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fix: use deepcopy when dumping mixed types #671

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merged 4 commits into from
Jun 6, 2024

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iProzd
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@iProzd iProzd commented Jun 6, 2024

Use deepcopy when dumping mixed types in system level. Fix #670 .

Typically, users use the following command to dump list of systems to mixed_type:

dpdata.MultiSystems(*systems).to_deepmd_npy_mixed("mixed_dir")

This command will rebuild a new system with a new data dict, thus it does not change the original system.data.

In #670 , when users use

system.to('deepmd/npy/mixed', 'dir') 

on a system in standard format, it would directly convert the original system.data into mixed types, thus the original system.data would be changed.

Use deepcopy to prevent this.

Summary by CodeRabbit

  • Bug Fixes

    • Enhanced data integrity by preserving the original content before processing.
  • Tests

    • Added new tests to ensure proper functionality of the data dumping process.

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codspeed-hq bot commented Jun 6, 2024

CodSpeed Performance Report

Merging #671 will not alter performance

Comparing iProzd:fix_mix_convert (29bcf6a) with devel (4bb4069)

Summary

✅ 2 untouched benchmarks

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codecov bot commented Jun 6, 2024

Codecov Report

Attention: Patch coverage is 50.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 84.30%. Comparing base (4bb4069) to head (c58a87f).

Current head c58a87f differs from pull request most recent head 29bcf6a

Please upload reports for the commit 29bcf6a to get more accurate results.

Files Patch % Lines
dpdata/deepmd/mixed.py 50.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##            devel     #671      +/-   ##
==========================================
- Coverage   84.31%   84.30%   -0.01%     
==========================================
  Files          81       81              
  Lines        7142     7144       +2     
==========================================
+ Hits         6022     6023       +1     
- Misses       1120     1121       +1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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coderabbitai bot commented Jun 6, 2024

Walkthrough

Walkthrough

The changes introduce a deep copy operation in the dump function of dpdata/deepmd/mixed.py to prevent data modification during processing. Additionally, new unit tests in tests/test_deepmd_mixed.py ensure the correct functionality of dumping single systems in mixed type format, addressing a bug where systems could not be appended to multi-systems after being dumped.

Changes

File Change Summary
dpdata/deepmd/mixed.py Added import copy and data = copy.deepcopy(data) within the dump function to preserve data.
tests/test_deepmd_mixed.py Added TestMixedSingleSystemsDump class with setUp and tearDown methods, and a test for dumping.

Assessment against linked issues

Objective (Issue #670) Addressed Explanation
Ensure systems can be appended to multi-systems after being dumped in mixed type format
Validate the functionality with unit tests

Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between c58a87f and 29bcf6a.

Files selected for processing (1)
  • tests/test_deepmd_mixed.py (1 hunks)
Additional comments not posted (3)
tests/test_deepmd_mixed.py (3)

334-336: Proper cleanup in tearDown method.


317-337: The structure of TestMixedSingleSystemsDump is well-organized for testing single system dumps.


318-333: Ensure the test dump operation in setUp is intended for setup only and not an actual test.

Verification successful

The test dump operation in setUp is only referenced within the setUp and tearDown methods, confirming it is intended for setup purposes only and not an actual test.

  • tests/test_deepmd_mixed.py:
    • Line 318: self.system_1.to("deepmd/npy/mixed", "tmp.deepmd.mixed.single")
    • Line 333: if os.path.exists("tmp.deepmd.mixed.single"):
    • Line 334: shutil.rmtree("tmp.deepmd.mixed.single")
Scripts executed

The following scripts were executed for the analysis:


Script:

#!/bin/bash
# Description: Verify if the test dump operation in `setUp` is used elsewhere or if it should be part of a test method.

# Test: Search for references to `tmp.deepmd.mixed.single`. Expect: No references outside of `setUp` and `tearDown`.
rg --type python $'tmp.deepmd.mixed.single'

Length of output: 73



Script:

#!/bin/bash
# Description: Verify if the test dump operation in `setUp` is used elsewhere or if it should be part of a test method.

# Test: Search for references to `tmp.deepmd.mixed.single`. Expect: No references outside of `setUp` and `tearDown`.
rg 'tmp.deepmd.mixed.single' --glob '*.py'

Length of output: 302


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@wanghan-iapcm wanghan-iapcm requested a review from njzjz June 6, 2024 09:25
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@wanghan-iapcm wanghan-iapcm left a comment

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A UT is necessary
it is designed to reproduce the issue in the old code, and to show the bug is fixed in the revised code.

@iProzd iProzd requested a review from wanghan-iapcm June 6, 2024 09:59
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@njzjz njzjz left a comment

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We may also consider copying the data in System.

@njzjz njzjz merged commit e19e34e into deepmodeling:devel Jun 6, 2024
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3 participants