pen-stack 0.1.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- pen_stack/__init__.py +2 -0
- pen_stack/_resources.py +34 -0
- pen_stack/active/__init__.py +20 -0
- pen_stack/active/acquire.py +165 -0
- pen_stack/active/brains.py +74 -0
- pen_stack/active/campaign.py +109 -0
- pen_stack/active/design.py +66 -0
- pen_stack/active/validate.py +104 -0
- pen_stack/adapt/__init__.py +14 -0
- pen_stack/adapt/finetune.py +33 -0
- pen_stack/adapt/ingest.py +86 -0
- pen_stack/adapt/pipeline.py +101 -0
- pen_stack/adapt/recalibrate.py +58 -0
- pen_stack/adapt/report.py +130 -0
- pen_stack/agent/__init__.py +1 -0
- pen_stack/agent/cite.py +175 -0
- pen_stack/agent/co_scientist.py +262 -0
- pen_stack/agent/epistemic.py +102 -0
- pen_stack/agent/guardrails.py +67 -0
- pen_stack/agent/mcp_server.py +215 -0
- pen_stack/agent/orchestrator.py +112 -0
- pen_stack/agent/orchestrator_live.py +56 -0
- pen_stack/agent/pen_agent.py +242 -0
- pen_stack/agent/scope.py +60 -0
- pen_stack/agent/tools.py +130 -0
- pen_stack/api/__init__.py +12 -0
- pen_stack/api/manifest.py +160 -0
- pen_stack/atlas/__init__.py +1 -0
- pen_stack/atlas/atlas.parquet +0 -0
- pen_stack/atlas/build_wtkb.py +80 -0
- pen_stack/atlas/crosslink.py +179 -0
- pen_stack/atlas/expand.py +190 -0
- pen_stack/atlas/guide_design.py +178 -0
- pen_stack/atlas/schema.py +59 -0
- pen_stack/atlas/scorecard.py +134 -0
- pen_stack/atlas/scorecard_v3.parquet +0 -0
- pen_stack/atlas/universe.py +75 -0
- pen_stack/atlas/universe_v3.parquet +0 -0
- pen_stack/atlas/variant_propose.py +155 -0
- pen_stack/atlas/writer_efficiency.py +184 -0
- pen_stack/atlas/writer_predict.py +229 -0
- pen_stack/atlas/writer_recommend.py +170 -0
- pen_stack/atlas/writer_verify.py +167 -0
- pen_stack/atlas/wtkb.parquet +0 -0
- pen_stack/bridge/__init__.py +1 -0
- pen_stack/bridge/activity.py +52 -0
- pen_stack/bridge/cli.py +65 -0
- pen_stack/bridge/fold_qc.py +53 -0
- pen_stack/bridge/guide_qc.py +87 -0
- pen_stack/bridge/ingest.py +139 -0
- pen_stack/bridge/offtarget.py +191 -0
- pen_stack/bridge/offtarget_energetics.py +105 -0
- pen_stack/bridge/ortholog_screen.py +73 -0
- pen_stack/bridge/pipeline.py +83 -0
- pen_stack/build/__init__.py +16 -0
- pen_stack/build/cloudlab.py +74 -0
- pen_stack/build/ingest.py +47 -0
- pen_stack/build/protocol.py +82 -0
- pen_stack/build/simlab.py +30 -0
- pen_stack/cli.py +126 -0
- pen_stack/data/__init__.py +1 -0
- pen_stack/data/encode.py +84 -0
- pen_stack/data/genome.py +71 -0
- pen_stack/data/ingest_chromatin.py +119 -0
- pen_stack/data/ingest_integration.py +112 -0
- pen_stack/data/ingest_safety_annot.py +201 -0
- pen_stack/data/ingest_trip.py +76 -0
- pen_stack/design/__init__.py +14 -0
- pen_stack/design/capsid_generate.py +62 -0
- pen_stack/design/generate.py +70 -0
- pen_stack/design/pareto.py +70 -0
- pen_stack/design/space.py +137 -0
- pen_stack/design/writer_variants.py +121 -0
- pen_stack/env/__init__.py +1 -0
- pen_stack/env/genome_writing_env.py +248 -0
- pen_stack/env/policies.py +94 -0
- pen_stack/graph/__init__.py +21 -0
- pen_stack/graph/build.py +133 -0
- pen_stack/graph/cell_types.py +58 -0
- pen_stack/graph/ingest.py +132 -0
- pen_stack/graph/query.py +148 -0
- pen_stack/graph/schema.py +100 -0
- pen_stack/loop/__init__.py +15 -0
- pen_stack/loop/continual.py +61 -0
- pen_stack/loop/cycle.py +84 -0
- pen_stack/loop/drift.py +41 -0
- pen_stack/mech/__init__.py +1 -0
- pen_stack/mech/classify_atlas.py +71 -0
- pen_stack/mech/pfam_whitelist.yaml +247 -0
- pen_stack/mech/whitelist.py +66 -0
- pen_stack/monitor/__init__.py +1 -0
- pen_stack/monitor/europepmc.py +32 -0
- pen_stack/monitor/run.py +57 -0
- pen_stack/monitor/triage.py +63 -0
- pen_stack/oracles/__init__.py +65 -0
- pen_stack/oracles/affinity.py +116 -0
- pen_stack/oracles/cache.py +53 -0
- pen_stack/oracles/energetics.py +33 -0
- pen_stack/oracles/genome.py +167 -0
- pen_stack/oracles/protein_design.py +136 -0
- pen_stack/oracles/reliability.py +64 -0
- pen_stack/oracles/rna.py +28 -0
- pen_stack/oracles/schema.py +77 -0
- pen_stack/oracles/status.py +123 -0
- pen_stack/oracles/structure.py +42 -0
- pen_stack/oracles/structure_run.py +76 -0
- pen_stack/oracles/vcell.py +74 -0
- pen_stack/planner/__init__.py +1 -0
- pen_stack/planner/ada_risk.py +64 -0
- pen_stack/planner/antipeg_oracle.py +75 -0
- pen_stack/planner/capsid_epitope_oracle.py +135 -0
- pen_stack/planner/cargo.py +56 -0
- pen_stack/planner/cargo_polish.py +146 -0
- pen_stack/planner/chromosome.py +106 -0
- pen_stack/planner/delivery.py +55 -0
- pen_stack/planner/delivery_constraints.py +110 -0
- pen_stack/planner/delivery_immune.py +61 -0
- pen_stack/planner/delivery_immunology.py +222 -0
- pen_stack/planner/delivery_predict.py +196 -0
- pen_stack/planner/delivery_vehicles.py +37 -0
- pen_stack/planner/genotoxicity_oracle.py +112 -0
- pen_stack/planner/immune_mhc2.py +154 -0
- pen_stack/planner/immune_profile.py +292 -0
- pen_stack/planner/innate_sensing.py +135 -0
- pen_stack/planner/multiplex.py +110 -0
- pen_stack/planner/optimize.py +278 -0
- pen_stack/planner/pipeline.py +87 -0
- pen_stack/planner/report.py +26 -0
- pen_stack/planner/router.py +57 -0
- pen_stack/planner/seroprevalence_oracle.py +92 -0
- pen_stack/planner/target_site.py +118 -0
- pen_stack/rag/__init__.py +1 -0
- pen_stack/rag/corpus.py +133 -0
- pen_stack/rag/embed.py +98 -0
- pen_stack/rag/ground.py +131 -0
- pen_stack/rag/index.py +53 -0
- pen_stack/rag/llm.py +215 -0
- pen_stack/rag/qa.py +105 -0
- pen_stack/rag/retrieve.py +48 -0
- pen_stack/rules/__init__.py +9 -0
- pen_stack/rules/evaluators.py +318 -0
- pen_stack/rules/loader.py +31 -0
- pen_stack/rules/schema.py +99 -0
- pen_stack/rules/solver.py +43 -0
- pen_stack/rules/spec.py +78 -0
- pen_stack/safety/__init__.py +21 -0
- pen_stack/safety/audit.py +90 -0
- pen_stack/safety/gate.py +58 -0
- pen_stack/safety/pfam_scan.py +157 -0
- pen_stack/safety/policy.py +69 -0
- pen_stack/safety/redteam.py +71 -0
- pen_stack/safety/registry.py +255 -0
- pen_stack/safety/screen.py +59 -0
- pen_stack/safety/standards.py +141 -0
- pen_stack/score/__init__.py +1 -0
- pen_stack/score/recalibrate.py +77 -0
- pen_stack/score/therapeutic.py +85 -0
- pen_stack/server/__init__.py +1 -0
- pen_stack/server/api.py +647 -0
- pen_stack/spec/__init__.py +18 -0
- pen_stack/spec/clarify.py +42 -0
- pen_stack/spec/extract.py +406 -0
- pen_stack/spec/resolvers/__init__.py +17 -0
- pen_stack/spec/resolvers/cell.py +51 -0
- pen_stack/spec/resolvers/chem.py +32 -0
- pen_stack/spec/resolvers/feature.py +36 -0
- pen_stack/spec/resolvers/gene.py +43 -0
- pen_stack/spec/resolvers/locus.py +29 -0
- pen_stack/spec/resolvers/phenotype.py +37 -0
- pen_stack/spec/satisfy.py +114 -0
- pen_stack/spec/service.py +33 -0
- pen_stack/spec/writespec.py +252 -0
- pen_stack/twin/__init__.py +14 -0
- pen_stack/twin/calibrate.py +61 -0
- pen_stack/twin/data/__init__.py +12 -0
- pen_stack/twin/data/position_effect.py +245 -0
- pen_stack/twin/mechanistic.py +147 -0
- pen_stack/twin/outcome.py +132 -0
- pen_stack/twin/position_effect.py +454 -0
- pen_stack/ui/__init__.py +1 -0
- pen_stack/ui/app.py +713 -0
- pen_stack/validate/__init__.py +1 -0
- pen_stack/validate/adapt_demo.py +69 -0
- pen_stack/validate/agent_eval.py +117 -0
- pen_stack/validate/bench_adversarial_tasks.py +118 -0
- pen_stack/validate/bench_coscientist_tasks.py +60 -0
- pen_stack/validate/bench_graph_tasks.py +64 -0
- pen_stack/validate/bench_rule_tasks.py +84 -0
- pen_stack/validate/bench_trust_tasks.py +92 -0
- pen_stack/validate/bench_writetype_tasks.py +101 -0
- pen_stack/validate/blind_gsh_discovery.py +261 -0
- pen_stack/validate/cargo_directionality.py +57 -0
- pen_stack/validate/closed_loop.py +63 -0
- pen_stack/validate/durability_baselines.py +185 -0
- pen_stack/validate/experiment_design.py +65 -0
- pen_stack/validate/expr_controls.py +39 -0
- pen_stack/validate/forward_hypotheses.py +104 -0
- pen_stack/validate/generative_design.py +62 -0
- pen_stack/validate/guide_qc_demo.py +69 -0
- pen_stack/validate/heldout_celltype_expr.py +32 -0
- pen_stack/validate/immune_calibration.py +133 -0
- pen_stack/validate/intent_specification.py +82 -0
- pen_stack/validate/known_biology_expr.py +38 -0
- pen_stack/validate/offtarget_energetics_eval.py +144 -0
- pen_stack/validate/out_of_scope_refusal.py +82 -0
- pen_stack/validate/outcome_calibration.py +194 -0
- pen_stack/validate/outcome_prediction.py +76 -0
- pen_stack/validate/paper3_benchmark.py +165 -0
- pen_stack/validate/paper4_real_validation.py +144 -0
- pen_stack/validate/paper4_validation.py +82 -0
- pen_stack/validate/protocol_safety.py +62 -0
- pen_stack/validate/safety_screening.py +72 -0
- pen_stack/validate/selective_prediction.py +104 -0
- pen_stack/validate/seq_vs_measured.py +134 -0
- pen_stack/validate/target_site_controls.py +65 -0
- pen_stack/validate/uncertainty_eval.py +244 -0
- pen_stack/validate/ungrounded_baseline.py +234 -0
- pen_stack/validate/within_locus_ranking.py +84 -0
- pen_stack/validate/writer_recovery.py +91 -0
- pen_stack/verify/__init__.py +5 -0
- pen_stack/verify/proof.py +206 -0
- pen_stack/verify/schema.py +53 -0
- pen_stack/verify/service.py +191 -0
- pen_stack/web/__init__.py +18 -0
- pen_stack/web/guide.py +110 -0
- pen_stack/web/llm.py +393 -0
- pen_stack/web/llm_provider.py +119 -0
- pen_stack/web/router.py +119 -0
- pen_stack/web/server.py +96 -0
- pen_stack/web/tools.py +197 -0
- pen_stack/wgenome/__init__.py +1 -0
- pen_stack/wgenome/chromatin_seq.py +83 -0
- pen_stack/wgenome/durability.py +108 -0
- pen_stack/wgenome/export_tracks.py +52 -0
- pen_stack/wgenome/features.py +82 -0
- pen_stack/wgenome/genotoxic_blocklist.py +88 -0
- pen_stack/wgenome/gsh_baseline.py +154 -0
- pen_stack/wgenome/mesh_features.py +61 -0
- pen_stack/wgenome/offtarget_assay.py +80 -0
- pen_stack/wgenome/offtarget_bridge.py +47 -0
- pen_stack/wgenome/offtarget_cast.py +97 -0
- pen_stack/wgenome/offtarget_data.py +148 -0
- pen_stack/wgenome/offtarget_enumerate.py +274 -0
- pen_stack/wgenome/offtarget_integrase.py +155 -0
- pen_stack/wgenome/offtarget_nuclease.py +123 -0
- pen_stack/wgenome/offtarget_paste.py +41 -0
- pen_stack/wgenome/offtarget_predict.py +282 -0
- pen_stack/wgenome/ood.py +135 -0
- pen_stack/wgenome/providers.py +278 -0
- pen_stack/wgenome/safety.py +69 -0
- pen_stack/wgenome/structure3d.py +212 -0
- pen_stack/wgenome/uncertainty.py +250 -0
- pen_stack/wgenome/writability.py +72 -0
- pen_stack-0.1.0.dist-info/METADATA +401 -0
- pen_stack-0.1.0.dist-info/RECORD +259 -0
- pen_stack-0.1.0.dist-info/WHEEL +5 -0
- pen_stack-0.1.0.dist-info/entry_points.txt +3 -0
- pen_stack-0.1.0.dist-info/licenses/LICENSE +21 -0
- pen_stack-0.1.0.dist-info/top_level.txt +1 -0
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