yaml version out of date

[Yi-FanLi]

When using the following package versions: Package Version

---

bcrypt 4.0.1 certifi 2023.11.17 cffi 1.16.0 charset-normalizer 3.3.2 cryptography 41.0.5 dargs 0.4.3 deepks 0.2.dev79+g7978b39 dpdispatcher 0.6.2 idna 3.4 numpy 1.26.2 paramiko 3.3.1 pip 23.3 pycparser 2.21 PyNaCl 1.5.0 PyYAML 6.0.1 requests 2.31.0 ruamel.yaml 0.18.5 ruamel.yaml.clib 0.2.8 setuptools 68.0.0 tqdm 4.66.1 typeguard 4.1.5 typing_extensions 4.8.0 urllib3 2.1.0 wheel 0.41.2

The following error will occur:

Traceback (most recent call last): File "/opt/mamba/envs/deepks/lib/python3.10/runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None, File "/opt/mamba/envs/deepks/lib/python3.10/runpy.py", line 86, in _run_code exec(code, run_globals) File "/opt/mamba/envs/deepks/lib/python3.10/site-packages/deepks/main.py", line 11, in main_cli() File "/opt/mamba/envs/deepks/lib/python3.10/site-packages/deepks/main.py", line 37, in main_cli sub_cli(args.args) File "/opt/mamba/envs/deepks/lib/python3.10/site-packages/deepks/main.py", line 254, in iter_cli argdict = deep_update(argdict, load_yaml(fl)) File "/opt/mamba/envs/deepks/lib/python3.10/site-packages/deepks/utils.py", line 138, in load_yaml res = yaml.safe_load(fp) File "/opt/mamba/envs/deepks/lib/python3.10/site-packages/ruamel/yaml/main.py", line 1105, in safe_load error_deprecation('safe_load', 'load', arg="typ='safe', pure=True") File "/opt/mamba/envs/deepks/lib/python3.10/site-packages/ruamel/yaml/main.py", line 1039, in error_deprecation raise AttributeError(s, name=None) AttributeError: "safe_load()" has been removed, use

yaml = YAML(typ='safe', pure=True) yaml.load(...)

instead of file "/opt/mamba/envs/deepks/lib/python3.10/site-packages/deepks/utils.py", line 138

    res = yaml.safe_load(fp)

The safe_load and safe_dump functions used in deepks/utils.py has been deprecated since yaml 0.15.0. See https://yaml.readthedocs.io/en/latest/api/. We should think about update the supported version of yaml package.

[y1xiaoc]

Good catch! Do you want to write a PR for this?