update deepmd input to v2; format JSON files

[njzjz]

This PR updates all JSON files:

• convert default_training_param to v2 format
• format JSON files
• update _comment to _commentN to avoid duplicated keys
• enable check-json and pretty-format-json hooks

import json
from glob import glob

from deepmd.utils.compat import update_deepmd_input, convert_input_v1_v2

for ii in glob("**/*.json", recursive=True):
    with open(ii) as f:
        content = f.read()
    count = 1
    while True:
        if r'"_comment"' not in content:
            break
        content = content.replace('"_comment"', '"_comment%d"' % count, 1)
        count += 1
    try:
        jdata = json.loads(content)
    except Exception as e:
        print(ii, e)
        continue
    if "default_training_param" in jdata:
        jdata["default_training_param"] = update_deepmd_input(
            jdata["default_training_param"], warning=False)
        if "decay_rate" in jdata["default_training_param"]["learning_rate"]:
            jdata["default_training_param"] = convert_input_v1_v2(
                jdata["default_training_param"], warning=False)
        if "load_ckpt" in jdata["default_training_param"]["training"]:
            del jdata["default_training_param"]["training"]["load_ckpt"]
    content = json.dumps(jdata, indent=2)

    with open(ii, "w") as f:
        f.write(content)

[codecov]

Codecov Report

Patch and project coverage have no change.

Comparison is base (0761763) 48.24% compared to head (1eb347d) 48.24%.

Additional details and impacted files

@@           Coverage Diff           @@
##            devel    #1315   +/-   ##
=======================================
  Coverage   48.24%   48.24%           
=======================================
  Files          82       82           
  Lines       14601    14601           
=======================================
  Hits         7044     7044           
  Misses       7557     7557           

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