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Allow nbdev_clean to accept multiple filenames or globs (#1480) #1488

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Allow nbdev_clean to accept multiple filenames or globs (#1480) #1488

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5718660
Allow nbdev_clean to accept multiple filenames and updated tests
jbwhit Jan 25, 2025
99259cc
Skip failing test in 10_processors.ipynb
jbwhit Jan 25, 2025
6fb9767
Remove test skip markers in 10_processors.ipynb
jbwhit Feb 27, 2025
30a1405
Fix nbdev_clean to support multiple notebook paths
jbwhit Mar 18, 2025
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6 changes: 4 additions & 2 deletions nbdev/clean.py
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Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,7 @@ def _nbdev_clean(nb, path=None, clear_all=None):
# %% ../nbs/api/11_clean.ipynb
@call_parse
def nbdev_clean(
fname:str=None, # A notebook name or glob to clean
fname=None, # A notebook path or a list of paths/globs to clean
clear_all:bool=False, # Remove all cell metadata and cell outputs?
disp:bool=False, # Print the cleaned outputs
stdin:bool=False # Read notebook from input stream
Expand All @@ -141,7 +141,9 @@ def nbdev_clean(
_write = partial(process_write, warn_msg='Failed to clean notebook', proc_nb=_clean)
if stdin: return _write(f_in=sys.stdin, f_out=sys.stdout)
if fname is None: fname = get_config().nbs_path
for f in globtastic(fname, file_glob='*.ipynb', skip_folder_re='^[_.]'): _write(f_in=f, disp=disp)
# Use listify to handle both single paths and lists of paths
for f in globtastic(listify(fname), file_glob='*.ipynb', skip_folder_re='^[_.]'):
_write(f_in=f, disp=disp)

# %% ../nbs/api/11_clean.ipynb
def clean_jupyter(path, model, **kwargs):
Expand Down
103 changes: 101 additions & 2 deletions nbs/api/11_clean.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -388,7 +388,7 @@
"#|export\n",
"@call_parse\n",
"def nbdev_clean(\n",
" fname:str=None, # A notebook name or glob to clean\n",
" fname=None, # A notebook path or a list of paths/globs to clean\n",
" clear_all:bool=False, # Remove all cell metadata and cell outputs?\n",
" disp:bool=False, # Print the cleaned outputs\n",
" stdin:bool=False # Read notebook from input stream\n",
Expand All @@ -399,7 +399,9 @@
" _write = partial(process_write, warn_msg='Failed to clean notebook', proc_nb=_clean)\n",
" if stdin: return _write(f_in=sys.stdin, f_out=sys.stdout)\n",
" if fname is None: fname = get_config().nbs_path\n",
" for f in globtastic(fname, file_glob='*.ipynb', skip_folder_re='^[_.]'): _write(f_in=f, disp=disp)"
" # Use listify to handle both single paths and lists of paths\n",
" for f in globtastic(listify(fname), file_glob='*.ipynb', skip_folder_re='^[_.]'): \n",
" _write(f_in=f, disp=disp)"
]
},
{
Expand Down Expand Up @@ -811,6 +813,103 @@
"test_eq(nb.cells[-1].output, ours.cells[-1].output)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#|hide\n",
"#|eval: false\n",
"def test_clean_multiple_paths():\n",
" \"\"\"Test that demonstrates the current failure and success of the fixed version.\"\"\"\n",
" with tempfile.TemporaryDirectory() as d, working_directory(d):\n",
" # Create test notebooks\n",
" nbs_path = Path('nbs')\n",
" nbs_path.mkdir()\n",
" \n",
" # Create two notebooks with metadata we expect to be cleaned\n",
" nb1 = nbs_path/'nb1.ipynb'\n",
" nb2 = nbs_path/'nb2.ipynb'\n",
" \n",
" meta = {'nbformat': 4, 'metadata': {\n",
" 'kernelspec': {'name': 'python3'}, \n",
" 'test_metadata': 'should_be_removed'\n",
" }}\n",
" \n",
" # Add execution_count that should be cleaned\n",
" cells = [\n",
" {'cell_type': 'code', 'execution_count': 1, 'source': 'print(\"test\")', 'outputs': [], 'metadata': {}}\n",
" ]\n",
" \n",
" # Write the test notebooks\n",
" for nb_path in [nb1, nb2]:\n",
" write_nb(dict2nb({'cells': cells, **meta}), nb_path)\n",
" \n",
" # CURRENT BEHAVIOR SIMULATION:\n",
" # This simulates the current nbdev_clean implementation\n",
" current_implementation = False\n",
" try:\n",
" # Original code passes fname directly to globtastic:\n",
" fname = [str(nb1), str(nb2)] # List of paths\n",
" # This will fail because globtastic expects a string/Path, not a list\n",
" for f in globtastic(fname, file_glob='*.ipynb', skip_folder_re='^[_.]'): \n",
" pass\n",
" current_implementation = True\n",
" except Exception:\n",
" # Expected to fail with the current implementation\n",
" current_implementation = False\n",
" \n",
" # FIXED BEHAVIOR SIMULATION:\n",
" # This simulates the fixed implementation using listify\n",
" fixed_implementation = False\n",
" try:\n",
" # The fix uses listify, which lets us process all paths\n",
" fname = [str(nb1), str(nb2)]\n",
" for f in globtastic(listify(fname), file_glob='*.ipynb', skip_folder_re='^[_.]'):\n",
" pass\n",
" fixed_implementation = True\n",
" except Exception:\n",
" fixed_implementation = False\n",
" \n",
" # Iterate manually over each path as a workaround for current implementation\n",
" workaround_implementation = False\n",
" try:\n",
" fname = [str(nb1), str(nb2)]\n",
" # Have to manually iterate over each path\n",
" for path in fname:\n",
" for f in globtastic(path, file_glob='*.ipynb', skip_folder_re='^[_.]'):\n",
" pass\n",
" workaround_implementation = True\n",
" except Exception:\n",
" workaround_implementation = False\n",
" \n",
" # Assertions to prove the issue and fix\n",
" assert not current_implementation, \"Current implementation unexpectedly works with list of paths\"\n",
" assert fixed_implementation, \"Fixed implementation fails with list of paths\"\n",
" assert workaround_implementation, \"Even the manual workaround fails\"\n",
" \n",
" # Now test with the fixed nbdev_clean function (assuming it's been updated with listify)\n",
" # These assertions should only pass with the fixed implementation\n",
" try:\n",
" # Call the actual nbdev_clean function (should be fixed version with listify)\n",
" nbdev_clean([str(nb1), str(nb2)])\n",
" \n",
" # Verify both notebooks were properly cleaned\n",
" for nb_path in [nb1, nb2]:\n",
" cleaned_nb = read_nb(nb_path)\n",
" assert 'test_metadata' not in cleaned_nb.metadata, f\"Metadata was not cleaned in {nb_path}\"\n",
" assert cleaned_nb.cells[0].get('execution_count') is None, f\"Execution count not cleared in {nb_path}\"\n",
" \n",
" # If we got here without exceptions, the fix works\n",
" fixed_function_works = True\n",
" except Exception as e:\n",
" fixed_function_works = False\n",
" print(f\"Error when running fixed nbdev_clean: {e}\")\n",
" \n",
" assert fixed_function_works, \"Fixed nbdev_clean function failed with multiple paths\""
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down