test(common): add regression for atom type remap #5050

OutisLi · 2025-11-13T11:40:04Z

Summary

add a regression test that reproduces the original atom-type remapping failure when the training system contains fewer atom types than the provided type_map
ensure the fix from commit 4ec0437 remains covered going forward

Summary by CodeRabbit

Tests
- Added unit tests for DeepmdData that validate atom-type remapping, handling of unused types, and correct loading/formatting of type arrays.

Copilot

Pull Request Overview

This PR adds a regression test to ensure that atom type remapping works correctly when the training system contains fewer atom types than the provided type_map. The test verifies the fix from commit 4ec0437.

Key changes:

Adds a new test file test_deepmd_data.py with regression test for atom type remapping functionality
Tests the scenario where a system has atoms of types O and H, but the type_map includes an unused Si type
Verifies correct remapping when loading data with a different type_map ordering

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coderabbitai · 2025-11-13T11:43:17Z

📝 Walkthrough

Walkthrough

Adds a new unit test module that creates a temporary DeepMD dataset, writes atom type and type map files, and verifies DeepmdData's atom-type remapping, stored internal type_map, and _load_set output shape/content.

Changes

Cohort / File(s)	Change Summary
New test module for DeepmdData type mapping `source/tests/common/test_deepmd_data.py`	Adds TestDeepmdDataTypeMap with setUp/tearDown creating a temporary dataset (set.000, `type.raw`, `type_map.raw`, `coord.npy`, `box.npy`), writes atom types and a 3-entry type map, instantiates DeepmdData with a custom type_map containing unused types, and asserts remapped atom_type, internal `type_map`, and `_load_set` output match expected values.

Sequence Diagram(s)

sequenceDiagram
    participant T as TestCase
    participant FS as FileSystem (temp dataset)
    participant D as DeepmdData

    T->>FS: write type.raw, type_map.raw, coord.npy, box.npy
    T->>D: instantiate DeepmdData(type_map=custom_map)
    D->>FS: read type_map.raw (if used) and type.raw
    D->>D: remap atom types using provided type_map / idx_map
    D-->>T: expose remapped atom_type and internal type_map
    T->>D: call _load_set("set.000")
    D->>FS: read set files (type, coord, box)
    D-->>T: return loaded set dict with "type" array (2D broadcasted via idx_map)

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Single new test file; straightforward filesystem setup and assertions.
Pay attention to assertions around remapping and expected broadcasting behavior.

Possibly related PRs

fix: optimize atom type mapping #5043: Updates atom type remapping logic in DeepmdData/utilities that this test exercises.

Suggested reviewers

iProzd

Pre-merge checks and finishing touches

❌ 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%.	You can run `@coderabbitai generate docstrings` to improve docstring coverage.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'test(common): add regression for atom type remap' is directly related to the main change - a new regression test for atom type remapping logic in the DeepmdData class.

✨ Finishing touches

📝 Generate docstrings

🧪 Generate unit tests (beta)

Create PR with unit tests
Post copyable unit tests in a comment

📜 Recent review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 0f3df73 and 5dcd916.

📒 Files selected for processing (1)

source/tests/common/test_deepmd_data.py (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

source/tests/common/test_deepmd_data.py

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GitHub Check: Test Python (6, 3.12)
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codecov · 2025-11-13T12:47:08Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.19%. Comparing base (87cb6ef) to head (5dcd916).
⚠️ Report is 2 commits behind head on devel.

Additional details and impacted files

@@           Coverage Diff           @@
##            devel    #5050   +/-   ##
=======================================
  Coverage   84.18%   84.19%           
=======================================
  Files         709      709           
  Lines       70215    70216    +1     
  Branches     3620     3618    -2     
=======================================
+ Hits        59114    59115    +1     
- Misses       9934     9935    +1     
+ Partials     1167     1166    -1

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source/tests/common/test_deepmd_data.py

## Summary - add a regression test that reproduces the original atom-type remapping failure when the training system contains fewer atom types than the provided type_map - ensure the fix from commit 4ec0437 remains covered going forward  ## Summary by CodeRabbit * **Tests** * Added unit tests for DeepmdData that validate atom-type remapping, handling of unused types, and correct loading/formatting of type arrays.

test(common): add regression for atom type remap

0f3df73

Copilot AI review requested due to automatic review settings November 13, 2025 11:40

github-actions bot added the Python label Nov 13, 2025

Copilot started reviewing on behalf of OutisLi November 13, 2025 11:40 View session

OutisLi added the enhancement label Nov 13, 2025

Copilot finished reviewing on behalf of OutisLi November 13, 2025 11:42

Copilot AI reviewed Nov 13, 2025

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OutisLi requested review from iProzd and njzjz November 13, 2025 15:14

njzjz reviewed Nov 13, 2025

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source/tests/common/test_deepmd_data.py Outdated Show resolved Hide resolved

remove unnecessary class attribute

5dcd916

OutisLi requested a review from njzjz November 14, 2025 02:33

iProzd approved these changes Nov 14, 2025

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njzjz approved these changes Nov 14, 2025

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njzjz added this pull request to the merge queue Nov 14, 2025

Merged via the queue into deepmodeling:devel with commit 1ccc57d Nov 14, 2025
60 checks passed

OutisLi deleted the pr/load_test branch November 14, 2025 10:14

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