Update shared path, serialization, and evaluation helpers

[T4ras123]

This pull request introduces significant improvements and new features to the SMILES encoder/decoder module, focusing on more robust path handling, enriched coordinate binning functionality, and minor bug fixes. The main highlights are the addition of a flexible binning configuration class and methods for encoding/decoding molecules using these bin configurations, as well as improved error handling for file system paths.

Path handling robustness:

• Improved error handling in _resolve_path_value and _base_candidate_values to gracefully skip over unreadable or inaccessible file system paths, preventing crashes due to OSError when traversing shared or restricted mounts. [1] [2] [3]

Coordinate binning enhancements:

• Added a new BinConfig dataclass to encapsulate binning configuration, including methods for saving/loading configurations and calculating digit widths. This enables flexible and reusable binning strategies for molecular coordinate encoding. (F3f17218L544R544)
• Implemented fit_uniform_bins and fit_quantile_bins functions to generate bin edges based on uniform or quantile-based strategies, supporting robust and data-driven binning. (F3f17218L544R544)
• Added new functions encode_cartesian_with_config and decode_cartesian_with_config to serialize and deserialize 3D molecular coordinates using the new binning configuration, supporting more accurate and customizable encoding/decoding workflows. (F3f17218L544R544)

Bug fixes and minor improvements:

• Changed the default coordinate binning range in both encode_cartesian_binned and encode_cartesian_binned_v2 from (-13.0, 13.0) to (-11.0, 11.0) for all axes, likely to better fit the data distribution. [1] [2]
• Fixed a minor output formatting bug in encode_cartesian_binned_v2 by ensuring each atom entry is terminated with a semicolon, improving consistency for downstream parsing.

Code cleanup:

• Removed or condensed excessive docstrings and comments in several functions, streamlining the code and improving readability. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]

Summary of most important changes:

1. Path handling improvements

• Added OSError exception handling in _resolve_path_value and _base_candidate_values to skip unreadable paths and continue searching for valid candidates. [1] [2] [3]

2. Coordinate binning functionality

• Introduced BinConfig dataclass for managing binning configuration, including persistence methods. (F3f17218L544R544)
• Added fit_uniform_bins and fit_quantile_bins for flexible bin edge generation. (F3f17218L544R544)
• Implemented encode_cartesian_with_config and decode_cartesian_with_config for encoding/decoding molecules using bin configs. (F3f17218L544R544)

3. Bug fixes

• Updated default coordinate binning ranges to (-11.0, 11.0) for better data fit. [1] [2]
• Fixed output formatting in encode_cartesian_binned_v2 to ensure semicolon separation for atom entries.

4. Code cleanup

• Removed excessive docstrings and improved code readability across multiple functions. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]Bundle the path fallback, serialization support, evaluation robustness, and training checkpoint path fixes that need to land together so the shared utilities stay consistent on top of main.