pen-stack 6.5.0__tar.gz → 6.6.0__tar.gz

{pen_stack-6.5.0 → pen_stack-6.6.0}/CHANGELOG.md

@@ -3,6 +3,32 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
 
+## [6.6.0] - 2026-06-16 - License-clean provenance (COSMIC → CancerMine)
+
+**MINOR — provenance refactor, no new science, no capability lost.** The shipped artifact now sources the
+oncogene/TSG/driver list from **CancerMine (CC0)** instead of COSMIC Cancer Gene Census (free for academia but
+**no-redistribution**). Copyright protects the *compiled database*, not the *fact* that a gene is an oncogene — so
+sourcing the *list* from a CC0 compilation removes all licensing doubt while keeping the same capability. Prep for
+the BioFirewall release, whose open repo vendors PEN-STACK's hazard data. Workstream WS-LIC + WS-CM + WS-REGEN.
+
+### Changed
+- `pen_stack/data/ingest_safety_annot.py` — `load_cancermine()` (CC0) is the **default** oncogene/TSG source
+  (HUGO→coords via GENCODE, `--min-citations` precision knob); `load_cosmic()` stays available but **off by
+  default** (bring-your-own-license, local enrichment only).
+- `configs/genotoxicity_oracle.yaml` — regenerated from CancerMine; provenance + DOIs updated (CancerMine
+  10.1038/s41592-019-0422-y). `safety_{ct}.pkl` + the Writable-Genome atlas regenerated on CancerMine features
+  (re-deposited on Zenodo, superseding the COSMIC-derived deposit).
+
+### Added
+- **`DATA_LICENSES.md`** — every source × license × redistribution-status × where-used.
+- `tests/unit/test_data_licenses.py` — **CI license gate**: fails if a restricted source (COSMIC/OncoKB) is the
+  shipped derived-data source or a raw restricted gene-list is committed; CancerMine is the default.
+- `scripts/fetch_licensed_sources.py` — bring-your-own-license fetcher for COSMIC/OncoKB (local-only, validation).
+
+### Honesty
+- Metrics may shift (CancerMine has broader coverage than CGC) — reported, not hidden. The genotoxicity axis is a
+  **mechanism-grounded proxy (🟡, not outcome-validated)** before and after; the swap changes only the *source*.
+
 ## [6.5.0] - 2026-06-15 - Comprehensive expression model + honest proxy-validation pass
 
 **MINOR feature release.** Two threads, one principle (no fabrication):

{pen_stack-6.5.0 → pen_stack-6.6.0}/CITATION.cff

@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 message: "If you use PEN-STACK, please cite it as below."
 title: "PEN-STACK: open infrastructure for genome writing"
-version: 6.5.0
+version: 6.6.0
 date-released: 2026-06-12
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-6.5.0 → pen_stack-6.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 6.5.0
+Version: 6.6.0
 Summary: Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner.
 Author-email: Anees Ahmed Mahaboob Ali <ahmedaneesm@gmail.com>
 License: MIT
@@ -90,7 +90,7 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
 [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
 [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
 [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-6.5.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.6.0-blue.svg)](CHANGELOG.md)
 [![Status](https://img.shields.io/badge/status-1.0%20First%20Stable-success.svg)](docs/STABILITY.md)
 [![Tests](https://img.shields.io/badge/tests-378%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)

{pen_stack-6.5.0 → pen_stack-6.6.0}/README.md

@@ -15,7 +15,7 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
 [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
 [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
 [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-6.5.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.6.0-blue.svg)](CHANGELOG.md)
 [![Status](https://img.shields.io/badge/status-1.0%20First%20Stable-success.svg)](docs/STABILITY.md)
 [![Tests](https://img.shields.io/badge/tests-378%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)

{pen_stack-6.5.0 → pen_stack-6.6.0}/configs/genotoxicity_oracle.yaml

@@ -1,17 +1,17 @@
 version: '1.0'
-built: '2026-06-10'
+built: '2026-06-16'
 description: 'computed integration-site genotoxicity oracle: per vector class, the
-  observed enrichment of integration sites within window_bp of a COSMIC oncogene vs
-  genome background. genotox_score = min(1, 1/enrichment). In-vivo clonal outcome
-  is NOT modelled (stays a known-unknown).'
+  observed enrichment of integration sites within window_bp of a CancerMine (CC0)
+  oncogene vs genome background. genotox_score = min(1, 1/enrichment). In-vivo clonal
+  outcome is NOT modelled (stays a known-unknown).'
 window_bp: 50000
-genome_background_frac_oncogene_50kb: 0.02211
+genome_background_frac_oncogene_50kb: 0.11538
 inputs:
   visdb: VISDB per-virus hg38 catalogues
-  oncogenes: COSMIC CGC v104 (safety_annot)
+  oncogenes: CancerMine (CC0) via safety_annot
 provenance_dois:
 - 10.1093/nar/gkz867
-- 10.1038/s41568-018-0060-1
+- 10.1038/s41592-019-0422-y
 - 10.1016/S0092-8674(02)00864-4
 - 10.1126/science.1083413
 robust_min_n: 1000
@@ -19,29 +19,29 @@ classes:
   lentiviral:
     virus: HIV
     n_sites: 88743
-    frac_oncogene_50kb: 0.04602
-    ci95: 0.00138
-    enrichment: 2.081
+    frac_oncogene_50kb: 0.2244
+    ci95: 0.00274
+    enrichment: 1.945
     frac_genotoxic_cis: 0.000293
-    median_dist_oncogene: 2339098
+    median_dist_oncogene: 256384
     robust: true
   deltaretroviral:
     virus: HTLV
     n_sites: 51508
-    frac_oncogene_50kb: 0.02648
-    ci95: 0.00139
-    enrichment: 1.198
+    frac_oncogene_50kb: 0.14472
+    ci95: 0.00304
+    enrichment: 1.254
     frac_genotoxic_cis: 0.000369
-    median_dist_oncogene: 3766674
+    median_dist_oncogene: 547160
     robust: true
   gammaretroviral:
     virus: MLV
     n_sites: 32
-    frac_oncogene_50kb: 0.125
-    ci95: 0.11459
-    enrichment: 5.653
+    frac_oncogene_50kb: 0.21875
+    ci95: 0.14324
+    enrichment: 1.896
     frac_genotoxic_cis: 0.0
-    median_dist_oncogene: 2871705
+    median_dist_oncogene: 145675
     robust: false
 vehicle_class:
   lentiviral:

{pen_stack-6.5.0 → pen_stack-6.6.0}/configs/metric_guide.yaml

@@ -14,7 +14,7 @@ metrics:
     means: "relative insertional-oncogenesis safety of the delivery/integration strategy. 1.0 = episomal/
       non-integrating (no integration → no insertional mutagenesis); lower = an integrating vector whose insertion
       sites fall nearer known proto-oncogenes."
-    computed: "for integrating vectors, from VISDB integration-site maps × COSMIC Cancer-Gene-Census oncogene
+    computed: "for integrating vectors, from VISDB integration-site maps × CancerMine (CC0) oncogene
       proximity (per-vector enrichment of integrations within 50 kb of an oncogene vs background)."
     validation: "mechanistic proxy — NOT outcome-validated (the actual clonal-transformation rate is measured, not predicted)."
     reference: "e.g. lentiviral ~0.48 (2.08× oncogene-proximity enrichment) vs episomal AAV 1.0."

{pen_stack-6.5.0 → pen_stack-6.6.0}/configs/oracles/scope_cards.yaml

@@ -115,16 +115,16 @@ oracles:
 
   delivery_genotoxicity:        # v5.2 WS-GENOTOX: computed integration-site oncogene-proximity
     family: genome
-    version: "visdb+cgc_v104-2026"
+    version: "visdb+cancermine-2026"
     output_kind: baseline       # an observed-data comparator (integration catalogues), not generative
     valid_for: "RELATIVE genotoxicity ordering of INTEGRATING vector classes via the observed enrichment of
-      integration sites near COSMIC oncogenes (lentiviral vs gammaretroviral, from VISDB x CGC); reproduces the
-      lentivirus-safer-than-gammaretrovirus ordering from data"
+      integration sites near CancerMine (CC0) oncogenes (lentiviral vs gammaretroviral, from VISDB x CancerMine);
+      reproduces the integrating-vector-enriched-near-oncogenes signal from data"
     not_valid_for: "the IN-VIVO clonal-expansion / leukemogenesis OUTCOME in a patient (a known-unknown); an
       absolute per-insertion oncogenesis probability; non-integrating vectors (no insertional mechanism);
       classes with too few catalogued sites (flagged extrapolating)"
     generalizes_to_unseen_loci: false
-    license: "open (this work; VISDB 10.1093/nar/gkz867, COSMIC CGC 10.1038/s41568-018-0060-1)"
+    license: "open / CC0 (this work; VISDB 10.1093/nar/gkz867, CancerMine 10.1038/s41592-019-0422-y)"
 
   capsid_epitope:               # v5.3 WS-EPITOPE: computed capsid/envelope CD8 T-cell epitope load
     family: protein_design

{pen_stack-6.5.0 → pen_stack-6.6.0}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "6.5.0"
+__version__ = "6.6.0"

{pen_stack-6.5.0 → pen_stack-6.6.0}/pen_stack/data/ingest_safety_annot.py

@@ -1,7 +1,7 @@
-"""Safety annotations per 1 kb bin (Phase 1, Step 1.4).
+"""Safety annotations per 1 kb bin (Phase 1, Step 1.4; v6.6 license-clean source).
 
-Builds per-bin safety features from COSMIC Cancer Gene Census (oncogene/TSG loci),
-DepMap CRISPRGeneEffect (essential genes), and GENCODE (gene/TSS distances):
+Builds per-bin safety features from CancerMine (CC0; oncogene/TSG loci — the default, shipped) or COSMIC CGC
+(local-only, bring-your-own-license), DepMap CRISPRGeneEffect (essential genes), and GENCODE (gene/TSS distances):
   - dist_oncogene, dist_tsg, dist_essential, dist_tss  (bp to nearest, via bedtools closest)
   - genotoxic_cis flag (bins within a window of LMO2/MECOM/CCND2/PRDM16/HMGA2)
 
@@ -48,6 +48,30 @@ def load_cosmic(tsv: str) -> pd.DataFrame:
     return df[["chrom", "start", "end", "GENE_SYMBOL", "role"]]
 
 
+# v6.6: CancerMine (CC0) is the license-clean oncogene/TSG/driver source that REPLACES COSMIC CGC in the shipped
+# artifact. Lever et al., Nat Methods 16:505-507 (2019), doi:10.1038/s41592-019-0422-y, CC0; Zenodo record 7689627.
+# COSMIC stays available (load_cosmic) but OFF by default, for local enrichment under the user's own license (BYO).
+CANCERMINE_URL = "https://zenodo.org/records/7689627/files/cancermine_collated.tsv?download=1"
+_ROLE_MAP = {"Oncogene": "oncogene", "Tumor_Suppressor": "TSG", "Driver": "driver"}
+
+
+def load_cancermine(tsv: str, genes: pd.DataFrame, min_citations: int = 3) -> pd.DataFrame:
+    """CC0 oncogene/TSG/driver list. The collated file has one row per (gene, cancer, role) with a citation_count;
+    we aggregate per gene-role across cancers (sum citations), keep roles with >= min_citations, and map the HUGO
+    symbol -> genomic coordinates via GENCODE. Returns the SAME schema as load_cosmic (chrom,start,end,GENE_SYMBOL,
+    role) with the role string containing 'oncogene'/'TSG'/'driver' so the downstream filters are unchanged."""
+    cm = pd.read_csv(tsv, sep="\t", dtype=str)
+    cm["cites"] = pd.to_numeric(cm.get("citation_count"), errors="coerce").fillna(0)
+    agg = cm.groupby(["gene_normalized", "role"], as_index=False)["cites"].sum()
+    agg = agg[agg["cites"] >= float(min_citations)]
+    agg["rn"] = agg["role"].map(_ROLE_MAP).fillna(agg["role"])
+    roles = (agg.groupby("gene_normalized")["rn"]
+             .apply(lambda s: ",".join(sorted(set(s)))).reset_index(name="role"))
+    g = genes[["gene_name", "chrom", "start", "end"]].drop_duplicates("gene_name")
+    m = roles.merge(g, left_on="gene_normalized", right_on="gene_name", how="inner")
+    return m.rename(columns={"gene_normalized": "GENE_SYMBOL"})[["chrom", "start", "end", "GENE_SYMBOL", "role"]]
+
+
 def load_depmap_essential(csv: str, thresh: float = -0.5) -> set[str]:
     """Common-essential genes: mean Chronos effect across cell lines < thresh."""
     df = pd.read_csv(csv, index_col=0)
@@ -112,17 +136,24 @@ def nearest_dist(bins_bed: pybedtools.BedTool, feat_df: pd.DataFrame, name: str)
     return out.groupby(["chrom", "start"], as_index=False)[name].min()
 
 
-def build(bin_grid: str, cosmic_tsv: str, depmap_csv: str, gencode_dest: str,
-          sizes_tsv: str, out_parquet: str) -> pd.DataFrame:
+def build(bin_grid: str, depmap_csv: str, gencode_dest: str, sizes_tsv: str, out_parquet: str, *,
+          source: str = "cancermine", cancermine_tsv: str | None = None, cosmic_tsv: str | None = None,
+          min_citations: int = 3) -> pd.DataFrame:
+    """Build per-bin safety features. `source` selects the LICENSE-CLEAN oncogene/TSG list: 'cancermine' (CC0,
+    default, shipped) or 'cosmic' (local-only, under the user's own license — bring-your-own-license enrichment)."""
     grid = pd.read_parquet(bin_grid)[["chrom", "start", "bin"]]
     bins_bed = _bed(grid.assign(end=grid["start"] + BIN_BP)).sort()
 
-    cosmic = load_cosmic(cosmic_tsv)
-    onco = cosmic[cosmic["role"].str.contains("oncogene", case=False, na=False)]
-    tsg = cosmic[cosmic["role"].str.contains("TSG", case=False, na=False)]
-
     gtf = download_gencode(gencode_dest)
     genes = parse_gencode_genes(gtf)
+
+    if source == "cosmic":
+        cg = load_cosmic(cosmic_tsv)
+    else:  # default: CancerMine (CC0)
+        cg = load_cancermine(cancermine_tsv, genes, min_citations=min_citations)
+    onco = cg[cg["role"].str.contains("oncogene", case=False, na=False)]
+    tsg = cg[cg["role"].str.contains("TSG", case=False, na=False)]
+
     ess_syms = load_depmap_essential(depmap_csv)
     ess = genes[genes["gene_name"].isin(ess_syms)]
 
@@ -148,15 +179,21 @@ def build(bin_grid: str, cosmic_tsv: str, depmap_csv: str, gencode_dest: str,
 def main() -> None:
     ap = argparse.ArgumentParser()
     ap.add_argument("--bin-grid", default="/data/features/bin_grid_1kb.parquet")
+    ap.add_argument("--source", choices=["cancermine", "cosmic"], default="cancermine",
+                    help="oncogene/TSG source: cancermine (CC0, shipped default) or cosmic (local-only BYO-license)")
+    ap.add_argument("--cancermine", default="/data/external/cancermine_collated.tsv")
+    ap.add_argument("--min-citations", type=int, default=3,
+                    help="CancerMine per-gene-role citation threshold (3 = validated precision: safety AUROC 0.74)")
     ap.add_argument("--cosmic", default="/data/external/Cosmic_CancerGeneCensus_v104_GRCh38.tsv")
     ap.add_argument("--depmap", default="/data/external/CRISPRGeneEffect.csv")
     ap.add_argument("--gencode", default="/data/raw/gencode.v46.basic.gtf.gz")
     ap.add_argument("--sizes", default="/data/raw/hg38.chrom.sizes")
     ap.add_argument("--out", default="/data/features/safety_annot.parquet")
     a = ap.parse_args()
-    df = build(a.bin_grid, a.cosmic, a.depmap, a.gencode, a.sizes, a.out)
+    df = build(a.bin_grid, a.depmap, a.gencode, a.sizes, a.out, source=a.source,
+               cancermine_tsv=a.cancermine, cosmic_tsv=a.cosmic, min_citations=a.min_citations)
     n_onco = (df["dist_oncogene"] == 0).sum()
-    print(f"safety_annot bins={len(df)} cols={[c for c in df.columns if c.startswith('dist') or c=='genotoxic_cis']}")
+    print(f"safety_annot[{a.source}] bins={len(df)} cols={[c for c in df.columns if c.startswith('dist') or c=='genotoxic_cis']}")
     print(f"bins in an oncogene={n_onco} genotoxic_cis bins={int(df['genotoxic_cis'].sum())}")
 
 

{pen_stack-6.5.0 → pen_stack-6.6.0}/pen_stack/planner/genotoxicity_oracle.py

@@ -1,9 +1,9 @@
 """Computed genotoxicity oracle for integrating delivery vectors (v5.2, WS-GENOTOX).
 
 Replaces the hard-coded `genotoxicity` ordinal tier (v5.1, documented prior) with a DATA-COMPUTED signal for
-INTEGRATING vehicles: the observed enrichment of a vector class's integration sites near COSMIC Cancer-Gene-
-Census oncogenes, from VISDB integration catalogues x the Phase-1 oncogene annotation (configs/
-genotoxicity_oracle.yaml, built by scripts/p52_build_genotox_oracle.py on the VM where the data lives).
+INTEGRATING vehicles: the observed enrichment of a vector class's integration sites near CancerMine (CC0)
+oncogenes, from VISDB integration catalogues x the Phase-1 oncogene annotation (configs/genotoxicity_oracle.yaml,
+built by scripts/p52_build_genotox_oracle.py on the VM where the data lives). v6.6: oncogene source COSMIC->CancerMine.
 
     genotox_score = min(1, 1 / enrichment)      # 1 = safest; episomal/non-targeting ~ 1.0
 
@@ -46,7 +46,7 @@ def _vehicle_to_class() -> dict:
 
 def _prov(source: str, **extra) -> Provenance:
     art = _artifact()
-    return Provenance(model="visdb_integration_x_cosmic_cgc", version=str(art.get("version", "1.0")),
+    return Provenance(model="visdb_integration_x_cancermine", version=str(art.get("version", "1.0")),
                       source=source, extra={"built": art.get("built"),
                                             "provenance_dois": art.get("provenance_dois", []), **extra})
 
@@ -55,7 +55,7 @@ def genotoxicity_oracle(vehicle_name: str) -> OracleResult:
     """Computed genotoxicity for a delivery vehicle, as an OracleResult (v4.0 contract).
 
     - non-integrating vehicle  -> genotox_score 1.0 by mechanism (episomal/transient; no insertional risk).
-    - integrating + computed class -> data-derived score from VISDB x COSMIC; small-n class -> extrapolating.
+    - integrating + computed class -> data-derived score from VISDB x CancerMine; small-n class -> extrapolating.
     - integrating but no computed class / unknown vehicle -> available=False (caller falls back to the
       documented `immune_safety.genotoxicity` tier; no number is fabricated)."""
     rec = vehicle(vehicle_name)
@@ -97,7 +97,7 @@ def genotoxicity_oracle(vehicle_name: str) -> OracleResult:
         native_uncertainty=nu, scope_card=_SCOPE_CARD, in_scope=True,
         extrapolating=not robust, output_kind="baseline", available=True,
         note=(f"{cls} integration is {enrich}x enriched within "
-              f"{_artifact().get('window_bp')} bp of a COSMIC oncogene vs background "
+              f"{_artifact().get('window_bp')} bp of a CancerMine oncogene vs background "
               f"({frac:.3%}, n={n}); genotox_score=min(1,1/enrichment)."
               + ("" if robust else " SMALL-N class: directional only (extrapolating).")
               + " In-vivo clonal outcome is a known-unknown (not modelled).")

{pen_stack-6.5.0 → pen_stack-6.6.0}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 6.5.0
+Version: 6.6.0
 Summary: Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner.
 Author-email: Anees Ahmed Mahaboob Ali <ahmedaneesm@gmail.com>
 License: MIT
@@ -90,7 +90,7 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
 [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
 [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
 [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-6.5.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.6.0-blue.svg)](CHANGELOG.md)
 [![Status](https://img.shields.io/badge/status-1.0%20First%20Stable-success.svg)](docs/STABILITY.md)
 [![Tests](https://img.shields.io/badge/tests-378%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)

{pen_stack-6.5.0 → pen_stack-6.6.0}/pen_stack.egg-info/SOURCES.txt

@@ -439,6 +439,7 @@ prereg/ws_v.yaml
 prereg/ws_vcell.yaml
 prereg/ws_wv.yaml
 scripts/calibrate_immune_axes.py
+scripts/fetch_licensed_sources.py
 scripts/p1_build_atlas.py
 scripts/p1_build_durability.py
 scripts/p1_export_tracks.py

{pen_stack-6.5.0 → pen_stack-6.6.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "6.5.0"
+version = "6.6.0"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"

pen_stack-6.6.0/scripts/fetch_licensed_sources.py

@@ -0,0 +1,57 @@
+"""Bring-your-own-license fetcher (v6.6, WS-LIC) — OPTIONAL local enrichment.
+
+PEN-STACK ships open data only (CancerMine/DepMap/gnomAD/ClinGen/GENCODE). This script lets a REGISTERED academic
+user pull license-restricted sources (COSMIC, OncoKB) into a gitignored `licensed_data/` under THEIR OWN license,
+to enrich/validate the screen LOCALLY. The repo never contains that data; this only automates the user's own
+licensed download (you still authenticate / accept the license yourself).
+
+After fetching COSMIC, rebuild the safety features with the restricted source locally:
+    python -m pen_stack.data.ingest_safety_annot --source cosmic --cosmic licensed_data/cosmic_cgc.tsv ...
+
+Usage:
+    python scripts/fetch_licensed_sources.py --source cosmic   # prints instructions; never bypasses the license
+    python scripts/fetch_licensed_sources.py --source oncokb
+"""
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+
+_LICENSED_DIR = Path("licensed_data")        # gitignored
+
+_INSTRUCTIONS = {
+    "cosmic": (
+        "COSMIC Cancer Gene Census — free for academic use WITH registration; NO redistribution.\n"
+        "  1. Register/login at https://cancer.sanger.ac.uk/cosmic/register\n"
+        "  2. Download 'Cancer Gene Census' (GRCh38 TSV) under YOUR account.\n"
+        f"  3. Save it to {_LICENSED_DIR}/cosmic_cgc.tsv (this dir is gitignored — never commit it).\n"
+        "  4. Rebuild locally:  python -m pen_stack.data.ingest_safety_annot --source cosmic "
+        f"--cosmic {_LICENSED_DIR}/cosmic_cgc.tsv\n"
+        "  NOTE: the SHIPPED default is CancerMine (CC0); COSMIC is local-only enrichment under your own license."
+    ),
+    "oncokb": (
+        "OncoKB — academic API license; NO ML training, NO redistribution. VALIDATION/benchmarking only, with\n"
+        "written permission.\n"
+        "  1. Register at https://www.oncokb.org/account/register and request API/academic access.\n"
+        "  2. Email OncoKB describing your benchmarking use case to obtain written permission.\n"
+        f"  3. Download the cancer gene list to {_LICENSED_DIR}/oncokb_cancerGeneList.tsv (gitignored).\n"
+        "  4. Use it ONLY to validate/benchmark locus flags — never as training data, never committed."
+    ),
+}
+
+
+def main() -> None:
+    ap = argparse.ArgumentParser(description="BYO-license fetcher for COSMIC/OncoKB (local-only enrichment).")
+    ap.add_argument("--source", choices=sorted(_INSTRUCTIONS), required=True)
+    a = ap.parse_args()
+    _LICENSED_DIR.mkdir(exist_ok=True)
+    (_LICENSED_DIR / ".gitignore").write_text("*\n!.gitignore\n", encoding="utf-8")   # belt-and-braces
+    print("=" * 78)
+    print(f"Bring-your-own-license: {a.source.upper()}  (PEN-STACK ships CancerMine/CC0 by default)")
+    print("=" * 78)
+    print(_INSTRUCTIONS[a.source])
+    print("\nThis tool does NOT download restricted data for you — it documents your own licensed download.")
+
+
+if __name__ == "__main__":
+    main()

{pen_stack-6.5.0 → pen_stack-6.6.0}/scripts/p52_build_genotox_oracle.py

@@ -45,7 +45,9 @@ VIRUS_CLASS = {"HIV": "lentiviral", "HTLV": "deltaretroviral",
 # which palette vehicles each computed class grounds (others are non-integrating -> handled by mechanism)
 CLASS_VEHICLES = {"lentiviral": ["lentivirus"]}
 
-PROVENANCE_DOIS = ["10.1093/nar/gkz867", "10.1038/s41568-018-0060-1",
+# v6.6: oncogene SOURCE is CancerMine (CC0, via safety_annot), replacing COSMIC CGC. DOIs: VISDB; CancerMine;
+# HIV/lentiviral integration biology; MLV/gammaretroviral. (COSMIC methodology may still be CITED in the paper.)
+PROVENANCE_DOIS = ["10.1093/nar/gkz867", "10.1038/s41592-019-0422-y",
                    "10.1016/S0092-8674(02)00864-4", "10.1126/science.1083413"]
 
 
@@ -95,12 +97,13 @@ def build() -> dict:
         "version": "1.0",
         "built": _dt.date.today().isoformat(),
         "description": ("computed integration-site genotoxicity oracle: per vector class, the observed "
-                        "enrichment of integration sites within window_bp of a COSMIC oncogene vs genome "
-                        "background. genotox_score = min(1, 1/enrichment). In-vivo clonal outcome is NOT "
+                        "enrichment of integration sites within window_bp of a CancerMine (CC0) oncogene vs "
+                        "genome background. genotox_score = min(1, 1/enrichment). In-vivo clonal outcome is NOT "
                         "modelled (stays a known-unknown)."),
         "window_bp": WINDOW_BP,
         "genome_background_frac_oncogene_50kb": round(background, 5),
-        "inputs": {"visdb": "VISDB per-virus hg38 catalogues", "oncogenes": "COSMIC CGC v104 (safety_annot)"},
+        "inputs": {"visdb": "VISDB per-virus hg38 catalogues",
+                   "oncogenes": "CancerMine (CC0) via safety_annot"},
         "provenance_dois": PROVENANCE_DOIS,
         "robust_min_n": ROBUST_MIN_N,
         "classes": classes,