Fixups for new RTD website (#1573)

* Fixups for new RTD website

* update docstrings

Author: michaeldeistler

docs/_templates/autosummary/class.rst

@@ -0,0 +1,8 @@
+{{ fullname }}
+{{ underline }}
+
+.. autoclass:: {{ fullname }}
+   :members:
+   :undoc-members:
+   :inherited-members:
+   :show-inheritance:

docs/conf.py

@@ -16,6 +16,8 @@
 # import os
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
+import os
+import shutil
 
 # -- Project information -----------------------------------------------------
 
@@ -98,3 +100,23 @@
 autodoc_typehints = "description"
 add_module_names = False
 autodoc_member_order = "bysource"
+
+
+def copy_data_folder(app, exception):
+    """Copy all images in `how_to_guide/data` to the `_build_` folder.
+
+    This function was written by ChatGPT."""
+    if exception is None:
+        source_dir = os.path.join(app.srcdir, 'how_to_guide', 'data')
+        dest_dir = os.path.join(app.outdir, 'how_to_guide', 'data')
+        if os.path.exists(source_dir):
+            os.makedirs(dest_dir, exist_ok=True)
+            for filename in os.listdir(source_dir):
+                shutil.copyfile(
+                    os.path.join(source_dir, filename), os.path.join(dest_dir, filename)
+                )
+
+
+def setup(app):
+    """Action to copy all images in `how_to_guide/data` to the `_build_` folder."""
+    app.connect('build-finished', copy_data_folder)

docs/how_to_guide/13_diagnostics_lc2st.ipynb

@@ -71,7 +71,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<img src=\"l_c2st_pp_plot.png\" width=\"500\">"
+    "<img src=\"data/l_c2st_pp_plot.png\" width=\"500\">"
    ]
   },
   {

docs/how_to_guide/15_expected_coverage.ipynb

@@ -2,15 +2,15 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "262a8be1",
+   "id": "7de8bf27",
    "metadata": {},
    "source": [
     "# How to run expected coverage"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "afdf4c0c",
+   "id": "e431d6e1",
    "metadata": {},
    "source": [
     "Expected coverage provides a simple and interpretable tool to diagnose issues in the posterior. In comparison to other diagnostic tools such as L-C2ST, it requires relatively few additional simulations (~200) and it does not rely on any additional hyperparameters (as TARP would) or additional neural network training.\n",
@@ -22,15 +22,15 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f897470f",
+   "id": "81d072a6",
    "metadata": {},
    "source": [
     "## Main syntax"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "4b758674",
+   "id": "a1e890c2",
    "metadata": {},
    "source": [
     "```python\n",
@@ -66,23 +66,23 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3a700ac9",
+   "id": "dd374b82",
    "metadata": {},
    "source": [
     "This will return a figure such as the following:"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "1614d726",
+   "id": "5db59c6e",
    "metadata": {},
    "source": [
-    "<img src=\"sbc_rank_plot.png\" width=\"500\">"
+    "<img src=\"data/sbc_rank_plot.png\" width=\"500\">"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "14c277ea",
+   "id": "1072f685",
    "metadata": {},
    "source": [
     "You can interpret this plots as follows:\n",

docs/how_to_guide/16_sbc.ipynb

@@ -2,15 +2,15 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "85533aa3",
+   "id": "7741d8ac",
    "metadata": {},
    "source": [
     "# How to run simulation-based calibration (SBC)"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "eee436d4",
+   "id": "aceee7d6",
    "metadata": {},
    "source": [
     "Similar to expected coverage, simulation-based calibration (SBC) provides a simple and interpretable tool to diagnose issues in the posterior. It also requires relatively few additional simulations (~200) and it does not rely on any additional hyperparameters (as TARP would) or additional neural network training.\n",
@@ -22,15 +22,15 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5586331e",
+   "id": "48d5f324",
    "metadata": {},
    "source": [
     "## Main syntax"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "2a4f6e84",
+   "id": "41f152b0",
    "metadata": {},
    "source": [
     "```python\n",
@@ -63,31 +63,31 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fbfbb941",
+   "id": "0d2ec9af",
    "metadata": {},
    "source": [
     "The only difference to running expected coverage is that we did not pass `run_sbc(..., reduce_fns=...)` and we visualize it differently by not passing `sbc_rank_plot(..., plot_type=\"cdf\")`"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "2f5d7d31",
+   "id": "2cdd5ca1",
    "metadata": {},
    "source": [
     "This will return a figure such as the following:"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "25fed9c0",
+   "id": "cb91ea03",
    "metadata": {},
    "source": [
-    "<img src=\"sbc_plot.png\" width=\"500\">"
+    "<img src=\"data/sbc_plot.png\" width=\"500\">"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "b8d2f1e9",
+   "id": "3467dcb5",
    "metadata": {},
    "source": [
     "This plots as many plots as there are parameters. For each of the parameters you can interpret the the shape of the red bars as follows:\n",
@@ -100,15 +100,15 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4fdb5991",
+   "id": "e758d940",
    "metadata": {},
    "source": [
     "## Example"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "d49e4382",
+   "id": "67c19086",
    "metadata": {},
    "source": [
     "For a detailed example and further explanation, see [this tutorial](https://sbi.readthedocs.io/en/latest/advanced_tutorials/11_diagnostics_simulation_based_calibration.html)."

docs/how_to_guide/17_tarp.ipynb

@@ -2,15 +2,15 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "2239191b",
+   "id": "8cd307dd",
    "metadata": {},
    "source": [
     "# How to run TARP"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "40eb9908",
+   "id": "59d719f3",
    "metadata": {},
    "source": [
     "TARP is an alternative calibration check proposed recently in https://arxiv.org/abs/2302.03026. \n",
@@ -30,7 +30,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "80dc7728",
+   "id": "5db62ea3",
    "metadata": {},
    "source": [
     "```python\n",
@@ -62,39 +62,39 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2d8ada2f",
+   "id": "c73833f8",
    "metadata": {},
    "source": [
     "This generates a plot like the following:"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "9f5fbbee",
+   "id": "a3589a9f",
    "metadata": {},
    "source": [
-    "<img src=\"tarp_plot.png\" width=\"400\">"
+    "<img src=\"data/tarp_plot.png\" width=\"400\">"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "d90cc58f",
+   "id": "ee39a40d",
    "metadata": {},
    "source": [
     "If the blue curve is above the diagonal, then the posterior estimate is under-confident. If it is under the diagonal, then the posterior estimate is over confident."
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "7f10f082",
+   "id": "2bf07d41",
    "metadata": {},
    "source": [
     "## Explanation"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "37c99744",
+   "id": "45c402a1",
    "metadata": {},
    "source": [
     "Given a test set $(\\theta^*, x^*)$ and a set of reference points $\\theta_r$, TARP calculates \n",