fix(data): Throw error when data's element is not present in `input.json/type_map` #4639

Chengqian-Zhang · 2025-03-06T10:57:22Z

See issue #4519 .
When there are elements in the data that are not present in input.json, no error will be reported. For example, when element D is in type_map.raw, but D is not in type_map of input.json, the training process is normal. This error appears when self.mixed_type=True.

Summary by CodeRabbit

New Features
- Introduced enhanced data validation to ensure the atom type mapping is complete and consistent. Users will now receive clear error notifications if there are discrepancies in the provided mapping.
Tests
- Added a new test class to verify correct data initialization and validate that errors are raised appropriately for invalid atom type mappings.

coderabbitai · 2025-03-06T10:59:14Z

📝 Walkthrough

Walkthrough

The changes add a validation step in the __init__ method of the DeepmdData class to ensure that every atom type declared in self.type_map is present in the provided type_map, raising a ValueError if not. In addition, new unit tests in the TestDataMixType class have been introduced to validate both successful initialization and error handling when an invalid type map is passed. An existing test was also updated to include this error check.

Changes

File	Change Summary
deepmd/utils/data.py	Added a validation step in the `DeepmdData.__init__` method to check that all entries in `self.type_map` exist in the provided `type_map`; raises a `ValueError` if missing.
source/tests/tf/test_deepmd_data.py	Introduced `TestDataMixType` with tests for proper initialization and error handling of the type map; modified an existing test to check for `ValueError` on invalid maps.

Sequence Diagram(s)

sequenceDiagram
    participant Caller
    participant DeepmdData.__init__

    Caller->>DeepmdData.__init__: Initialize with type_map & self.type_map
    DeepmdData.__init__->>DeepmdData.__init__: Check if type_map and self.type_map are non-empty
    DeepmdData.__init__->>DeepmdData.__init__: Validate each element in self.type_map against provided type_map
    alt Missing types found
        DeepmdData.__init__->>Caller: Raise ValueError with missing types
    else
        DeepmdData.__init__->>Caller: Proceed with initialization
    end

Possibly related PRs

docs: improve error message for inconsistent type maps #4074: The changes in the main PR, which introduce validation for the type_map in the DeepmdData class, are related to the enhancements made in the retrieved PR that improve error messaging for type map inconsistencies, as both address error handling related to type maps.

Suggested reviewers

njzjz
iProzd

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Chengqian-Zhang · 2025-03-06T11:00:26Z

This bug appends because there is no error reported in np.searchsorted method even when type_map and self.type_map are totally different.

coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (2)

source/tests/tf/test_deepmd_data.py (2)
455-458: Address unused variable warning.

The variable dd is assigned but never used, triggering a static analysis warning.
-    def test_init_type_map_error(self) -> None:
-        with self.assertRaises(ValueError):
-            dd = DeepmdData(self.data_name, type_map=["foo"])
+    def test_init_type_map_error(self) -> None:
+        with self.assertRaises(ValueError):
+            DeepmdData(self.data_name, type_map=["foo"])
🧰 Tools

🪛 Ruff (0.8.2)

457-457: Local variable dd is assigned to but never used

Remove assignment to unused variable dd

(F841)

180-183: Address unused variable warning in TestData class.

Similar to the other test, the variable dd is assigned but never used.
-    def test_init_type_map_error(self) -> None:
-        with self.assertRaises(ValueError):
-            dd = DeepmdData(self.data_name, type_map=["bar"])
+    def test_init_type_map_error(self) -> None:
+        with self.assertRaises(ValueError):
+            DeepmdData(self.data_name, type_map=["bar"])
🧰 Tools

🪛 Ruff (0.8.2)

182-182: Local variable dd is assigned to but never used

Remove assignment to unused variable dd

(F841)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 65812b8 and 534d620.

📒 Files selected for processing (2)

deepmd/utils/data.py (1 hunks)
source/tests/tf/test_deepmd_data.py (2 hunks)

🧰 Additional context used

🪛 Ruff (0.8.2)

source/tests/tf/test_deepmd_data.py

182-182: Local variable dd is assigned to but never used

Remove assignment to unused variable dd

(F841)

457-457: Local variable dd is assigned to but never used

Remove assignment to unused variable dd

(F841)

⏰ Context from checks skipped due to timeout of 90000ms (16)

GitHub Check: Build wheels for cp310-manylinux_aarch64
GitHub Check: Test Python (5, 3.12)
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GitHub Check: Analyze (python)
GitHub Check: Analyze (c-cpp)
GitHub Check: Test C++ (false)
GitHub Check: Test C++ (true)
GitHub Check: Build C library (2.14, >=2.5.0rc0,<2.15, libdeepmd_c_cu11.tar.gz)
GitHub Check: Build C library (2.18, libdeepmd_c.tar.gz)

🔇 Additional comments (3)

deepmd/utils/data.py (1)

92-96: Well-implemented validation check.

This change adds proper validation to ensure all elements in self.type_map are present in the provided type_map. The error message clearly identifies which elements are missing, helping users quickly diagnose the issue.

source/tests/tf/test_deepmd_data.py (2)

180-183: Good addition of error handling test case.

Adding a test case that verifies the ValueError is raised when an incomplete type map is provided ensures the new validation in DeepmdData is working as expected.

🧰 Tools

🪛 Ruff (0.8.2)

182-182: Local variable dd is assigned to but never used

Remove assignment to unused variable dd

(F841)

385-454: Well-designed test class for mixed type testing.

This new test class properly sets up test data with mixed atom types and validates the behavior of DeepmdData when working with mixed types. The setup method is thorough in creating all necessary test files and data.

source/tests/tf/test_deepmd_data.py

coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

source/tests/tf/test_deepmd_data.py (1)
385-461: Well-structured test class for mixed type scenario.

Good addition of the TestDataMixType class that specifically tests the behavior when handling mixed atom types. The setup method properly initializes test data including coordinates, boxes, and real atom types across multiple sets. The test methods appropriately verify both the successful initialization with a valid type map and error handling with an invalid type map.

One suggestion: consider adding a test case that verifies the error message content to ensure it provides clear guidance to users.

You could enhance the error test by verifying the specific error message:
 def test_init_type_map_error(self) -> None:
-    with self.assertRaises(ValueError):
+    with self.assertRaisesRegex(ValueError, "Some atom types.*not found in.*type_map"):
         DeepmdData(self.data_name, type_map=["foo"])

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

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Reviewing files that changed from the base of the PR and between 534d620 and 7ce0ea2.

📒 Files selected for processing (1)

source/tests/tf/test_deepmd_data.py (2 hunks)

⏰ Context from checks skipped due to timeout of 90000ms (18)

GitHub Check: Build wheels for cp310-manylinux_aarch64
GitHub Check: Build wheels for cp311-win_amd64
GitHub Check: Build wheels for cp311-macosx_arm64
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GitHub Check: Test C++ (false)
GitHub Check: Build wheels for cp311-manylinux_x86_64
GitHub Check: Test C++ (true)
GitHub Check: Build wheels for cp311-manylinux_x86_64
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GitHub Check: Build C library (2.14, >=2.5.0rc0,<2.15, libdeepmd_c_cu11.tar.gz)
GitHub Check: Analyze (javascript-typescript)
GitHub Check: Build C library (2.18, libdeepmd_c.tar.gz)
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🔇 Additional comments (3)

source/tests/tf/test_deepmd_data.py (3)

180-183: Good addition of error test case.

This test verifies that a ValueError is thrown when an invalid type map (with only one type) is provided, which helps catch configuration errors early.

446-454: Thorough verification of type mapping properties.

The test properly verifies all relevant properties related to type mapping:

enforce_type_map flag is correctly set

type_map contents match expected values

mixed_type is correctly set to True

Type index mappings are correctly established

This ensures that the type mapping system works as intended.

455-458: Appropriate error test matches the existing TestData error test.

This test correctly verifies that an error is thrown when an invalid type map is provided, aligning with the similar test in the TestData class.

njzjz · 2025-03-06T11:45:31Z

This bug appends because there is no error reported in np.searchsorted method even when type_map and self.type_map are totally different.

There is another np.searchsorted that may also be critical. cc @iProzd

deepmd-kit/deepmd/tf/fit/ener.py

Lines 1007 to 1009 in 70bc6d8

    
           idx_type_map = sorter[ 
        
               np.searchsorted(full_type_map, origin_type_map, sorter=sorter) 
        
           ]

codecov · 2025-03-06T11:57:37Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.64%. Comparing base (65812b8) to head (7ce0ea2).
Report is 75 commits behind head on devel.

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #4639      +/-   ##
==========================================
- Coverage   84.78%   84.64%   -0.14%     
==========================================
  Files         688      688              
  Lines       66091    66094       +3     
  Branches     3539     3539              
==========================================
- Hits        56032    55944      -88     
- Misses       8918     9013      +95     
+ Partials     1141     1137       -4

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…son/type_map` (deepmodeling#4639) See issue deepmodeling#4519 . When there are elements in the data that are not present in input.json, no error will be reported. For example, when element D is in type_map.raw, but D is not in type_map of input.json, the training process is normal. This error appears when `self.mixed_type=True`.  ## Summary by CodeRabbit - **New Features** - Introduced enhanced data validation to ensure the atom type mapping is complete and consistent. Users will now receive clear error notifications if there are discrepancies in the provided mapping. - **Tests** - Added a new test class to verify correct data initialization and validate that errors are raised appropriately for invalid atom type mappings.  --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (cherry picked from commit e4eb01f)

Chengqian-Zhang added 2 commits March 6, 2025 18:45

Fix bug 4519

a8e86b5

Delete blank line

184359a

github-actions bot added the Python label Mar 6, 2025

Merge branch 'devel' into 4519

460b76c

[pre-commit.ci] auto fixes from pre-commit.com hooks

534d620

for more information, see https://pre-commit.ci

Chengqian-Zhang requested a review from njzjz March 6, 2025 11:02

coderabbitai bot reviewed Mar 6, 2025

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github-advanced-security bot found potential problems Mar 6, 2025

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source/tests/tf/test_deepmd_data.py Fixed Show fixed Hide fixed

source/tests/tf/test_deepmd_data.py Fixed Show fixed Hide fixed

Chengqian-Zhang requested a review from wanghan-iapcm March 6, 2025 11:03

Fix code scanning

7ce0ea2

coderabbitai bot reviewed Mar 6, 2025

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wanghan-iapcm approved these changes Mar 6, 2025

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njzjz approved these changes Mar 6, 2025

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njzjz linked an issue Mar 6, 2025 that may be closed by this pull request

[BUG] No error reported when data's element is not present in input.json #4519

Closed

njzjz enabled auto-merge March 6, 2025 11:56

njzjz added this pull request to the merge queue Mar 6, 2025

Merged via the queue into deepmodeling:devel with commit e4eb01f Mar 6, 2025
60 checks passed

njzjz added this to the v3.0.3 milestone May 21, 2025

fix(data): Throw error when data's element is not present in input.json/type_map #4639

fix(data): Throw error when data's element is not present in input.json/type_map #4639

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fix(data): Throw error when data's element is not present in `input.json/type_map` #4639

fix(data): Throw error when data's element is not present in `input.json/type_map` #4639

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