Fix: add seaborn to requirements (needed by embed_protein_vec.py)

Fix: pin pydantic==2.10.6 to fix HF Spaces API crash

API implementation fix

Fix: replace gr.JSON with gr.Code to fix API schema crash on HF Spaces

Fix: replace removed gr.update() with component constructors for Gradio 5.x

docs: add Gradio 4.x breaking changes to LEARNINGS.md

Fix: remove deprecated height param from gr.Dataframe

docs: add HuggingFace deployment lessons to LEARNINGS.md

Fix: make visualization/collaborative imports optional

Fix: add transformers to requirements.txt

Fix HuggingFace Spaces deployment

Add HuggingFace Spaces configuration to README

Clean up search summary output

Improve Gradio UI with modern design and better UX

Fix Gradio interface to work with upstream/main threshold format

Merge upstream/main into gradio - bring in all core improvements

docs: add CLEAN setup details and Docker/Apptainer usage

docs: add Protein-Vec model weights Zenodo link with wget commands

docs: clarify cpr search accepts both FASTA and embeddings

docs: add development workflow patterns to CLAUDE.md

docs: consolidate documentation and add working patterns

chore: clean up redundant scripts and consolidate thresholds

fix: update CLI tests for --input flag and --no-filter

docs: improve Apptainer usage instructions

fix: FDR computation bug, clean up CLEAN/DALI notebooks

docs: add session summary of cleanup work

chore: clean up stale results, add partial FNR script

data: add JCVI Syn3.0 test sequences with documentation

docs: add test example using included JCVI Syn3.0 data

fix: use actual computed FNR thresholds in docs

refactor: consolidate CLI to single 'cpr search' command

docs: comprehensive GETTING_STARTED.md update

fix: use faiss-cpu in Apptainer (pip compatible)

fix: use N=100 for FDR (matches paper), 100 trials, partial thresholds

perf: optimize FDR computation and add DALI documentation

feat: add --alpha-levels option for custom threshold computation

feat: add FNR threshold computation and partial match support

fix: remove unsupported --no-mount flag from apptainer build

fix: Apptainer build mount points and SLURM resource limits

fix: use only verified FDR threshold, warn for other alpha values

feat: add one-step cpr find command and FDR-level search

refactor: cleanup repo, add SLURM scripts, document reproducibility

fix: use shared conda path in SLURM script

fix: CLI tests and FAISS edge case handling

feat: add CLEAN embedding support and CLI tests

fix: use correct calibration dataset (pfam_new_proteins.npy)

fix: handle numpy array in FDR investigation script

feat: add Docker/Apptainer support and FDR investigation tools

docs: update verification notes with FDR calibration results

feat: add verification scripts and multi-model embedding support