add support for multiple input molecules

[rvhonorato]

===autogenerated description===

This pull request includes multiple changes to improve the testing framework, update the documentation, and refactor the codebase for better performance and readability. The most important changes are summarized below:

Testing Framework Improvements:

• .github/workflows/ci.yml: Separated unit tests and integration tests, added detailed pytest options, and included hypothesis statistics.
• pyproject.toml: Added a marker for integration tests to the pytest configuration.

Documentation Updates:

• README.md: Updated usage instructions, added examples for running prodigy on single and multiple structures, and improved the help message format. [1] [2] [3] [4] [5]

Codebase Refactoring:

• src/prodigy_prot/cli.py: Refactored the CLI to handle both single structure files and directories, improved logging, and streamlined argument parsing. [1] [2] [3]
• src/prodigy_prot/modules/freesasa_tools.py: Replaced subprocess calls with the freesasa Python API for better integration and removed obsolete code.
• src/prodigy_prot/modules/parsers.py: Added a function to get the appropriate parser based on file extension and improved structure validation and logging. [1] [2]

These changes collectively enhance the project's maintainability, usability, and testing capabilities.

[Copilot]

Copilot reviewed 14 out of 14 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (1)

tests/test_prodigy.py:226

• The variable 'diffs' is referenced without being initialized, which will result in a runtime error during test execution. Consider initializing 'diffs' (e.g., as an empty dictionary with lists for each key) before iterating over it.

for k in diffs.keys():