add debugging exercises

Author: fabridamicelli

book/111_debugging.ipynb

@@ -227,85 +227,89 @@
     "2) Set a breakpoint inside `main` to use the debugger\n",
     "3) Step through the code using `n (next)` and another time using `s (step)`\n",
     "4) Set a second breakpoint inside `main`and run again the code but this time use `c (continue)`\n",
-    "5) Download [this public dataset](https://github.com/fabridamicelli/ds005588/archive/refs/heads/broken-data.zip) into the folder `/pycourse/data/` (create it if you don't yet have it).\n",
+    "5) Download [this public dataset](https://github.com/OpenNeuroDatasets/ds005588) as zip file into the folder `/pycourse/data/` (create it if you don't yet have it)\n",
     "\n",
-    "This dataset was modified and has some problems apparently.\n",
-    "Here's a bit of code to unzip it and read through the files."
+    "Here's a bit of code to unzip the file."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
-   "id": "bbe54d2f-f5a4-44f1-a015-8a4d19e1097a",
+   "execution_count": 1,
+   "id": "6ed1ee58-e172-48ca-8d02-735cefc5ec1e",
    "metadata": {},
    "outputs": [],
    "source": [
-    "path = \"/home/fdamicel/projects/pycourse/data/ds005588-broken-data.zip\"\n",
-    "target = \"/home/fdamicel/projects/pycourse/data\""
+    "from pathlib import Path\n",
+    "import zipfile\n",
+    "\n",
+    "def unzip(source_file, target_dir):\n",
+    "    with zipfile.ZipFile(source_file) as file:\n",
+    "        file.extractall(target_dir)\n",
+    "\n",
+    "project_path = Path(\"pycourse\")\n",
+    "\n",
+    "source = project_path/\"data/ds005588-main.zip\"\n",
+    "target = project_path/\"data\"\n",
+    "unzip(source, target)"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 7,
-   "id": "e7ad9b30-c041-4edc-83d4-2cfdf984dac7",
+   "cell_type": "markdown",
+   "id": "2ef4d196-964a-49ae-9c50-3b4c772f14f5",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "import zipfile"
+    "Now, your collaborator has written this script to extract the mean value of the \"SAR\" entry from across all subjects bold data.\n",
+    "\n",
+    "6) Put this script into the folder (create if it does not yet exist) `pycourse/scripts/sar_mean.py` and make the necessary modifications to make it run as a script.\n",
+    "\n",
+    "7) Run it using `uv run scripts/sar_mean.py` and see it fail. Set a breakpoint inside the `get_subjects_sar_mean` function. Run it again and try to find the bug inside the debugger.\n",
+    "\n",
+    "8) Add some error handling to make sure the script runs."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "123149ab-4410-4444-9348-099cbf067f91",
+   "id": "4877305d-66bb-47ab-95c9-ae9377323bef",
    "metadata": {},
    "outputs": [],
    "source": [
-    "with zipfile.ZipFile(path) as file:\n",
-    "    file.extractall(target)"
+    "import json\n",
+    "from glob import glob\n",
+    "from pathlib import Path\n",
+    "\n",
+    "def get_subjects_sar_mean(data_dir):\n",
+    "    # Grab all files matching this filename pattern\n",
+    "    files = glob(str(data_dir/\"**/*_bold.json\"), recursive=True)\n",
+    "    \n",
+    "    sar_sum = 0\n",
+    "    n = 0\n",
+    "    for file in files:\n",
+    "        content = json.loads(Path(file).read_text())\n",
+    "        sar_sum += content[\"SAR\"]\n",
+    "        n += 1\n",
+    "    return sar_sum/n\n",
+    "\n",
+    "# TODO: add whatever code you need to make this code a proper script\n",
+    "# that prints the sar-mean when run"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 13,
-   "id": "8d95f7c4-977f-4cc5-8f8e-80e87ec7d40a",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 14,
-   "id": "3f764de2-552c-49ab-ae8c-8d8455d254c3",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 15,
-   "id": "4fbd3efe-bd52-4414-99a5-42058984a3c8",
+   "cell_type": "markdown",
+   "id": "1e080ee5-eea8-4f16-bb1d-a992e4eed409",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "UnicodeDecodeError",
-     "evalue": "'utf-8' codec can't decode byte 0xb9 in position 10: invalid start byte",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
-      "\u001b[31mUnicodeDecodeError\u001b[39m                        Traceback (most recent call last)",
-      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[15]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m1\u001b[39m lines = \u001b[43mf\u001b[49m\u001b[43m.\u001b[49m\u001b[43mreadlines\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
-      "\u001b[36mFile \u001b[39m\u001b[32m<frozen codecs>:325\u001b[39m, in \u001b[36mdecode\u001b[39m\u001b[34m(self, input, final)\u001b[39m\n",
-      "\u001b[31mUnicodeDecodeError\u001b[39m: 'utf-8' codec can't decode byte 0xb9 in position 10: invalid start byte"
-     ]
-    }
-   ],
-   "source": []
+   "source": [
+    "To recap, so far our project should have these files:\n",
+    "\n",
+    "![](./images/files.png)\n",
+    "\n",
+    "![](./images/tree-2.png)"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4877305d-66bb-47ab-95c9-ae9377323bef",
+   "id": "43472f65-ea2f-4706-bb6a-7cf9a28e05b3",
    "metadata": {},
    "outputs": [],
    "source": []