From 48d912956c6238c122f77818b65471fd403d3425 Mon Sep 17 00:00:00 2001 From: Jammy2211 Date: Fri, 24 Jul 2026 16:39:50 +0100 Subject: [PATCH] docs: merge adjacent documentation blocks --- .../tutorial_0_visualization.ipynb | 7 ------ .../tutorial_1_grids_and_galaxies.ipynb | 7 ------ .../tutorial_2_data.ipynb | 7 ------ .../tutorial_3_fitting.ipynb | 7 ------ .../tutorial_4_methods.ipynb | 7 ------ .../tutorial_5_summary.ipynb | 7 ------ .../tutorial_1_non_linear_search.ipynb | 7 ------ .../tutorial_2_practicalities.ipynb | 24 +++---------------- .../tutorial_3_realism_and_complexity.ipynb | 7 ------ .../tutorial_4_dealing_with_failure.ipynb | 7 ------ .../tutorial_6_masking.ipynb | 7 ------ .../tutorial_7_results.ipynb | 7 ------ .../tutorial_8_need_for_speed.ipynb | 7 ------ .../tutorial_1_search_chaining.ipynb | 7 ------ .../tutorial_2_prior_passing.ipynb | 7 ------ .../tutorial_3_x2_galaxies.ipynb | 7 ------ .../tutorial_1_pixelizations.ipynb | 7 ------ .../tutorial_2_mappers.ipynb | 7 ------ .../tutorial_3_inversions.ipynb | 7 ------ .../tutorial_4_bayesian_regularization.ipynb | 7 ------ .../tutorial_5_model_fit.ipynb | 7 ------ .../chapter_optional/tutorial_searches.ipynb | 7 ------ notebooks/simulators/sersic.ipynb | 7 ------ notebooks/simulators/sersic_x2.ipynb | 7 ------ notebooks/simulators/simple.ipynb | 7 ------ .../tutorial_2_practicalities.py | 2 -- 26 files changed, 3 insertions(+), 191 deletions(-) diff --git a/notebooks/chapter_1_introduction/tutorial_0_visualization.ipynb b/notebooks/chapter_1_introduction/tutorial_0_visualization.ipynb index aed1212..22295bd 100644 --- a/notebooks/chapter_1_introduction/tutorial_0_visualization.ipynb +++ b/notebooks/chapter_1_introduction/tutorial_0_visualization.ipynb @@ -294,13 +294,6 @@ "Great! Hopefully, visualization in **PyAutoGalaxy** is displaying nicely for us to get on with the **HowToGalaxy**\n", "lecture series." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_1_introduction/tutorial_1_grids_and_galaxies.ipynb b/notebooks/chapter_1_introduction/tutorial_1_grids_and_galaxies.ipynb index 2424de1..0371fb3 100644 --- a/notebooks/chapter_1_introduction/tutorial_1_grids_and_galaxies.ipynb +++ b/notebooks/chapter_1_introduction/tutorial_1_grids_and_galaxies.ipynb @@ -1089,13 +1089,6 @@ "Once you are more experienced, you should read up on over-sampling in more detail via \n", "the `autogalaxy_workspace/*/guides/over_sampling.ipynb` notebook." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_1_introduction/tutorial_2_data.ipynb b/notebooks/chapter_1_introduction/tutorial_2_data.ipynb index 2217381..49e3d57 100644 --- a/notebooks/chapter_1_introduction/tutorial_2_data.ipynb +++ b/notebooks/chapter_1_introduction/tutorial_2_data.ipynb @@ -634,13 +634,6 @@ "\n", "- **Output**: We saved the simulated data to `.fits` files, the standard format used by astronomers for storing images." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_1_introduction/tutorial_3_fitting.ipynb b/notebooks/chapter_1_introduction/tutorial_3_fitting.ipynb index ca3de09..df78e09 100644 --- a/notebooks/chapter_1_introduction/tutorial_3_fitting.ipynb +++ b/notebooks/chapter_1_introduction/tutorial_3_fitting.ipynb @@ -1102,13 +1102,6 @@ "- **Model Fitting**: We performed a basic model fit on a simple dataset, adjusting the model parameters to improve the\n", " fit quality." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_1_introduction/tutorial_4_methods.ipynb b/notebooks/chapter_1_introduction/tutorial_4_methods.ipynb index a4626e0..03ae894 100644 --- a/notebooks/chapter_1_introduction/tutorial_4_methods.ipynb +++ b/notebooks/chapter_1_introduction/tutorial_4_methods.ipynb @@ -79,13 +79,6 @@ "source": [ "__Wrap Up__" ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_1_introduction/tutorial_5_summary.ipynb b/notebooks/chapter_1_introduction/tutorial_5_summary.ipynb index c77d257..b6b198b 100644 --- a/notebooks/chapter_1_introduction/tutorial_5_summary.ipynb +++ b/notebooks/chapter_1_introduction/tutorial_5_summary.ipynb @@ -283,13 +283,6 @@ "\n", "Even the smallest bit of exposure via a GitHub star can help our project grow!" ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_2_modeling/tutorial_1_non_linear_search.ipynb b/notebooks/chapter_2_modeling/tutorial_1_non_linear_search.ipynb index 7c04d30..1da2914 100644 --- a/notebooks/chapter_2_modeling/tutorial_1_non_linear_search.ipynb +++ b/notebooks/chapter_2_modeling/tutorial_1_non_linear_search.ipynb @@ -995,13 +995,6 @@ "scientific research and data analysis. In the next tutorials, these concepts will be further expanded upon to \n", "deepen your understanding and provide more advanced techniques for model fitting and analysis." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_2_modeling/tutorial_2_practicalities.ipynb b/notebooks/chapter_2_modeling/tutorial_2_practicalities.ipynb index 9184718..d3abf8d 100644 --- a/notebooks/chapter_2_modeling/tutorial_2_practicalities.ipynb +++ b/notebooks/chapter_2_modeling/tutorial_2_practicalities.ipynb @@ -535,16 +535,8 @@ "parameter `n`). These mappings ate specified in the `config/notation.yaml` file and can be customized by users.\n", "\n", "The superscripts of labels correspond to the name each component was given in the model (e.g. for the `Isothermal`\n", - "mass its name `mass` defined when making the `Model` above is used)." - ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [ + "mass its name `mass` defined when making the `Model` above is used).\n", "\n", - "# %%\n", - "'''\n", "__Other Practicalities__\n", "\n", "The following are examples of other practicalities which I will document fully in this example script in the future,\n", @@ -569,18 +561,8 @@ "- How to navigate the output folder and examine model-fit results to assess quality.\n", "\n", "- How to estimate the run-time of a model-fit before initiating it, and change settings to make it faster or run the\n", - " analysis in parallel.\n", - "'''" - ], - "outputs": [], - "execution_count": null - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null + " analysis in parallel." + ] } ], "metadata": { diff --git a/notebooks/chapter_2_modeling/tutorial_3_realism_and_complexity.ipynb b/notebooks/chapter_2_modeling/tutorial_3_realism_and_complexity.ipynb index d317be4..0d92f8f 100644 --- a/notebooks/chapter_2_modeling/tutorial_3_realism_and_complexity.ipynb +++ b/notebooks/chapter_2_modeling/tutorial_3_realism_and_complexity.ipynb @@ -427,13 +427,6 @@ " disk, bulge, bar, star-forming knot) and there may even be more than 1 galaxy! Do you think there is any hope of \n", " us navigating a parameter space if the galaxies contributes 30+ parameters?" ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_2_modeling/tutorial_4_dealing_with_failure.ipynb b/notebooks/chapter_2_modeling/tutorial_4_dealing_with_failure.ipynb index fc56c1d..95adc71 100644 --- a/notebooks/chapter_2_modeling/tutorial_4_dealing_with_failure.ipynb +++ b/notebooks/chapter_2_modeling/tutorial_4_dealing_with_failure.ipynb @@ -727,13 +727,6 @@ "To wrap up chapter 2, we have a few more tutorials, where we will discuss masking in more detail, the `Result` object\n", "and how to make **PyAutoGalaxy** run faster." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_2_modeling/tutorial_6_masking.ipynb b/notebooks/chapter_2_modeling/tutorial_6_masking.ipynb index f94ce90..f92eb1b 100644 --- a/notebooks/chapter_2_modeling/tutorial_6_masking.ipynb +++ b/notebooks/chapter_2_modeling/tutorial_6_masking.ipynb @@ -261,13 +261,6 @@ " 1) Customizing the mask for the analysis of one galaxy gets the analysis running fast and can provide accurate \n", " non-linear sampling. However, for a large sample of galaxies, this high level of customization may take a lot of time. " ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_2_modeling/tutorial_7_results.ipynb b/notebooks/chapter_2_modeling/tutorial_7_results.ipynb index 75bd00b..e34854a 100644 --- a/notebooks/chapter_2_modeling/tutorial_7_results.ipynb +++ b/notebooks/chapter_2_modeling/tutorial_7_results.ipynb @@ -259,13 +259,6 @@ "This is because it makes it simple to perform all analyse in a Jupyter notebook, which is the most flexible and \n", "versatile way to check results and make figures." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_2_modeling/tutorial_8_need_for_speed.ipynb b/notebooks/chapter_2_modeling/tutorial_8_need_for_speed.ipynb index 3fac868..bb8d393 100644 --- a/notebooks/chapter_2_modeling/tutorial_8_need_for_speed.ipynb +++ b/notebooks/chapter_2_modeling/tutorial_8_need_for_speed.ipynb @@ -124,13 +124,6 @@ "\n", "_setup_colab.setup(\"howtogalaxy\")" ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_3_search_chaining/tutorial_1_search_chaining.ipynb b/notebooks/chapter_3_search_chaining/tutorial_1_search_chaining.ipynb index 67a977c..0238764 100644 --- a/notebooks/chapter_3_search_chaining/tutorial_1_search_chaining.ipynb +++ b/notebooks/chapter_3_search_chaining/tutorial_1_search_chaining.ipynb @@ -550,13 +550,6 @@ "Fortunately, we can pass priors in **PyAutoGalaxy** without specifying the specific values. The API for this technique,\n", "called prior passing, is the topic of the next tutorial." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_3_search_chaining/tutorial_2_prior_passing.ipynb b/notebooks/chapter_3_search_chaining/tutorial_2_prior_passing.ipynb index f81df25..f8e4f18 100644 --- a/notebooks/chapter_3_search_chaining/tutorial_2_prior_passing.ipynb +++ b/notebooks/chapter_3_search_chaining/tutorial_2_prior_passing.ipynb @@ -526,13 +526,6 @@ "\n", "And with that, we're done. Chaining priors is a bit of an art form, but one that works really well. " ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_3_search_chaining/tutorial_3_x2_galaxies.ipynb b/notebooks/chapter_3_search_chaining/tutorial_3_x2_galaxies.ipynb index 1c3df17..52fb697 100644 --- a/notebooks/chapter_3_search_chaining/tutorial_3_x2_galaxies.ipynb +++ b/notebooks/chapter_3_search_chaining/tutorial_3_x2_galaxies.ipynb @@ -491,13 +491,6 @@ "\n", "We have successfully fitted multiple galaxies, but fitting each one-by-one." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_4_pixelizations/tutorial_1_pixelizations.ipynb b/notebooks/chapter_4_pixelizations/tutorial_1_pixelizations.ipynb index 95d36e9..77c6482 100644 --- a/notebooks/chapter_4_pixelizations/tutorial_1_pixelizations.ipynb +++ b/notebooks/chapter_4_pixelizations/tutorial_1_pixelizations.ipynb @@ -314,13 +314,6 @@ " 1) The rectangular pixelization`s edges are aligned with the most exterior coordinates of the source-grid. This is \n", " intentional, why do you think this is?" ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_4_pixelizations/tutorial_2_mappers.ipynb b/notebooks/chapter_4_pixelizations/tutorial_2_mappers.ipynb index cad0c38..dabb7d2 100644 --- a/notebooks/chapter_4_pixelizations/tutorial_2_mappers.ipynb +++ b/notebooks/chapter_4_pixelizations/tutorial_2_mappers.ipynb @@ -334,13 +334,6 @@ " on the pixel-grid. So, how does knowing how each pixel maps to the image actually help us? If you`ve not got \n", " any bright ideas, then worry not, that exactly what we're going to cover in the next tutorial." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_4_pixelizations/tutorial_3_inversions.ipynb b/notebooks/chapter_4_pixelizations/tutorial_3_inversions.ipynb index 904aa73..a1cf859 100644 --- a/notebooks/chapter_4_pixelizations/tutorial_3_inversions.ipynb +++ b/notebooks/chapter_4_pixelizations/tutorial_3_inversions.ipynb @@ -398,13 +398,6 @@ "`autogalaxy_workspace/*/imaging/log_likelihood_function/inversion.ipynb` which gives a visual step-by-step\n", "guide of the process alongside equations and references to literature on the subject." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_4_pixelizations/tutorial_4_bayesian_regularization.ipynb b/notebooks/chapter_4_pixelizations/tutorial_4_bayesian_regularization.ipynb index 8cd2387..cc1c58f 100644 --- a/notebooks/chapter_4_pixelizations/tutorial_4_bayesian_regularization.ipynb +++ b/notebooks/chapter_4_pixelizations/tutorial_4_bayesian_regularization.ipynb @@ -441,13 +441,6 @@ "this framework throughout, **PyAutoGalaxy** objectively determines the final model following the principles of Bayesian\n", "analysis and Occam\u2019s Razor." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_4_pixelizations/tutorial_5_model_fit.ipynb b/notebooks/chapter_4_pixelizations/tutorial_5_model_fit.ipynb index bf0a152..22d70db 100644 --- a/notebooks/chapter_4_pixelizations/tutorial_5_model_fit.ipynb +++ b/notebooks/chapter_4_pixelizations/tutorial_5_model_fit.ipynb @@ -363,13 +363,6 @@ "\n", "And with that, we now have a pipeline to model galaxies using an inversion! " ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/chapter_optional/tutorial_searches.ipynb b/notebooks/chapter_optional/tutorial_searches.ipynb index 1d7b679..ae73c21 100644 --- a/notebooks/chapter_optional/tutorial_searches.ipynb +++ b/notebooks/chapter_optional/tutorial_searches.ipynb @@ -471,13 +471,6 @@ "For the vast majority of models in **PyAutoGalaxy**, the default nested sampling search `Nautilus` is recommended, as\n", "it is robust, efficient and requires little manual tuning." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/simulators/sersic.ipynb b/notebooks/simulators/sersic.ipynb index 35cb5ad..d76bb8f 100644 --- a/notebooks/simulators/sersic.ipynb +++ b/notebooks/simulators/sersic.ipynb @@ -324,13 +324,6 @@ "source": [ "The dataset can be viewed in the folder `autogalaxy_workspace/imaging/simple__sersic`." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/simulators/sersic_x2.ipynb b/notebooks/simulators/sersic_x2.ipynb index 53521e5..33abbba 100644 --- a/notebooks/simulators/sersic_x2.ipynb +++ b/notebooks/simulators/sersic_x2.ipynb @@ -332,13 +332,6 @@ "source": [ "The dataset can be viewed in the folder `autogalaxy_workspace/imaging/sersic_x2`." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/notebooks/simulators/simple.ipynb b/notebooks/simulators/simple.ipynb index 735f679..5825ac7 100644 --- a/notebooks/simulators/simple.ipynb +++ b/notebooks/simulators/simple.ipynb @@ -420,13 +420,6 @@ "See `scripts/guides/api/data_structures.py` for the broader \"JIT-it-\n", "yourself\" pattern." ] - }, - { - "cell_type": "code", - "metadata": {}, - "source": [], - "outputs": [], - "execution_count": null } ], "metadata": { diff --git a/scripts/chapter_2_modeling/tutorial_2_practicalities.py b/scripts/chapter_2_modeling/tutorial_2_practicalities.py index 1b5dce0..5a8c1ae 100644 --- a/scripts/chapter_2_modeling/tutorial_2_practicalities.py +++ b/scripts/chapter_2_modeling/tutorial_2_practicalities.py @@ -362,9 +362,7 @@ The superscripts of labels correspond to the name each component was given in the model (e.g. for the `Isothermal` mass its name `mass` defined when making the `Model` above is used). -""" -""" __Other Practicalities__ The following are examples of other practicalities which I will document fully in this example script in the future,