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cron test error: pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb #308
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Describe the bug
from the nightly log: https://github.com/Project-MONAI/MONAI/runs/3319164834?check_suite_focus=true
real 1m25.421s
user 1m36.764s
sys 0m13.458s
Running ./pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb
Checking PEP8 compliance...
Running notebook...
Error: Couldn't find the keyword "max_epochs", and the notebook wasn't on the list of expected exemptions ("doesnt_contain_max_epochs")..
Check failed!
Executing: 0%| | 0/13 [00:00<?, ?cell/s]
Executing: 8%|▊ | 1/13 [00:01<00:12, 1.07s/cell]
Executing: 38%|███▊ | 5/13 [00:18<00:16, 2.07s/cell]
Executing: 46%|████▌ | 6/13 [00:19<00:11, 1.70s/cell]
Executing: 62%|██████▏ | 8/13 [00:20<00:06, 1.29s/cell]
Executing: 85%|████████▍ | 11/13 [00:20<00:01, 1.10cell/s]
Executing: 85%|████████▍ | 11/13 [00:20<00:03, 1.87s/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 [5]":
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-5-e9fcc49d73ee> in <module>
1 # Load NVTX Push/Pop Range Summary
----> 2 summary = pd.read_csv("profile_report_nvtxppsum.csv")
3 # display(summary)
4
5 # Set the Range (which is the name of each range) as the index
/opt/conda/lib/python3.8/site-packages/pandas/io/parsers.py in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)
686 )
687
--> 688 return _read(filepath_or_buffer, kwds)
689
690
/opt/conda/lib/python3.8/site-packages/pandas/io/parsers.py in _read(filepath_or_buffer, kwds)
452
453 # Create the parser.
--> 454 parser = TextFileReader(fp_or_buf, **kwds)
455
456 if chunksize or iterator:
/opt/conda/lib/python3.8/site-packages/pandas/io/parsers.py in __init__(self, f, engine, **kwds)
946 self.options["has_index_names"] = kwds["has_index_names"]
947
--> 948 self._make_engine(self.engine)
949
950 def close(self):
/opt/conda/lib/python3.8/site-packages/pandas/io/parsers.py in _make_engine(self, engine)
1178 def _make_engine(self, engine="c"):
1179 if engine == "c":
-> 1180 self._engine = CParserWrapper(self.f, **self.options)
1181 else:
1182 if engine == "python":
/opt/conda/lib/python3.8/site-packages/pandas/io/parsers.py in __init__(self, src, **kwds)
2008 kwds["usecols"] = self.usecols
2009
-> 2010 self._reader = parsers.TextReader(src, **kwds)
2011 self.unnamed_cols = self._reader.unnamed_cols
2012
pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader.__cinit__()
pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source()
FileNotFoundError: [Errno 2] No such file or directory: 'profile_report_nvtxppsum.csv'
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