BUG: build encountering JSON error in a notebook

sjsrey commented 5 years ago

(pysal-notebooks) src/notebooks - [master●] » python lib/build.py --build
python scripts/generate_book.py
Convert and copy notebook/md files...
 69%|██████████████████████████████████████████████████████▋                        | 36/52 [00:25<00:11,  1.38it/s]Traceback (most recent call last):
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/nbformat/reader.py", line 14, in parse_json
    nb_dict = json.loads(s, **kwargs)
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/json/__init__.py", line 348, in loads
    return _default_decoder.decode(s)
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/json/decoder.py", line 353, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes: line 244 column 1 (char 31035)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "scripts/generate_book.py", line 242, in <module>
    cleaner = NotebookCleaner(tmp_notebook)
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/nbclean/clean.py", line 19, in __init__
    self.ntbk = _check_nb_file(ntbk)
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/nbclean/utils.py", line 8, in _check_nb_file
    ntbk = nbf.read(ntbk, nbf.NO_CONVERT)
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/nbformat/__init__.py", line 139, in read
    return read(f, as_version, **kwargs)
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/nbformat/__init__.py", line 141, in read
    return reads(fp.read(), as_version, **kwargs)
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/nbformat/__init__.py", line 74, in reads
    nb = reader.reads(s, **kwargs)
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/nbformat/reader.py", line 58, in reads
    nb_dict = parse_json(s, **kwargs)
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/nbformat/reader.py", line 17, in parse_json
    raise NotJSONError(("Notebook does not appear to be JSON: %r" % s)[:77] + "...")
nbformat.reader.NotJSONError: Notebook does not appear to be JSON: '{\n "cells": [\n  {\n   "cell_type": "c...
Exception ignored in: <function tqdm.__del__ at 0x10be78598>
Traceback (most recent call last):
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/tqdm/_tqdm.py", line 931, in __del__
    self.close()
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/tqdm/_tqdm.py", line 1133, in close
    self._decr_instances(self)
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/tqdm/_tqdm.py", line 496, in _decr_instances
    cls.monitor.exit()
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/site-packages/tqdm/_monitor.py", line 52, in exit
    self.join()
  File "/anaconda3/envs/pysal-notebooks/lib/python3.7/threading.py", line 1029, in join
    raise RuntimeError("cannot join current thread")
RuntimeError: cannot join current thread
make: *** [book] Error 1

darribas commented 5 years ago

Yes! Sorry forgot to document. This has to do with this issue: pysal/spint#16. Until it's resolved, removing that single notebook (glm_speed.ipynb) should work. Please report back if there're further problems or feel free to close the issue when worked out.

weikang9009 commented 5 years ago

Works great on my mac after deleting glm_speed.ipynb!

jGaboardi commented 5 years ago

Resolved via pysal/spint#19

pysal / notebooks

BUG: build encountering JSON error in a notebook #52