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

chore: clean up redundant scripts and consolidate thresholds

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

chore: clean up stale results, add partial FNR script

refactor: consolidate CLI to single 'cpr search' command

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

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

feat: add verification scripts and multi-model embedding support

feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%)

new clean branch

savez

bunch of renaming and refactoring

created dockerfile and dockerignore

second attempt at fdr/fnr generating script

rewrote precompute fdr into shell script

refactored gradio code to use pre-existing files

completed fnr and fdr thresholds scripts. currently testing both

finished fnr threshold function w/ exact + partial

updated fdr calc to support exact + partial

completed script v1 for generating fdr thresholds

third overall update

Merge branch 'main' of https://github.com/LoocasGoose/conformal-protein-retrieval

first attempt at gradio website. basic functionalities for UI/UX present

scripts for embedding, search, translation

script had bug ugh

fully working scripts for searching and getting probs with known lambda

fix search script

Merge branch 'main' of github.com:ronboger/conformal-protein-retrieval

log partial

log both p0, p1

move to argparser

changes to script

precompute SVA probs for linspace of similarities

search script

adds a script for getting probabilities given a similarity score