improve configurations of Python lint tools

[njzjz]

1. use black-pre-commit-mirror instead of black which is faster;
2. first ruff and then black;
3. remove tool.ruff.target-version which can be detected automatically;
4. add RUF and NPY rules to tool.ruff.select;
5. set tool.ruff.pydocstyle.convention to numpy, which can automatically add several rules to ignore.

[codecov]

Codecov Report

Patch coverage: 86.95% and no project coverage change.

Comparison is base (1a4a7ca) 75.49% compared to head (c6a79aa) 75.49%.
Report is 1 commits behind head on devel.

❗ Current head c6a79aa differs from pull request most recent head f51b9df. Consider uploading reports for the commit f51b9df to get more accurate results

Additional details and impacted files

@@           Coverage Diff           @@
##            devel    #2823   +/-   ##
=======================================
  Coverage   75.49%   75.49%           
=======================================
  Files         242      242           
  Lines       24163    24163           
  Branches     1533     1533           
=======================================
  Hits        18241    18241           
  Misses       5006     5006           
  Partials      916      916           

Files Changed	Coverage Δ
deepmd/calculator.py	80.55% <ø> (ø)
deepmd/entrypoints/ipi.py	0.00% <0.00%> (ø)
deepmd/fit/dos.py	48.40% <ø> (ø)
deepmd/loss/ener.py	68.23% <ø> (ø)
deepmd/utils/data_system.py	84.00% <0.00%> (ø)
deepmd/utils/path.py	91.45% <0.00%> (ø)
deepmd/utils/spin.py	86.36% <ø> (ø)
deepmd/descriptor/se_a.py	95.72% <100.00%> (ø)
deepmd/descriptor/se_a_ebd.py	67.13% <100.00%> (ø)
deepmd/descriptor/se_atten.py	93.97% <100.00%> (ø)
... and 10 more

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