None index with adaptive mutation

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PyGAD 3.5.0

Refactor the pygad.py script

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Add read permissions to workflows

Fix documentation errors in 'Other Attributes'

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1. Support passing a class to the fitness, crossover, and mutation. #342
2. A new class called `Validation` is created in the new `pygad/utils/validation.py` script. It has a method called `validate_parameters()` to validate all the parameters passed while instantiating the `pygad.GA` class.
3. Refactoring the `pygad.py` script by moving a lot of functions and methods to other classes in other scripts.
  4. The `summary()` method was moved to `Helper` class in the `pygad/helper/misc.py` script.
  5. The validation code in the `__init__()` method of the `pygad.GA` class is moved to the new `validate_parameters()` method in the new `Validation` class in the new `pygad/utils/validation.py` script. Moreover, the `validate_multi_stop_criteria()` method is also moved to the same class.
  6. The GA main workflow is moved into the new `GAEngine` class in the new `pygad/utils/engine.py` script. Specifically, these methods are moved from the `pygad.GA` class to the new `GAEngine` class:
         1. `run()`
            1. `run_loop_head()`
            2. `run_select_parents()`
            3. `run_crossover()`
            4. `run_mutation()`
            5. `run_update_population()`
         2. `initialize_population()`
         3. `cal_pop_fitness()`
         4. `best_solution()`
         5. `round_genes()`
7. The `pygad.GA` class now extends the two new classes `utils.validation.Validation` and `utils.engine.GAEngine`.
8. The version of the `pygad.utils` submodule is upgraded from `1.3.0` to `1.4.0`.
9. The version of the `pygad.helper` submodule is upgraded from `1.2.0` to `1.3.0`.
10. The version of the `pygad.visualize` submodule is upgraded from `1.1.0` to `1.1.1`.
11. The version of the `pygad.nn` submodule is upgraded from `1.2.1` to `1.2.2`.
12. The version of the `pygad.cnn` submodule is upgraded from `1.1.0` to `1.1.1`.
13. The version of the `pygad.torchga` submodule is upgraded from `1.4.0` to `1.4.1`.
14. The version of the `pygad.kerasga` submodule is upgraded from `1.3.0` to `1.3.1`.
15. Update the elitism after the evolution ends to fix issue where the best solution returned by the `best_solution()` method is not correct. #337
16. Fix a bug in calling the `numpy.reshape()` function. The parameter `newshape` is removed since it is no longer supported started from NumPy `2.4.0`. https://numpy.org/doc/stable/release/2.4.0-notes.html#removed-newshape-parameter-from-numpy-reshape
17. A minor change in the documentation is made to replace the `newshape` parameter when calling `numpy.reshape()`.
18. Fix a bug in the `visualize/plot.py` script that causes a warning to be given when the plot leged is used with single-objective problems.
19. A new method called `initialize_parents_array()` is added to the `Helper` class in the `pygad/helper/misc.py` script. It is usually called from the methods in the `ParentSelection` class in the `pygad/utils/parent_selection.py` script to initialize the parents array.
20. Add more tests about:
          1. Operators (crossover, mutation, and parent selection).
          2. The `best_solution()` method.
          3. Parallel processing.
          4. The `GANN` module.
          5. The plots created by the `visualize`.

21. Instead of using repeated code for converting the data type and rounding the genes during crossover and mutation, the `change_gene_dtype_and_round()` method is called from the `pygad.helper.misc.Helper` class.
22. Fix some documentation issues. #336
23. Update the documentation to reflect the recent additions and changes to the library structure.

PyGAD 3.6.0