From 0765d96151284255af2b1404661d294200decab4 Mon Sep 17 00:00:00 2001 From: Jammy2211 Date: Thu, 30 Jul 2026 11:03:18 +0100 Subject: [PATCH] docs: fix dead internal references in script docstrings The README half of this drift class is fixed and now gated at PR time (PyAutoHands#213). This is the remaining surface: dead file/folder references in scripts/**/*.py docstrings and comments, which the gate deliberately does not cover. Driven by `pyauto-brain hygiene refs --json`, which reported 129 findings across 7 repos. Verified classes: - log_likelihood_function -> likelihood_function (the scripts drop the log_) - notation/label.yaml -> notation.yaml (config went folder -> file) - config/generag.yaml -> config/general.yaml (autolens->autogalaxy clone residue, here in script prose) - autofit_workspace/*/plots -> plot (the package is singular) - feature/pixelization/... -> features/ ; subhalo/detection -> detect - guides/source_science -> the topic packages (source_science.py lives in imaging/, interferometer/, group/ -- never guides/) - preprocess / propocess -> imaging/data_preparation - modeling/imaging/{customize,searches} -> guides/modeling/... - imaging/advanced/database -> guides/results/database - simulators -> simulator (singular) - dataset directories quoted without their `dataset/` prefix -- the folder is written by a simulator, so the fix is qualification, not a restore Eleven needed prose rewriting rather than a re-point, because the target does not exist in any form: autogalaxy has no CPU-fast pixelization example (now points at the autolens one), point_source has no likelihood_function walkthrough (points at cluster/likelihood_function, titled "Log Likelihood Function: Cluster Point Source"), no subhalo/detect/examples folder exists, mat_wrap.yaml was retired in favour of general.yaml, config/priors has no `default` subfolder, and z_projects/ is not part of this workspace (the Euclid pipeline has its own repo). Notebooks and the navigator catalogue regenerated, since docstring text feeds notebooks/, llms-full.txt and workspace_index.json. Verified: hygiene refs reports 0 findings across all 7 repos (from 129), and check_navigator.py --banners=fail passes on all 6 gated repos. Co-Authored-By: Claude Opus 5 --- .../tutorial_4_dealing_with_failure.ipynb | 2 +- notebooks/chapter_2_lens_modeling/tutorial_7_results.ipynb | 2 +- notebooks/simulator/lens_sersic.ipynb | 2 +- notebooks/simulator/lens_x2.ipynb | 2 +- notebooks/simulator/no_lens_light.ipynb | 2 +- notebooks/simulator/no_lens_light__mass_sis.ipynb | 2 +- notebooks/simulator/source_complex.ipynb | 4 ++-- .../tutorial_4_dealing_with_failure.py | 2 +- scripts/chapter_2_lens_modeling/tutorial_7_results.py | 2 +- scripts/simulator/lens_sersic.py | 2 +- scripts/simulator/lens_x2.py | 2 +- scripts/simulator/no_lens_light.py | 2 +- scripts/simulator/no_lens_light__mass_sis.py | 2 +- scripts/simulator/source_complex.py | 4 ++-- 14 files changed, 16 insertions(+), 16 deletions(-) diff --git a/notebooks/chapter_2_lens_modeling/tutorial_4_dealing_with_failure.ipynb b/notebooks/chapter_2_lens_modeling/tutorial_4_dealing_with_failure.ipynb index 4ada2d5..0e4c53a 100644 --- a/notebooks/chapter_2_lens_modeling/tutorial_4_dealing_with_failure.ipynb +++ b/notebooks/chapter_2_lens_modeling/tutorial_4_dealing_with_failure.ipynb @@ -200,7 +200,7 @@ "In a previous tutorial, we learned how to fully customize priors. Let's apply this knowledge \n", "now. I've set up a custom search below with priors adjusted to give the non-linear search a better chance of finding \n", "the global maxima solution. I'll also explain how each prior has been changed from the default values specified in\n", - " the `config/priors/default` configuration files.\n", + " the `config/priors` configuration files.\n", "\n", "We will call our lens and source galaxies `lens` and `source` this time, for shorter more readable code.\n", "\n", diff --git a/notebooks/chapter_2_lens_modeling/tutorial_7_results.ipynb b/notebooks/chapter_2_lens_modeling/tutorial_7_results.ipynb index 0985b99..fd3c7dd 100644 --- a/notebooks/chapter_2_lens_modeling/tutorial_7_results.ipynb +++ b/notebooks/chapter_2_lens_modeling/tutorial_7_results.ipynb @@ -240,7 +240,7 @@ "advanced queries, so specific results can be loaded and inspected.\n", "\n", "We won't go into any more detail on the database in this tutorial. If you think the database will be useful, checkout \n", - "the full set of database tutorials which can be found in the folder `autolens_workspace/*/imaging/advanced/database`. \n", + "the full set of database tutorials which can be found in the folder `autolens_workspace/*/guides/results/database`. \n", "\n", "Here, you'll learn how to:\n", "\n", diff --git a/notebooks/simulator/lens_sersic.ipynb b/notebooks/simulator/lens_sersic.ipynb index e1451cd..927643a 100644 --- a/notebooks/simulator/lens_sersic.ipynb +++ b/notebooks/simulator/lens_sersic.ipynb @@ -367,7 +367,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The dataset can be viewed in the folder `autolens_workspace/imaging/lens_sersic`." + "The dataset can be viewed in the folder `autolens_workspace/dataset/imaging/lens_sersic`." ] } ], diff --git a/notebooks/simulator/lens_x2.ipynb b/notebooks/simulator/lens_x2.ipynb index 34629bd..759824f 100644 --- a/notebooks/simulator/lens_x2.ipynb +++ b/notebooks/simulator/lens_x2.ipynb @@ -352,7 +352,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The dataset can be viewed in the folder `autolens_workspace/imaging/x2_lens_galaxies`." + "The dataset can be viewed in the folder `autolens_workspace/dataset/imaging/x2_lens_galaxies`." ] } ], diff --git a/notebooks/simulator/no_lens_light.ipynb b/notebooks/simulator/no_lens_light.ipynb index d9de134..28451a8 100644 --- a/notebooks/simulator/no_lens_light.ipynb +++ b/notebooks/simulator/no_lens_light.ipynb @@ -436,7 +436,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The dataset can be viewed in the folder `autolens_workspace/imaging/simple__no_lens_light`." + "The dataset can be viewed in the folder `autolens_workspace/dataset/imaging/simple__no_lens_light`." ] } ], diff --git a/notebooks/simulator/no_lens_light__mass_sis.ipynb b/notebooks/simulator/no_lens_light__mass_sis.ipynb index 6fbe806..2caa1d7 100644 --- a/notebooks/simulator/no_lens_light__mass_sis.ipynb +++ b/notebooks/simulator/no_lens_light__mass_sis.ipynb @@ -350,7 +350,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The dataset can be viewed in the folder `autolens_workspace/imaging/simple__no_lens_light`." + "The dataset can be viewed in the folder `autolens_workspace/dataset/imaging/simple__no_lens_light`." ] } ], diff --git a/notebooks/simulator/source_complex.ipynb b/notebooks/simulator/source_complex.ipynb index 8cc805f..dc6eb31 100644 --- a/notebooks/simulator/source_complex.ipynb +++ b/notebooks/simulator/source_complex.ipynb @@ -11,7 +11,7 @@ "other examples, being composed of 4 Sersics.\n", "\n", "It is used to illustrate features which reconstruct the source galaxy's light using a pixelizaiton, for example\n", - "in the script `autolens_workspace/notebooks/modeling/features/pixelization`.\n", + "in the script `autolens_workspace/notebooks/imaging/features/pixelization`.\n", "\n", "__Contents__\n", "\n", @@ -378,7 +378,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The dataset can be viewed in the folder `autolens_workspace/imaging/source_complex`." + "The dataset can be viewed in the folder `autolens_workspace/dataset/imaging/source_complex`." ] } ], diff --git a/scripts/chapter_2_lens_modeling/tutorial_4_dealing_with_failure.py b/scripts/chapter_2_lens_modeling/tutorial_4_dealing_with_failure.py index 5837756..4c4ba7d 100644 --- a/scripts/chapter_2_lens_modeling/tutorial_4_dealing_with_failure.py +++ b/scripts/chapter_2_lens_modeling/tutorial_4_dealing_with_failure.py @@ -103,7 +103,7 @@ In a previous tutorial, we learned how to fully customize priors. Let's apply this knowledge now. I've set up a custom search below with priors adjusted to give the non-linear search a better chance of finding the global maxima solution. I'll also explain how each prior has been changed from the default values specified in - the `config/priors/default` configuration files. + the `config/priors` configuration files. We will call our lens and source galaxies `lens` and `source` this time, for shorter more readable code. diff --git a/scripts/chapter_2_lens_modeling/tutorial_7_results.py b/scripts/chapter_2_lens_modeling/tutorial_7_results.py index 11b7cd2..f784a99 100644 --- a/scripts/chapter_2_lens_modeling/tutorial_7_results.py +++ b/scripts/chapter_2_lens_modeling/tutorial_7_results.py @@ -143,7 +143,7 @@ advanced queries, so specific results can be loaded and inspected. We won't go into any more detail on the database in this tutorial. If you think the database will be useful, checkout -the full set of database tutorials which can be found in the folder `autolens_workspace/*/imaging/advanced/database`. +the full set of database tutorials which can be found in the folder `autolens_workspace/*/guides/results/database`. Here, you'll learn how to: diff --git a/scripts/simulator/lens_sersic.py b/scripts/simulator/lens_sersic.py index e32c962..1c7ca24 100644 --- a/scripts/simulator/lens_sersic.py +++ b/scripts/simulator/lens_sersic.py @@ -182,5 +182,5 @@ ) """ -The dataset can be viewed in the folder `autolens_workspace/imaging/lens_sersic`. +The dataset can be viewed in the folder `autolens_workspace/dataset/imaging/lens_sersic`. """ diff --git a/scripts/simulator/lens_x2.py b/scripts/simulator/lens_x2.py index 7bde40c..661b1a0 100644 --- a/scripts/simulator/lens_x2.py +++ b/scripts/simulator/lens_x2.py @@ -188,5 +188,5 @@ ) """ -The dataset can be viewed in the folder `autolens_workspace/imaging/x2_lens_galaxies`. +The dataset can be viewed in the folder `autolens_workspace/dataset/imaging/x2_lens_galaxies`. """ diff --git a/scripts/simulator/no_lens_light.py b/scripts/simulator/no_lens_light.py index 3592d03..8f56a1a 100644 --- a/scripts/simulator/no_lens_light.py +++ b/scripts/simulator/no_lens_light.py @@ -228,5 +228,5 @@ ) """ -The dataset can be viewed in the folder `autolens_workspace/imaging/simple__no_lens_light`. +The dataset can be viewed in the folder `autolens_workspace/dataset/imaging/simple__no_lens_light`. """ diff --git a/scripts/simulator/no_lens_light__mass_sis.py b/scripts/simulator/no_lens_light__mass_sis.py index fa0f519..6e3bc0b 100644 --- a/scripts/simulator/no_lens_light__mass_sis.py +++ b/scripts/simulator/no_lens_light__mass_sis.py @@ -164,5 +164,5 @@ ) """ -The dataset can be viewed in the folder `autolens_workspace/imaging/simple__no_lens_light`. +The dataset can be viewed in the folder `autolens_workspace/dataset/imaging/simple__no_lens_light`. """ diff --git a/scripts/simulator/source_complex.py b/scripts/simulator/source_complex.py index 2ac973a..e2a4b27 100644 --- a/scripts/simulator/source_complex.py +++ b/scripts/simulator/source_complex.py @@ -6,7 +6,7 @@ other examples, being composed of 4 Sersics. It is used to illustrate features which reconstruct the source galaxy's light using a pixelizaiton, for example -in the script `autolens_workspace/notebooks/modeling/features/pixelization`. +in the script `autolens_workspace/notebooks/imaging/features/pixelization`. __Contents__ @@ -194,5 +194,5 @@ ) """ -The dataset can be viewed in the folder `autolens_workspace/imaging/source_complex`. +The dataset can be viewed in the folder `autolens_workspace/dataset/imaging/source_complex`. """