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High-level description

This file contains unit tests for the utility functions defined in cassiopeia/mixins/utilities.py. It tests the functionality of various utility functions related to handling ambiguous states in character matrices and finding duplicate groups.

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Symbols

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TestMixinUtilities

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Description

This is a test class that inherits from unittest.TestCase. It contains several test methods to verify the functionality of utility functions from the cassiopeia.mixins.utilities module.

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Internal Logic

The class defines three test methods:
  1. test_is_ambiguous_state: Tests the is_ambiguous_state function.
  2. test_unravel_states: Tests the unravel_ambiguous_states function.
  3. test_find_duplicated_character_states: Tests the find_duplicate_groups function.

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test_is_ambiguous_state

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Description

This method tests the is_ambiguous_state function from the utilities module.

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Internal Logic

  • Asserts that (1, 2) is recognized as an ambiguous state.
  • Asserts that 1 is not recognized as an ambiguous state.

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test_unravel_states

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Description

This method tests the unravel_ambiguous_states function from the utilities module.

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Internal Logic

  • Tests the function with an array containing both ambiguous and non-ambiguous states.
  • Tests the function with an array containing only non-ambiguous states.
  • Asserts that the output matches the expected unraveled list in both cases.

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test_find_duplicated_character_states

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Description

This method tests the find_duplicate_groups function from the utilities module.

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Internal Logic

  • Creates a sample character matrix using pandas DataFrame.
  • Calls the find_duplicate_groups function on the character matrix.
  • Checks if the returned duplicate mappings contain the expected entries.
  • Verifies that the keys and values in the duplicate mappings match the expected groups.

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Dependencies

DependencyPurpose
unittestProvides the testing framework
pandasUsed to create and manipulate the character matrix
cassiopeia.mixins.utilitiesModule containing the utility functions being tested

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Error Handling

The test methods use assertions to verify the correctness of the utility functions. If any assertion fails, an AssertionError will be raised, indicating a test failure.

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Notes

  • The test file uses the unittest framework, which is a standard Python testing library.
  • The tests cover various scenarios, including ambiguous states and duplicate character states in matrices.
  • The test_find_duplicated_character_states method uses a complex character matrix with ambiguous states to thoroughly test the find_duplicate_groups function.