From 4f029f404ba9498541a12b4391de5234162a9d06 Mon Sep 17 00:00:00 2001
From: Mike Fienen <mnfienen@usgs.gov>
Date: Sat, 3 Feb 2024 10:34:43 -0600
Subject: [PATCH 1/2] incorporated testing for notebook output prior to
 clearing output

---
 notebooks/clear_all_notebooks.py | 25 +++++++++++++++++++++----
 1 file changed, 21 insertions(+), 4 deletions(-)

diff --git a/notebooks/clear_all_notebooks.py b/notebooks/clear_all_notebooks.py
index cd548d0..3bb016a 100644
--- a/notebooks/clear_all_notebooks.py
+++ b/notebooks/clear_all_notebooks.py
@@ -1,5 +1,7 @@
 import os
 import pathlib as pl
+import json
+
 notebook_count = 0
 # add the basenames of any notebooks we want to keep the results of 
 # all solutions are still not being cleared
@@ -14,12 +16,27 @@
     '10_modpath-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        
+
 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:
-                print(f"clearing {nb}")
-                os.system(f"jupyter nbconvert --clear-output --inplace {nb._str}")
-                notebook_count += 1
+            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")
\ No newline at end of file

From cf97eef60604dab78cd2bbdec581fd66ef998b07 Mon Sep 17 00:00:00 2001
From: Mike Fienen <mnfienen@usgs.gov>
Date: Sat, 3 Feb 2024 10:39:49 -0600
Subject: [PATCH 2/2] typo in test_notebooks_output.py and added flopy project
 structured overview to xfail notebooks for testing due to important but
 incomplete code blocks

---
 tests/test_notebook_output.py | 2 +-
 tests/test_notebooks.py       | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/test_notebook_output.py b/tests/test_notebook_output.py
index 8265c33..c8103b9 100644
--- a/tests/test_notebook_output.py
+++ b/tests/test_notebook_output.py
@@ -49,6 +49,6 @@ def test_notebook_output(notebook):
         for item in data['cells']:
             for k, v in item.items():
                 if item['cell_type'] == 'code':
-                    assert not any (item['outputs']), (f"{notebook} as output "
+                    assert not any (item['outputs']), (f"{notebook} has output "
                                 "but is not listed in notebooks/clean_all_notebooks.py "
                                 "as excepted!")
diff --git a/tests/test_notebooks.py b/tests/test_notebooks.py
index b5017a6..9e56219 100644
--- a/tests/test_notebooks.py
+++ b/tests/test_notebooks.py
@@ -13,6 +13,7 @@
     '06_matplotlib.ipynb': 'notebook intentionally incomplete',
     '00_python_basics_review__solutions.ipynb': 'intentional error',
     '01_functions_script__solution.ipynb': 'intentional error',
+    '06-Project-structured.ipynb': 'intentionally incomplete information'
     
     
 }