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Merge upstream/main into gradio - bring in all core improvements
- Takes upstream/main (ronboger) as source of truth for core functionality - Keeps Gradio UI work from hf-space branch - Merged dependencies in environment.yml and requirements.txt - Added fair-esm for CLEAN embedding support Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>9895fb8
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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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Merge gradio-ron branch: add Gradio UI, reorganize notebooks
- Add Gradio interface with backend (collaborative, visualization) - Add Dockerfile and environment.yml - Reorganize notebooks into notebooks/ directory - Add FDR/FNR threshold scripts - Add requirements.txt Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>3553828
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bunch of renaming and refactoring
30c3022
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plot generation
699cf6d -
plot generation
918ef70
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utils, afdb embed
e1a1c53 -
utils, afdb embed
6803c88
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Merge branch 'clean' into main
b7d1f4c -
Merge branch 'clean' into main
e32037c -
merge conflict
8c74a78 -
merge conflict
fcb4e73 -
adding new clean stuff
4c04c6b -
adding new clean stuff
4a84e4d
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refactoring + sva
c993f80
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price benchmark
4dddfaa -
price benchmark
18250df -
price benchmark
2d73d85 -
clean benchmarking on new against max-sep
a4d72ff -
clean benchmarking on new against max-sep
9024e67 -
clean benchmarking on new against max-sep
2e7fa7b
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clean basic LTT
eaf2758 -
clean basic LTT
b5bebdc -
clean basic LTT
4520ee8
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clean true labels for loss
9d0cec1 -
clean true labels for loss
a651760 -
clean true labels for loss
2da269e
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clean data work
0b69392 -
clean data work
6c268fb -
clean data work
b84608f