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API implementation fix
a5b0ee4 -
Fix: replace removed gr.update() with component constructors for Gradio 5.x
gr.update() was removed in Gradio 5.x, causing "No API found" error on HuggingFace Spaces when clicking SCOPE or Custom database options. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>40cdbbd -
docs: add Gradio 4.x breaking changes to LEARNINGS.md
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>be42188 -
docs: add HuggingFace deployment lessons to LEARNINGS.md
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>5bfd99b -
Fix HuggingFace Spaces deployment
- Update requirements.txt for HF compatibility - Allow results/*.csv in .gitignore for threshold files - Add learnings documentation Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>fd7bdaf
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docs: consolidate documentation and add working patterns
- Update CLAUDE.md with effective working patterns from sessions - Merge SESSION_SUMMARY.md into DEVELOPMENT.md changelog - Archive outdated docs/QUICKSTART.md (superseded by GETTING_STARTED.md) - Add docs/archive/ to .gitignore Key additions to CLAUDE.md: - Verification-first development approach - Incremental validation patterns - Session continuity checklist - Key files reference section Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>59b2337
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refactor: cleanup repo, add SLURM scripts, document reproducibility
Major cleanup and improvements for the CPR repository: ## Cleanup - Remove duplicate notebooks from root dirs (afdb/, scope/, clean_selection/) These are archived in notebooks_archive/ (now gitignored) Organized versions remain in notebooks/ - Delete legacy dockerfile (keep modern Dockerfile with PyTorch base) - Remove large binary files from git tracking (84MB+ .npy, .pkl files) - Update .gitignore for build artifacts, caches, model files ## New Features - Add SLURM scripts for HPC workflows: - slurm_build_apptainer.sh: Build container on compute node - slurm_compute_fdr_thresholds.sh: Compute FDR threshold lookup table - Add compute_fdr_table.py: Generate FDR thresholds at standard alpha levels - Add docs/REPRODUCIBILITY.md: Document expected variability in results ## Documentation Updates (CLAUDE.md) - Add $HOME2 storage instructions (avoid disk quota on $HOME) - Add SLURM requirement for GPU/CPU-intensive tasks - Document available partitions (standard, gpu, memory) ## …f7a768a
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docs: update verification notes with FDR calibration results
FDR calibration from scratch completed: - Risk: 0.0948 (≤ α=0.1, controlled) - Lhat: 0.9999654 (paper uses 0.999980, more conservative) - Both thresholds control FDR at target level Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>5f84065 -
feat: add verification scripts and multi-model embedding support
- Add DALI prefiltering verification (Tables 4-6: 82.8% TPR, 31.5% DB reduction) - Add CLEAN enzyme classification verification (Tables 1-2: hierarchical loss) - Add multi-model embedding support: protein-vec, clean, esm - Add SLURM job scripts for FDR/FNR calibration - Update verification notes with all paper claim results Verified paper claims: - Syn3.0: 59/149 = 39.6% ✓ - DALI: 81.8% TPR, 31.5% reduction ✓ - CLEAN: risk controlled at α=1.0 ✓ Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>3f702bf -
feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%)
## Paper Verification - Verified Figure 2A: 59/149 = 39.6% JCVI Syn3.0 genes annotated at FDR α=0.1 - FDR threshold λ = 0.999980225003127 matches paper ## New Features - CLI with commands: embed, search, prob, calibrate, verify - `cpr prob`: Convert similarity scores to Venn-Abers probabilities - `cpr calibrate`: Compute FDR/FNR thresholds for new embedding models - SLURM scripts for cluster deployment (slurm_verify.sh, slurm_embed.sh) ## Bug Fixes - Fixed `get_thresh_FDR()` to handle both 1D and 2D arrays - Fixed numpy deprecation: `interpolation=` → `method=` in np.quantile() - Fixed `__init__.py` to not require gradio for core imports - Fixed `setup.py` conflict with pyproject.toml (removed src/ reference) - Fixed test expectation in test_threshold_decreases_with_lower_alpha ## Documentation - Added DATA.md: Documents GitHub vs Zenodo file requirements - Added docs/VERIFICATION_NOTES.md: Technical notes on what verification does - Updated CLAUDE.md with session log ## Tests - Al…c95d941
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feat: add test infrastructure, docs, and modern packaging
This commit sets up the foundation for a major refactoring effort to make the Conformal Protein Retrieval codebase more usable and maintainable. ## Added - pyproject.toml: Modern Python packaging with CLI entry point (`cpr`) - Optional dependency groups: [gui], [api], [dev], [all] - pytest and code quality tool configuration - tests/: Comprehensive test suite - conftest.py: Pytest fixtures for FASTA, embeddings, and calibration data - test_util.py: Tests for all core functions in protein_conformal/util.py - FASTA parsing - FAISS operations - FDR/FNR threshold calculations - Venn-Abers probability predictions - Hierarchical loss functions - docs/: User documentation - INSTALLATION.md: Complete installation guide with Zenodo data links - QUICKSTART.md: Usage examples for common workflows - DEVELOPMENT.md: Development notes and refactoring plan ## Removed - src/protein_conformal/: Duplicate of protein_conformal/ (2280 lines) - pfam/tmp.py: Temporary debug…f4b267d