update docs, remove deepcopy

[rodvrees]

This pull request introduces several improvements, bug fixes, and documentation updates for version 2.0.2 of the project. The most significant changes include the integration of Sphinx documentation with the changelog, optimization of PSM list filtering for better memory efficiency, updates to code examples and docstrings to match the current API, and a fix for CLI argument passing. Additionally, several docstring and error message improvements were made for clarity.

Documentation improvements:

• Added Sphinx documentation integration, including automatic inclusion of CHANGELOG.md in the docs, and updated the documentation index to link to the changelog. [1] [2] [3]
• Updated code examples in docstrings and documentation to use the current API (e.g., replacing predict_ccs with predict). [1] [2] [3]
• Changed CSV code block in README.md to a generic text block for improved rendering.

Performance and API changes:

• Optimized PSM list filtering in validate_psm_list to mutate instead of generating deep copies, reducing memory usage for large datasets. Added notes to clarify in-place mutation behavior. [1] [2] [3] [4] [5]
• Improved logic for handling PSMs with missing fields and clarified error messages.

Bug fixes:

• Fixed CLI argument passing to the predict function when calibration data is not provided.

Other:

• Bumped version to 2.0.2 in pyproject.toml.
• Updated changelog with all recent changes.