_mtp.py from_config() feature update #618
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Signed-off-by: David <[email protected]>
Signed-off-by: David <[email protected]>
Signed-off-by: David <[email protected]>
Signed-off-by: David <[email protected]>
WalkthroughThe recent updates focus on improving element ordering control in Changes
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Signed-off-by: David <[email protected]>
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Actionable comments posted: 7
Out of diff range and nitpick comments (9)
tests/apps/pes/test_mtp.py (9)
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1-1: Add a module-level docstring to provide an overview of the module's purpose and functionality.
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25-25: Add a docstring to thesetUpClassmethod to explain its functionality, particularly how it sets up the test environment.
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31-31: Add a docstring to thetearDownClassmethod to describe its role in cleaning up after tests are run.
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35-35: Add a docstring to thesetUpmethod to explain how it initializes the conditions for each test.
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49-49: Add a docstring to thetest_write_read_cfgsmethod to describe what this test verifies.
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60-60: ReplaceassertAlmostEqualwith a regularassertfor consistency with other tests and to simplify the code.- self.assertAlmostEqual(energy1, energy2) + assert energy1 == energy2
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66-66: Add a docstring to thetest_trainmethod to explain what aspects of thetrainmethod it tests.
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79-79: Add a docstring to thetest_evaluatemethod to describe its purpose and the conditions under which it operates.
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99-99: Add a docstring to thetest_predict_efsmethod to explain what this test checks and how it uses thepredict_efsmethod.
tests/apps/pes/test_mtp.py
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| @@ -112,6 +113,10 @@ | |||
| def test_from_config(self): | |||
| mtp = MTPotential.from_config(config_file, elements=["Mo"]) | |||
| assert mtp.param is not None | |||
| mtp = MTPotential.from_config(config_file_4, elements=['Nb','O','Li','Cl']) | |||
| assert mtp.param is not None and mtp.elements == ['Li','Nb','Cl','O'] | |||
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Break down the assertion into multiple parts for clarity and to isolate which part of the assertion might fail.
- assert mtp.param is not None and mtp.elements == ['Li','Nb','Cl','O']
+ assert mtp.param is not None
+ assert mtp.elements == ['Li','Nb','Cl','O']Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| assert mtp.param is not None and mtp.elements == ['Li','Nb','Cl','O'] | |
| assert mtp.param is not None | |
| assert mtp.elements == ['Li','Nb','Cl','O'] |
tests/apps/pes/test_mtp.py
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| mtp = MTPotential.from_config(config_file_4, elements=['Nb','O','Li','Cl']) | ||
| assert mtp.param is not None and mtp.elements == ['Li','Nb','Cl','O'] | ||
| mtp = MTPotential.from_config(config_file_4, elements=['Nb','O','Li','Cl'], default_element_ordering=False) | ||
| assert mtp.param is not None and mtp.elements == ['Nb','O','Li','Cl'] |
There was a problem hiding this comment.
Break down the assertion into multiple parts for clarity and to isolate which part of the assertion might fail.
- assert mtp.param is not None and mtp.elements == ['Nb','O','Li','Cl']
+ assert mtp.param is not None
+ assert mtp.elements == ['Nb','O','Li','Cl']Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| assert mtp.param is not None and mtp.elements == ['Nb','O','Li','Cl'] | |
| assert mtp.param is not None | |
| assert mtp.elements == ['Nb','O','Li','Cl'] |
Signed-off-by: David <[email protected]>
maml/apps/pes/_mtp.py
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| f"Order for the elements has been altered from {elements} to {ordered_elements} to ensure" | ||
| + " consistency with default element ordering in maml during MTP fitting. Change the" |
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Consider using implicit string concatenation for better readability.
- f"Order for the elements has been altered from {elements} to {ordered_elements} to ensure"
- + " consistency with default element ordering in maml during MTP fitting. Change the"
+ f"Order for the elements has been altered from {elements} to {ordered_elements} to ensure consistency with default element ordering in maml during MTP fitting. Change the"Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| f"Order for the elements has been altered from {elements} to {ordered_elements} to ensure" | |
| + " consistency with default element ordering in maml during MTP fitting. Change the" | |
| f"Order for the elements has been altered from {elements} to {ordered_elements} to ensure consistency with default element ordering in maml during MTP fitting. Change the" |
|
Thanks for the PR David @dsun980701. Please try to make the linting tests pass, and then we can ask Shyue Ping for a review. |
Signed-off-by: David <[email protected]>
|
Thank you for reviewing @JiQi535. I have changed my code to address the linting issue. However, as of now, the linting is failing not from my changes, but from "maml/apps/symbolic/init." and "maml/utils/_signal_processing.py". Please let me know if there is anything that I can do about these issues! |
Signed-off-by: David <[email protected]>
|
Hi @dsun980701, can you please try to pull the latest changes from the main branch? I think I have fixed the united tests and now at least the pytest should work. |
Summary
Major changes:
Checklist
ruff.mypy.duecredit@due.dcitedecorators to reference relevant papers by DOI (example)Tip: Install
pre-commithooks to auto-check types and linting before every commit:Summary by CodeRabbit
New Features
MTPotentialclass based on Pauling electronegativity, enhancing consistency in molecular simulations.Bug Fixes
get_sp_methodfunction in the signal processing module to accept a more flexible range of callable types, improving its utility and compatibility.Tests
MTPotentialclass to ensure robustness and reliability.