fix: simulators call af.ex.util, and the chain-run resolves in a notebook (PENDING RELEASE)

llms-full.txt

@@ -44,4 +44,3 @@ AUTO-GENERATED by PyAutoHands — do not edit by hand; regenerate with generate.
   - Contents: Gaussian x1, Gaussian x1 (0), Gaussian x1 (1), Gaussian x1 (2), Gaussian x1 (Identical 0), Gaussian x1 (Identical 1), Gaussian x1 (Identical 2), Gaussian x1 + Exponential x1, Gaussian x2 + Exponential x1, Gaussian x2, Gaussian x3, Gaussian x5, Gaussian x1 unconvolved, Gaussian x1 convolved, Gaussian x1 with feature, Gaussian x2 split, Gaussian x1 time
 - [__Simulators__](scripts/simulators/simulators_sample.py): These scripts simulates many 1D Gaussian datasets with a low signal to noise ratio, which are used to demonstrate model-fitting.
   - Contents: Gaussian x1 low snr (centre fixed to 50.0), Gaussian x1 low snr (centre drawn from parent Gaussian distribution to 50.0), Gaussian x2 offset centre
-- [util](scripts/simulators/util.py): (no summary in script docstring)

notebooks/simulators/simulators.ipynb

@@ -76,7 +76,6 @@
     "\n",
     "# from autofit import setup_notebook; setup_notebook()\n",
     "\n",
-    "import util\n",
     "from os import path\n",
     "\n",
     "import autofit as af"
@@ -97,7 +96,9 @@
    "source": [
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=10.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)"
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")"
    ],
    "outputs": [],
    "execution_count": null
@@ -115,7 +116,9 @@
    "source": [
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_0\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=1.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)"
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")"
    ],
    "outputs": [],
    "execution_count": null
@@ -133,7 +136,9 @@
    "source": [
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=5.0)\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_1\")\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)"
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")"
    ],
    "outputs": [],
    "execution_count": null
@@ -151,7 +156,9 @@
    "source": [
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=10.0)\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_2\")\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)"
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")"
    ],
    "outputs": [],
    "execution_count": null
@@ -169,7 +176,9 @@
    "source": [
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_identical_0\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=10.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)"
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")"
    ],
    "outputs": [],
    "execution_count": null
@@ -187,7 +196,9 @@
    "source": [
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_identical_1\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=10.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)"
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")"
    ],
    "outputs": [],
    "execution_count": null
@@ -205,7 +216,9 @@
    "source": [
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_identical_2\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=10.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)"
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")"
    ],
    "outputs": [],
    "execution_count": null
@@ -224,7 +237,7 @@
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=10.0)\n",
     "exponential = af.ex.Exponential(centre=50.0, normalization=40.0, rate=0.05)\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1__exponential_x1\")\n",
-    "util.simulate_dataset_1d_via_profile_1d_list_from(\n",
+    "af.ex.util.simulate_dataset_1d_via_profile_1d_list_from(\n",
     "    profile_1d_list=[gaussian, exponential], dataset_path=dataset_path\n",
     ")"
    ],
@@ -246,7 +259,7 @@
     "gaussian_1 = af.ex.Gaussian(centre=20.0, normalization=30.0, sigma=5.0)\n",
     "exponential = af.ex.Exponential(centre=70.0, normalization=40.0, rate=0.005)\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x2__exponential_x1\")\n",
-    "util.simulate_dataset_1d_via_profile_1d_list_from(\n",
+    "af.ex.util.simulate_dataset_1d_via_profile_1d_list_from(\n",
     "    profile_1d_list=[gaussian_0, gaussian_1, exponential], dataset_path=dataset_path\n",
     ")"
    ],
@@ -267,7 +280,7 @@
     "gaussian_0 = af.ex.Gaussian(centre=50.0, normalization=20.0, sigma=1.0)\n",
     "gaussian_1 = af.ex.Gaussian(centre=50.0, normalization=40.0, sigma=5.0)\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x2\")\n",
-    "util.simulate_dataset_1d_via_profile_1d_list_from(\n",
+    "af.ex.util.simulate_dataset_1d_via_profile_1d_list_from(\n",
     "    profile_1d_list=[gaussian_0, gaussian_1], dataset_path=dataset_path\n",
     ")"
    ],
@@ -289,7 +302,7 @@
     "gaussian_1 = af.ex.Gaussian(centre=50.0, normalization=40.0, sigma=5.0)\n",
     "gaussian_2 = af.ex.Gaussian(centre=50.0, normalization=60.0, sigma=10.0)\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x3\")\n",
-    "util.simulate_dataset_1d_via_profile_1d_list_from(\n",
+    "af.ex.util.simulate_dataset_1d_via_profile_1d_list_from(\n",
     "    profile_1d_list=[gaussian_0, gaussian_1, gaussian_2], dataset_path=dataset_path\n",
     ")"
    ],
@@ -313,7 +326,7 @@
     "gaussian_3 = af.ex.Gaussian(centre=50.0, normalization=80.0, sigma=15.0)\n",
     "gaussian_4 = af.ex.Gaussian(centre=50.0, normalization=100.0, sigma=20.0)\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x5\")\n",
-    "util.simulate_dataset_1d_via_profile_1d_list_from(\n",
+    "af.ex.util.simulate_dataset_1d_via_profile_1d_list_from(\n",
     "    profile_1d_list=[gaussian_0, gaussian_1, gaussian_2, gaussian_3, gaussian_4],\n",
     "    dataset_path=dataset_path,\n",
     ")"
@@ -334,7 +347,9 @@
    "source": [
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_unconvolved\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=3.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)"
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")"
    ],
    "outputs": [],
    "execution_count": null
@@ -352,7 +367,7 @@
    "source": [
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_convolved\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=3.0)\n",
-    "util.simulate_data_1d_with_kernel_via_gaussian_from(\n",
+    "af.ex.util.simulate_data_1d_with_kernel_via_gaussian_from(\n",
     "    gaussian=gaussian, dataset_path=dataset_path\n",
     ")"
    ],
@@ -373,7 +388,7 @@
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_with_feature\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=25.0, sigma=10.0)\n",
     "gaussian_feature = af.ex.Gaussian(centre=70.0, normalization=0.3, sigma=0.5)\n",
-    "util.simulate_dataset_1d_via_profile_1d_list_from(\n",
+    "af.ex.util.simulate_dataset_1d_via_profile_1d_list_from(\n",
     "    profile_1d_list=[gaussian, gaussian_feature], dataset_path=dataset_path\n",
     ")"
    ],
@@ -394,7 +409,7 @@
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x2_split\")\n",
     "gaussian_0 = af.ex.Gaussian(centre=25.0, normalization=50.0, sigma=12.5)\n",
     "gaussian_1 = af.ex.Gaussian(centre=75.0, normalization=50.0, sigma=12.5)\n",
-    "util.simulate_dataset_1d_via_profile_1d_list_from(\n",
+    "af.ex.util.simulate_dataset_1d_via_profile_1d_list_from(\n",
     "    profile_1d_list=[gaussian_0, gaussian_1], dataset_path=dataset_path\n",
     ")\n"
    ],
@@ -414,15 +429,21 @@
    "source": [
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_time\", \"time_0\")\n",
     "gaussian = af.ex.Gaussian(centre=40.0, normalization=50.0, sigma=20.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)\n",
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")\n",
     "\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_time\", \"time_1\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=50.0, sigma=20.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)\n",
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")\n",
     "\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_time\", \"time_2\")\n",
     "gaussian = af.ex.Gaussian(centre=60.0, normalization=50.0, sigma=20.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)\n"
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")\n"
    ],
    "outputs": [],
    "execution_count": null
@@ -440,15 +461,21 @@
    "source": [
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_variable\", \"sigma_0\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=50.0, sigma=10.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)\n",
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")\n",
     "\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_variable\", \"sigma_1\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=50.0, sigma=20.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)\n",
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")\n",
     "\n",
     "dataset_path = path.join(\"dataset\", \"example_1d\", \"gaussian_x1_variable\", \"sigma_2\")\n",
     "gaussian = af.ex.Gaussian(centre=50.0, normalization=50.0, sigma=30.0)\n",
-    "util.simulate_dataset_1d_via_gaussian_from(gaussian=gaussian, dataset_path=dataset_path)"
+    "af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    gaussian=gaussian, dataset_path=dataset_path\n",
+    ")"
    ],
    "outputs": [],
    "execution_count": null
@@ -460,7 +487,12 @@
     "__Sample Datasets (Chapter 3)__\n",
     "\n",
     "Chain-run the sample simulator so every tutorial's `simulators.py` subprocess\n",
-    "call also produces the `dataset_*/` sample folders used by chapter 3."
+    "call also produces the `dataset_*/` sample folders used by chapter 3.\n",
+    "\n",
+    "The path is relative to the repository root, which every execution context sets as the working\n",
+    "directory: scripts are run from the root, the notebook kernel is pinned there, and Colab chdirs\n",
+    "there. It must not be derived from the script's own file path, which a notebook kernel does not\n",
+    "define."
    ]
   },
   {
@@ -470,7 +502,7 @@
     "import runpy\n",
     "\n",
     "runpy.run_path(\n",
-    "    path.join(path.dirname(path.abspath(__file__)), \"simulators_sample.py\"),\n",
+    "    path.join(\"scripts\", \"simulators\", \"simulators_sample.py\"),\n",
     "    run_name=\"__main__\",\n",
     ")\n"
    ],

notebooks/simulators/simulators_sample.ipynb

@@ -66,8 +66,7 @@
     "import numpy as np\n",
     "from os import path\n",
     "\n",
-    "import autofit as af\n",
-    "import util"
+    "import autofit as af"
    ],
    "outputs": [],
    "execution_count": null
@@ -93,7 +92,7 @@
     "        \"dataset\", \"example_1d\", f\"gaussian_x1__low_snr\", f\"dataset_{i}\"\n",
     "    )\n",
     "    gaussian = af.ex.Gaussian(centre=50.0, normalization=0.5, sigma=5.0)\n",
-    "    util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
     "        gaussian=gaussian, dataset_path=dataset_path\n",
     "    )"
    ],
@@ -133,7 +132,7 @@
     "\n",
     "    gaussian = gaussian_parent_model.random_instance()\n",
     "\n",
-    "    util.simulate_dataset_1d_via_gaussian_from(\n",
+    "    af.ex.util.simulate_dataset_1d_via_gaussian_from(\n",
     "        gaussian=gaussian, dataset_path=dataset_path\n",
     "    )\n"
    ],
@@ -184,7 +183,7 @@
     "    gaussian_0 = af.ex.Gaussian(centre=40.0, normalization=1.0, sigma=sigma_0_value)\n",
     "    gaussian_1 = af.ex.Gaussian(centre=60.0, normalization=1.0, sigma=sigma_1_value)\n",
     "\n",
-    "    util.simulate_dataset_1d_via_profile_1d_list_from(\n",
+    "    af.ex.util.simulate_dataset_1d_via_profile_1d_list_from(\n",
     "        profile_1d_list=[gaussian_0, gaussian_1], dataset_path=dataset_path\n",
     "    )\n"
    ],