diff --git a/CITATIONS.md b/CITATIONS.md new file mode 100644 index 000000000..5124098cf --- /dev/null +++ b/CITATIONS.md @@ -0,0 +1,26 @@ +# 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 ( and ) 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. + +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 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 under +citation key `Anowar2019`. + +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] ;). diff --git a/CITATIONS.rst b/CITATIONS.rst deleted file mode 100644 index cdaa1aada..000000000 --- a/CITATIONS.rst +++ /dev/null @@ -1,31 +0,0 @@ -.. _references: - -Citations & References -====================== - -The bibtex entries for **PyAutoLens** and its affiliated software packages can be found -`here `_, with example text for citing **PyAutoLens** -in `.tex format here `_ format here and -`.md format here `_. 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 `_ 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. - -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``. - -The citations.bib file above also includes my work on `using strong lensing to study galaxy structure -`_. If you're feeling kind, please go ahead and stick -a citation in your introduction using \citep{Nightingale2019} or [@Nightingale2019] ;). - diff --git a/MANIFEST.in b/MANIFEST.in index d599fbf9e..1f0f44000 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..2f266fed0 --- /dev/null +++ b/README.md @@ -0,0 +1,60 @@ +# PyAutoLens-JAX: Open-Source Strong Lensing + +[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PyAutoLabs/autolens_workspace/blob/2026.5.1.4/start_here.ipynb) +[![Documentation Status](https://readthedocs.org/projects/pyautolens/badge/?version=latest)](https://pyautolens.readthedocs.io/en/latest/?badge=latest) +[![Tests](https://github.com/Jammy2211/PyAutoLens/actions/workflows/main.yml/badge.svg)](https://github.com/Jammy2211/PyAutoLens/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.02825/status.svg)](https://doi.org/10.21105/joss.02825) +[![Zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4548697.svg)](https://doi.org/10.5281/zenodo.4548697) +[![arXiv](https://img.shields.io/badge/arXiv-1708.07377-blue)](https://arxiv.org/abs/1708.07377) +[![Project Status: Active](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) +[![Python Versions](https://img.shields.io/pypi/pyversions/autolens)](https://pypi.org/project/autolens/) +[![PyPI Version](https://img.shields.io/pypi/v/autolens.svg)](https://pypi.org/project/autolens/) + +[Installation Guide](https://pyautolens.readthedocs.io/en/latest/installation/overview.html) | +[readthedocs](https://pyautolens.readthedocs.io/en/latest/index.html) | +[Introduction on Colab](https://colab.research.google.com/github/PyAutoLabs/autolens_workspace/blob/2026.5.1.4/start_here.ipynb) | +[HowToLens](https://pyautolens.readthedocs.io/en/latest/howtolens/howtolens.html) + + + +When two or more galaxies are aligned perfectly down our line-of-sight, the background galaxy appears multiple times. + +This is called strong gravitational lensing and **PyAutoLens** makes it **simple** to model strong gravitational lenses, using JAX to **accelerate lens modeling on GPUs**. + +## Getting Started + +The following links are useful for new starters: + +- [The PyAutoLens readthedocs](https://pyautolens.readthedocs.io/en/latest): which includes [an overview of PyAutoLens's core features](https://pyautolens.readthedocs.io/en/latest/overview/overview_1_start_here.html), [a new user starting guide](https://pyautolens.readthedocs.io/en/latest/overview/overview_2_new_user_guide.html) and [an installation guide](https://pyautolens.readthedocs.io/en/latest/installation/overview.html). +- [The introduction Jupyter Notebook on Google Colab](https://colab.research.google.com/github/PyAutoLabs/autolens_workspace/blob/2026.5.1.4/start_here.ipynb): try **PyAutoLens** in a web browser (without installation). +- [The autolens_workspace GitHub repository](https://github.com/PyAutoLabs/autolens_workspace): example scripts covering every **PyAutoLens** use case. +- [The HowToLens GitHub repository](https://github.com/PyAutoLabs/HowToLens): a Jupyter notebook lecture series teaching strong lensing and lens modeling from the ground up. + +## Community & Support + +Support for **PyAutoLens** is available via our Slack workspace, where the community shares updates, discusses +gravitational lensing 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/PyAutoLens/issues). + +## HowToLens + +For users less familiar with gravitational lensing, Bayesian inference and scientific analysis +you may wish to read through the **HowToLens** lectures. These teach you the basic principles of gravitational lensing +and Bayesian inference, with the content pitched at undergraduate level and above. + +A complete overview of the lectures [is provided on the HowToLens readthedocs page](https://pyautolens.readthedocs.io/en/latest/howtolens/howtolens.html), and the notebooks themselves live in the [PyAutoLabs/HowToLens](https://github.com/PyAutoLabs/HowToLens) repository. + +## Citations + +Information on how to cite **PyAutoLens** in publications can be found [on the citations page](https://github.com/Jammy2211/PyAutoLens/blob/main/CITATIONS.md). + +## Contributing + +Information on how to contribute to **PyAutoLens** can be found [on the contributing page](https://github.com/Jammy2211/PyAutoLens/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 678cdb5ab..000000000 --- a/README.rst +++ /dev/null @@ -1,101 +0,0 @@ -PyAutoLens-JAX: Open-Source Strong Lensing -========================================== - -.. |nbsp| unicode:: 0xA0 - :trim: - -.. |colab| image:: https://colab.research.google.com/assets/colab-badge.svg - :target: https://colab.research.google.com/github/PyAutoLabs/autolens_workspace/blob/2026.5.1.4/start_here.ipynb - -.. |RTD| image:: https://readthedocs.org/projects/pyautolens/badge/?version=latest - :target: https://pyautolens.readthedocs.io/en/latest/?badge=latest - :alt: Documentation Status - -.. |Tests| image:: https://github.com/Jammy2211/PyAutoLens/actions/workflows/main.yml/badge.svg - :target: https://github.com/Jammy2211/PyAutoLens/actions - -.. |Build| image:: https://github.com/Jammy2211/PyAutoBuild/actions/workflows/release.yml/badge.svg - :target: https://github.com/Jammy2211/PyAutoBuild/actions - -.. |code-style| image:: https://img.shields.io/badge/code%20style-black-000000.svg - :target: https://github.com/psf/black - -.. |JOSS| image:: https://joss.theoj.org/papers/10.21105/joss.02825/status.svg - :target: https://doi.org/10.21105/joss.02825 - -.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4548697.svg - :target: https://doi.org/10.5281/zenodo.4548697 - :alt: Zenodo DOI - -.. |arXiv| image:: https://img.shields.io/badge/arXiv-1708.07377-blue - :target: https://arxiv.org/abs/1708.07377 - -.. 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/autolens - :target: https://pypi.org/project/autolens/ - :alt: Python Versions - -.. image:: https://img.shields.io/pypi/v/autolens.svg - :target: https://pypi.org/project/autolens/ - :alt: PyPI Version - -|colab| |RTD| |Tests| |Build| |code-style| |JOSS| |DOI| |arXiv| - -`Installation Guide `_ | -`readthedocs `_ | -`Introduction on Colab `_ | -`HowToLens `_ - -.. image:: https://github.com/Jammy2211/PyAutoLogo/blob/main/gifs/pyautolens.gif?raw=true - :width: 900 - -When two or more galaxies are aligned perfectly down our line-of-sight, the background galaxy appears multiple times. - -This is called strong gravitational lensing and **PyAutoLens** makes it **simple** to model strong gravitational lenses, using JAX to **accelerate lens modeling on GPUs**. - -Getting Started ---------------- - -The following links are useful for new starters: - -- `The PyAutoLens readthedocs `_: which includes `an overview of PyAutoLens's core features `_, `a new user starting guide `_ and `an installation guide `_. - -- `The introduction Jupyter Notebook on Google Colab `_: try **PyAutoLens** in a web browser (without installation). - -- `The autolens_workspace GitHub repository `_: example scripts covering every **PyAutoLens** use case. - -- `The HowToLens GitHub repository `_: a Jupyter notebook lecture series teaching strong lensing and lens modeling from the ground up. - -Community & Support -------------------- - -Support for **PyAutoLens** is available via our Slack workspace, where the community shares updates, discusses -gravitational lensing 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 `_. - -HowToLens ---------- - -For users less familiar with gravitational lensing, Bayesian inference and scientific analysis -you may wish to read through the **HowToLens** lectures. These teach you the basic principles of gravitational lensing -and Bayesian inference, with the content pitched at undergraduate level and above. - -A complete overview of the lectures `is provided on the HowToLens readthedocs page `_, and the notebooks themselves live in the `PyAutoLabs/HowToLens `_ repository. - -Citations ---------- - -Information on how to cite **PyAutoLens** in publications can be found `on the citations page `_. - -Contributing ------------- - -Information on how to contribute to **PyAutoLens** 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/docs/conf.py b/docs/conf.py index 5d3266834..ef3fa30cb 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 92833aa9c..4af9d8876 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" name = "autolens" dynamic = ["version"] description="Open-Source Strong Lensing" -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 = [