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The GUI is not a current focus. This removes the entire optimhc/gui/ package (18 files, ~2300 lines), the `optimhc gui` CLI command, the optional [gui] dependency group (streamlit, plotly, watchdog), and all GUI references from README, docs, and pyproject.toml. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Migrate Google-style docstrings (Parameters:/Returns: without underlines) to NumPy style (Parameters\n----------) in config.py, basic.py, DeepLC.py, and spectral_similarity.py (13 docstrings total). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Rename PWM.py, DeepLC.py, netMHCpan.py, and netMHCIIpan.py to their lowercase equivalents (pwm.py, deeplc.py, netmhcpan.py, netmhciipan.py). Update all import statements in feature_generation.py and module paths in docs/api/features.md accordingly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Auto-format base_feature_generator.py, factory.py, and spectral_similarity.py to comply with ruff style (line wrapping adjustments). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Need to update logging because the import logic has changed. Logging should now be configured at the entry point of OptiMHC, in cli.py, rather than during module import. |
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| def setup_logging(): | ||
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| level=logging.INFO, |
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The CLI now hard-codes logging.INFO in setup_logging(), and pipeline/experiment call this before any config-driven level is applied, so both --logLevel and logLevel in YAML are effectively ignored. In workflows that rely on quieter logs (e.g., ERROR) or verbose diagnostics (DEBUG), this regression changes runtime behavior and makes the existing configuration knob misleading because it no longer controls logging output.
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This PR introduces a Factory + Registry pattern for feature generators, replacing the if/elif chain in the orchestrator with a clean and extensible architecture (#8). It also removes the experimental Streamlit GUI and unifies code style.