Merge pull request #89 from CUQI-DTU/fenics_example

FEniCS notebook update. Update note on pre-run notebooks with new style

Author: amal-ghamdi

chapter01/overview_of_cuqipy.md

@@ -40,15 +40,15 @@ CUQIpy is built to address the need for:
 * CUQIpy consists of many modules for modeling, solving, and analyzing Bayesian inverse problems.
 * These modules mostly correspond to typical components/tools needed for modeling and solving Bayesian inverse problems.
 * Each module contains classes and functions that are used to perform specific tasks.
-* click [here](https://cuqi-dtu.github.io/CUQIpy/api/index.html) for an overview of the modules available in CUQIpy.
+* Click [here](https://cuqi-dtu.github.io/CUQIpy/api/index.html) for an overview of the modules available in CUQIpy.
 
 ![CUQIpy modules](../images/cuqipy_modules.png)
 
 ## CUQIpy plugins <a class="anchor" id="r-cuqipy-plugins"></a>
 
 * In addition to the CUQIpy modules, CUQIpy also has plugins that extend the functionality of the framework. 
 * These plugins allow integration of third-party software and tools with CUQIpy.
-* click [here](https://cuqi-dtu.github.io/CUQIpy/#cuqipy-plugins) to see the list of plugins available in CUQIpy.
+* Click [here](https://cuqi-dtu.github.io/CUQIpy/#cuqipy-plugins) to see the list of plugins available in CUQIpy.
 
 ![CUQIpy plugins](../images/cuqipy_modules_plugin.png)
 

chapter04/PDE/core_pde.ipynb

@@ -7,8 +7,6 @@
    "source": [
     "# Solving PDE-based BIP using core CUQIpy\n",
     "\n",
-    "**note**:\n",
-    "- This notebook was run on a local machine and not using github actions for this book due to its long execution time.\n",
     "\n",
     "Here we build a Bayesian problem in which the forward model is a partial differential equation (PDE) model, the 1D heat problem in particular.\n",
     "\n",
@@ -33,7 +31,13 @@
    "metadata": {},
    "source": [
     "<div style=\"border: 2px solid #FFB74D; background-color: #FFF3E0; border-radius: 8px; padding: 10px; font-family: Arial, sans-serif; color: #333; box-shadow: 2px 2px 8px rgba(0, 0, 0, 0.1); max-width: 750px; margin: 0 auto;\">\n",
-    "  <strong style=\"color: #E65100;\">⚠️ Note:</strong> This notebook uses MCMC samplers from the new <code>cuqi.experimental.mcmc</code> module, which are expected to become the default soon. Check out the <a href=\"https://cuqi-dtu.github.io/CUQIpy/api/_autosummary/cuqi.experimental.mcmc.html#module-cuqi.experimental.mcmc\">documentation</a> for more details.\n",
+    "  <strong style=\"color: #E65100;\">⚠️ Note:</strong> \n",
+    "  \n",
+    " - This notebook was run on a local machine and not using github actions for this book due to its long execution time.\n",
+    "\n",
+    " - This notebook uses MCMC samplers from the new <code>cuqi.experimental.mcmc</code> module, which are expected to become the default soon. Check out the <a href=\"https://cuqi-dtu.github.io/CUQIpy/api/_autosummary/cuqi.experimental.mcmc.html#module-cuqi.experimental.mcmc\">documentation</a> for more details.\n",
+    "\n",
+    "\n",
     "</div>"
    ]
   },

chapter04/Plugins/CUQIpy-CIL/demo_ct.ipynb

@@ -15,9 +15,6 @@
    "id": "99cf022a-d1d1-4adf-bbe5-798f0853833f",
    "metadata": {},
    "source": [
-    "**note**: \n",
-    "- This notebook was run on some machine and not using github actions for this book. To run this notebook on your machine, you need to have [CUQIpy-CIL installed](https://github.com/CUQI-DTU/CUQIpy-CIL).\n",
-    "\n",
     "[The Core Imaging Library (CIL)](https://www.ccpi.ac.uk/cil) is an open-source python library for processing and reconstruction of CT data (and other inverse problems).\n",
     "\n",
     "\n",
@@ -41,7 +38,12 @@
    "metadata": {},
    "source": [
     "<div style=\"border: 2px solid #FFB74D; background-color: #FFF3E0; border-radius: 8px; padding: 10px; font-family: Arial, sans-serif; color: #333; box-shadow: 2px 2px 8px rgba(0, 0, 0, 0.1); max-width: 750px; margin: 0 auto;\">\n",
-    "  <strong style=\"color: #E65100;\">⚠️ Note:</strong> This notebook uses MCMC samplers from the new <code>cuqi.experimental.mcmc</code> module, which are expected to become the default soon. Check out the <a href=\"https://cuqi-dtu.github.io/CUQIpy/api/_autosummary/cuqi.experimental.mcmc.html#module-cuqi.experimental.mcmc\">documentation</a> for more details.\n",
+    "  <strong style=\"color: #E65100;\">⚠️ Note:</strong> \n",
+    "  \n",
+    "- This notebook was run on some machine and not using github actions for this book. To run this notebook on your machine, you need to have [CUQIpy-CIL installed](https://github.com/CUQI-DTU/CUQIpy-CIL).\n",
+    "\n",
+    "- This notebook uses MCMC samplers from the new <code>cuqi.experimental.mcmc</code> module, which are expected to become the default soon. Check out the <a href=\"https://cuqi-dtu.github.io/CUQIpy/api/_autosummary/cuqi.experimental.mcmc.html#module-cuqi.experimental.mcmc\">documentation</a> for more details.\n",
+    "\n",
     "</div>"
    ]
   },

chapter04/Plugins/CUQIpy-FEniCS/poisson_2D_fenics.ipynb

@@ -7,8 +7,7 @@
    "source": [
     "# Hamiltonian Monte Carlo with CUQIpy-PyTorch\n",
     "\n",
-    "**note**: \n",
-    "- This notebook was run on some machine and not using github actions for this book. To run this notebook on your machine, you need to have [CUQIpy-PyTorch installed](https://github.com/CUQI-DTU/CUQIpy-PyTorch).\n",
+    "\n",
     "\n",
     "In this notebook, we use [CUQIpy-PyTorch](https://github.com/CUQI-DTU/CUQIpy-PyTorch) to extend CUQIpy by adding the ability to use PyTorch as a backend for array operations. PyTorch enables two main things: 1) GPU acceleration and 2) automatic differentiation. GPU acceleration is self-explanatory, but automatic differentiation deserves some explanation.\n",
     "\n",
@@ -43,7 +42,13 @@
    "metadata": {},
    "source": [
     "<div style=\"border: 2px solid #FFB74D; background-color: #FFF3E0; border-radius: 8px; padding: 10px; font-family: Arial, sans-serif; color: #333; box-shadow: 2px 2px 8px rgba(0, 0, 0, 0.1); max-width: 750px; margin: 0 auto;\">\n",
-    "  <strong style=\"color: #E65100;\">⚠️ Note:</strong> This notebook uses MCMC samplers from the new <code>cuqi.experimental.mcmc</code> module, which are expected to become the default soon. Check out the <a href=\"https://cuqi-dtu.github.io/CUQIpy/api/_autosummary/cuqi.experimental.mcmc.html#module-cuqi.experimental.mcmc\">documentation</a> for more details.\n",
+    "  <strong style=\"color: #E65100;\">⚠️ Note:</strong> \n",
+    "\n",
+    "- This notebook was run on some machine and not using github actions for this book. To run this notebook on your machine, you need to have [CUQIpy-PyTorch installed](https://github.com/CUQI-DTU/CUQIpy-PyTorch).\n",
+    "  \n",
+    "-  This notebook uses MCMC samplers from the new <code>cuqi.experimental.mcmc</code> module, which are expected to become the default soon. Check out the <a href=\"https://cuqi-dtu.github.io/CUQIpy/api/_autosummary/cuqi.experimental.mcmc.html#module-cuqi.experimental.mcmc\">documentation</a> for more details.\n",
+    "\n",
+    "\n",
     "</div>"
    ]
   },
@@ -1320,7 +1325,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.4"
+   "version": "3.9.16"
   },
   "orig_nbformat": 4,
   "vscode": {