PyAutoLabs · Jammy2211 · Jul 25, 2026 · Jul 25, 2026
diff --git a/notebooks/chapter_1_introduction/tutorial_1_grids_and_galaxies.ipynb b/notebooks/chapter_1_introduction/tutorial_1_grids_and_galaxies.ipynb
@@ -1104,7 +1104,7 @@
     "adaptive over sampling scheme with high accuracy across all use cases.\n",
     "\n",
     "Once you are more experienced, you should read up on over-sampling in more detail via\n",
-    "the `autolens_workspace/*/guides/over_sampling.ipynb` notebook."
+    "the `autolens_workspace/*/guides/advanced/over_sampling.ipynb` notebook."
    ]
   }
  ],

diff --git a/notebooks/chapter_2_lens_modeling/tutorial_1_non_linear_search.ipynb b/notebooks/chapter_2_lens_modeling/tutorial_1_non_linear_search.ipynb
@@ -521,7 +521,7 @@
     "fitted the data.\n",
     "\n",
     "A detailed step-by-step visual guide of the likelihood function is provided \n",
-    "at `autolens_workspace/*/imaging/log_likelihood_function/parametric.ipynb`."
+    "at `autolens_workspace/*/imaging/likelihood_function.ipynb`."
    ]
   },
   {

diff --git a/notebooks/chapter_2_lens_modeling/tutorial_2_practicalities.ipynb b/notebooks/chapter_2_lens_modeling/tutorial_2_practicalities.ipynb
@@ -384,11 +384,11 @@
     "limiting, as the notebook cell will only complete once the fit finishes, preventing you from advancing through the \n",
     "tutorial or running additional code.\n",
     "\n",
-    "To work around this, we recommend running tutorial scripts as standalone Python scripts, found \n",
-    "in `autolens_workspace/scripts/howtogalaxy`. These scripts mirror the notebook tutorials but run independently of \n",
+    "To work around this, we recommend running tutorial scripts as standalone Python scripts, found\n",
+    "in the `scripts/` folder of the HowToLens repository. These scripts mirror the notebook tutorials but run independently of\n",
     "Jupyter notebooks. For example, you can start a script with:\n",
     "\n",
-    "`python3 scripts/howtogalaxy/chapter_2_modeling/tutorial_2_practicalities.py`\n",
+    "`python3 scripts/chapter_2_lens_modeling/tutorial_2_practicalities.py`\n",
     "\n",
     "Using scripts allows results to be saved to the hard drive in the `output` folder, enabling you to inspect results \n",
     "immediately once the script completes. When rerun, the script loads results directly from disk, so any Jupyter \n",

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
@@ -708,7 +708,7 @@
     "find the global maximum lens model. However, this also means the search will take longer!\n",
     "\n",
     "Below, we configure a more thorough Nautilus search with `n_live=200`. These settings and what they change are \n",
-    "discussed in the optional tutorial `howtolens/chapter_optional/tutorial_searches.ipynb`.\n",
+    "discussed in the optional tutorial `chapter_optional/tutorial_searches.ipynb`.\n",
     "\n",
     "Due to the long run times of this search, the output is commented out below. Feel free to uncomment it to run the \n",
     "script faster."

diff --git a/notebooks/chapter_2_lens_modeling/tutorial_5_linear_profiles.ipynb b/notebooks/chapter_2_lens_modeling/tutorial_5_linear_profiles.ipynb
@@ -801,7 +801,7 @@
     "in a much simpler non-linear parameter space which has far less significant parameter degeneracies!\n",
     "\n",
     "We strongly recommend that you adopt an MGE in your own lens modeling pipelines from here on. The script \n",
-    "`autolens_workspace/*/modeling/features/multi_gaussian_expansion.py` gives examples on fitting even more complex\n",
+    "`autolens_workspace/*/imaging/features/multi_gaussian_expansion/modeling.py` gives examples on fitting even more complex\n",
     "MGE models, where for example the Gaussians have different axis-ratios and position angles.\n",
     "\n",
     "__Disadvantage of Basis Functions__\n",
@@ -833,7 +833,7 @@
     "features of a galaxy. They do so over a wide range of scales, and can often represent  features in source galaxies \n",
     "that a single Sersic function or MGE cannot.\n",
     "\n",
-    "An example using shapelets is given at `autolens_workspace/scripts/modeling/features/shapelets.py`.\n",
+    "An example using shapelets is given at `autolens_workspace/scripts/imaging/features/advanced/shapelets/modeling.py`.\n",
     " \n",
     "Feel free to experiment with using shapelets as the source galaxy by yourself. However they incur higher computational \n",
     "overheads than the MGE and include a free parameter which governs the size of the basis functions and therefore source,\n",

diff --git a/notebooks/chapter_4_pixelizations/tutorial_3_inversions.ipynb b/notebooks/chapter_4_pixelizations/tutorial_3_inversions.ipynb
@@ -512,7 +512,7 @@
     "__Detailed Explanation__\n",
     "\n",
     "If you are interested in a more detailed description of how inversions work, then checkout the file\n",
-    "`autolens_workspace/*/imaging/log_likelihood_function/inversion.ipynb` which gives a visual step-by-step\n",
+    "`autolens_workspace/*/imaging/features/pixelization/likelihood_function.ipynb` which gives a visual step-by-step\n",
     "guide of the process alongside equations and references to literature on the subject."
    ]
   }

diff --git a/notebooks/chapter_4_pixelizations/tutorial_8_model_fit.ipynb b/notebooks/chapter_4_pixelizations/tutorial_8_model_fit.ipynb
@@ -9,7 +9,7 @@
     "\n",
     "You should now perform lens modeling using a pixelization, which is described fully in the example:\n",
     "\n",
-    "`autolens_workspace/*/imaging/features/pixelizations/modeling.py`\n",
+    "`autolens_workspace/*/imaging/features/pixelization/modeling.py`\n",
     "\n",
     "__Wrap Up__\n",
     "\n",

diff --git a/notebooks/simulator/lens_sersic.ipynb b/notebooks/simulator/lens_sersic.ipynb
@@ -32,7 +32,7 @@
     "\n",
     "__Start Here Notebook__\n",
     "\n",
-    "If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook."
+    "If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook."
    ]
   },
   {

diff --git a/notebooks/simulator/lens_x2.ipynb b/notebooks/simulator/lens_x2.ipynb
@@ -40,7 +40,7 @@
     "\n",
     "__Start Here Notebook__\n",
     "\n",
-    "If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook."
+    "If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook."
    ]
   },
   {

diff --git a/notebooks/simulator/no_lens_light.ipynb b/notebooks/simulator/no_lens_light.ipynb
@@ -10,7 +10,7 @@
     "This script simulates `Imaging` of a 'galaxy-scale' which is identical to the `simple` simulated in the `start_here.py`\n",
     "script, but where the lens galaxy's light is omitted.\n",
     "\n",
-    "It is used in `autolens_workspace/notebooks/modeling/features/no_lens_light.ipynb` to illustrate how to fit a\n",
+    "It is used in `autolens_workspace/notebooks/imaging/features/no_lens_light/modeling.ipynb` to illustrate how to fit a\n",
     "lens model to data where the lens galaxy's light is not present (e.g. because it is too faint to be detected).\n",
     "\n",
     "__Contents__\n",
@@ -33,7 +33,7 @@
     "\n",
     "__Start Here Notebook__\n",
     "\n",
-    "If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook."
+    "If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook."
    ]
   },
   {
@@ -340,7 +340,8 @@
     "__Mask Extra Galaxies__\n",
     "\n",
     "This dataset has no extra galaxies, but pixelization tutorials that load it (e.g.\n",
-    "`imaging/features/pixelization/modeling.py`, `imaging/features/pixelization/fit.py`) demonstrate the\n",
+    "`autolens_workspace/scripts/imaging/features/pixelization/modeling.py`,\n",
+    "`autolens_workspace/scripts/imaging/features/pixelization/fit.py`) demonstrate the\n",
     "noise-scaling API by applying a `mask_extra_galaxies` mask to the dataset. Output an empty (all-False,\n",
     "no-pixels-masked) mask so those tutorials can call `apply_noise_scaling(mask=...)` without crashing on a\n",
     "missing FITS file. The mask shape tracks `dataset.shape_native`, so `PYAUTO_SMALL_DATASETS=1` is honoured\n",

diff --git a/notebooks/simulator/no_lens_light__mass_sis.ipynb b/notebooks/simulator/no_lens_light__mass_sis.ipynb
@@ -31,7 +31,7 @@
     "\n",
     "__Start Here Notebook__\n",
     "\n",
-    "If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook."
+    "If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook."
    ]
   },
   {

diff --git a/notebooks/simulator/source_complex.ipynb b/notebooks/simulator/source_complex.ipynb
@@ -35,7 +35,7 @@
     "\n",
     "__Start Here Notebook__\n",
     "\n",
-    "If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook."
+    "If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook."
    ]
   },
   {

diff --git a/scripts/chapter_1_introduction/tutorial_1_grids_and_galaxies.py b/scripts/chapter_1_introduction/tutorial_1_grids_and_galaxies.py
@@ -668,5 +668,5 @@
 adaptive over sampling scheme with high accuracy across all use cases.
 
 Once you are more experienced, you should read up on over-sampling in more detail via
-the `autolens_workspace/*/guides/over_sampling.ipynb` notebook.
+the `autolens_workspace/*/guides/advanced/over_sampling.ipynb` notebook.
 """
diff --git a/scripts/chapter_2_lens_modeling/tutorial_1_non_linear_search.py b/scripts/chapter_2_lens_modeling/tutorial_1_non_linear_search.py
@@ -357,7 +357,7 @@
 fitted the data.
 
 A detailed step-by-step visual guide of the likelihood function is provided 
-at `autolens_workspace/*/imaging/log_likelihood_function/parametric.ipynb`.
+at `autolens_workspace/*/imaging/likelihood_function.ipynb`.
 """
 analysis = al.AnalysisImaging(dataset=dataset)
 

diff --git a/scripts/chapter_2_lens_modeling/tutorial_2_practicalities.py b/scripts/chapter_2_lens_modeling/tutorial_2_practicalities.py
@@ -253,11 +253,11 @@
 limiting, as the notebook cell will only complete once the fit finishes, preventing you from advancing through the 
 tutorial or running additional code.
 
-To work around this, we recommend running tutorial scripts as standalone Python scripts, found 
-in `autolens_workspace/scripts/howtogalaxy`. These scripts mirror the notebook tutorials but run independently of 
+To work around this, we recommend running tutorial scripts as standalone Python scripts, found
+in the `scripts/` folder of the HowToLens repository. These scripts mirror the notebook tutorials but run independently of
 Jupyter notebooks. For example, you can start a script with:
 
-`python3 scripts/howtogalaxy/chapter_2_modeling/tutorial_2_practicalities.py`
+`python3 scripts/chapter_2_lens_modeling/tutorial_2_practicalities.py`
 
 Using scripts allows results to be saved to the hard drive in the `output` folder, enabling you to inspect results 
 immediately once the script completes. When rerun, the script loads results directly from disk, so any Jupyter 

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
@@ -402,7 +402,7 @@
 find the global maximum lens model. However, this also means the search will take longer!
 
 Below, we configure a more thorough Nautilus search with `n_live=200`. These settings and what they change are 
-discussed in the optional tutorial `howtolens/chapter_optional/tutorial_searches.ipynb`.
+discussed in the optional tutorial `chapter_optional/tutorial_searches.ipynb`.
 
 Due to the long run times of this search, the output is commented out below. Feel free to uncomment it to run the 
 script faster.

diff --git a/scripts/chapter_2_lens_modeling/tutorial_5_linear_profiles.py b/scripts/chapter_2_lens_modeling/tutorial_5_linear_profiles.py
@@ -496,7 +496,7 @@
 in a much simpler non-linear parameter space which has far less significant parameter degeneracies!
 
 We strongly recommend that you adopt an MGE in your own lens modeling pipelines from here on. The script 
-`autolens_workspace/*/modeling/features/multi_gaussian_expansion.py` gives examples on fitting even more complex
+`autolens_workspace/*/imaging/features/multi_gaussian_expansion/modeling.py` gives examples on fitting even more complex
 MGE models, where for example the Gaussians have different axis-ratios and position angles.
 
 __Disadvantage of Basis Functions__
@@ -528,7 +528,7 @@
 features of a galaxy. They do so over a wide range of scales, and can often represent  features in source galaxies 
 that a single Sersic function or MGE cannot.
 
-An example using shapelets is given at `autolens_workspace/scripts/modeling/features/shapelets.py`.
+An example using shapelets is given at `autolens_workspace/scripts/imaging/features/advanced/shapelets/modeling.py`.
 
 Feel free to experiment with using shapelets as the source galaxy by yourself. However they incur higher computational 
 overheads than the MGE and include a free parameter which governs the size of the basis functions and therefore source,

diff --git a/scripts/chapter_4_pixelizations/tutorial_3_inversions.py b/scripts/chapter_4_pixelizations/tutorial_3_inversions.py
@@ -305,6 +305,6 @@
 __Detailed Explanation__
 
 If you are interested in a more detailed description of how inversions work, then checkout the file
-`autolens_workspace/*/imaging/log_likelihood_function/inversion.ipynb` which gives a visual step-by-step
+`autolens_workspace/*/imaging/features/pixelization/likelihood_function.ipynb` which gives a visual step-by-step
 guide of the process alongside equations and references to literature on the subject.
 """
diff --git a/scripts/chapter_4_pixelizations/tutorial_8_model_fit.py b/scripts/chapter_4_pixelizations/tutorial_8_model_fit.py
@@ -1,13 +1,13 @@
-"""
-Tutorial 8: Model-Fit
-=====================
-
-You should now perform lens modeling using a pixelization, which is described fully in the example:
-
-`autolens_workspace/*/imaging/features/pixelizations/modeling.py`
-
-__Wrap Up__
-
-Once complete, you can then move on to the next HowToLens tutorial and gain more insight into adaptive
-pixelizations.
-"""
+"""
+Tutorial 8: Model-Fit
+=====================
+
+You should now perform lens modeling using a pixelization, which is described fully in the example:
+
+`autolens_workspace/*/imaging/features/pixelization/modeling.py`
+
+__Wrap Up__
+
+Once complete, you can then move on to the next HowToLens tutorial and gain more insight into adaptive
+pixelizations.
+"""
diff --git a/scripts/simulator/lens_sersic.py b/scripts/simulator/lens_sersic.py
@@ -27,7 +27,7 @@
 
 __Start Here Notebook__
 
-If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook.
+If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook.
 """
 
 from autolens import jax_wrapper  # Sets JAX environment before other imports

diff --git a/scripts/simulator/lens_x2.py b/scripts/simulator/lens_x2.py
@@ -35,7 +35,7 @@
 
 __Start Here Notebook__
 
-If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook.
+If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook.
 """
 
 from pathlib import Path

diff --git a/scripts/simulator/no_lens_light.py b/scripts/simulator/no_lens_light.py
@@ -5,7 +5,7 @@
 This script simulates `Imaging` of a 'galaxy-scale' which is identical to the `simple` simulated in the `start_here.py`
 script, but where the lens galaxy's light is omitted.
 
-It is used in `autolens_workspace/notebooks/modeling/features/no_lens_light.ipynb` to illustrate how to fit a
+It is used in `autolens_workspace/notebooks/imaging/features/no_lens_light/modeling.ipynb` to illustrate how to fit a
 lens model to data where the lens galaxy's light is not present (e.g. because it is too faint to be detected).
 
 __Contents__
@@ -28,7 +28,7 @@
 
 __Start Here Notebook__
 
-If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook.
+If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook.
 """
 
 from autolens import jax_wrapper  # Sets JAX environment before other imports
@@ -165,7 +165,8 @@
 __Mask Extra Galaxies__
 
 This dataset has no extra galaxies, but pixelization tutorials that load it (e.g.
-`imaging/features/pixelization/modeling.py`, `imaging/features/pixelization/fit.py`) demonstrate the
+`autolens_workspace/scripts/imaging/features/pixelization/modeling.py`,
+`autolens_workspace/scripts/imaging/features/pixelization/fit.py`) demonstrate the
 noise-scaling API by applying a `mask_extra_galaxies` mask to the dataset. Output an empty (all-False,
 no-pixels-masked) mask so those tutorials can call `apply_noise_scaling(mask=...)` without crashing on a
 missing FITS file. The mask shape tracks `dataset.shape_native`, so `PYAUTO_SMALL_DATASETS=1` is honoured

diff --git a/scripts/simulator/no_lens_light__mass_sis.py b/scripts/simulator/no_lens_light__mass_sis.py
@@ -26,7 +26,7 @@
 
 __Start Here Notebook__
 
-If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook.
+If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook.
 """
 
 from autolens import jax_wrapper  # Sets JAX environment before other imports

diff --git a/scripts/simulator/source_complex.py b/scripts/simulator/source_complex.py
@@ -30,7 +30,7 @@
 
 __Start Here Notebook__
 
-If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook.
+If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook.
 """
 
 from autolens import jax_wrapper  # Sets JAX environment before other imports
-Original file line number
+Diff line change
@@ Expand Up / @@ -32,7 +32,7 @@ @@
         "\n",
         "__Start Here Notebook__\n",
         "\n",
-        "If any code in this script is unclear, refer to the `simulators/start_here.ipynb` notebook."
+        "If any code in this script is unclear, refer to the `autolens_workspace/*/imaging/simulator.ipynb` notebook."
        ]
       },
       {
@@ Expand Down @@