxy modeling and analysis, and helps troubleshoot problems. + +Slack is invitation-only. If you'd like to join, please send an email requesting an invite. + +For installation issues, bug reports, or feature requests, please raise an issue on the [GitHub issues page](https://github.com/Jammy2211/PyAutoGalaxy/issues). + +## HowToGalaxy + +For users less familiar with galaxy analysis, Bayesian inference, and scientific analysis, you may wish to read through +the **HowToGalaxy** lectures. These introduce the basic principles of galaxy modeling and Bayesian inference, with +the material pitched at undergraduate level and above. + +A complete overview of the lectures [is provided on the HowToGalaxy readthedocs page](https://pyautogalaxy.readthedocs.io/en/latest/howtogalaxy/howtogalaxy.html), and the notebooks themselves live in the [PyAutoLabs/HowToGalaxy](https://github.com/PyAutoLabs/HowToGalaxy) repository. + +## Citations + +Information on how to cite **PyAutoGalaxy** in publications can be found [on the citations page](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/CITATIONS.md). + +## Contributing + +Information on how to contribute to **PyAutoGalaxy** can be found [on the contributing page](https://github.com/Jammy2211/PyAutoGalaxy/blob/main/CONTRIBUTING.md). + +Hands on support for contributions is available via our Slack workspace, again please email to request an invite. diff --git a/README.rst b/README.rst deleted file mode 100644 index 9ab699208..000000000 --- a/README.rst +++ /dev/null @@ -1,113 +0,0 @@ -PyAutoGalaxy: Open-Source Multi Wavelength Galaxy Structure & Morphology -======================================================================== - -.. image:: https://colab.research.google.com/assets/colab-badge.svg - :target: https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.1.4/start_here.ipynb - -.. image:: https://readthedocs.org/projects/pyautogalaxy/badge/?version=latest - :target: https://pyautogalaxy.readthedocs.io/en/latest/?badge=latest - :alt: Documentation Status - -.. image:: https://github.com/Jammy2211/PyAutoGalaxy/actions/workflows/main.yml/badge.svg - :target: https://github.com/Jammy2211/PyAutoGalaxy/actions - -.. image:: https://github.com/Jammy2211/PyAutoBuild/actions/workflows/release.yml/badge.svg - :target: https://github.com/Jammy2211/PyAutoBuild/actions - -.. image:: https://img.shields.io/badge/code%20style-black-000000.svg - :target: https://github.com/psf/black - -.. image:: https://joss.theoj.org/papers/10.21105/joss.04475/status.svg - :target: https://doi.org/10.21105/joss.04475 - -.. image:: https://pyopensci.org/badges/peer-reviewed.svg - :target: https://github.com/pyOpenSci/software-submission/issues/235 - :alt: pyOpenSci Peer-Reviewed - -.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7546914.svg - :target: https://doi.org/10.5281/zenodo.7546914 - :alt: Zenodo DOI - -.. image:: https://www.repostatus.org/badges/latest/active.svg - :target: https://www.repostatus.org/#active - :alt: Project Status: Active - -.. image:: https://img.shields.io/pypi/pyversions/autogalaxy - :target: https://pypi.org/project/autogalaxy/ - :alt: Python Versions - -.. image:: https://img.shields.io/pypi/v/autogalaxy.svg - :target: https://pypi.org/project/autogalaxy/ - :alt: PyPI Version - -`Installation Guide `_ | -`readthedocs `_ | -`Introduction on Colab `_ | -`HowToGalaxy `_ - -**PyAutoGalaxy** is software for analysing the morphologies and structures of galaxies: - -.. image:: https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/hstcombined.png?raw=true - :target: https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/hstcombined.png - -**PyAutoGalaxy** also fits interferometer data from observatories such as ALMA: - -.. image:: https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/almacombined.png?raw=true - :target: https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/almacombined.png - -Getting Started ---------------- - -The following links are useful for new starters: - -- `The PyAutoGalaxy readthedocs `_, which includes `an overview of PyAutoGalaxy's core features `_, `a new user starting guide `_ and `an installation guide `_. - -- `The introduction Jupyter Notebook on Google Colab `_, where you can try **PyAutoGalaxy** in a web browser (without installation). - -- `The autogalaxy_workspace GitHub repository `_: example scripts covering every **PyAutoGalaxy** use case. - -- `The HowToGalaxy GitHub repository `_: a Jupyter notebook lecture series teaching galaxy modeling from the ground up. - -Core Aims ---------- - -**PyAutoGalaxy** has three core aims: - -- **Big Data**: Scaling automated Sérsic fitting to extremely large datasets, *accelerated with JAX on GPUs and using tools like an SQL database to **build a scalable scientific workflow***. - -- **Model Complexity**: Fitting complex galaxy morphology models (e.g. Multi Gaussian Expansion, Shapelets, Ellipse Fitting, Irregular Meshes) that go beyond just simple Sérsic fitting. - -- **Data Variety**: Support for many data types (e.g. CCD imaging, interferometry, multi-band imaging) which can be fitted independently or simultaneously. - -A complete overview of the software's aims is provided in our `Journal of Open Source Software paper `_. - -Community & Support -------------------- - -Support for **PyAutoGalaxy** is available via our Slack workspace, where the community shares updates, discusses -galaxy modeling and analysis, and helps troubleshoot problems. - -Slack is invitation-only. If you’d like to join, please send an email requesting an invite. - -For installation issues, bug reports, or feature requests, please raise an issue on the `GitHub issues page `_. - -HowToGalaxy ------------ - -For users less familiar with galaxy analysis, Bayesian inference, and scientific analysis, you may wish to read through -the **HowToGalaxy** lectures. These introduce the basic principles of galaxy modeling and Bayesian inference, with -the material pitched at undergraduate level and above. - -A complete overview of the lectures `is provided on the HowToGalaxy readthedocs page `_, and the notebooks themselves live in the `PyAutoLabs/HowToGalaxy `_ repository. - -Citations ---------- - -Information on how to cite **PyAutoGalaxy** in publications can be found `on the citations page `_. - -Contributing ------------- - -Information on how to contribute to **PyAutoGalaxy** can be found `on the contributing page `_. - -Hands on support for contributions is available via our Slack workspace, again please email to request an invite. \ No newline at end of file diff --git a/autogalaxy/config/README.md b/autogalaxy/config/README.md new file mode 100644 index 000000000..4b8202c77 --- /dev/null +++ b/autogalaxy/config/README.md @@ -0,0 +1,13 @@ +The `config` folder contains configuration files which customize default **PyAutoLens**. + +# Folders + +- `priors`: Configs defining default priors assumed on every model component and set of parameters. +- `visualize`: Configs defining what images are output by a lens model fit. + +# Files + +- `general.yaml`: Customizes general **PyAutoLens** settings. +- `grids.yaml`: Customize default behaviour of grids when used for calculations. +- `logging.yaml`: Customizes the logging behaviour. +- `notation.yaml`: Configs defining labels and formatting of model parameters when used for visualization. diff --git a/autogalaxy/config/README.rst b/autogalaxy/config/README.rst deleted file mode 100644 index c6dd5c196..000000000 --- a/autogalaxy/config/README.rst +++ /dev/null @@ -1,16 +0,0 @@ -The ``config`` folder contains configuration files which customize default **PyAutoLens**. - -Folders -------- - -- ``priors``: Configs defining default priors assumed on every model component and set of parameters. -- ``visualize``: Configs defining what images are output by a lens model fit. - -Files ------ - -- ``general.yaml``: Customizes general **PyAutoLens** settings. -- ``grids.yaml``: Customize default behaviour of grids when used for calculations. -- ``logging.yaml``: Customizes the logging behaviour. -- ``notation.yaml``: Configs defining labels and formatting of model parameters when used for visualization. - diff --git a/autogalaxy/config/priors/README.md b/autogalaxy/config/priors/README.md new file mode 100644 index 000000000..bb06e891c --- /dev/null +++ b/autogalaxy/config/priors/README.md @@ -0,0 +1,41 @@ +The prior config files contain the default priors and related variables for every light profile and mass profile +when it is used as a model. + +They appear as follows: + +```bash +Sersic: + effective_radius: + type: Uniform + lower_limit: 0.0 + upper_limit: 100.0 + width_modifier: + type: Absolute + value: 20.0 + limits: + lower: -inf + upper: inf +``` + +The sections of this example config set the following: + +> type {Uniform, Gaussian, LogUniform} +> +> : The default prior given to this parameter when used by the non-linear search. In the example above, a +> UniformPrior is used with lower_limit of 0.0 and upper_limit of 4.0. A GaussianPrior could be used by +> putting "Gaussian" in the "type" box, with "mean" and "sigma" used to set the default values. Any prior can be +> set in an analogous fashion (see the example configs). +> +> width_modifier +> +> : When the results of a search are passed to a subsequent search to set up the priors of its non-linear search, +> this entry describes how the Prior is passed. +> +> limits +> +> : When the results of a search are passed to a subsequent search, they are passed using a GaussianPrior. The +> limits set the physical lower and upper limits of this GaussianPrior, such that parameter samples +> can not go beyond these limits. + +The files `template_module.yaml` and `TemplateObject.yaml` give templates one can use to set up prior default +configs for your own model components. diff --git a/autogalaxy/config/priors/README.rst b/autogalaxy/config/priors/README.rst deleted file mode 100644 index 0b492084a..000000000 --- a/autogalaxy/config/priors/README.rst +++ /dev/null @@ -1,36 +0,0 @@ -The prior config files contain the default priors and related variables for every light profile and mass profile -when it is used as a model. - -They appear as follows: - -.. code-block:: bash - - Sersic: - effective_radius: - type: Uniform - lower_limit: 0.0 - upper_limit: 100.0 - width_modifier: - type: Absolute - value: 20.0 - limits: - lower: -inf - upper: inf - -The sections of this example config set the following: - - type {Uniform, Gaussian, LogUniform} - The default prior given to this parameter when used by the non-linear search. In the example above, a - UniformPrior is used with lower_limit of 0.0 and upper_limit of 4.0. A GaussianPrior could be used by - putting "Gaussian" in the "type" box, with "mean" and "sigma" used to set the default values. Any prior can be - set in an analogous fashion (see the example configs). - width_modifier - When the results of a search are passed to a subsequent search to set up the priors of its non-linear search, - this entry describes how the Prior is passed. - limits - When the results of a search are passed to a subsequent search, they are passed using a GaussianPrior. The - limits set the physical lower and upper limits of this GaussianPrior, such that parameter samples - can not go beyond these limits. - -The files ``template_module.yaml`` and ``TemplateObject.yaml`` give templates one can use to set up prior default -configs for your own model components. \ No newline at end of file diff --git a/autogalaxy/config/priors/ellipse/README.rst b/autogalaxy/config/priors/ellipse/README.md similarity index 59% rename from autogalaxy/config/priors/ellipse/README.rst rename to autogalaxy/config/priors/ellipse/README.md index 1fbbe5828..00e7f1fd3 100644 --- a/autogalaxy/config/priors/ellipse/README.rst +++ b/autogalaxy/config/priors/ellipse/README.md @@ -1,6 +1,6 @@ -The ``ellipse`` folder contains configuration files for the default priors assumed for ``ellipse`` objects. - -These model components are used for ellipse isophote fitting, which models the surface brightness of a galaxy as a -series of ellipses, which can include multipole perturbations. - -The main object used for modeling is the `Ellipse` object, with a list of `Ellipse` objects used to model the galaxy. \ No newline at end of file +The `ellipse` folder contains configuration files for the default priors assumed for `ellipse` objects. + +These model components are used for ellipse isophote fitting, which models the surface brightness of a galaxy as a +series of ellipses, which can include multipole perturbations. + +The main object used for modeling is the `Ellipse` object, with a list of `Ellipse` objects used to model the galaxy. diff --git a/autogalaxy/config/priors/galaxy/README.md b/autogalaxy/config/priors/galaxy/README.md new file mode 100644 index 000000000..795b87539 --- /dev/null +++ b/autogalaxy/config/priors/galaxy/README.md @@ -0,0 +1,5 @@ +The `galaxy` folder contains configuration files for the default priors assumed for `Galaxy` object properties **PyAutoGalaxy**. + +# Folders + +- `redshift`: Configs for priors on the redshift of a galaxy, when treated as a free parameter. diff --git a/autogalaxy/config/priors/galaxy/README.rst b/autogalaxy/config/priors/galaxy/README.rst deleted file mode 100644 index b65d67ea0..000000000 --- a/autogalaxy/config/priors/galaxy/README.rst +++ /dev/null @@ -1,6 +0,0 @@ -The ``galaxy`` folder contains configuration files for the default priors assumed for ``Galaxy`` object properties **PyAutoGalaxy**. - -Folders -------- - -- ``redshift``: Configs for priors on the redshift of a galaxy, when treated as a free parameter. \ No newline at end of file diff --git a/autogalaxy/config/priors/light/README.md b/autogalaxy/config/priors/light/README.md new file mode 100644 index 000000000..255f6da44 --- /dev/null +++ b/autogalaxy/config/priors/light/README.md @@ -0,0 +1,9 @@ +The `light` folder contains configuration files for the default priors assumed for light profiles in **PyAutoGalaxy** (e.g. `Sersic`, `Gaussian`). + +# Folders + +- `standard`: Configs for standard light profiles (specified via `ag.lp.`), which include an `intensity` parameter to control their overall amount of emission. +- `linear`: Configs for linear light profiles (specified via `ag.lp_linear.`),, where the `intensity` parameter is implicitly solved for via linear algebra. +- `shapelets`: Configs for shapelets (specified via `ag.lp_linear.`), which decomposed the light of a galaxy via shapelet basis functions. +- `operated`: Configs for operated light profiles (specified via `ag.lp_operated.`), where the light profile represents the already PSF convolved emission. +- `linear_operated`: Configs for linear operated light profiles (specified via `ag.lp_linear_operated.`), which behave like operated light profiles but with a linearly solved for `intensity`. diff --git a/autogalaxy/config/priors/light/README.rst b/autogalaxy/config/priors/light/README.rst deleted file mode 100644 index 42258bb75..000000000 --- a/autogalaxy/config/priors/light/README.rst +++ /dev/null @@ -1,10 +0,0 @@ -The ``light`` folder contains configuration files for the default priors assumed for light profiles in **PyAutoGalaxy** (e.g. ``Sersic``, ``Gaussian``). - -Folders -------- - -- ``standard``: Configs for standard light profiles (specified via ``ag.lp.``), which include an ``intensity`` parameter to control their overall amount of emission. -- ``linear``: Configs for linear light profiles (specified via ``ag.lp_linear.``),, where the ``intensity`` parameter is implicitly solved for via linear algebra. -- ``shapelets``: Configs for shapelets (specified via ``ag.lp_linear.``), which decomposed the light of a galaxy via shapelet basis functions. -- ``operated``: Configs for operated light profiles (specified via ``ag.lp_operated.``), where the light profile represents the already PSF convolved emission. -- ``linear_operated``: Configs for linear operated light profiles (specified via ``ag.lp_linear_operated.``), which behave like operated light profiles but with a linearly solved for ``intensity``. \ No newline at end of file diff --git a/autogalaxy/config/priors/mass/README.md b/autogalaxy/config/priors/mass/README.md new file mode 100644 index 000000000..56278f808 --- /dev/null +++ b/autogalaxy/config/priors/mass/README.md @@ -0,0 +1,8 @@ +The `mass` folder contains configuration files for the default priors assumed for mass profiles in **PyAutoGalaxy**. + +# Folders + +- `dark`: Configs for mass profiles that typically represent dark matter (e.g. `NFW`, `gNFW`). +- `stellar`: Configs for mass profiles that typically represent stellar matter (e.g. ``` Sersic`, ``Gaussian ```). +- `total`: Configs for mass profiles that typically represent the total (e.g. stellar and dark matter) mass distribution (e.g. ``` Isothermal`, ``PowerLaw ```). +- `sheets`: Configs for mass profiles that represent sheet-like mass components (e.g. ``` ExternalShear`, ``MassSheet ```). diff --git a/autogalaxy/config/priors/mass/README.rst b/autogalaxy/config/priors/mass/README.rst deleted file mode 100644 index 6c8b9fd30..000000000 --- a/autogalaxy/config/priors/mass/README.rst +++ /dev/null @@ -1,9 +0,0 @@ -The ``mass`` folder contains configuration files for the default priors assumed for mass profiles in **PyAutoGalaxy**. - -Folders -------- - -- ``dark``: Configs for mass profiles that typically represent dark matter (e.g. ``NFW``, ``gNFW``). -- ``stellar``: Configs for mass profiles that typically represent stellar matter (e.g. ``Sersic`, ``Gaussian``). -- ``total``: Configs for mass profiles that typically represent the total (e.g. stellar and dark matter) mass distribution (e.g. ``Isothermal`, ``PowerLaw``). -- ``sheets``: Configs for mass profiles that represent sheet-like mass components (e.g. ``ExternalShear`, ``MassSheet``). \ No newline at end of file diff --git a/autogalaxy/config/priors/mesh/README.md b/autogalaxy/config/priors/mesh/README.md new file mode 100644 index 000000000..ac0d7fc93 --- /dev/null +++ b/autogalaxy/config/priors/mesh/README.md @@ -0,0 +1,3 @@ +The `mesh` folder contains configuration files for the default priors assumed for `mesh` objects. + +These model components reconstruct a galaxy's emission using a rectangular grid, Delaunay triangulation or Voronoi mesh. diff --git a/autogalaxy/config/priors/mesh/README.rst b/autogalaxy/config/priors/mesh/README.rst deleted file mode 100644 index 820f43690..000000000 --- a/autogalaxy/config/priors/mesh/README.rst +++ /dev/null @@ -1,3 +0,0 @@ -The ``mesh`` folder contains configuration files for the default priors assumed for ``mesh`` objects. - -These model components reconstruct a galaxy's emission using a rectangular grid, Delaunay triangulation or Voronoi mesh. \ No newline at end of file diff --git a/autogalaxy/config/priors/regularization/README.md b/autogalaxy/config/priors/regularization/README.md new file mode 100644 index 000000000..bec44e5ff --- /dev/null +++ b/autogalaxy/config/priors/regularization/README.md @@ -0,0 +1,3 @@ +The `regularization` folder contains configuration files for the default priors assumed for `regularization` objects. + +These model components regularize the smoothness of a galaxy's emission when it is reconstructed using a `mesh` object. diff --git a/autogalaxy/config/priors/regularization/README.rst b/autogalaxy/config/priors/regularization/README.rst deleted file mode 100644 index f15562e25..000000000 --- a/autogalaxy/config/priors/regularization/README.rst +++ /dev/null @@ -1,3 +0,0 @@ -The ``regularization`` folder contains configuration files for the default priors assumed for ``regularization`` objects. - -These model components regularize the smoothness of a galaxy's emission when it is reconstructed using a ``mesh`` object. \ No newline at end of file diff --git a/autogalaxy/config/visualize/README.md b/autogalaxy/config/visualize/README.md new file mode 100644 index 000000000..c99ad0275 --- /dev/null +++ b/autogalaxy/config/visualize/README.md @@ -0,0 +1,10 @@ +The `config` folder contains configuration files which customize default **PyAutoLens**. + +# Files + +- `general.yaml`: Customizes general visualization settings (e.g. the matplotlib backend). +- `include.yaml`: Customize features that appears on plotted images by default (e.g. a mask, a grid). +- `plots.yaml`: Customize which figures are output during a model-fit. +- `mat_wrap.yaml`: Specify the default matplotlib settings when figures and subplots are plotted. +- `mat_wrap_1d.yaml`: Specify the default matplotlib settings when 1D figures and subplots are plotted. +- `mat_wrap_2d.yaml`: Specify the default matplotlib settings when 2D figures and subplots are plotted. diff --git a/autogalaxy/config/visualize/README.rst b/autogalaxy/config/visualize/README.rst deleted file mode 100644 index 1fa4f11d3..000000000 --- a/autogalaxy/config/visualize/README.rst +++ /dev/null @@ -1,11 +0,0 @@ -The ``config`` folder contains configuration files which customize default **PyAutoLens**. - -Files ------ - -- ``general.yaml``: Customizes general visualization settings (e.g. the matplotlib backend). -- ``include.yaml``: Customize features that appears on plotted images by default (e.g. a mask, a grid). -- ``plots.yaml``: Customize which figures are output during a model-fit. -- ``mat_wrap.yaml``: Specify the default matplotlib settings when figures and subplots are plotted. -- ``mat_wrap_1d.yaml``: Specify the default matplotlib settings when 1D figures and subplots are plotted. -- ``mat_wrap_2d.yaml``: Specify the default matplotlib settings when 2D figures and subplots are plotted. \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index 3f70babd7..19681c6c7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -101,8 +101,7 @@ ".DS_Store", "CODE_OF_CONDUCT.md", "CONTRIBUTING.md", - "CITATIONS.rst", - "README.rst", + "CITATIONS.md", "README.md", ] diff --git a/pyproject.toml b/pyproject.toml index 9cead4f22..a901e6816 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" name = "autogalaxy" dynamic = ["version"] description="Open-Source Multi Wavelength Galaxy Structure & Morphology" -readme = { file = "README.rst", content-type = "text/x-rst" } +readme = { file = "README.md", content-type = "text/markdown" } license = { text = "MIT" } requires-python = ">=3.9" authors = [