feat(jax/array-api): se_e2_r #4257
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Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces significant modifications to the Changes
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🔇 Additional comments (6)
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
deepmd/jax/descriptor/se_e2_r.py (1)
27-41: Add docstring and improve error handling.The
__setattr__method handles special attributes but lacks documentation and robust error handling.Consider adding a docstring and error handling:
def __setattr__(self, name: str, value: Any) -> None: + """Custom attribute setter for JAX array compatibility. + + Args: + name: Attribute name to set + value: Value to assign + + Handles special cases: + - dstd/davg: Converts to JAX arrays and wraps in ArrayAPIVariable + - embeddings: Deserializes through NetworkCollection + - env_mat: Ignored (no storage) + - emask: Converts to PairExcludeMask + """ if name in {"dstd", "davg"}: + try: value = to_jax_array(value) if value is not None: value = ArrayAPIVariable(value) + except Exception as e: + raise ValueError(f"Failed to convert {name} to JAX array: {e}") elif name in {"embeddings"}: if value is not None: + try: value = NetworkCollection.deserialize(value.serialize()) + except Exception as e: + raise ValueError(f"Failed to deserialize embeddings: {e}") elif name == "env_mat": # env_mat doesn't store any value pass elif name == "emask": + if not hasattr(value, 'ntypes') or not hasattr(value, 'exclude_types'): + raise ValueError("emask value must have ntypes and exclude_types attributes") value = PairExcludeMask(value.ntypes, value.exclude_types)
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📒 Files selected for processing (5)
- deepmd/dpmodel/descriptor/se_r.py (5 hunks)
- deepmd/jax/descriptor/init.py (1 hunks)
- deepmd/jax/descriptor/se_e2_r.py (1 hunks)
- source/tests/array_api_strict/descriptor/se_e2_r.py (1 hunks)
- source/tests/consistent/descriptor/test_se_r.py (4 hunks)
🔇 Additional comments (14)
deepmd/jax/descriptor/__init__.py (1)
8-10: LGTM! Clean and consistent changes.The addition of
DescrptSeRfollows the established module structure, with proper import organization and export declaration in__all__.Also applies to: 14-14
source/tests/array_api_strict/descriptor/se_e2_r.py (3)
1-16: LGTM! Well-organized imports.The imports are properly organized and all necessary dependencies are included for the array API strict implementation.
19-32: LGTM! Clean implementation of array API strict compatibility.The attribute handling logic is well-structured and covers all necessary cases for array API compatibility.
19-32: Verify base class and utility function implementations.Let's ensure the implementation is consistent with the base class and utility functions.
✅ Verification successful
Let me gather more specific information about the utility functions and base class implementation.
Let me try one more search to find the base class implementation.
Let me check the actual base class implementation since we found it's imported from deepmd.dpmodel.descriptor.se_r.
Based on all the gathered information, I can now provide the final response:
Implementation is consistent with the codebase
The implementation correctly extends the base functionality by:
- Properly inheriting from
DescrptSeRDP(which is an alias forDescrptSeRfrom dpmodel)- Using verified utility functions:
to_array_api_strict_arrayfor array conversionPairExcludeMaskfor mask handlingNetworkCollectionfor network serialization- Adding array-api-strict specific attribute handling while maintaining the base class behavior through
super().__setattr__🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify base class implementation and utility function usage # Check base class implementation echo "Checking base class implementation..." ast-grep --pattern 'class DescrptSeRDP { $$$ def __setattr__($$$) { $$$ } $$$ }' # Check utility function implementations echo "Checking utility function implementations..." rg -l "to_array_api_strict_array" --type py rg -l "PairExcludeMask" --type py rg -l "NetworkCollection" --type pyLength of output: 3298
Script:
#!/bin/bash # Check the implementation of to_array_api_strict_array echo "Checking to_array_api_strict_array implementation..." rg "def to_array_api_strict_array" -A 5 --type py # Check PairExcludeMask implementation in the same directory echo "Checking PairExcludeMask implementation..." rg "class PairExcludeMask" -A 5 source/tests/array_api_strict/utils/exclude_mask.py # Check NetworkCollection implementation echo "Checking NetworkCollection implementation..." rg "class NetworkCollection" -A 5 source/tests/array_api_strict/utils/network.py # Check base class DescrptSeRDP implementation echo "Checking DescrptSeRDP implementation..." fd "se_e2_r.py" --type f --exec rg "class DescrptSeRDP" -A 10 {}Length of output: 1535
Script:
#!/bin/bash # Search for DescrptSeRDP in the entire codebase echo "Searching for DescrptSeRDP class..." rg "class DescrptSeRDP" -A 10 --type py # Also check if it's imported from somewhere echo "Checking DescrptSeRDP imports..." rg "from.*import.*DescrptSeRDP" --type pyLength of output: 584
Script:
#!/bin/bash # Check the actual base class implementation echo "Checking base class in deepmd.dpmodel.descriptor.se_r..." rg "class DescrptSeR" -A 15 deepmd/dpmodel/descriptor/se_r.py # Also check if there's any __setattr__ in the base class echo "Checking __setattr__ in base class..." ast-grep --pattern 'class DescrptSeR { $$$ def __setattr__($$$) { $$$ } $$$ }' deepmd/dpmodel/descriptor/se_r.pyLength of output: 999
deepmd/jax/descriptor/se_e2_r.py (2)
1-26: LGTM! Well-structured class setup with dual registration.The class is properly set up with necessary imports and decorators. The dual registration under both "se_e2_r" and "se_r" names ensures backward compatibility.
26-41: Verify complete attribute handling coverage.Since this class extends
DescrptSeRDP, we should verify that all necessary attributes are properly handled in the JAX implementation.Let's check the parent class attributes:
✅ Verification successful
Based on the search results, I can now generate the final response since I have a comprehensive view of all attributes in the parent class.
The JAX implementation properly handles all critical attributes
The
__setattr__implementation correctly handles the key attributes that require special treatment in the JAX context:
dstd,davg: Converted to JAX arraysembeddings: Properly deserialized for network collectionenv_mat: Correctly skipped as it doesn't store valuesemask: Properly instantiated with PairExcludeMaskAll other attributes from the parent class (rcut, sel, neuron, etc.) can use the default attribute setting behavior since they don't require special JAX handling.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Find all attributes accessed in the parent class # to ensure complete coverage in the JAX implementation # Search for self.* assignments in the parent class echo "Searching for attribute assignments in parent class:" rg "self\." "deepmd/dpmodel/descriptor/se_r.py" -A 2 # Search for @property decorators to find property attributes echo -e "\nSearching for properties in parent class:" rg "@property" "deepmd/dpmodel/descriptor/se_r.py" -A 2Length of output: 5070
source/tests/consistent/descriptor/test_se_r.py (4)
56-56: LGTM! Class name updated to match the descriptor type.The class name change from
TestSeAtoTestSeRcorrectly reflects the type of descriptor being tested.
97-116: LGTM! Skip properties follow consistent implementation pattern.The new skip properties for JAX and Array API Strict follow the same pattern as existing skip properties, correctly handling test skipping based on both installation status and type_one_side parameter.
120-121: LGTM! Backend implementations are consistent.The new JAX and Array API Strict backend implementations follow the established pattern:
- Class attributes correctly reference the respective descriptor classes
- Evaluation methods properly utilize the descriptor-specific evaluation helpers
Also applies to: 186-203
186-203: Verify test coverage for new backends.Please ensure that the test suite executes all test cases for the new JAX and Array API Strict backends.
✅ Verification successful
Let me check the actual test implementations to better understand the coverage.
Based on the test implementation details shown in the output, I can now provide a final response:
Test coverage for new backends is properly implemented
The test suite includes comprehensive test coverage for both JAX and Array API Strict backends:
- Both backends have consistency tests with reference implementations (
test_jax_consistent_with_ref,test_array_api_strict_consistent_with_ref)- Both backends have self-consistency tests (
test_jax_self_consistent,test_array_api_strict_self_consistent)- Tests include proper skipping mechanisms for unsupported backends
- The test implementations follow the same pattern as other established backends (TF, PyTorch)
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check test coverage for JAX and Array API Strict backends # Expected: Test methods that use eval_jax and eval_array_api_strict # Search for test methods that use the new evaluation methods echo "Test methods using JAX backend:" rg -l "self\.eval_jax\(" source/tests/ echo "Test methods using Array API Strict backend:" rg -l "self\.eval_array_api_strict\(" source/tests/Length of output: 334
Script:
#!/bin/bash # Check the implementation details of the test methods echo "Content of source/tests/consistent/common.py showing test methods:" rg -B 5 -A 10 "def test.*" source/tests/consistent/common.py # Check if there are any test base classes or mixins that might be used echo -e "\nPotential test base classes:" rg -l "class.*Test" source/tests/ # Check for any parametrized tests echo -e "\nParametrized tests:" rg "pytest.mark.parametrize" source/tests/Length of output: 19133
deepmd/dpmodel/descriptor/se_r.py (4)
9-9: LGTM: Clean import additions for array API compatibilityThe new imports properly support the transition to array API compatibility, enabling better backend support.
Also applies to: 17-20
149-165: LGTM: Improved network initialization and type handlingGood improvements:
- Better code organization with local variable initialization
- Added proper seed propagation for reproducibility
- Added cumulative sum for efficient type-based indexing
Also applies to: 175-175
286-288: LGTM: Clean array API integrationThe array API integration is properly implemented with correct namespace handling and reshape operations.
382-383: LGTM: Proper array conversion in serializationThe use of
to_numpy_arrayensures correct array conversion during serialization, maintaining consistency with the array API compatibility changes.
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Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## devel #4257 +/- ##
=======================================
Coverage 84.23% 84.23%
=======================================
Files 548 549 +1
Lines 51425 51456 +31
Branches 3051 3051
=======================================
+ Hits 43317 43345 +28
Misses 7150 7150
- Partials 958 961 +3 ☔ View full report in Codecov by Sentry. |
Summary by CodeRabbit
New Features
DescrptSeR, enhancing compatibility with JAX and Array API.Bug Fixes
Tests
DescrptSeRdescriptor, including support for JAX and Array API Strict backends.DescrptSeRdescriptor.