fix: 781 pymatgen structure bug #782
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CodSpeed Performance ReportMerging #782 will not alter performanceComparing Summary
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📝 WalkthroughWalkthroughThe pull request introduces modifications to the PyMatGen integration within the dpdata library. Changes span across multiple files, focusing on improving structure conversion, handling periodic boundary conditions, and expanding test coverage. The modifications enhance the library's ability to work with different atomic structures, particularly in converting between dpdata and PyMatGen formats. The changes include updates to conversion methods, PBC handling, and the addition of new test cases and element type mappings. Changes
Sequence DiagramsequenceDiagram
participant System as dpdata.System
participant PyMatGen as PyMatGen Structure
participant Converter as Structure Converter
System->>Converter: Convert to PyMatGen
Converter->>Converter: Check PBC conditions
Converter->>Converter: Map atomic symbols
Converter->>Converter: Generate metadata
Converter->>PyMatGen: Return converted structure
This sequence diagram illustrates the high-level conversion process between dpdata System and PyMatGen Structure, highlighting the key steps of PBC checking, symbol mapping, and metadata generation introduced in the changes. Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? 🪧 TipsChatThere are 3 ways to chat with CodeRabbit:
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #782 +/- ##
==========================================
- Coverage 85.13% 85.13% -0.01%
==========================================
Files 81 81
Lines 7535 7539 +4
==========================================
+ Hits 6415 6418 +3
- Misses 1120 1121 +1 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 1
🧹 Nitpick comments (1)
tests/test_pymatgen_structure.py (1)
31-43: Enhance test coverage for PBC scenarios.While the new test class provides good coverage for basic structure conversion, consider adding explicit test methods for:
- Structures with different PBC configurations
- Error cases for partial PBC
Example test methods:
def test_pbc_fully_periodic(self): # Test structure with all PBC True pass def test_pbc_non_periodic(self): # Test structure with all PBC False pass def test_pbc_partial_raises_error(self): # Test structure with mixed PBC raises ValueError pass
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📒 Files selected for processing (5)
dpdata/plugins/pymatgen.py(1 hunks)dpdata/pymatgen/structure.py(1 hunks)tests/pymatgen_data/deepmd/type.raw(1 hunks)tests/pymatgen_data/deepmd/type_map.raw(1 hunks)tests/test_pymatgen_structure.py(2 hunks)
✅ Files skipped from review due to trivial changes (2)
- tests/pymatgen_data/deepmd/type.raw
- tests/pymatgen_data/deepmd/type_map.raw
🧰 Additional context used
🪛 GitHub Check: codecov/patch
dpdata/pymatgen/structure.py
[warning] 16-17: dpdata/pymatgen/structure.py#L16-L17
Added lines #L16 - L17 were not covered by tests
[warning] 19-19: dpdata/pymatgen/structure.py#L19
Added line #L19 was not covered by tests
🔇 Additional comments (3)
dpdata/pymatgen/structure.py (2)
8-8: LGTM: More reliable species access.The change from
site.species_stringtoii.specie.symbolprovides more direct and reliable access to the atomic symbol.
27-28: LGTM: Consistent info_dict additions.The new fields
origandnopbcenhance the structure information and maintain consistency with system requirements.dpdata/plugins/pymatgen.py (1)
37-37: LGTM: Improved species list construction.The list comprehension is a more concise and Pythonic way to construct the species list while maintaining the same functionality.
| if all(structure.pbc): | ||
| pbc = True | ||
| elif not any(structure.pbc): | ||
| pbc = False | ||
| else: | ||
| raise ValueError(f"Partial pbc condition {structure.pbc} is not supported") |
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💡 Codebase verification
Add test coverage for PBC validation in pymatgen structure conversion.
The review comment is accurate. While there are tests for fully periodic and non-periodic cases in the codebase, there is no test coverage for:
- Mixed PBC conditions (e.g. [True, False, True])
- ValueError being raised for partial PBC cases
Please add test cases in tests/test_pymatgen_structure.py to verify this validation logic.
🔗 Analysis chain
Add test coverage for PBC validation.
The new PBC validation logic is a good addition, but static analysis indicates missing test coverage for the partial PBC case.
Let's verify the test coverage:
Consider adding test cases for:
- Fully periodic structure (all True)
- Non-periodic structure (all False)
- Partial periodic structure (mixed True/False) to verify error handling
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for test cases covering PBC validation
rg -l "pbc.*True|pbc.*False" tests/
Length of output: 261
Script:
#!/bin/bash
# Find pymatgen structure-specific test files
fd test.*pymatgen tests/
# Search for actual test cases with PBC validation in pymatgen tests
echo "=== Test content ==="
rg -A 5 -B 5 "def test.*pbc|assert.*pbc" tests/ --type py
Length of output: 4417
🧰 Tools
🪛 GitHub Check: codecov/patch
[warning] 16-17: dpdata/pymatgen/structure.py#L16-L17
Added lines #L16 - L17 were not covered by tests
[warning] 19-19: dpdata/pymatgen/structure.py#L19
Added line #L19 was not covered by tests
Summary by CodeRabbit
New Features
Tests
Bug Fixes