Start cleaning things up

[theodore-s-beers]

Summary by Sourcery

Clean up and improve type hints, error handling, and code quality across the DataFed TorchFlow library

Bug Fixes:

• Fixed potential None-related errors in various methods
• Added missing initializations
• Corrected some type-related edge cases

Enhancements:

• Added type hints to method signatures
• Improved error handling with explicit None checks
• Refactored type checking using isinstance()
• Simplified some conditional logic

Chores:

• Updated dependencies in setup.cfg
• Added development tools like pyright and ruff

[sourcery-ai]

Reviewer's Guide

This pull request implements enhancements by adding type hints across modules, introducing validation checks for crucial parameters, and refining code style. Project dependencies have also been updated.

Updated Class Diagram for PyTorchModelLogger

classDiagram
    class PyTorchModelLogger {
        +__init__(self, ..., input_data_shape: Optional_tuple_int_Ellipsis, ...)
        +getMetadata(self, local_vars: Optional_list_tuple_str_Any, model_hyperparameters: Optional_dict_str_Any, **kwargs)
        +save_notebook(self)
    }
    note for PyTorchModelLogger "Type hints updated for parameters in __init__ and getMetadata. Added input validation for some parameters."
    note for PyTorchModelLogger.getMetadata "Raises ValueError if local_vars or model_hyperparameters is None."
    note for PyTorchModelLogger.save_notebook "Raises ValueError if notebook metadata cannot be fetched."

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Updated Class Diagram for DataFed

classDiagram
    class API {
        %% Base class, details not shown as not modified in this PR
    }
    class DataFed {
        +__init__(self, ..., datafed_path: str, ..., dataset_id_or_path: Optional_str, ...)
        +user_id(self) : str
        +check_string_for_dot_or_slash(self, s)
        +data_record_create(self, ..., record_title: Optional_str, ...)
        +data_record_update(self, ..., record_title: Optional_str, ...)
        +required_keys(self, dict_list, required_keys)
        +getData(self, dataset_id: Optional_str)
    }
    DataFed --|> API
    note for DataFed "Type hints added/updated for several methods. Methods 'check_string_for_dot_or_slash' and 'required_keys' changed from static to instance methods. Input validation added."
    note for DataFed.user_id "Property; raises RuntimeError if authenticated user info cannot be fetched."
    note for DataFed.data_record_create "Raises ValueError if record_title is None."
    note for DataFed.data_record_update "Raises ValueError if record_title is None."
    note for DataFed.getData "Raises ValueError if dataset_id_or_path is not set and dataset_id is None."

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Updated Class Diagram for UniversalEncoder

classDiagram
    class JSONEncoder {
        %% Base class from json module, details not shown
    }
    class UniversalEncoder {
        +default(self, o)
    }
    UniversalEncoder --|> JSONEncoder
    note for UniversalEncoder "Parameter 'obj' in 'default' method renamed to 'o'."

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File-Level Changes

Change	Details	Files
Added type annotations and input validation checks.	Applied type hints to function signatures, return types, and attributes. Implemented runtime checks for None values in critical parameters, raising ValueError or RuntimeError.	src/datafed_torchflow/pytorch.py src/datafed_torchflow/datafed.py
Improved code style, Pythonic idioms, and addressed minor logical issues.	Replaced type() in [] constructs with isinstance() for type checking. Modified dictionary update operations for broader Python version compatibility. Standardized f-string formatting for floating-point numbers in example notebooks. Ensured variables are initialized before use to prevent potential errors. Refactored a static method to an instance method where appropriate. Minor cosmetic changes such as parameter renaming and spacing adjustments.	src/datafed_torchflow/pytorch.py src/datafed_torchflow/datafed.py src/datafed_torchflow/JSON.py examples/PyTorchModelLogger.ipynb examples/PyTorchModelLogger.old.ipynb src/datafed_torchflow/computer.py
Updated project dependencies and development tooling.	Added pyright, ruff, and sphinx to the list of dependencies. Reordered items within the install_requires section.	setup.cfg

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[sourcery-ai]

Hey @theodore-s-beers - I've reviewed your changes - here's some feedback:

• The 'Bandaid fix' comment regarding self.data_path in DataFed.getData should be addressed with a more permanent solution.
• Consider providing a more descriptive PR title and a brief summary in the description to outline the main changes, as 'Start cleaning things up' is quite general.
• The required_keys method in DataFed no longer references self after the @staticmethod decorator was removed; evaluate if it should be a static method or a standalone utility function.

Here's what I looked at during the review

• 🟡 General issues: 3 issues found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Documentation: all looks good

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[theodore-s-beers]

Going to merge this. There may be details to revert later, given some of the guards I've added, but I think it's better to start by imposing constraints.