chore(typing): check nested dpdata packages

[njzjz-bot]

Fixes #1004.

Expand Pyright coverage to nested parser/plugin modules and pin the type-check workflow checkout action.

Tests: pyright (passes with recursive include).

Why existing tests missed it: The old glob selected only top-level modules, silently excluding most format and plugin code.

Coding agent: Codex
Codex version: codex-cli 0.144.4
Model: gpt-5.6-sol
Reasoning effort: xhigh

Summary by CodeRabbit

• Chores
  • Expanded automated type-checking coverage for additional application modules.
  • Added configuration notes clarifying incremental coverage and excluded areas.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 211ffe0e-117b-46e5-ae99-d34b5ba3f6aa

📥 Commits

Reviewing files that changed from the base of the PR and between c77e038 and 20cb31a.

📒 Files selected for processing (1)

• pyproject.toml

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📝 Walkthrough

Walkthrough

Pyright configuration now includes additional nested modules under dpdata/formats, dpdata/md, and dpdata/plugins, with comments documenting incremental coverage and excluded parser directories.

Changes

Pyright coverage

Layer / File(s)	Summary
Include nested dpdata modules pyproject.toml	The Pyright include list expands beyond top-level dpdata/*.py to selected format, md, and plugin subtrees, with explanatory comments for coverage scope and exclusions.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Suggested reviewers: outisli

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Out of Scope Changes check	⚠️ Warning	The PR also pins the type-check workflow checkout action, which is unrelated to the linked pyright coverage issue.	Move the checkout-action pinning to a separate PR or explain it in a linked issue so this change stays scoped to Pyright coverage.

✅ 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 clearly reflects the main change: expanding typing coverage for nested dpdata packages.
Linked Issues check	✅ Passed	The pyright include expansion and explanatory comments address issue #1004 by covering nested format, plugin, and md modules.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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[codspeed-hq]

Merging this PR will improve performance by 14.7%

⚠️ Unknown Walltime execution environment detected

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For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

⚠️ Different runtime environments detected

Some benchmarks with significant performance changes were compared across different runtime environments,
which may affect the accuracy of the results.

Open the report in CodSpeed to investigate

⚡ 1 improved benchmark
✅ 1 untouched benchmark

Performance Changes

	Mode	Benchmark	BASE	HEAD	Efficiency
⚡	WallTime	test_import	11.5 ms	10.1 ms	+14.7%

Tip

Curious why this is faster? Comment @codspeedbot explain why this is faster on this PR, or directly use the CodSpeed MCP with your agent.

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_{Comparing njzjz-bot:fix/issue-1004 (20cb31a) with master (c77e038)}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 87.63%. Comparing base (c77e038) to head (20cb31a).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1028   +/-   ##
=======================================
  Coverage   87.63%   87.63%           
=======================================
  Files          90       90           
  Lines        9209     9209           
=======================================
  Hits         8070     8070           
  Misses       1139     1139           

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[njzjz]

I don't think it can be done without carefully checking the types.

[njzjz]

Agreed that enabling the entire nested package tree requires careful type review. Commit d35b9f1 takes an incremental approach: it adds only nested modules that currently have zero Pyright diagnostics and documents why the remaining parser directories are deferred for format-specific typing work. The resulting Pyright CI job is green.

Coding agent: Codex
Codex version: codex-cli 0.144.6
Model: gpt-5.6-sol
Reasoning effort: xhigh