Fix search-mode reliability for BLAST, UniProt, AFDB, and small maps - #103
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Replace hanging blastp -remote with NCBI WWW/QBlast by default, harden UniProt idmapping/metadata and AlphaFold PDB downloads, and keep tiny maps from crashing UMAP/Leiden. Proven while wiring ProteinCartography into Arcadia Studio full cartography on Modal. Co-authored-by: Cursor <cursoragent@cursor.com>
Query AlphaFold's prediction API first so isoform entries like Q9Y6V0-3 are not written as 404 error bodies. Stop scaling t-SNE perplexity for every N<250. Share one PC_BLAST_SOFT_FAIL opt-in so an empty BLAST TSV cannot succeed in run_blast and then abort extract_blast_hits. Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
…s import. Unpinned matplotlib now requires numpy>=1.25 while this env pins 1.23.5; setuptools 81 dropped pkg_resources, which umap-learn still imports. Same pins as #101. Co-authored-by: Cursor <cursoragent@cursor.com>
This was referenced Aug 17, 2026
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Summary
PC_BLAST_BACKEND=www,PC_BLAST_DB=refseq_protein) with timeout/heartbeat; keepblastp -remotevia env. OptionalPC_BLAST_SOFT_FAIL=1continues Foldseek-only when NCBI fails. Empty BLAST results no longer abort extract.model_v6, fall back tov4/ prediction API; never write HTML/XML error bodies as PDBs (poisoned Foldseek → N≈1)./uniprotkb/accessionsinstead of 100-OR search.These fixes were developed while running ProteinCartography v0.5.0 search-mode on Modal for Arcadia Studio (
fullcartography). Upstreammainalready has AFDB v6 URL + FoldseekF1-modelparse; this PR covers what still breaks real cloud/search runs.Test plan
ruff check ProteinCartography/ruff formatpytestunit tests:test_blast_utils,test_extract_blast_hits,test_packagingmake test)run-slow-testslabel before merge for live API smokeEnv knobs (optional)
PC_BLAST_BACKENDwwwwww/remote/autoPC_BLAST_DBrefseq_protein(www)nrfor broader historical searchPC_BLAST_SOFT_FAIL0(run) / empty extract allowed1to continue after BLAST failurePC_UNIPROT_MAP_*/PC_UNIPROT_META_*Made with Cursor