breaking: use all sets for training and test

[njzjz]

Fix #3860.

Remove train_dirs and test_dir in DeepmdData.

Summary by CodeRabbit

• New Features

  • All data sets are now trained and tested by default, simplifying the training process.

• Bug Fixes

  • Improved logic for handling training directories and test set merging.

• Tests

  • Added new test cases for the updated data handling methods.
  • Updated existing tests to reflect changes in data set handling and batch sizes.

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Commits

Files that changed from the base of the PR and between 9d001ca and 4c59892.

Walkthrough

The recent changes in deepmd/utils/data.py and corresponding test files involve the deprecation of the trn_all_set parameter in the DeepmdData class, leading to a unified approach where all sets are trained and tested. This simplifies the logic for handling training directories and ensures that test sets are merged from all directories before shuffling. These updates address the issue where only the last set was tested, ensuring comprehensive testing across all sets.

Changes

Files/Modules	Change Summary
deepmd/utils/data.py	Deprecated trn_all_set parameter, simplified logic for handling training directories, unified test set loading and shuffling.
source/tests/tf/test_deepmd_data.py	Updated tests to reflect changes in directory handling, test set merging, and batch size checks.
source/tests/tf/test_deepmd_data_sys.py	Adjusted batch sizes and array concatenations for coordinate and test data retrieval to align with new logic.

Sequence Diagram(s) (Beta)

sequenceDiagram
    participant User
    participant DeepmdData
    participant TestSet

    User->>DeepmdData: Initialize without trn_all_set
    DeepmdData->>DeepmdData: Simplify training directory logic
    User->>DeepmdData: Request test set
    DeepmdData->>TestSet: Merge test sets from all directories
    TestSet->>DeepmdData: Return merged and shuffled test set
    DeepmdData->>User: Provide comprehensive test set

Loading

Assessment against linked issues

Objective	Addressed	Explanation
Only the last set of a LabeledSystem is tested in 'dp test' (#3860)	✅

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 82.66%. Comparing base (674bad7) to head (4c59892).
Report is 119 commits behind head on devel.

Additional details and impacted files

@@           Coverage Diff           @@
##            devel    #3862   +/-   ##
=======================================
  Coverage   82.66%   82.66%           
=======================================
  Files         517      517           
  Lines       49724    49720    -4     
  Branches     2984     2984           
=======================================
- Hits        41105    41102    -3     
+ Misses       7709     7708    -1     
  Partials      910      910           

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