Genetics Implementation

[allisterakun]

Context

Issue(s) closed by this pull request: closes #

What

Why

How

Test plan

Input Changes

Output Changes

• N/A

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[github-actions]

Current Coverage: 99%

Mypy errors on genetics_implementation branch: 1677
Mypy errors on dev branch: 1677
No difference in error counts

[github-actions]

Current Coverage: 99%

Mypy errors on genetics_implementation branch: 1740
Mypy errors on dev branch: 1682
58 more errors on genetics_implementation branch

[github-actions]

🚨 Unauthorized changes detected in protected files. Please remove these changes if they are not intended.
🚨 Flake8 linting errors were found. Please fix the linting issues.

[github-actions]

Current Coverage: 99%

Mypy errors on genetics_implementation branch: 1739
Mypy errors on dev branch: 1681
58 more errors on genetics_implementation branch

[github-actions]

🚨 Unauthorized changes detected in protected files. Please remove these changes if they are not intended.

[YijingGong]

Original PR: #2608
See design doc, PR description, and discussion there.

[jadamchick]

I just tried to run the branch as-is, and got the following error (pasted below). Looks like input manager is still looking for animal_net_merit in the metadata?

Starting task: 1/1
[23-Mar-2026_Mon_15-31-27.033331][ERROR][freestall] Metadata blobs error. Missing required file blobs: ['animal_net_merit']. Please add all missing file blobs to metadata.
[23-Mar-2026_Mon_15-31-27.045494][ERROR][freestall] Failed to finish task: 1/1 with output prefix: freestall. Failed to recover from error: Missing required file blobs: ['animal_net_merit']; traceback: Traceback (most recent call last):
  File "C:\Users\jms349\GitHub\RuFaS\RUFAS\task_manager.py", line 590, in task
    is_data_valid = TaskManager.handle_input_data_audit(args, input_manager, output_manager, True)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\jms349\GitHub\RuFaS\RUFAS\task_manager.py", line 753, in handle_input_data_audit
    is_data_valid = input_manager.start_data_processing(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\jms349\GitHub\RuFaS\RUFAS\input_manager.py", line 128, in start_data_processing
    self._validate_required_file_blobs(set(self.__metadata[ADDRESS_TO_INPUTS].keys()))
  File "C:\Users\jms349\GitHub\RuFaS\RUFAS\input_manager.py", line 182, in _validate_required_file_blobs
    raise ValueError(f"Missing required file blobs: {list(missing_blobs)}")
ValueError: Missing required file blobs: ['animal_net_merit']

[allisterakun]

I just tried to run the branch as-is, and got the following error (pasted below). Looks like input manager is still looking for animal_net_merit in the metadata?

Starting task: 1/1
[23-Mar-2026_Mon_15-31-27.033331][ERROR][freestall] Metadata blobs error. Missing required file blobs: ['animal_net_merit']. Please add all missing file blobs to metadata.
[23-Mar-2026_Mon_15-31-27.045494][ERROR][freestall] Failed to finish task: 1/1 with output prefix: freestall. Failed to recover from error: Missing required file blobs: ['animal_net_merit']; traceback: Traceback (most recent call last):
  File "C:\Users\jms349\GitHub\RuFaS\RUFAS\task_manager.py", line 590, in task
    is_data_valid = TaskManager.handle_input_data_audit(args, input_manager, output_manager, True)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\jms349\GitHub\RuFaS\RUFAS\task_manager.py", line 753, in handle_input_data_audit
    is_data_valid = input_manager.start_data_processing(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\jms349\GitHub\RuFaS\RUFAS\input_manager.py", line 128, in start_data_processing
    self._validate_required_file_blobs(set(self.__metadata[ADDRESS_TO_INPUTS].keys()))
  File "C:\Users\jms349\GitHub\RuFaS\RUFAS\input_manager.py", line 182, in _validate_required_file_blobs
    raise ValueError(f"Missing required file blobs: {list(missing_blobs)}")
ValueError: Missing required file blobs: ['animal_net_merit']

Should be fixed now!

[github-actions]

Current Coverage: %

Mypy errors on genetics_implementation branch: 1269
Mypy errors on dev branch: 1214
55 more errors on genetics_implementation branch

[github-actions]

🚨 Unauthorized changes detected in protected files. Please remove these changes if they are not intended.
🚨 Some tests have failed.