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Make sex parameter required in encode_sex function
Unverified signature- Remove 'Unknown' as valid sex option, only accept 'Male' or 'Female' - Raise ValueError if invalid sex value is provided - Update documentation to clarify sex is required parameter466e964
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Add GitHub Actions workflows and comprehensive test suite
Unverified signature- Add CI/CD workflows for tests, code quality, and Docker builds - Add comprehensive Makefile with test, lint, format, and Docker targets - Add new test files for CLI, fixtures, UI components, and UI events - Refactor batch analysis into main analysis module - Update model manager and inference modules - Add .dockerignore for cleaner Docker builds - Update dependencies in uv.lock4780d8d
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Fix circular import by moving get_data_directory to separate module
Unverified signatureMoved get_data_directory() function from gradio_app.py to a new data_directory.py module to avoid circular imports. The circular import occurred because gradio_app.py imports from ui/utils.py, which was trying to import back from gradio_app.py. Changes: - Create src/mosaic/data_directory.py with get_data_directory() and set_data_directory() functions - Update gradio_app.py to import and use set_data_directory() - Update all other modules (aeon.py, data.py, utils.py, analysis.py) to import from data_directory module instead of gradio_app 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>52f8cb9 -
Fix model file location to use HuggingFace cache directory
Unverified signatureChanged all model file references from hardcoded local data/ directory to use HuggingFace cache directory. This fixes the issue where files couldn't be found after downloading from HuggingFace Hub. Changes: - Add get_data_directory() function to gradio_app.py that checks MOSAIC_DATA_DIR environment variable first, then falls back to local data/ for development - Update gradio_app.py to download to HF cache (removed local_dir parameter) and set MOSAIC_DATA_DIR environment variable - Update all model file references in aeon.py, data.py, utils.py, and analysis.py to use get_data_directory() instead of hardcoded paths 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>751062d
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Define DEFAULT_TISSUE_SITE_IDX constant for "Not Applicable" tissue site
copilot-swe-agent[bot] +1: raylimCo-authored-by: raylim <3074310+raylim@users.noreply.github.com>e1efb8d -
Merge pull request #10 from pathology-data-mining/copilot/sub-pr-7-another-one
Unverified signatureAdd error handling for missing CSV mapping files2f88344 -
Add error handling for missing CSV files in get_tissue_site_map and get_sex_map
copilot-swe-agent[bot] +1: raylimCo-authored-by: raylim <3074310+raylim@users.noreply.github.com>85adf5f -
Update src/mosaic/inference/data.py
Unverified signatureCo-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>7b9f0ea -
Add comprehensive sex and tissue site parameter support
Unverified signatureThis commit enhances the Aeon inference pipeline with complete support for sex and tissue site parameters across the entire application: - Add sex and tissue site encoding functions with CSV-based mapping - Update Aeon model to load correct target mappings from metadata - Add CLI arguments for sex and tissue site in gradio_app.py - Add validation for sex and tissue site in settings - Update dependencies: add lightning, seaborn, and statsmodels - Fix tissue site map file path references 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>a2b6947
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Complete implementation of sex and tissue site parameters
Unverified signature- Add UI dropdowns for Sex and Tissue Site selection - Update settings dataframe to include Sex and Tissue Site columns - Pass sex and tissue_site parameters through the analysis pipeline - Convert sex string to index (0=Male, 1=Female, None=Unknown) - Convert tissue site string to index using tissue site mapping - Add get_tissue_sites() helper function in ui/utils.py - Update all inference pipeline functions to handle these parameters - Pass sex and tissue_site_idx to Aeon model for improved inference49fbf68
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Add sex and tissue site parameters to Aeon inference
Unverified signature- Add encoding functions to data.py (encode_sex, encode_tissue_site, tissue_site_to_one_hot) - Update TileFeatureTensorDataset to optionally include SEX and TISSUE_SITE fields - Add sex and tissue_site_idx parameters to Aeon run() function - Thread sex and tissue_site through analysis pipeline (Aeon only, Paladin unchanged) - Add Sex and Tissue Site dropdowns to UI - Add validation for Sex and Tissue Site in settings CSV - Update SETTINGS_COLUMNS to include new fieldsde40714
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Add comprehensive documentation improvements
copilot-swe-agent[bot] +1: raylim- Fix installation instructions in README (correct repo URL) - Fix command name inconsistency (mosaic_app -> mosaic) - Add detailed examples section to README - Add CSV file format documentation - Add cancer subtypes reference - Add troubleshooting section - Add advanced usage examples - Create CONTRIBUTING.md with development guidelines - Add comprehensive docstrings to all modules - Add module-level docstrings to core modules Co-authored-by: raylim <3074310+raylim@users.noreply.github.com>71ae2f0
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initial commit
Unverified signature6bd4e42