Script to test notebooks

how-to/1_Read_and_visualise/ZeissDataReader.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -43,7 +43,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -68,14 +68,17 @@
        "True"
       ]
      },
-     "execution_count": 25,
+     "execution_count": null,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
     "from cil.utilities import dataexample\n",
-    "dataexample.WALNUT.download_data(data_dir='.', prompt=False)"
+    "from pathlib import Path\n",
+    "\n",
+    "data_dir = Path.home() / \".cache\" / \"cil\" # choose a location to save the dataset\n",
+    "dataexample.WALNUT.download_data(data_dir=str(data_dir), prompt=False)"
    ]
   },
   {
@@ -89,12 +92,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "from cil.io import ZEISSDataReader\n",
-    "file_name = \"./walnut/valnut/valnut_2014-03-21_643_28/tomo-A/valnut_tomo-A.txrm\"\n",
+    "file_name = Path(data_dir) / \"./walnut/valnut/valnut_2014-03-21_643_28/tomo-A/valnut_tomo-A.txrm\"\n",
     "data_reader = ZEISSDataReader(file_name=file_name)\n",
     "data = data_reader.read()"
    ]
@@ -108,7 +111,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -124,10 +127,10 @@
     {
      "data": {
       "text/plain": [
-       "<cil.utilities.display.show_geometry at 0x7f1850cf77d0>"
+       "<cil.utilities.display.show_geometry at 0x7f86d9a6f2b0>"
       ]
      },
-     "execution_count": 27,
+     "execution_count": null,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -146,7 +149,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -162,10 +165,10 @@
     {
      "data": {
       "text/plain": [
-       "<cil.utilities.display.show2D at 0x7f185169d700>"
+       "<cil.utilities.display.show2D at 0x7f86d8431ae0>"
       ]
      },
-     "execution_count": 28,
+     "execution_count": null,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -186,7 +189,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -202,10 +205,10 @@
     {
      "data": {
       "text/plain": [
-       "<cil.utilities.display.show2D at 0x7f1850c85ee0>"
+       "<cil.utilities.display.show2D at 0x7f86d9a6eda0>"
       ]
      },
-     "execution_count": 29,
+     "execution_count": null,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -226,7 +229,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -242,10 +245,10 @@
     {
      "data": {
       "text/plain": [
-       "<cil.utilities.display.show2D at 0x7f18458d7fb0>"
+       "<cil.utilities.display.show2D at 0x7f86d39331c0>"
       ]
      },
-     "execution_count": 30,
+     "execution_count": null,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -266,7 +269,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -276,7 +279,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -292,10 +295,10 @@
     {
      "data": {
       "text/plain": [
-       "<cil.utilities.display.show_geometry at 0x7f1850d0aba0>"
+       "<cil.utilities.display.show_geometry at 0x7f86d34171f0>"
       ]
      },
-     "execution_count": 32,
+     "execution_count": null,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -307,7 +310,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "cil_demos",
+   "display_name": "cil_dev",
    "language": "python",
    "name": "python3"
   },
@@ -321,7 +324,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.7"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+addopts = --nbmake --nbmake-kernel=cil_demos --nbmake-timeout=900

test_notebooks.py

@@ -0,0 +1,64 @@
+import pytest
+import nbformat
+import os
+import re
+import shutil
+
+folders = ['demos', 'how-to']
+skip_notebooks = ['demos/2_Iterative/04_SPDHG.ipynb'
+]
+
+def run_tmp_notebook(notebook_path):    
+    tmp_notebook_path = notebook_path.replace('.ipynb', '_tmp.ipynb')
+    shutil.copy(notebook_path, tmp_notebook_path)
+
+    with open(tmp_notebook_path, 'r') as f:
+        notebook = nbformat.read(f, as_version=4)
+
+    for cell in notebook.cells:
+        if cell.cell_type == 'code':
+            # Update filepath
+            if '/mnt/materials/' in cell.source:
+                cell.source = re.sub(r'/mnt/materials/', '/mnt/share/materials/', cell.source)
+
+            # Replace commented %load lines with the correct snippet
+            if '# %load' in cell.source:
+                snippet_file = cell.source.split('snippets/')[1].split('\'')[0]
+                snippet_path = os.path.join(os.path.dirname(notebook_path), 'snippets', snippet_file)
+                if os.path.exists(snippet_path):
+                    with open(snippet_path, 'r') as snippet_file:
+                        snippet_code = snippet_file.read()
+                    cell.source = cell.source.replace('# %load', '') 
+                    cell.source = snippet_code  
+                else:
+                    print(f"Warning: Snippet path {snippet_path} does not exist.")
+
+            # Clear cells containing ellipses
+            if '...' in cell.source:
+                cell.source = ""  
+
+    with open(tmp_notebook_path, 'w') as f:
+        nbformat.write(notebook, f)
+
+    print(f"\t\t Testing notebook: {tmp_notebook_path}")
+    pytest.main([tmp_notebook_path])
+
+    os.remove(tmp_notebook_path)
+
+def test_notebook_runs():
+    for folder in folders: 
+        print(f"Searching in folder: {folder}")
+        for root, dirs, files in os.walk(folder):
+            print(f"\tIn directory: {root}")
+            for file in files:
+                if not file.endswith('.ipynb'):
+                    continue
+                if file.endswith('_tmp.ipynb'):
+                    continue
+
+                notebook_path = os.path.join(root, file)             
+                if notebook_path in skip_notebooks:
+                    print(f"\t\t Skipping notebook: {notebook_path}")
+                else:
+                    run_tmp_notebook(notebook_path)
+