Be clearer when there is an error with the user supplied json file

[patrickfuchs]

Making a try with a toy (user supplied) json file:

$ buildH -c 3Conly.pdb -d 3Conly.def -lt Berger_3Conly.json  -l PO3C
usage: buildH [-h] -c COORD [-t TRAJ] -l LIPID [-lt LIPID_TOPOLOGY [LIPID_TOPOLOGY ...]] -d DEFOP [-opx OPDBXTC] [-o OUT]
              [-b BEGIN] [-e END] [-pi PICKLE]
buildH: error: Berger_3Conly.json is in a bad format.

This error message is not very precise. The user can't find where the error comes from in the json file.

When doing this by hand:

>>> f = open("Berger_3Conly.json")
>>> json.load(f)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/fuchs/software/miniconda3/envs/buildh/lib/python3.9/json/__init__.py", line 293, in load
    return loads(fp.read(),
  File "/home/fuchs/software/miniconda3/envs/buildh/lib/python3.9/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/home/fuchs/software/miniconda3/envs/buildh/lib/python3.9/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/fuchs/software/miniconda3/envs/buildh/lib/python3.9/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 4 column 1 (char 61)

Here we can see that it comes from line 4 column 1. Easier to debug.
In fact the error was coming from a comma at the end of the last line :

{
    "resname": ["PO3C"],
    "C26": ["CH2", "C25", "C27"],
}

It makes me think to warn the user about this: don't put a comma on the last line!

[HubLot]

Yes, I hide the traceback of the exception thrown by the JSON parser. I thought it would make the output unreadable with uninformative lines. JSON format is pretty well-known so I thought it will be easy to spot a mistake in it.

We can keep the traceback if you think it's not enough.

[patrickfuchs]

I agree the Traceback is polluted by too much text. But on the other hand, knowing the problem comes from line x column y is very useful in a file with a few dozens of lines. If we could keep only the last line json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes: line 4 column 1 (char 61) which is informative, that would be ideal. Don't know if it's doable though.