Merge pull request #50 from Chaste/fix-tutorial-generation

Fix markdown and jupyter generation
Chaste · Nov 28, 2023 · 104d19a · 104d19a
2 parents 535065f + c548be0
commit 104d19a
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Showing 28 changed files with 4,881 additions and 274 deletions.
diff --git a/.github/workflows/update-pychaste-tutorials.yml b/.github/workflows/update-pychaste-tutorials.yml
@@ -44,10 +44,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Download pychaste-tutorials markdown
+      - name: Download pychaste-tutorials-markdown
         uses: actions/download-artifact@v3
         with:
-          name: pychaste-tutorials markdown
+          name: pychaste-tutorials-markdown
 
       - name: Checkout website repository
         uses: actions/checkout@v4

diff --git a/doc/tutorials/TestCellSortingTutorial.ipynb b/doc/tutorials/TestCellSortingTutorial.ipynb
@@ -2,15 +2,17 @@
  "cells": [
   {
    "cell_type": "markdown",
+   "id": "296c5d00",
    "metadata": {},
    "source": [
-    "This tutorial is automatically generated from the file test/python/cell_based/tutorials/TestCellSortingTutorial.py.\n",
+    "This tutorial is automatically generated from the file ../test/python/cell_based/tutorials/TestCellSortingTutorial.py.\n",
     "\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
+   "id": "85518493",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -22,6 +24,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "425c7509",
    "metadata": {},
    "source": [
     "\n",
@@ -37,7 +40,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
+   "id": "ad3b4b3d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -52,6 +56,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "0859ed0f",
    "metadata": {},
    "source": [
     "## Test 1 - Cell sorting\n",
@@ -62,7 +67,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
+   "id": "914c5dbe",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,6 +78,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "6b89b200",
    "metadata": {},
    "source": [
     "First, we generate a `Potts` mesh. To create a `PottsMesh`, we can use the `PottsMeshGenerator`.\n",
@@ -82,7 +89,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
+   "id": "53498c64",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -92,6 +100,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "55826799",
    "metadata": {},
    "source": [
     "Having created a mesh, we now create some cells. To do this, we the `CellsGenerator` helper class,\n",
@@ -101,7 +110,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
+   "id": "83100d25",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -112,6 +122,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "ab73135c",
    "metadata": {},
    "source": [
     "Before we make a CellPopulation we make a cell label and then assign this label to some randomly chosen cells.\n",
@@ -120,7 +131,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
+   "id": "4c965778",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -132,6 +144,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "63891d61",
    "metadata": {},
    "source": [
     "Now we have a mesh and a set of cells to go with it, we can create a `CellPopulation`.\n",
@@ -140,7 +153,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
+   "id": "56507a69",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -149,6 +163,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "84a90a0d",
    "metadata": {},
    "source": [
     "In order to visualize labelled cells we need to use the following command.\n",
@@ -157,7 +172,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
+   "id": "46963d23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -166,6 +182,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "6571a038",
    "metadata": {},
    "source": [
     "PyChaste can do simple 3D rendering with VTK. We set up a VtkScene so that we can\n",
@@ -175,19 +192,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
+   "id": "13078a02",
    "metadata": {},
    "outputs": [],
    "source": [
     "scene= chaste.visualization.VtkScene2()\n",
     "scene.SetCellPopulation(cell_population)\n",
     "scene.GetCellPopulationActorGenerator().SetShowPottsMeshEdges(True)\n",
     "nb_manager = chaste.visualization.JupyterNotebookManager()\n",
-    "#nb_manager.vtk_show(scene, height=600)"
+    "nb_manager.vtk_show(scene, height=600)"
    ]
   },
   {
    "cell_type": "markdown",
+   "id": "73bf51b5",
    "metadata": {},
    "source": [
     "We then pass in the cell population into an `OffLatticeSimulation`, and set the output directory and end time\n",
@@ -196,7 +215,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
+   "id": "4c4b7723",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -208,6 +228,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "9a2f7393",
    "metadata": {},
    "source": [
     "We must now create one or more update rules, which determine the Hamiltonian in the Potts simulation.\n",
@@ -219,7 +240,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
+   "id": "4e6905d0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -231,6 +253,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "ce8333cb",
    "metadata": {},
    "source": [
     "We repeat the process for any other update rules.\n",
@@ -239,7 +262,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
+   "id": "85b15aac",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -254,6 +278,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "0c443ccd",
    "metadata": {},
    "source": [
     "Set up plotting\n",
@@ -262,7 +287,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": null,
+   "id": "0ccc598e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -274,6 +300,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "ac2f8034",
    "metadata": {},
    "source": [
     "To run the simulation, we call `Solve()`.\n",
@@ -282,57 +309,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": null,
+   "id": "aad50aa1",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "TypeError",
-     "evalue": "Unable to convert function return value to a Python type! The signature was\n\t(self: chaste.visualization._chaste_project_PyChaste_visualization.VtkScene2) -> vtkSmartPointer<vtkRenderer>",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-15-44e7981dfade>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0mscene\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mStart\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0msimulator\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSolve\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      3\u001b[0m \u001b[0;31m# Tear down the test\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0mchaste\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcell_based\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mTearDownNotebookTest\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/Code/chaste-build/projects/PyChaste/python/chaste/visualization/fortests.py\u001b[0m in \u001b[0;36mUpdateAtEndOfTimeStep\u001b[0;34m(self, cell_population)\u001b[0m\n\u001b[1;32m    179\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    180\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moutput_format\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'png'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 181\u001b[0;31m                 \u001b[0mIPython\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdisplay\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdisplay\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplotting_manager\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvtk_show\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGetVtkScene\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_format\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moutput_format\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    182\u001b[0m             \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    183\u001b[0m                 \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplotting_manager\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvtk_show\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGetVtkScene\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_format\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moutput_format\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/Code/chaste-build/projects/PyChaste/python/chaste/visualization/fortests.py\u001b[0m in \u001b[0;36mvtk_show\u001b[0;34m(self, scene, width, height, output_format, increment)\u001b[0m\n\u001b[1;32m    132\u001b[0m                 \u001b[0mrenderWindow\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvtk\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvtkRenderWindow\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    133\u001b[0m                 \u001b[0mrenderWindow\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSetOffScreenRendering\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 134\u001b[0;31m                 \u001b[0mrenderWindow\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mAddRenderer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mscene\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mGetRenderer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    135\u001b[0m                 \u001b[0mrenderWindow\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSetSize\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwidth\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mheight\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    136\u001b[0m                 \u001b[0mrenderWindow\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mRender\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mTypeError\u001b[0m: Unable to convert function return value to a Python type! The signature was\n\t(self: chaste.visualization._chaste_project_PyChaste_visualization.VtkScene2) -> vtkSmartPointer<vtkRenderer>"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "scene.Start()\n",
     "simulator.Solve()\n",
     "# Tear down the test \n",
     "chaste.cell_based.TearDownNotebookTest()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.6.9"
-  }
- },
+ "metadata": {},
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 5
 }
diff --git a/doc/tutorials/TestCellSortingTutorial.md b/doc/tutorials/TestCellSortingTutorial.md
@@ -1,9 +1,14 @@
+
 ---
-layout: page-full-width 
-title: Test Cell Sorting Tutorial
+title : "Test Cell Sorting Tutorial"
+summary: ""
+draft: false
+images: []
+toc: true
+layout: "single"
 ---
-This tutorial is automatically generated from the file test/python/cell_based/tutorials/TestCellSortingTutorial.py.
-[Go to the Jupyter Notebook version.]({{ site.baseurl}}/documentation/md_tutorials/TestCellSortingTutorial_nb.html)
+
+This tutorial is automatically generated from the file ../test/python/cell_based/tutorials/TestCellSortingTutorial.py .
 Note that the code is given in full at the bottom of the page.