diff --git a/CITATIONS.md b/CITATIONS.md index 7f8822c4..2bd173e4 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,9 +1,9 @@ # Citations & References The bibtex entries for **PyAutoFit** and its affiliated software packages can be found -[here](https://github.com/rhayes777/PyAutoFit/blob/main/files/citations.bib), with example text for citing **PyAutoFit** -in [.tex format here](https://github.com/rhayes777/PyAutoFit/blob/main/files/citation.tex) format here and -[.md format here](https://github.com/rhayes777/PyAutoFit/blob/main/files/citations.md). +[here](https://github.com/PyAutoLabs/PyAutoFit/blob/main/files/citations.bib), with example text for citing **PyAutoFit** +in [.tex format here](https://github.com/PyAutoLabs/PyAutoFit/blob/main/files/citation.tex) format here and +[.md format here](https://github.com/PyAutoLabs/PyAutoFit/blob/main/files/citations.md). As shown in the examples, we would greatly appreciate it if you mention **PyAutoFit** by name and include a link to our GitHub page! diff --git a/CLAUDE.md b/CLAUDE.md index b849787f..5b59086b 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -68,7 +68,7 @@ ls failed/ ```yaml autofit: - ScriptName # Reason it cannot run yet - - ScriptName # bug https://github.com/rhayes777/PyAutoFit/issues/NNN + - ScriptName # bug https://github.com/PyAutoLabs/PyAutoFit/issues/NNN ``` Scripts with a bug link or the word "bug"/"issue"/"fix" in the comment are flagged as `[TODO - should run after a future PR]` in the output. diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index dd7e19d5..b281bd3b 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). **PyAutoFit 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/README.md b/README.md index 24e2b9dc..6bdea382 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # PyAutoFit Workspace -[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PyAutoLabs/autofit_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/autofit_workspace/blob/2026.5.14.2/notebooks/overview/overview_1_the_basics.ipynb) [![JOSS](https://joss.theoj.org/papers/10.21105/joss.02550/status.svg)](https://doi.org/10.21105/joss.02550) [Installation Guide](https://pyautofit.readthedocs.io/en/latest/installation/overview.html) | @@ -67,7 +67,7 @@ This version of the workspace are built and tested for using **PyAutoFit v2026.5 ## Support Support for installation issues and integrating your modeling software with **PyAutoFit** is available by -[raising an issue on the autofit_workspace GitHub page](https://github.com/Jammy2211/autofit_workspace/issues). or +[raising an issue on the autofit_workspace GitHub page](https://github.com/PyAutoLabs/autofit_workspace/issues). or joining the **PyAutoFit** [Slack channel](https://pyautofit.slack.com/), where we also provide the latest updates on **PyAutoFit**. diff --git a/notebooks/overview/overview_1_the_basics.ipynb b/notebooks/overview/overview_1_the_basics.ipynb index 9541e7a8..b8a9f205 100644 --- a/notebooks/overview/overview_1_the_basics.ipynb +++ b/notebooks/overview/overview_1_the_basics.ipynb @@ -883,7 +883,7 @@ "\n", "__Resources__\n", "\n", - "The `autofit_workspace: `_ repository on GitHub provides numerous \n", + "The `autofit_workspace: `_ repository on GitHub provides numerous \n", "examples demonstrating more complex model-fitting tasks.\n", "\n", "This includes cookbooks, which provide a concise reference guide to the **PyAutoFit** API for advanced model-fitting:\n", diff --git a/notebooks/overview/overview_2_scientific_workflow.ipynb b/notebooks/overview/overview_2_scientific_workflow.ipynb index 8b31cce3..d90e4f5e 100644 --- a/notebooks/overview/overview_2_scientific_workflow.ipynb +++ b/notebooks/overview/overview_2_scientific_workflow.ipynb @@ -265,7 +265,7 @@ "source": [ "The screenshot below shows the output folder where all output is enabled:\n", "\n", - ".. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoFit/main/docs/overview/image/output_example.png\n", + ".. image:: https://raw.githubusercontent.com/PyAutoLabs/PyAutoFit/main/docs/overview/image/output_example.png\n", " :width: 400\n", " :alt: Alternative text\n", "\n", diff --git a/notebooks/overview/overview_3_statistical_methods.ipynb b/notebooks/overview/overview_3_statistical_methods.ipynb index b4052cba..8dfe79be 100644 --- a/notebooks/overview/overview_3_statistical_methods.ipynb +++ b/notebooks/overview/overview_3_statistical_methods.ipynb @@ -20,7 +20,7 @@ "\n", "A full description of using graphical models is given below:\n", "\n", - "https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/graphical_models.ipynb\n", + "https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/graphical_models.ipynb\n", "\n", "Hierarchical Models\n", "-------------------\n", @@ -44,7 +44,7 @@ "\n", "A full description of using model comparison is given below:\n", "\n", - "https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/model_comparison.ipynb\n", + "https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/model_comparison.ipynb\n", "\n", "Interpolation\n", "-------------\n", @@ -60,7 +60,7 @@ "\n", "**PyAutoFit**'s interpolation feature allows for this, and a full description of its use is given below:\n", "\n", - "https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/interpolate.ipynb\n", + "https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/interpolate.ipynb\n", "\n", "Search Grid Search\n", "------------------\n", @@ -80,7 +80,7 @@ "\n", "A full description of using search grid searches is given below:\n", "\n", - "https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/search_grid_search.ipynb\n", + "https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/search_grid_search.ipynb\n", "\n", "Search Chaining\n", "---------------\n", @@ -96,7 +96,7 @@ "\n", "A full description of using search chaining is given below:\n", "\n", - "https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/search_grid_search.ipynb\n", + "https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/search_grid_search.ipynb\n", "\n", "Sensitivity Mapping\n", "-------------------\n", @@ -114,7 +114,7 @@ "\n", "A full description of using sensitivity mapping is given below:\n", "\n", - "https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/sensitivity_mapping.ipynb\n", + "https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/sensitivity_mapping.ipynb\n", "\n", "__Contents__\n", "\n", diff --git a/notebooks/searches/mle.ipynb b/notebooks/searches/mle.ipynb index 685a7146..a4907694 100644 --- a/notebooks/searches/mle.ipynb +++ b/notebooks/searches/mle.ipynb @@ -15,7 +15,7 @@ "\n", "Relevant links:\n", "\n", - " - Drawer: https://github.com/rhayes777/PyAutoFit/blob/main/autofit/non_linear/optimize/drawer/drawer.py\n", + " - Drawer: https://github.com/PyAutoLabs/PyAutoFit/blob/main/autofit/non_linear/optimize/drawer/drawer.py\n", " - L-BFGS: https://docs.scipy.org/doc/scipy/reference/optimize.minimize-lbfgsb.html\n", "\n", "__Contents__\n", diff --git a/scripts/overview/overview_1_the_basics.py b/scripts/overview/overview_1_the_basics.py index 794d8332..2ae32a62 100644 --- a/scripts/overview/overview_1_the_basics.py +++ b/scripts/overview/overview_1_the_basics.py @@ -583,7 +583,7 @@ def log_likelihood_function(self, instance) -> float: __Resources__ -The `autofit_workspace: `_ repository on GitHub provides numerous +The `autofit_workspace: `_ repository on GitHub provides numerous examples demonstrating more complex model-fitting tasks. This includes cookbooks, which provide a concise reference guide to the **PyAutoFit** API for advanced model-fitting: diff --git a/scripts/overview/overview_2_scientific_workflow.py b/scripts/overview/overview_2_scientific_workflow.py index c8a77cd5..870c0313 100644 --- a/scripts/overview/overview_2_scientific_workflow.py +++ b/scripts/overview/overview_2_scientific_workflow.py @@ -196,7 +196,7 @@ def on_the_fly_output(self, instance): """ The screenshot below shows the output folder where all output is enabled: -.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoFit/main/docs/overview/image/output_example.png +.. image:: https://raw.githubusercontent.com/PyAutoLabs/PyAutoFit/main/docs/overview/image/output_example.png :width: 400 :alt: Alternative text diff --git a/scripts/overview/overview_3_statistical_methods.py b/scripts/overview/overview_3_statistical_methods.py index 82952b18..9ba603bd 100644 --- a/scripts/overview/overview_3_statistical_methods.py +++ b/scripts/overview/overview_3_statistical_methods.py @@ -15,7 +15,7 @@ A full description of using graphical models is given below: -https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/graphical_models.ipynb +https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/graphical_models.ipynb Hierarchical Models ------------------- @@ -39,7 +39,7 @@ A full description of using model comparison is given below: -https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/model_comparison.ipynb +https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/model_comparison.ipynb Interpolation ------------- @@ -55,7 +55,7 @@ **PyAutoFit**'s interpolation feature allows for this, and a full description of its use is given below: -https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/interpolate.ipynb +https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/interpolate.ipynb Search Grid Search ------------------ @@ -75,7 +75,7 @@ A full description of using search grid searches is given below: -https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/search_grid_search.ipynb +https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/search_grid_search.ipynb Search Chaining --------------- @@ -91,7 +91,7 @@ A full description of using search chaining is given below: -https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/search_grid_search.ipynb +https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/search_grid_search.ipynb Sensitivity Mapping ------------------- @@ -109,7 +109,7 @@ A full description of using sensitivity mapping is given below: -https://github.com/Jammy2211/autofit_workspace/blob/release/notebooks/features/sensitivity_mapping.ipynb +https://github.com/PyAutoLabs/autofit_workspace/blob/main/notebooks/features/sensitivity_mapping.ipynb __Contents__ diff --git a/scripts/searches/mle.py b/scripts/searches/mle.py index 54181496..9e90f0da 100644 --- a/scripts/searches/mle.py +++ b/scripts/searches/mle.py @@ -10,7 +10,7 @@ Relevant links: - - Drawer: https://github.com/rhayes777/PyAutoFit/blob/main/autofit/non_linear/optimize/drawer/drawer.py + - Drawer: https://github.com/PyAutoLabs/PyAutoFit/blob/main/autofit/non_linear/optimize/drawer/drawer.py - L-BFGS: https://docs.scipy.org/doc/scipy/reference/optimize.minimize-lbfgsb.html __Contents__