save_history fails with TypeError

[smoia]

Expected Behavior

Export the history of hte physio object into a json file

Actual Behavior

Fails with TypeError:

In [20]: pk.save_history('sub-001_ses-01_task-rest_recording-ppg_physio.json', p)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[20], line 1
----> 1 pk.save_history('sub-001_ses-01_task-rest_recording-ppg_physio.json', p)

File ~/Scrivania/gitlab/peakdet/peakdet/io.py:220, in save_history(file, data)
    218 file += ".json" if not file.endswith(".json") else ""
    219 with open(file, "w") as dest:
--> 220     json.dump(data.history, dest, indent=4)
    221 logger.info(f"Saved {data} history in {file}")
    223 return file

File /usr/lib/python3.10/json/__init__.py:179, in dump(obj, fp, skipkeys, ensure_ascii, check_circular, allow_nan, cls, indent, separators, default, sort_keys, **kw)
    173     iterable = cls(skipkeys=skipkeys, ensure_ascii=ensure_ascii,
    174         check_circular=check_circular, allow_nan=allow_nan, indent=indent,
    175         separators=separators,
    176         default=default, sort_keys=sort_keys, **kw).iterencode(obj)
    177 # could accelerate with writelines in some versions of Python, at
    178 # a debuggability cost
--> 179 for chunk in iterable:
    180     fp.write(chunk)

File /usr/lib/python3.10/json/encoder.py:429, in _make_iterencode.<locals>._iterencode(o, _current_indent_level)
    427     yield _floatstr(o)
    428 elif isinstance(o, (list, tuple)):
--> 429     yield from _iterencode_list(o, _current_indent_level)
    430 elif isinstance(o, dict):
    431     yield from _iterencode_dict(o, _current_indent_level)

File /usr/lib/python3.10/json/encoder.py:325, in _make_iterencode.<locals>._iterencode_list(lst, _current_indent_level)
    323         else:
    324             chunks = _iterencode(value, _current_indent_level)
--> 325         yield from chunks
    326 if newline_indent is not None:
    327     _current_indent_level -= 1

File /usr/lib/python3.10/json/encoder.py:325, in _make_iterencode.<locals>._iterencode_list(lst, _current_indent_level)
    323         else:
    324             chunks = _iterencode(value, _current_indent_level)
--> 325         yield from chunks
    326 if newline_indent is not None:
    327     _current_indent_level -= 1

File /usr/lib/python3.10/json/encoder.py:405, in _make_iterencode.<locals>._iterencode_dict(dct, _current_indent_level)
    403         else:
    404             chunks = _iterencode(value, _current_indent_level)
--> 405         yield from chunks
    406 if newline_indent is not None:
    407     _current_indent_level -= 1

File /usr/lib/python3.10/json/encoder.py:325, in _make_iterencode.<locals>._iterencode_list(lst, _current_indent_level)
    323         else:
    324             chunks = _iterencode(value, _current_indent_level)
--> 325         yield from chunks
    326 if newline_indent is not None:
    327     _current_indent_level -= 1

File /usr/lib/python3.10/json/encoder.py:438, in _make_iterencode.<locals>._iterencode(o, _current_indent_level)
    436         raise ValueError("Circular reference detected")
    437     markers[markerid] = o
--> 438 o = _default(o)
    439 yield from _iterencode(o, _current_indent_level)
    440 if markers is not None:

File /usr/lib/python3.10/json/encoder.py:179, in JSONEncoder.default(self, o)
    160 def default(self, o):
    161     """Implement this method in a subclass such that it returns
    162     a serializable object for ``o``, or calls the base implementation
    163     (to raise a ``TypeError``).
   (...)
    177 
    178     """
--> 179     raise TypeError(f'Object of type {o.__class__.__name__} '
    180                     f'is not JSON serializable')

TypeError: Object of type int64 is not JSON serializable

With history:

In [21]: p.history
Out[21]: 
[('interpolate_physio', {'kind': 'linear', 'target_fs': 40}),
 ('filter_physio', {'cutoffs': 5, 'method': 'lowpass'}),
 ('peakfind_physio', {'dist': 1}),
 ('delete_peaks', {'remove': [58, 146, 179, 212, 259, 364, 389]}),
 ('add_peaks', {'add': [183]})]

@rmarkello I know you retired from this world, but if you could help us understand where the issue arises, that'd be awesome!

[smoia]

So #77 did not actually solve the issue.
The issue clearly pops up when the "add_peak" function runs, as the indexes created by it are np.int64.
I'll revert everything done.

[me-pic]

@smoia Can take a look at this today if you need. I might have run into a similar issue at some point