Document CLI and harden parsing behaviors

[danielmcauley]

Summary

• describe CLI entry point, README fixes, and parsing/SEM adjustments, aligning exports and metadata contracts as in plan
• note that package metadata and CI now reference Python 3.9+, install dev deps for testing
  Testing
• Not run (not requested)

[danielmcauley]

@codex review

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. You're on a roll.

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[Copilot]

Pull request overview

This PR documents the CLI entrypoint, hardens parsing behaviors, and aligns package metadata with Python 3.9+ requirements. It includes a critical bug fix for mouse exclusion logic and introduces robust path/filename parsing utilities.

Changes:

• Added CLI module with basic entrypoint structure for future expansion
• Refactored path parsing to use regex-based pattern matching instead of brittle index-based splitting
• Fixed critical bug where mouse_ids_to_remove parameter kept excluded mice instead of removing them
• Hardened SEM calculation to return NaN for edge cases (arrays with ≤1 elements)
• Updated Python version requirement to 3.9+ and modernized type hints to use PEP 585 style
• Cleaned up package exports in __all__ and moved pytest-mock to dev dependencies
• Added comprehensive test coverage for new and modified functionality

Reviewed changes

Copilot reviewed 13 out of 14 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/test_package_exports.py	New tests validating __all__ exports exist and are unique
tests/test_fiber_photometry.py	Added tests for process_block_path and process_all_blocks with improved mocking
tests/test_data_processing.py	Added tests for mouse exclusion, filename parsing validation, and path parsing errors
tests/test_data_loading.py	Added tests for absolute path handling and missing day/cohort validation
tests/test_cli.py	New tests for CLI help output and invalid argument handling
spout_mouse/cli.py	New CLI module with basic argument parser and main entrypoint
spout_mouse/data_loading.py	Refactored to use regex-based extract_day_and_cohort_from_path() function
spout_mouse/data_processing.py	Fixed mouse exclusion bug, added _extract_mouse_id_from_filename() with validation
spout_mouse/analysis.py	Added edge case handling for SEM calculation when array length ≤1
spout_mouse/__init__.py	Removed internal API functions and GOOGLE_SHEET_URL from __all__ exports
setup.cfg	Updated Python version classifiers to 3.9-3.11, moved pytest-mock to dev extras
requirements.txt	Removed pytest-mock (now in dev dependencies only)
.github/workflows/pytest.yml	Updated to Python 3.11 and install dev dependencies with editable mode
README.md	Added CLI section, updated get_experiment_data example, removed non-existent function references

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[danielmcauley]

@codex fix failing tests

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[molliebernstein]

lgtm