fix(deepmd): expose unlabeled mixed-system loading

[njzjz-bot]

Fixes #817.

Document and forward labeled=False through MultiSystems classmethod loading and add an NPY mixed no-label round-trip.

Tests: cd tests && python -m unittest test_deepmd_mixed

Why existing tests missed it: Existing mixed tests used labeled data; the unlabeled HDF5 test did not cover the reported NPY classmethod path.

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

Summary by CodeRabbit

• New Features

  • Added support for loading datasets without labels, returning coordinate-only systems when labeled=False.
  • Preserved labeled loading as the default behavior.

• Tests

  • Added coverage for round-trip loading of unlabeled mixed datasets, including coordinates, cells, and atom types.

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Review details

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 166583a1-5bad-4bf7-8cca-cfcf278fe4d7

📥 Commits

Reviewing files that changed from the base of the PR and between 7df2224 and fd7ce66.

📒 Files selected for processing (2)

• dpdata/system.py
• tests/test_deepmd_mixed.py

📝 Walkthrough

Walkthrough

MultiSystems file loading now accepts a keyword-only labeled flag, forwards it through format loading, and supports coordinate-only mixed DeepMD datasets. A regression test verifies unlabeled round-trip loading returns a System without energies while preserving atom types, cells, and coordinates.

Changes

Unlabeled MultiSystems loading

Layer / File(s)	Summary
Loading API propagation dpdata/system.py	from_file and load_systems_from_file accept labeled and forward it to from_fmt_obj, with documentation for unlabeled loading.
Unlabeled mixed-data regression test tests/test_deepmd_mixed.py	Adds a temporary-directory round-trip test for coordinate-only mixed DeepMD data and verifies the loaded System fields.

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

Sequence Diagram(s)

sequenceDiagram
  participant Caller
  participant MultiSystems
  participant FormatLoader
  Caller->>MultiSystems: from_file(labeled=False)
  MultiSystems->>MultiSystems: load_systems_from_file(labeled=False)
  MultiSystems->>FormatLoader: from_fmt_obj(labeled=False)
  FormatLoader-->>Caller: coordinate-only System

Loading

Suggested labels: dpdata, enhancement

Suggested reviewers: njzjz

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the main change: enabling unlabeled mixed-system loading.
Linked Issues check	✅ Passed	The PR adds labeled=False loading support and a regression test for unlabeled DeepMD mixed data, matching issue #817.
Out of Scope Changes check	✅ Passed	The changes stay focused on unlabeled mixed-system loading and the corresponding test, with no obvious unrelated additions.
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 not alter performance

⚠️ 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.

✅ 2 untouched benchmarks

---

_{Comparing njzjz-bot:fix/issue-817 (fd7ce66) with master (d2105f6)}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.95%. Comparing base (b3c88c6) to head (fd7ce66).
⚠️ Report is 10 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1033      +/-   ##
==========================================
- Coverage   87.01%   86.95%   -0.06%     
==========================================
  Files          90       90              
  Lines        8330     9183     +853     
==========================================
+ Hits         7248     7985     +737     
- Misses       1082     1198     +116     

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[wanghan-iapcm]

The added labeled keyword-only signature + docstrings are correct, safe, and a reasonable way to expose the unlabeled path for the #817 feature request. But the capability already worked via **kwargs on master, so the new test isn't a genuine regression test and #817's default call is unchanged -- see inline.

[wanghan-iapcm]

Verified the fix at head: the new test fails on the pre-fix merge base b3c88c6 (KeyError: 'labeled') and passes here, so it genuinely guards the change. Approving. One follow-up note inline that is worth tightening but not a blocker.

[wanghan-iapcm]

Thanks, this addresses both of my earlier points -- the signature is explicit now, and the default call gives a real pointer instead of a bare energies not found in data.

One thing to tighten: this wrapper is gated on the format name but not on the cause. Any DataError raised while loading a mixed dataset now gets "pass labeled=False" appended -- including a genuinely labeled dataset that fails for an unrelated reason, e.g. a corrupt or truncated force.npy. In that case the message sends the user in exactly the wrong direction. Narrowing to the missing-label case (checking for the absent energy/force file, or matching the specific condition) would be safer, and no test currently covers that misleading path.

Two smaller notes:

• The hint only fires via from_file / load_systems_from_file; MultiSystems().from_fmt_obj(...) still emits the bare message.
• The concatenation is missing a separator, so it currently reads energies not found in data For coordinate-only mixed datasets, pass labeled=False.