nightly test error: profiling_camelyon_pipeline.ipynb #317
Description
Describe the bug
Running ./pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb
Checking PEP8 compliance...
Running notebook...
Executing: 0%| | 0/18 [00:00<?, ?cell/s]
Executing: 6%|▌ | 1/18 [00:00<00:16, 1.04cell/s]
Executing: 33%|███▎ | 6/18 [00:07<00:12, 1.06s/cell]
Executing: 39%|███▉ | 7/18 [00:08<00:10, 1.04cell/s]
Executing: 50%|█████ | 9/18 [00:18<00:19, 2.17s/cell]
Executing: 61%|██████ | 11/18 [01:28<01:24, 12.10s/cell]
Executing: 67%|██████▋ | 12/18 [01:30<00:53, 9.00s/cell]
Executing: 89%|████████▉ | 16/18 [01:30<00:12, 6.31s/cell]
Executing: 89%|████████▉ | 16/18 [01:30<00:11, 5.69s/cell]
Traceback (most recent call last):
File "/opt/conda/bin/papermill", line 8, in <module>
sys.exit(papermill())
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 21, in new_func
return f(get_current_context(), *args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill
execute_notebook(
File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 122, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [7]":
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-7-e9fcc49d73ee> in <module>
10
11 # Normalize each transform range with total average time (percentage of transfom time)
---> 12 summary = summary[["Average", "Minimum", "Maximum", "StdDev"]] / summary["Average"].sum() * 100
13 summary
/opt/conda/lib/python3.8/site-packages/pandas/core/frame.py in __getitem__(self, key)
2910 if is_iterator(key):
2911 key = list(key)
-> 2912 indexer = self.loc._get_listlike_indexer(key, axis=1, raise_missing=True)[1]
2913
2914 # take() does not accept boolean indexers
/opt/conda/lib/python3.8/site-packages/pandas/core/indexing.py in _get_listlike_indexer(self, key, axis, raise_missing)
1252 keyarr, indexer, new_indexer = ax._reindex_non_unique(keyarr)
1253
-> 1254 self._validate_read_indexer(keyarr, indexer, axis, raise_missing=raise_missing)
1255 return keyarr, indexer
1256
/opt/conda/lib/python3.8/site-packages/pandas/core/indexing.py in _validate_read_indexer(self, key, indexer, axis, raise_missing)
1302 if raise_missing:
1303 not_found = list(set(key) - set(ax))
-> 1304 raise KeyError(f"{not_found} not in index")
1305
1306 # we skip the warning on Categorical
KeyError: "['StdDev'] not in index"
Additional context
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