updated notebook clearing script to be more in-depth. Also, output detector was not working so just run on all

Author: mnfienen

notebooks/clear_all_notebooks.py

@@ -1,6 +1,7 @@
 import os
 import pathlib as pl
 import json
+import subprocess
 
 notebook_count = 0
 # add the basenames of any notebooks we want to keep the results of 
@@ -18,30 +19,22 @@
     '10_modpath_particle_tracking-demo.ipynb'
     ]
 
-def check_nb_for_output(notebook):
-    has_output = False
-    # run autotest on each notebook
-    with open(notebook) as src:
-        data = src.read()
-        data = json.loads(data)
-        for item in data['cells']:
-            for k, v in item.items():
-                if item['cell_type'] == 'code':
-                    if any (item['outputs']):
-                        has_output = True
-    return has_output        
-
-
 if __name__ == "__main__":
-    
-    for [path, subdirs, files] in os.walk('.'):
-        for cf in files:
-            if cf.lower().endswith('.ipynb') and '.ipynb_checkpoint' not in path:
-                nb = pl.Path(path) / cf
-                if ('solutions' not in str(nb) and 
-                    nb.name not in skip_notebooks and 
-                    check_nb_for_output(nb) is True):
-                        print(f"clearing {nb}")
-                        os.system(f"jupyter nbconvert --clear-output --inplace {nb._str}")
-                        notebook_count += 1
-    print(notebook_count," notebooks cleared")
+    nbdir = pl.Path(".")
+    nbs = nbdir.rglob("*.ipynb")
+    for nb in nbs:
+        if ('solutions' not in str(nb) and 
+                    nb.name not in skip_notebooks):
+            print("clearing", nb)
+            cmd = (
+                "jupyter",
+                "nbconvert",
+                "--ClearOutputPreprocessor.enabled=True",
+                "--ClearMetadataPreprocessor.enabled=True",
+                "--ClearMetadataPreprocessor.preserve_nb_metadata_mask={('kernelspec')}",
+                "--inplace",
+                nb,
+            )
+            proc = subprocess.run(cmd)
+            assert proc.returncode == 0, f"Error running command: {' '.join(cmd)}"
+        

notebooks/part0_python_intro/00_python_basics_review.ipynb

@@ -1379,18 +1379,6 @@
    "display_name": "Python 3 (ipykernel)",
    "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": "3.11.10"
   }
  },
  "nbformat": 4,

notebooks/part0_python_intro/00_skills_test_on_basics.ipynb

@@ -91,9 +91,7 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "b755a4ce",
-   "metadata": {
-    "scrolled": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# finally split on \"whitespace\" resulting in a list of words\n",
@@ -287,18 +285,6 @@
    "display_name": "Python 3 (ipykernel)",
    "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": "3.11.13"
   }
  },
  "nbformat": 4,

notebooks/part0_python_intro/01_functions_scripts.ipynb

@@ -694,18 +694,6 @@
    "display_name": "pyclass",
    "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": "3.12.11"
   }
  },
  "nbformat": 4,

notebooks/part0_python_intro/02_Namespace_objects_modules_packages.ipynb

@@ -1605,18 +1605,6 @@
    "display_name": "Python 3 (ipykernel)",
    "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": "3.11.7"
   }
  },
  "nbformat": 4,

notebooks/part0_python_intro/03_useful-std-library-modules.ipynb

@@ -1252,18 +1252,6 @@
    "display_name": "pyclass",
    "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": "3.11.7"
   }
  },
  "nbformat": 4,

notebooks/part0_python_intro/04_files_and_strings.ipynb

@@ -843,18 +843,6 @@
    "display_name": "Python 3 (ipykernel)",
    "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": "3.12.1"
   }
  },
  "nbformat": 4,

notebooks/part0_python_intro/05_numpy.ipynb

@@ -1760,18 +1760,6 @@
    "display_name": "Python 3 (ipykernel)",
    "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": "3.12.11"
   }
  },
  "nbformat": 4,

notebooks/part0_python_intro/06_matplotlib.ipynb

@@ -1180,18 +1180,6 @@
    "display_name": "lisus_p2",
    "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": "3.11.10"
   }
  },
  "nbformat": 4,

notebooks/part0_python_intro/06b_matplotlib_animation.ipynb

@@ -94,11 +94,7 @@
    "source": []
   }
  ],
- "metadata": {
-  "language_info": {
-   "name": "python"
-  }
- },
+ "metadata": {},
  "nbformat": 4,
  "nbformat_minor": 2
 }