Feature/updated gradio app #1
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Pull request overview
This PR introduces a Gradio-based web application for cosinor analysis, adds comprehensive documentation to existing modules, and refactors the codebase by consolidating utilities and removing demo/example code. The changes significantly expand functionality for live-cell and omics dataset analysis while improving code maintainability through enhanced docstrings and type hints.
Key Changes
- Added Gradio web application support with dependencies (gradio>=5.50.0, openpyxl>=3.1.5)
- Introduced two new modules:
livecell_dataset.pyandlivecell_cosinor_analysis.pyfor time-series cosinor analysis - Comprehensive documentation added via NumPy-style docstrings across
omics_differential_rhytmicity.pyandomics_dataset.py
Reviewed changes
Copilot reviewed 27 out of 34 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| uv.lock | Added Gradio ecosystem dependencies (fastapi, aiofiles, uvicorn, websockets, etc.) and updated Python version markers |
| tests/unit_tests/test_states_info.py | Removed demo tests for example city/state functionality |
| tests/unit_tests/test_data_loading.py | Removed basic CSV loading tests |
| tests/fixtures/example_fixture.py | Removed example fixture demonstrating pytest patterns |
| tests/conftest.py | Simplified to register actual test fixtures instead of examples |
| test-reports/report.xml | Updated test results showing 89 passing tests (up from 7) |
| src/cosinor_lite/visualisation.py | Deleted; functionality consolidated into omics_differential_rhytmicity.py |
| src/cosinor_lite/utils.py | Deleted; utility functions moved into omics_differential_rhytmicity.py |
| src/cosinor_lite/states_info.py | Removed demo utility for US state capitals |
| src/cosinor_lite/cities.json | Removed demo data file |
| src/cosinor_lite/models.py | Deleted; model classes consolidated into omics_differential_rhytmicity.py |
| src/cosinor_lite/omics_differential_rhytmicity.py | Major enhancement with comprehensive docstrings, type hints, and consolidated model definitions |
| src/cosinor_lite/omics_dataset.py | Added NumPy-style docstrings and improved method documentation |
| src/cosinor_lite/livecell_dataset.py | New module for live-cell time-series dataset handling with validation and plotting |
| src/cosinor_lite/livecell_cosinor_analysis.py | New module implementing cosinor model fitting (24h, free-period, damped) for live-cell data |
| pyproject.toml | Added gradio and openpyxl dependencies; configured interrogate for docstring coverage |
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Updated readme.md with Hugging Face Spaces link