From aff4fd8fc85f06a2c0da20a0e99e66026216ba5c Mon Sep 17 00:00:00 2001 From: Jammy2211 Date: Wed, 29 Jul 2026 20:02:13 +0100 Subject: [PATCH 1/2] docs: fix README drift The READMEs described a tree that no longer exists. Surfaced by the widened hygiene refs scanner (PyAutoBrain#178, #180); same sweep as autolens_workspace#372 / autogalaxy_workspace#179. config/**/README.md inventories rewritten to list what actually ships: - config/README.md listed `grids` (gone), `non-linear` (it is `non_linear`) and `notation` (now notation.yaml, a file), and omitted output.yaml/build - config/non_linear/ ships only GridSearch.yaml, not mcmc/nest/mle.yaml - config/visualize/ ships general.yaml and plots_search.yaml (plus plots.yaml where present), not include.yaml/mat_wrap*.yaml Navigator catalogue regenerated, since README text feeds llms-full.txt and workspace_index.json. Prerequisite for widening PyAutoHands' check_navigator.py gate: it is repo-agnostic and runs on six repos, so this drift had to clear before the gate could see these shapes without turning these repos red. Co-Authored-By: Claude Opus 5 --- config/README.md | 7 ++++--- config/non_linear/README.md | 11 ++++++----- config/visualize/README.md | 6 +----- llms-full.txt | 2 +- notebooks/README.md | 1 - scripts/README.md | 1 - 6 files changed, 12 insertions(+), 16 deletions(-) diff --git a/config/README.md b/config/README.md index 41d2a15..32d9a64 100644 --- a/config/README.md +++ b/config/README.md @@ -2,13 +2,14 @@ The `config` folder contains configuration files which customize default **PyAut # Folders -- `grids`: Configs for default behaviour of grids when used for ray-tracing. -- `non-linear`: Configs for default non-linear search (e.g. MCMC, nested sampling) settings. -- `notation`: Configs defining labels and formatting of model parameters when used for visualization. +- `non_linear`: Configs for default non-linear search (e.g. MCMC, nested sampling) settings. - `priors`: Configs defining default priors assumed on every model component and set of parameters. - `visualize`: Configs defining what images are output by a model fit. +- `build`: Configs used by the automated build and test system (not relevant to normal use). # Files - `general.yaml`: Customizes general **PyAutoLens** settings. - `logging.yaml`: Customizes the logging behaviour of **PyAutoLens**. +- `notation.yaml`: Defines labels and formatting of model parameters when used for visualization. +- `output.yaml`: Customizes what a model-fit writes to the output folder. diff --git a/config/non_linear/README.md b/config/non_linear/README.md index f69c3b3..c7e7a57 100644 --- a/config/non_linear/README.md +++ b/config/non_linear/README.md @@ -1,8 +1,9 @@ -The `non_linear` folder contains configuration files which customize the default behaviour of non-linear searches in -**PyAutoLens**. +The `non_linear` folder contains configuration files which customize the default behaviour of non-linear +searches in **PyAutoLens**. + +Defaults for individual searches (e.g. Nautilus, Emcee, LBFGS) ship with **PyAutoFit** itself; this folder +holds only the workspace-level overrides. # Files -- `mcmc.yaml`: Settings default behaviour of MCMC non-linear searches (e.g. Emcee). -- `nest.yaml`: Settings default behaviour of nested sampler non-linear searches (e.g. Dynesty). -- `mle.yaml`: Settings default behaviour of maximum likelihood estimator (mle) searches (e.g. LBFGS). +- `GridSearch.yaml`: Settings for the non-linear search grid search. diff --git a/config/visualize/README.md b/config/visualize/README.md index 6fa8589..b0a4869 100644 --- a/config/visualize/README.md +++ b/config/visualize/README.md @@ -1,11 +1,7 @@ -The `config` folder contains configuration files which customize default **PyAutoLens**. +The `visualize` folder contains configuration files which customize what a model-fit outputs. # 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. - `plots_search.yaml`: Customize which non-linear search 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/llms-full.txt b/llms-full.txt index 20b2f42..543445c 100644 --- a/llms-full.txt +++ b/llms-full.txt @@ -1,6 +1,6 @@ AUTO-GENERATED by PyAutoHands — do not edit by hand; regenerate with generate.py. -# HowToLens Lectures — Full Catalogue +# PyAutoLens Workspace — Full Catalogue > Complete, generated listing of every script (and its matching notebook) in this > workspace, grouped by top-level `scripts/` folder. This is the expanded companion to diff --git a/notebooks/README.md b/notebooks/README.md index 56dd067..c103a00 100644 --- a/notebooks/README.md +++ b/notebooks/README.md @@ -7,7 +7,6 @@ a strong lens. - `chapter_2_lens_modeling`: How to model strong lenses, including a primer on Bayesian non-linear analysis. - `chapter_3_search_chaining`: How to fit complex lens models using non-linear search chaining. - `chapter_4_pixelizations`: How to perform pixelized reconstructions of the source-galaxy. -- `chapter_5_hyper_mode`: How to use **PyAutoLens** advanced modeling features that adapt the model to the strong lens being analysed. - `chapter_optional`: Optional tutorials. # Full Explanation diff --git a/scripts/README.md b/scripts/README.md index 56dd067..c103a00 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -7,7 +7,6 @@ a strong lens. - `chapter_2_lens_modeling`: How to model strong lenses, including a primer on Bayesian non-linear analysis. - `chapter_3_search_chaining`: How to fit complex lens models using non-linear search chaining. - `chapter_4_pixelizations`: How to perform pixelized reconstructions of the source-galaxy. -- `chapter_5_hyper_mode`: How to use **PyAutoLens** advanced modeling features that adapt the model to the strong lens being analysed. - `chapter_optional`: Optional tutorials. # Full Explanation From 017e7d3220fb481c032a7043a507208f02fa5b38 Mon Sep 17 00:00:00 2001 From: Jammy2211 Date: Wed, 29 Jul 2026 20:03:40 +0100 Subject: [PATCH 2/2] chore: regenerate catalogue with the repo's declared generator project The previous commit regenerated with the library project name (autolens / autogalaxy / autofit) rather than the project this repo declares in .github/workflows/navigator_check.yml (howtolens / howtogalaxy / howtofit), which rewrote the catalogue title and failed the staleness check. Co-Authored-By: Claude Opus 5 --- llms-full.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/llms-full.txt b/llms-full.txt index 543445c..20b2f42 100644 --- a/llms-full.txt +++ b/llms-full.txt @@ -1,6 +1,6 @@ AUTO-GENERATED by PyAutoHands — do not edit by hand; regenerate with generate.py. -# PyAutoLens Workspace — Full Catalogue +# HowToLens Lectures — Full Catalogue > Complete, generated listing of every script (and its matching notebook) in this > workspace, grouped by top-level `scripts/` folder. This is the expanded companion to