chore: enable safe Ruff autofix rules

[njzjz-bot]

Summary

Enable eight Ruff rules that have safe, automatic fixes in the repository's pinned Ruff v0.15.18:

• PIE808, PT022, RET502, SIM910, TD006
• PLR1711, PLR1733, PLR2044

Intentional follow-up

This PR deliberately changes only pyproject.toml; it does not include the 128 existing code fixes. The configured pre-commit.ci autofix should apply those fixes to this PR, which provides an end-to-end confirmation that the automated repair is clean.

COM812 is intentionally excluded because ruff-format is already enabled and Ruff recommends against combining the formatter with this trailing-comma rule. Rules whose fixes are classified as unsafe in Ruff v0.15.18 are also excluded.

Validation

• git diff --check
• ruff v0.15.18 check --output-format json . reports exactly 128 intentional diagnostics from the eight newly enabled rules; no --fix was run.

Authored by OpenClaw (model: custom-chat-jinzhezeng-group/gpt-5.6-terra)

Summary by CodeRabbit

• Bug Fixes

  • Improved attribute assignment handling to fully control weight/bias-related updates during tracing.
  • Ensured neighborhood-distance resolution is initialized from available runtime/tensor sources and saved consistently.
  • Improved test isolation by clearing leaked device contexts before tests.

• Refactor

  • Simplified option lookups (optional fields/seed/precision mappings) and equivalent loop-bound expressions across models/kernels.

• Chores

  • Expanded linting rules and removed stray placeholder comments/formatting artifacts across docs and code.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Repository UI

Review profile: CHILL

Plan: Pro

Run ID: a8496c92-cd2f-4ee3-9909-3788939a4cb9

📥 Commits

Reviewing files that changed from the base of the PR and between 9a4ec77 and 986e664.

📒 Files selected for processing (2)

• deepmd/tf/nvnmd/descriptor/se_a.py
• deepmd/tf/nvnmd/descriptor/se_atten.py

💤 Files with no reviewable changes (2)

• deepmd/tf/nvnmd/descriptor/se_atten.py
• deepmd/tf/nvnmd/descriptor/se_a.py

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📝 Walkthrough

Walkthrough

This PR applies mechanical Python and Triton syntax simplifications, makes selected attribute-assignment exits explicit, updates NVNMD descriptor range initialization, expands Ruff lint rules, and cleans up test fixtures, helpers, comments, and equivalent loop forms.

Changes

Runtime consistency and syntax cleanup

Layer / File(s)	Summary
Python runtime and data-path updates deepmd/jax/..., deepmd/pd/..., deepmd/pt/..., deepmd/tf/..., deepmd/utils/...	Simplifies dict.get() calls, removes explicit None returns, adds explicit attribute-assignment exits, and preserves existing downstream behavior.
Kernel and tabulation loop normalization deepmd/kernels/triton/..., deepmd/pt/optimizer/..., deepmd/tf/utils/..., deepmd/utils/tabulate_math.py	Rewrites equivalent range(0, ...) expressions using single-argument range(...) forms.
NVNMD descriptor initialization and cleanup deepmd/tf/nvnmd/..., deepmd/tf/op/...	Resolves NVNMD neighborhood-distance bounds and updates configuration state; removes placeholder comment lines from NVNMD implementation paths.
Lint and supporting configuration pyproject.toml, doc/conf.py	Enables eight additional Ruff rules and removes a standalone configuration comment.
Test helpers and fixture cleanup source/tests/...	Updates mock state, comparison variables, equivalent loop forms, device-context cleanup fixtures, and placeholder test comments.

Estimated code review effort: 2 (Simple) | ~10 minutes

Possibly related PRs

• deepmodeling/deepmd-kit#5344: Updates the same DeviceContext leak cleanup fixtures in source/tests/pt_expt/conftest.py.
• deepmodeling/deepmd-kit#5598: Touches DPZBLLinearEnergyAtomicModel.__setattr__ handling for zbl_weight.

Suggested reviewers: iProzd, njzjz

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 42.22% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately summarizes the main change: enabling safe Ruff autofix rules.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

---

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[njzjz]

pre-commit.ci autofix

[codecov]

Codecov Report

❌ Patch coverage is 81.66667% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.56%. Comparing base (0c5a914) to head (986e664).

Files with missing lines	Patch %	Lines
deepmd/kernels/triton/sezm/so2_rotation.py	0.00%	6 Missing ⚠️
deepmd/tf/utils/tabulate.py	77.77%	2 Missing ⚠️
deepmd/pt/optimizer/hybrid_muon.py	0.00%	1 Missing ⚠️
deepmd/tf2/atomic_model/linear_atomic_model.py	0.00%	1 Missing ⚠️
deepmd/utils/tabulate_math.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #5774      +/-   ##
==========================================
- Coverage   79.69%   79.56%   -0.14%     
==========================================
  Files        1020     1020              
  Lines      116359   116357       -2     
  Branches     4303     4305       +2     
==========================================
- Hits        92736    92581     -155     
- Misses      22076    22226     +150     
- Partials     1547     1550       +3     

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