Run notebook directly

.github/workflows/JupyterTest.yml

@@ -10,42 +10,50 @@ on:
 
 jobs:
   build:
-    runs-on: windows-latest
-
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
     steps:
     - name: Checkout repository
       uses: actions/checkout@v3
 
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: '3.8'
+        python-version: ${{ matrix.python-version }}
 
     - name: Create data directory if it doesn't exist
       run: |
-        mkdir -p data    
+        mkdir -p UnitTest/data    
 
     - name: Cache data
       id: cache-data
       uses: actions/cache@v3
       with:
         path: ./data
-        key: ${{ runner.os }}-data-${{ hashFiles('testfile.txt') }}
+        key: ${{ runner.os }}-data-${{ github.run_number }}-${{ hashFiles('testfile.txt') }}
         restore-keys: |
-          ${{ runner.os }}-data-2
+          ${{ runner.os }}-data-${{ github.run_number }}-
 
-    - name: Install dependencies
-      run: | 
-        pip install jupyter nbconvert tqdm
+    - name: Set PIPX_HOME to a path without spaces
+      run: |
+        export PIPX_HOME=$HOME/.local/pipx
+        mkdir -p $PIPX_HOME
+        pip install pipx
+        pipx install jupyter
+        pipx runpip jupyter install numpy matplotlib ducc0 healpy
 
-    - name: Convert notebook to script
+    - name: Run notebook directly
       run: |
-        jupyter nbconvert --to script UnitTest/NotebookToTest.ipynb
+        export PIPX_HOME=$HOME/.local/pipx
+        pipx run jupyter execute UnitTest/NotebookToTest.ipynb
 
-    - name: Print converted script
+    - name: Convert notebook to script to see logs
       run: |
-        cat UnitTest/NotebookToTest.py
-        
+        jupyter nbconvert --to script UnitTest/NotebookToTest.ipynb
+
     - name: Run converted script
       run: |
         python UnitTest/NotebookToTest.py

UnitTest/NotebookToTest.ipynb

@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 1,
    "id": "2292a595",
    "metadata": {},
    "outputs": [
@@ -40,6 +40,7 @@
    ],
    "source": [
     "import os\n",
+    "import numpy\n",
     "print(os.getcwd())"
    ]
   },
@@ -48,36 +49,40 @@
    "execution_count": 2,
    "id": "90bb750c",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'import urllib.request\\nfrom tqdm import tqdm\\n# Define a progress bar function\\nclass DownloadProgressBar(tqdm):\\n    def update_to(self, b=1, bsize=1, tsize=None):\\n        if tsize is not None:\\n            self.total = tsize\\n        self.update(b * bsize - self.n)'"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "import urllib.request\n",
+    "'''import urllib.request\n",
     "from tqdm import tqdm\n",
     "# Define a progress bar function\n",
     "class DownloadProgressBar(tqdm):\n",
     "    def update_to(self, b=1, bsize=1, tsize=None):\n",
     "        if tsize is not None:\n",
     "            self.total = tsize\n",
-    "        self.update(b * bsize - self.n)"
+    "        self.update(b * bsize - self.n)'''"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 4,
    "id": "747c02f6",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Could not find cached data\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "testfile.txt: 16.4kB [00:00, 35.8kB/s]                            \n"
+      "Data is already cached.\n"
      ]
     }
    ],
@@ -86,26 +91,18 @@
     "if not os.path.exists(data_path):\n",
     "    print(\"Could not find cached data - downloading ...............\")\n",
     "    url = \"https://www.w3.org/WAI/ER/tests/xhtml/testfiles/resources/pdf/dummy.pdf\"\n",
-    "    with DownloadProgressBar(unit='B', unit_scale=True, miniters=1, desc=data_path) as t:\n",
-    "        urllib.request.urlretrieve(url, data_path, reporthook=t.update_to)\n",
+    "    #with DownloadProgressBar(unit='B', unit_scale=True, miniters=1, desc=data_path) as t:\n",
+    "    urllib.request.urlretrieve(url, data_path, reporthook=t.update_to)\n",
     "else:\n",
     "    print(\"Data is already cached.\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "94ac107d",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "catalog.fits: 57.3kB [00:01, 53.2kB/s]                            \n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": []
   },
   {