fix(dpdata): use public format APIs

[njzjz-bot]

Problem

• dpdata 1.0 removes legacy backend import paths such as dpdata.abacus.stru, which breaks DP-GEN imports with the latest dpdata release.
• Directly importing backend parser modules is brittle across dpdata releases; DP-GEN should use dpdata's registered public format interface instead.

Change

• Replace direct ABACUS STRU and VASP POSCAR helper imports with dpdata.System(..., fmt=...) / System.to(...) calls.
• Replace direct SIESTA output parsing with dpdata.LabeledSystem(..., fmt="siesta/output").
• Keep the ABACUS SCF type_map path compatible with dpdata 1.x by normalizing atom_types before applying the type map.

Test

• With dpdata==1.0.2: python -m pytest tests/data/test_disturb_abacus.py tests/auto_test/test_abacus.py tests/generator/test_post_fp.py::TestPostFPABACUS::test_nframs_with_failed_job tests/generator/test_post_fp.py::TestPostFPSIESTA -q
• With dpdata==0.2.25: same targeted pytest command above.
• uvx ruff check dpgen/auto_test/lib/abacus.py dpgen/generator/lib/abacus_scf.py dpgen/generator/run.py

Authored by OpenClaw (model: gpt-5.5)

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request refactors import paths across three modules to use dpdata's new formats namespace. ABACUS STRU and VASP POSCAR imports are updated in auto_test/lib/abacus.py and abacus_scf.py. SIESTA output parsing imports and usage are updated in run.py. No logic changes occur.

Changes

dpdata Import Path Migration

Layer / File(s)	Summary
Abacus Import Refactoring dpgen/auto_test/lib/abacus.py, dpgen/generator/lib/abacus_scf.py	Imports for make_unlabeled_stru and poscar are migrated from dpdata.abacus.stru and dpdata.vasp to dpdata.formats.abacus.stru and dpdata.formats.vasp respectively.
SIESTA Import and Usage Update dpgen/generator/run.py	Import for dpdata.formats.siesta.output is added, and the obtain_frame(...) call site in the FP post-processing is updated to use the new module path.

🎯 1 (Trivial) | ⏱️ ~3 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% 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
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.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'fix(dpdata): use public format APIs' accurately summarizes the main change - updating DP-GEN to use dpdata's new public format module paths instead of legacy imports.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 49.80%. Comparing base (f4f74a2) to head (1053cfd).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1880      +/-   ##
==========================================
- Coverage   49.81%   49.80%   -0.01%     
==========================================
  Files          83       83              
  Lines       14988    14986       -2     
==========================================
- Hits         7466     7464       -2     
  Misses       7522     7522              

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[coderabbitai]

Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@dpgen/generator/lib/abacus_scf.py`:
- Line 6: The import path is wrong: replace the non-existent module
dpdata.formats.abacus.stru with dpdata.abacus.stru wherever get_frame_from_stru
and make_unlabeled_stru are imported (e.g., in the module that currently imports
from dpdata.formats.abacus.stru and the similar import in the other test
module). Update the import statement to import get_frame_from_stru and
make_unlabeled_stru from dpdata.abacus.stru so the runtime can find those
symbols.

In `@dpgen/generator/run.py`:
- Line 32: The import dpdata.formats.siesta.output is invalid and should be
changed to dpdata.siesta.output; update the import statement in
dpgen/generator/run.py to import from dpdata.siesta.output and ensure any
references that expect the old package path (the code that uses the siesta
output module later in this file) continue to refer to the same symbols from the
corrected import; this fixes the ImportError when importing dpgen.generator.run.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: a4f52112-0576-4de0-9ae8-9490252c1365

📥 Commits

Reviewing files that changed from the base of the PR and between f4f74a2 and 538c76d.

📒 Files selected for processing (3)

• dpgen/auto_test/lib/abacus.py
• dpgen/generator/lib/abacus_scf.py
• dpgen/generator/run.py