From 81f10611598c5e62480e9d39c6b7399f8232bd85 Mon Sep 17 00:00:00 2001 From: Jammy2211 Date: Fri, 15 May 2026 08:31:24 +0100 Subject: [PATCH] =?UTF-8?q?docs:=20audit-driven=20URL=20fixes=20(Jammy2211?= =?UTF-8?q?=20=E2=86=92=20PyAutoLabs,=20/release/=20=E2=86=92=20/main/,=20?= =?UTF-8?q?etc.)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Apply scripted URL rewrites surfaced by the new admin_jammy/software/url_check/ audit tool. All changes are doc-only (README, *.md, *.rst, plus docstring URLs in source files). No behaviour changes. Line endings preserved. Patterns applied: - hhttps:// → https:// (user-reported typo in overview_2_new_user_guide.md) - Jammy2211/ → PyAutoLabs/ (workspaces migrated orgs) - Jammy2211|rhayes777/ → PyAutoLabs/ - /blob/release/ and /tree/release/ → /main/ (release branch removed) - joshspeagle/nautilus → johannesulf/nautilus (sampler moved orgs) - rhayes777/PyAutoBuild → PyAutoLabs/PyAutoBuild - bokeh CoC moved to /docs/CODE_OF_CONDUCT.md - numfocus CoC moved to numfocus.org/code-of-conduct - www.sphinx-doc.org /en/main → /en/master - pyautofit.readthedocs.io renames (cookbook_1_basics → cookbooks/model, overview/model_fit → overview/the_basics, etc.) - autofit_workspace overview/{simple,complex}/{fit,result}.ipynb → new flat structure - workspaces modeling/imaging/features/.ipynb → imaging/features//modeling.ipynb - workspaces multi/modeling/features/.ipynb → multi/features//modeling.ipynb - workspaces multi/modeling/start_here.ipynb → multi/start_here.ipynb - workspaces tree/main/notebooks/plot → notebooks/guides/plot - Colab badge URL: workspace-root start_here.ipynb → notebooks//start_here.ipynb Tool + report: PyAutoLabs/admin_jammy#21 Issue: PyAutoLabs/PyAutoLens#508 Co-Authored-By: Claude Opus 4.7 (1M context) --- CITATIONS.md | 6 +++--- CODE_OF_CONDUCT.md | 4 ++-- CONTRIBUTING.md | 4 ++-- README.md | 18 +++++++++--------- docs/api/plot.rst | 4 ++-- docs/conf.py | 4 ++-- docs/general/citations.md | 6 +++--- docs/general/configs.md | 2 +- docs/general/credits.md | 2 +- docs/general/model_cookbook.md | 10 +++++----- docs/general/workspace.md | 6 +++--- docs/index.md | 8 ++++---- docs/installation/conda.md | 2 +- docs/installation/overview.md | 6 +++--- docs/installation/pip.md | 2 +- docs/installation/source.md | 12 ++++++------ docs/installation/troubleshooting.md | 2 +- docs/overview/overview_1_start_here.md | 14 +++++++------- docs/overview/overview_2_new_user_guide.md | 6 +++--- docs/overview/overview_3_features.md | 14 +++++++------- files/citations.md | 6 +++--- paper/README.md | 2 +- paper/paper.md | 8 ++++---- 23 files changed, 74 insertions(+), 74 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index cb6645ecd..3c42e40e6 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,9 +1,9 @@ # 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). +[here](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/files/citations.bib), with example text for citing **PyAutoGalaxy** +in [.tex format here](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/files/citations.tex) format here and +[.md format here](https://github.com/PyAutoLabs/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! diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 90d92efd9..386d6bb79 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -301,7 +301,7 @@ the situation is not yet resolved. ## License -This code of conduct has been adapted from [*NUMFOCUS code of conduct*](https://github.com/numfocus/numfocus/blob/main/manual/numfocus-coc.md#the-short-version), -which is adapted from numerous sources, including the [*Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license*](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy), the [*Contributor Covenant version 1.2.0*](http://contributor-covenant.org/version/1/2/0/), the [*Bokeh Code of Conduct*](https://github.com/bokeh/bokeh/blob/main/CODE_OF_CONDUCT.md), the [*SciPy Code of Conduct*](https://github.com/jupyter/governance/blob/main/conduct/enforcement.md), the [*Carpentries Code of Conduct*](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#enforcement-manual), and the [*NeurIPS Code of Conduct*](https://neurips.cc/public/CodeOfConduct). +This code of conduct has been adapted from [*NUMFOCUS code of conduct*](https://numfocus.org/code-of-conduct), +which is adapted from numerous sources, including the [*Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license*](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy), the [*Contributor Covenant version 1.2.0*](http://contributor-covenant.org/version/1/2/0/), the [*Bokeh Code of Conduct*](https://github.com/bokeh/bokeh/blob/main/docs/CODE_OF_CONDUCT.md), the [*SciPy Code of Conduct*](https://github.com/jupyter/governance/blob/main/conduct/enforcement.md), the [*Carpentries Code of Conduct*](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#enforcement-manual), and the [*NeurIPS Code of Conduct*](https://neurips.cc/public/CodeOfConduct). **PyAutoGalaxy Code of Conduct is licensed under the [Creative Commons Attribution 3.0 Unported License](https://creativecommons.org/licenses/by/3.0/).** \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a5e70a3ec..b17157c00 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -74,7 +74,7 @@ Contributions are welcome and greatly appreciated! ### Report Bugs -Report bugs at https://github.com/Jammy2211/PyAutoGalaxy/issues +Report bugs at https://github.com/PyAutoLabs/PyAutoGalaxy/issues If you are playing with the PyAutoGalaxy library and find a bug, please reporting it including: @@ -86,7 +86,7 @@ reporting it including: ### Propose New Features The best way to send feedback is to open an issue at -https://github.com/Jammy2211/PyAutoGalaxy +https://github.com/PyAutoLabs/PyAutoGalaxy with tag *enhancement*. If you are proposing a nnew feature: diff --git a/README.md b/README.md index 181bb31f5..f37431af9 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ # 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/2026.5.14.2/start_here.ipynb) +[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/notebooks/imaging/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) +[![Tests](https://github.com/PyAutoLabs/PyAutoGalaxy/actions/workflows/main.yml/badge.svg)](https://github.com/PyAutoLabs/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) @@ -14,23 +14,23 @@ [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/2026.5.14.2/start_here.ipynb) | +[Introduction on Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/notebooks/imaging/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) +[![HST Combined](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/paper/hstcombined.png?raw=true)](https://github.com/PyAutoLabs/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) +[![ALMA Combined](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/paper/almacombined.png?raw=true)](https://github.com/PyAutoLabs/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/2026.5.14.2/start_here.ipynb), where you can try **PyAutoGalaxy** in a web browser (without installation). +- [The introduction Jupyter Notebook on Google Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/notebooks/imaging/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. @@ -51,7 +51,7 @@ 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). +For installation issues, bug reports, or feature requests, please raise an issue on the [GitHub issues page](https://github.com/PyAutoLabs/PyAutoGalaxy/issues). ## HowToGalaxy @@ -63,10 +63,10 @@ A complete overview of the lectures [is provided on the HowToGalaxy readthedocs ## 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). +Information on how to cite **PyAutoGalaxy** in publications can be found [on the citations page](https://github.com/PyAutoLabs/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). +Information on how to contribute to **PyAutoGalaxy** can be found [on the contributing page](https://github.com/PyAutoLabs/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/docs/api/plot.rst b/docs/api/plot.rst index 5e9d6b3c9..b605a1659 100644 --- a/docs/api/plot.rst +++ b/docs/api/plot.rst @@ -5,12 +5,12 @@ Plotting **PyAutoGalaxy** custom visualization library. Step-by-step Juypter notebook guides illustrating all objects listed on this page are -provided on the `autogalaxy_workspace: plot tutorials `_ and +provided on the `autogalaxy_workspace: plot tutorials `_ and it is strongly recommended you use those to learn plot customization. **Examples / Tutorials:** -- `autogalaxy_workspace: plot tutorials `_ +- `autogalaxy_workspace: plot tutorials `_ Plotters [aplt] --------------- diff --git a/docs/conf.py b/docs/conf.py index 972e61f39..7b0e442fb 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -4,7 +4,7 @@ # # This file only contains a selection of the most common options. For a full # list see the documentation: -# https://www.sphinx-doc.org/en/main/usage/configuration.html +# https://www.sphinx-doc.org/en/master/usage/configuration.html # -- Path setup -------------------------------------------------------------- @@ -65,7 +65,7 @@ intersphinx_mapping = { "python": ("https://docs.python.org/3", None), - "sphinx": ("https://www.sphinx-doc.org/en/main", None), + "sphinx": ("https://www.sphinx-doc.org/en/master", None), } # -- Options for TODOs ------------------------------------------------------- diff --git a/docs/general/citations.md b/docs/general/citations.md index 47020c993..3367f6ebd 100644 --- a/docs/general/citations.md +++ b/docs/general/citations.md @@ -3,9 +3,9 @@ # 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). +[here](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/files/citations.bib), with example text for citing **PyAutoGalaxy** +in [.tex format here](https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/files/citations.tex) format here and +[.md format here](https://github.com/PyAutoLabs/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`. diff --git a/docs/general/configs.md b/docs/general/configs.md index 43c03c4ba..4bdfb490f 100644 --- a/docs/general/configs.md +++ b/docs/general/configs.md @@ -4,7 +4,7 @@ visualization and other aspects of **PyAutoGalaxy**. Descriptions of every configuration file and their input parameters are provided in the `README.md` in -the [config directory of the workspace](https://github.com/Jammy2211/autogalaxy_workspace/tree/release/config) +the [config directory of the workspace](https://github.com/PyAutoLabs/autogalaxy_workspace/tree/main/config) ## Setup diff --git a/docs/general/credits.md b/docs/general/credits.md index 6fdd4dc2a..c34a5af74 100644 --- a/docs/general/credits.md +++ b/docs/general/credits.md @@ -6,7 +6,7 @@ [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. +[Richard Hayes](https://github.com/rhayes777): Lead developer & [PyAutoFit](https://github.com/PyAutoLabs/PyAutoFit) guru. [Aristeidis Amvrosiadis](https://github.com/Sketos): Interferometer Analysis. diff --git a/docs/general/model_cookbook.md b/docs/general/model_cookbook.md index b6b60bf57..3dfad7c4e 100644 --- a/docs/general/model_cookbook.md +++ b/docs/general/model_cookbook.md @@ -224,8 +224,8 @@ profiles. The following example notebooks show how to compose and fit these models: - - + + ## Model Linking (Advanced) @@ -233,7 +233,7 @@ When performing non-linear search chaining, the inferred model of one phase can The following example notebooks show how to compose and fit these models: - + ## Across Datasets (Advanced) @@ -242,7 +242,7 @@ but certain parameters are free to vary across the datasets. The following example notebooks show how to compose and fit these models: - + ## Relations (Advanced) @@ -251,7 +251,7 @@ We can compose models where the free parameter(s) vary according to a user-speci The following example notebooks show how to compose and fit these models: - + ## PyAutoFit API diff --git a/docs/general/workspace.md b/docs/general/workspace.md index cee5c1228..52fbf8b6c 100644 --- a/docs/general/workspace.md +++ b/docs/general/workspace.md @@ -2,7 +2,7 @@ # Workspace Tour -You should have downloaded and configured the [autogalaxy workspace](https://github.com/Jammy2211/autogalaxy_workspace) +You should have downloaded and configured the [autogalaxy workspace](https://github.com/PyAutoLabs/autogalaxy_workspace) when you installed **PyAutoGalaxy**. If you didn't, checkout the [installation instructions](https://pyautogalaxy.readthedocs.io/en/latest/general/installation.html#installation-with-pip) for how to downloaded and configure the workspace. @@ -18,7 +18,7 @@ There are numerous example describing how to perform calculations, galaxy modeli **PyAutoGalaxy** features. All examples are provided as Python scripts and Jupyter notebooks. A full description of the scripts available is given on -the [autogalaxy workspace GitHub page](https://github.com/Jammy2211/autogalaxy_workspace). +the [autogalaxy workspace GitHub page](https://github.com/PyAutoLabs/autogalaxy_workspace). ## Config @@ -31,7 +31,7 @@ Here, you'll find the configuration files which customize: > - The generaltrue config which customizes other aspects of **PyAutoGalaxy**. Descriptions of every configuration file and their input parameters are provided in the `README.md` in -the [config directory of the workspace](https://github.com/Jammy2211/autogalaxy_workspace/tree/release/config) +the [config directory of the workspace](https://github.com/PyAutoLabs/autogalaxy_workspace/tree/main/config) ## Dataset diff --git a/docs/index.md b/docs/index.md index 78fbab806..c4b46cd6b 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,10 +1,10 @@ --- substitutions: pic1: |- - ```{image} https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/hstcombined.png?raw=true + ```{image} https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/paper/hstcombined.png?raw=true ``` pic2: |- - ```{image} https://github.com/Jammy2211/PyAutoGalaxy/blob/main/paper/almacombined.png?raw=true + ```{image} https://github.com/PyAutoLabs/PyAutoGalaxy/blob/main/paper/almacombined.png?raw=true ``` --- @@ -23,7 +23,7 @@ substitutions: 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 Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/start_here.ipynb), where you can try **PyAutoGalaxy** in a web browser (without installation). +- [The introduction Jupyter Notebook on Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/notebooks/imaging/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. @@ -134,7 +134,7 @@ galaxies_plotter.figures_2d(image=True) ``` To perform model-fitting, `PyAutoGalaxy` adopts the probabilistic programming -language `PyAutoFit` (). `PyAutoFit` allows users to compose a +language `PyAutoFit` (). `PyAutoFit` allows users to compose a model from `LightProfile` and `Galaxy` objects, customize the model parameterization and fit it to data via a non-linear search (e.g., `dynesty` [@dynesty], `emcee` [@emcee], `PySwarms` [@pyswarms]). By composing a model with `Pixelization` objects, the galaxy's light is reconstructed using a non-parametric rectangular diff --git a/docs/installation/conda.md b/docs/installation/conda.md index e32142cbd..506a3e83a 100644 --- a/docs/installation/conda.md +++ b/docs/installation/conda.md @@ -54,7 +54,7 @@ the `autogalaxy_workspace`, reducing the download size): ```bash cd /path/on/your/computer/you/want/to/put/the/autogalaxy_workspace -git clone https://github.com/Jammy2211/autogalaxy_workspace --depth 1 +git clone https://github.com/PyAutoLabs/autogalaxy_workspace --depth 1 cd autogalaxy_workspace ``` diff --git a/docs/installation/overview.md b/docs/installation/overview.md index 377c0fd69..b764cb599 100644 --- a/docs/installation/overview.md +++ b/docs/installation/overview.md @@ -22,11 +22,11 @@ our [building from source installation guide](https://pyautogalaxy.readthedocs.i **PyAutoGalaxy** has the following dependencies: -**PyAutoConf** +**PyAutoConf** -**PyAutoFit** +**PyAutoFit** -**PyAutoArray** +**PyAutoArray** **dynesty** diff --git a/docs/installation/pip.md b/docs/installation/pip.md index da5f63691..548bc1ff5 100644 --- a/docs/installation/pip.md +++ b/docs/installation/pip.md @@ -41,7 +41,7 @@ the `autogalaxy_workspace`, reducing the download size): ```bash cd /path/on/your/computer/you/want/to/put/the/autogalaxy_workspace -git clone https://github.com/Jammy2211/autogalaxy_workspace --depth 1 +git clone https://github.com/PyAutoLabs/autogalaxy_workspace --depth 1 cd autogalaxy_workspace ``` diff --git a/docs/installation/source.md b/docs/installation/source.md index 6ae981aad..a418cd958 100644 --- a/docs/installation/source.md +++ b/docs/installation/source.md @@ -8,9 +8,9 @@ contribute the development **PyAutoGalaxy** or experiment with yourself! A large amount of **PyAutoGalaxy** functionality is contained in its parent projects: -**PyAutoFit** +**PyAutoFit** -**PyAutoArray** +**PyAutoArray** If you wish to build from source all code you may need to build from source these 3 additional projects. We include below instructions for building just **PyAutoGalaxy** from source or building all projects. @@ -26,7 +26,7 @@ pip install --upgrade pip First, clone (or fork) the **PyAutoGalaxy** GitHub repository: ```bash -git clone https://github.com/Jammy2211/PyAutoGalaxy +git clone https://github.com/PyAutoLabs/PyAutoGalaxy ``` Next, install the **PyAuto** parent projects via pip: @@ -88,9 +88,9 @@ pip install --upgrade pip First, clone (or fork) all 4 GitHub repositories: ```bash -git clone https://github.com/rhayes777/PyAutoFit -git clone https://github.com/Jammy2211/PyAutoArray -git clone https://github.com/Jammy2211/PyAutoGalaxy +git clone https://github.com/PyAutoLabs/PyAutoFit +git clone https://github.com/PyAutoLabs/PyAutoArray +git clone https://github.com/PyAutoLabs/PyAutoGalaxy ``` Next, install **PyAutoConf** via pip: diff --git a/docs/installation/troubleshooting.md b/docs/installation/troubleshooting.md index 028a902d8..3e8fc5508 100644 --- a/docs/installation/troubleshooting.md +++ b/docs/installation/troubleshooting.md @@ -21,7 +21,7 @@ instead, or visa versa. ## Support If you are still having issues with installation, please raise an issue on the -[PyAutoGalaxy issues page](https://github.com/Jammy2211/PyAutoGalaxy/issues) with a description of the +[PyAutoGalaxy issues page](https://github.com/PyAutoLabs/PyAutoGalaxy/issues) with a description of the problem and your system setup (operating system, Python version, etc.). ## Current Working Directory diff --git a/docs/overview/overview_1_start_here.md b/docs/overview/overview_1_start_here.md index 0ec100d22..4bfc2c99b 100644 --- a/docs/overview/overview_1_start_here.md +++ b/docs/overview/overview_1_start_here.md @@ -4,7 +4,7 @@ **PyAutoGalaxy** is software for analysing the morphologies and structures of galaxies: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/paper/hstcombined.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/paper/hstcombined.png :alt: Alternative text :width: 400 ``` @@ -51,7 +51,7 @@ aplt.plot_grid(grid=grid, title="Uniform Grid") The `Grid2D` looks like this: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/0_grid.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/docs/overview/images/overview_1/0_grid.png :alt: Alternative text :width: 600 ``` @@ -102,7 +102,7 @@ aplt.plot_array(array=sersic_light_profile.image_2d_from(grid=grid), title="Sers The light profile appears as follows: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/1_image_2d.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/docs/overview/images/overview_1/1_image_2d.png :alt: Alternative text :width: 600 ``` @@ -134,7 +134,7 @@ aplt.plot_array(array=galaxy.image_2d_from(grid=grid), title="Galaxy Image") The galaxy, with both a bulge and disk, appears as follows: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/2_image_2d.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/docs/overview/images/overview_1/2_image_2d.png :alt: Alternative text :width: 600 ``` @@ -147,7 +147,7 @@ aplt.subplot_galaxy_light_profiles(galaxy=galaxy, grid=grid) The light profiles appear as follows: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/3_subplot_image.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/docs/overview/images/overview_1/3_subplot_image.png :alt: Alternative text :width: 600 ``` @@ -176,7 +176,7 @@ galaxies = ag.Galaxies( aplt.plot_array(array=galaxies.image_2d_from(grid=grid), title="Galaxies Image") ``` -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/4_image_2d.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/docs/overview/images/overview_1/4_image_2d.png :alt: Alternative text :width: 600 ``` @@ -242,7 +242,7 @@ aplt.plot_array(array=galaxies.image_2d_from(grid=grid), title="Galaxies Image") The image of the merging galaxy system appears as follows: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_1/5_image_2d.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/docs/overview/images/overview_1/5_image_2d.png :alt: Alternative text :width: 600 ``` diff --git a/docs/overview/overview_2_new_user_guide.md b/docs/overview/overview_2_new_user_guide.md index a45f6a54c..ee5d17bd9 100644 --- a/docs/overview/overview_2_new_user_guide.md +++ b/docs/overview/overview_2_new_user_guide.md @@ -12,9 +12,9 @@ the most appropriate starting point, answer one simple question: You now need to decide what type of data you are interested in: -- **CDD Imaging**: For image data from telescopes like Hubble and James Webb, go to [imaging/start_here.ipynb](https://github.com/Jammy2211/autogalaxy_workspace/blob/release/notebooks/imaging/start_here.ipynb). -- **Interferometer**: For radio / sub-mm interferometer from instruments like ALMA, go to [interferometer/start_here.ipynb](https://github.com/Jammy2211/autogalaxy_workspace/blob/release/notebooks/interferometer/start_here.ipynb). -- **Multi-Band Imaging**: For galaxies observed in multiple wavebands go to [multi_band//start_here.ipynb](hhttps://github.com/Jammy2211/autogalaxy_workspace/blob/release/notebooks/point_source/start_here.ipynb). +- **CDD Imaging**: For image data from telescopes like Hubble and James Webb, go to [imaging/start_here.ipynb](https://github.com/PyAutoLabs/autogalaxy_workspace/blob/main/notebooks/imaging/start_here.ipynb). +- **Interferometer**: For radio / sub-mm interferometer from instruments like ALMA, go to [interferometer/start_here.ipynb](https://github.com/PyAutoLabs/autogalaxy_workspace/blob/main/notebooks/interferometer/start_here.ipynb). +- **Multi-Band Imaging**: For galaxies observed in multiple wavebands go to [multi/start_here.ipynb](https://github.com/PyAutoLabs/autogalaxy_workspace/blob/main/notebooks/multi/start_here.ipynb). ## Google Colab diff --git a/docs/overview/overview_3_features.md b/docs/overview/overview_3_features.md index 5b1d70df8..5110eaccd 100644 --- a/docs/overview/overview_3_features.md +++ b/docs/overview/overview_3_features.md @@ -27,7 +27,7 @@ links to the relevant workspace examples. Modeling interferometer data from submillimeter (e.g. ALMA) and radio (e.g. LOFAR) observatories: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/paper/almacombined.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/paper/almacombined.png :alt: Alternative text :width: 600 ``` @@ -43,12 +43,12 @@ Checkout the `autogalaxy_workspace/*/interferometer` package to get started. Modeling imaging datasets observed at different wavelengths (e.g. HST F814W and F150W) simultaneously or simultaneously analysing imaging and interferometer data: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_3/g_image.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/docs/overview/images/overview_3/g_image.png :alt: Alternative text :width: 400 ``` -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_3/r_image.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/docs/overview/images/overview_3/r_image.png :alt: Alternative text :width: 400 ``` @@ -65,7 +65,7 @@ feature and it is recommended you first get to grips with the core API. Ellipse fitting is a technique which fits many ellipses to a galaxy's emission to determine its ellipticity, position angle and centre, without assuming a parametric form for its light (e.g. a Sersic profile): -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_3/ellipse.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/docs/overview/images/overview_3/ellipse.png :alt: Alternative text :width: 600 ``` @@ -84,7 +84,7 @@ Checkout `autogalaxy_workspace/notebooks/features/ellipse_fitting.ipynb` to lear An MGE decomposes the light of a galaxy into tens or hundreds of two dimensional Gaussians: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/docs/overview/images/overview_3/mge.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/docs/overview/images/overview_3/mge.png :alt: Alternative text :width: 600 ``` @@ -102,7 +102,7 @@ Checkout `autogalaxy_workspace/notebooks/features/multi_gaussian_expansion.ipynb Shapelets are a set of orthogonal basis functions that can be combined the represent galaxy structures: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoLens/main/docs/overview/images/overview_3/shapelets.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoLens/main/docs/overview/images/overview_3/shapelets.png :alt: Alternative text :width: 600 ``` @@ -145,7 +145,7 @@ The image below shows a non parametric of a galaxy observed in the Hubble Ultra fitted accurately using light profiles, whereas its asymmetric and irregular spiral arm features are accurately captured using a rectangular mesh: -```{image} https://raw.githubusercontent.com/Jammy2211/PyAutoGalaxy/main/paper/hstcombined.png +```{image} https://raw.githubusercontent.com/PyAutoLabs/PyAutoGalaxy/main/paper/hstcombined.png :alt: Alternative text :width: 600 ``` diff --git a/files/citations.md b/files/citations.md index 68c78b7e9..61dd1044a 100644 --- a/files/citations.md +++ b/files/citations.md @@ -1,6 +1,6 @@ **Insert in the main body of the paper:** -We use the lens modeling software `PyAutoLens` https://github.com/Jammy2211/PyAutoLens) [@pyautolens] [@Nightingale2015] [@Nightingale2018] to... +We use the lens modeling software `PyAutoLens` https://github.com/PyAutoLabs/PyAutoLens) [@pyautolens] [@Nightingale2015] [@Nightingale2018] to... **At the end of the paper (delete as appropriate, see https://pyautofit.readthedocs.io/en/latest/general/citations.html):** @@ -16,8 +16,8 @@ This work uses the following software packages: - `matplotlib` https://github.com/matplotlib/matplotlib [@matplotlib] - `numba` https://github.com/numba/numba [@numba] - `NumPy` https://github.com/numpy/numpy [@numpy] -- `PyAutoFit` https://github.com/rhayes777/PyAutoFit [@pyautofit] -- `PyAutoGalaxy` https://github.com/Jammy2211/PyAutoGalaxy [@Nightingale2018] [@pyautogalaxy] +- `PyAutoFit` https://github.com/PyAutoLabs/PyAutoFit [@pyautofit] +- `PyAutoGalaxy` https://github.com/PyAutoLabs/PyAutoGalaxy [@Nightingale2018] [@pyautogalaxy] - `PyNUFFT` https://github.com/jyhmiinlin/pynufft [@pynufft] - `PySwarms` https://github.com/ljvmiranda921/pyswarms [@pyswarms] - `Python` https://www.python.org/ [@python] diff --git a/paper/README.md b/paper/README.md index 7dc06cb6b..6615715e8 100644 --- a/paper/README.md +++ b/paper/README.md @@ -1,5 +1,5 @@ PyAutoGalaxy JOSS Paper ===================== -Paper accompanying [PyAutoGalaxy](https://github.com/Jammy2211/PyAutoGalaxy) for submission to the Journal of Open Source +Paper accompanying [PyAutoGalaxy](https://github.com/PyAutoLabs/PyAutoGalaxy) for submission to the Journal of Open Source Software (JOSS). \ No newline at end of file diff --git a/paper/paper.md b/paper/paper.md index a33566cff..fa3d8a5b3 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -56,7 +56,7 @@ affiliations: index: 4 date: 12 May 2022 -codeRepository: https://github.com/Jammy2211/PyAutoGalaxy +codeRepository: https://github.com/PyAutoLabs/PyAutoGalaxy license: MIT bibliography: paper.bib --- @@ -75,7 +75,7 @@ massively parallel model-fitting and an SQLite3 database that allows large suite queried and analysed. Accompanying `PyAutoGalaxy` is the [autogalaxy workspace](https://github.com/PyAutoLabs/autogalaxy_workspace), which includes example scripts and galaxy datasets covering every use case. The [`HowToGalaxy`](https://github.com/PyAutoLabs/HowToGalaxy) repository provides a separate Jupyter notebook lecture series which introduces non-experts to galaxy morphology studies using `PyAutoGalaxy`. Readers can try `PyAutoGalaxy` right now by going -to [the introduction Jupyter notebook on Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/start_here.ipynb) or +to [the introduction Jupyter notebook on Colab](https://colab.research.google.com/github/PyAutoLabs/autogalaxy_workspace/blob/2026.5.14.2/notebooks/imaging/start_here.ipynb) or checkout the [readthedocs](https://pyautogalaxy.readthedocs.io/en/latest/) for a complete overview of `PyAutoGalaxy`'s features. @@ -130,7 +130,7 @@ handles unit conversions and calculations are optimized using the packages `NumP and `PyNUFFT` [@pynufft]. To perform model-fitting, `PyAutoGalaxy` adopts the probabilistic programming -language `PyAutoFit` (https://github.com/rhayes777/PyAutoFit). `PyAutoFit` allows users to compose a +language `PyAutoFit` (https://github.com/PyAutoLabs/PyAutoFit). `PyAutoFit` allows users to compose a model from `LightProfile` and `Galaxy` objects, customize the model parameterization and fit it to data via a non-linear search, for example, `dynesty` [@dynesty], `emcee` [@emcee] or `PySwarms` [@pyswarms]. By composing a model with `Pixelization` objects, the galaxy's light is reconstructed using a non-parametric rectangular @@ -144,7 +144,7 @@ Automated fitting of complex galaxy models is possible using `PyAutoFit`'s searc a galaxy into a chained sequence of non-linear searches. These fits pass information gained about simpler models fitted by earlier searches to subsequent searches, which fit progressively more complex models. By granularizing the model-fitting procedure, automated pipelines that fit complex galaxy models without human intervention can be carefully -crafted, with example pipelines found on the [autogalaxy workspace](https://github.com/Jammy2211/autogalaxy_workspace). +crafted, with example pipelines found on the [autogalaxy workspace](https://github.com/PyAutoLabs/autogalaxy_workspace). To ensure the analysis and interpretation of fits to large galaxy datasets is feasible, `PyAutoFit`'s database tools write modeling results to a relational database which can be queried from a storage drive to a Python script or Jupyter notebook. This uses memory-light `Python` generators, ensuring it is practical for results containing hundreds of thousands of galaxies.