Allow saving of imported mat files as json

[Wealing]

When importing .mat models, the membranePot type is numpy's int16. The change makes it a standard int so that it can be saved as json.

[codecov]

Codecov Report

Merging #42 into master will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master      #42   +/-   ##
=======================================
  Coverage   70.92%   70.92%           
=======================================
  Files          46       46           
  Lines        3401     3401           
=======================================
  Hits         2412     2412           
  Misses        989      989           

Impacted Files	Coverage Δ
pytfa/io/base.py	92.62% <100.00%> (ø)

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[psalvy]

Hi!
Thanks for this contribution. Could you provide more context as to why this is necessary ? I could not reproduce the bug with this MWE:

%run tutorial_basics.py
from pytfa.io.json import save_json_model, load_json_model
save_json_model(mytfa, 'tmp.json')
m = load_json_model('tmp.json')

I indeed see the mat file is decoded as a numpy int, but the encoding of the JSON and decoding casts it directly to a Python int.
Cheers,
Pierre

[Wealing]

It might be a python 3.8 error:

Traceback (most recent call last):
  File "/Users/home/switchdrive/Cadiz/me/code/examples/write_redgem_to_json.py", line 16, in <module>
    save_json_model(model, 'redgem16_error.json')
  File "/Users/home/switchdrive/Cadiz/repos/cobrapy/cobra/io/json.py", line 110, in save_json_model
    json.dump(obj, file_handle, **dump_opts)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/__init__.py", line 179, in dump
    for chunk in iterable:
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 431, in _iterencode
    yield from _iterencode_dict(o, _current_indent_level)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  [Previous line repeated 1 more time]
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 438, in _iterencode
    o = _default(o)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type int16 is not JSON serializable

[psalvy]

Yes indeed, I found evidence of it here
Can you just change the int casting to float, since potentials are a continuous physical property ? then I'll merge the PR :)
Cheers,
Pierre

[Wealing]

Ok, good to go!

[psalvy]

Thanks!