pen-stack 6.2.0__tar.gz → 6.2.2__tar.gz

{pen_stack-6.2.0 → pen_stack-6.2.2}/CHANGELOG.md

@@ -3,6 +3,31 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
 
+## [6.2.2] - 2026-06-12 - v6.2.2: safe-harbour locus-nickname resolution (patch)
+
+**Usability fix.** Site Finder / `/plan` / `/writable` returned 0 plans for `AAVS1` because it is a genomic
+safe-harbour *locus nickname*, not an HGNC gene symbol, so the gene→coordinate lookup (`gene_coords`, 60,888
+symbols) could not resolve it — honest empty, but unhelpful for the most-typed safe harbour. (The cell-type
+atlases are complete; real symbols like `PCSK9`/`HBB`/`CCR5`/`CLYBL` resolved fine.)
+
+### Fixed
+- `pen_stack/planner/optimize.py`: `resolve_gene()` maps well-documented safe-harbour nicknames to their host
+  gene (`AAVS1`→`PPP1R12C` 19q13.42; `H11`/`Hipp11`→`EIF4ENIF1` 22q12) at every gene→coordinate lookup
+  (`gene_region`, `plan`, `crosslink.loci_for_gene`); real symbols pass through unchanged. Regression test
+  `tests/unit/test_ws_api.py::test_safe_harbour_nickname_resolves_to_host_gene`.
+
+## [6.2.1] - 2026-06-12 - v6.2.1: JSON-safe atlas/crosslink endpoints (patch)
+
+**Bug fix.** The `/atlas`, `/writable`, and `/crosslink/loci` endpoints returned raw DataFrame records, which
+leak non-finite floats (`NaN`/`inf`) present in `atlas.parquet`; the JSON encoder rejects these
+(`ValueError: Out of range float values are not JSON compliant` → HTTP 500). Surfaced on the v6.2 Web Platform's
+Writer Atlas and Site Finder pages.
+
+### Fixed
+- `pen_stack/server/api.py`: a `_records()` helper serializes DataFrame rows JSON-safely (via pandas `to_json`,
+  so `NaN`/`inf` → `null` and numpy scalars → native), applied to `/atlas`, `/writable`, `/crosslink/loci`.
+  Regression test `tests/unit/test_ws_api.py::test_records_helper_is_json_safe_with_non_finite_floats`.
+
 ## [6.2.0] - 2026-06-11 - v6.2: The Web Platform (the human surface)
 
 **Post-1.0 adoption surface for bench scientists.** A complete, friendly web application — a grounded co-scientist

{pen_stack-6.2.0 → pen_stack-6.2.2}/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: 6.2.0
+version: 6.2.2
 date-released: 2026-06-11
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-6.2.0 → pen_stack-6.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 6.2.0
+Version: 6.2.2
 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
@@ -90,9 +90,9 @@ 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-6.2.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.2.2-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-368%20passing-success.svg)](tests/)
+[![Tests](https://img.shields.io/badge/tests-370%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)
 [![Runtime: Docker](https://img.shields.io/badge/runtime-docker-2496ED.svg)](docker/)
 [![Validation: pre-registered](https://img.shields.io/badge/validation-pre--registered-critical.svg)](prereg/)

{pen_stack-6.2.0 → pen_stack-6.2.2}/README.md

@@ -15,9 +15,9 @@ 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-6.2.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.2.2-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-368%20passing-success.svg)](tests/)
+[![Tests](https://img.shields.io/badge/tests-370%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)
 [![Runtime: Docker](https://img.shields.io/badge/runtime-docker-2496ED.svg)](docker/)
 [![Validation: pre-registered](https://img.shields.io/badge/validation-pre--registered-critical.svg)](prereg/)

{pen_stack-6.2.0 → pen_stack-6.2.2}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "6.2.0"
+__version__ = "6.2.2"

{pen_stack-6.2.0 → pen_stack-6.2.2}/pen_stack/atlas/crosslink.py

@@ -99,13 +99,10 @@ def writers_for_locus(chrom: str, bin_idx: int, ct: str = "k562") -> pd.DataFram
 
 def loci_for_gene(gene: str, ct: str = "k562", gene_coords: str | Path | None = None) -> pd.DataFrame:
     """Writable bins overlapping a gene body (forward query helper)."""
-    if gene_coords:
-        gc_path = Path(gene_coords)
-    else:
-        from pen_stack.planner.optimize import gene_coords_path
-        gc_path = gene_coords_path()
+    from pen_stack.planner.optimize import gene_coords_path, resolve_gene
+    gc_path = Path(gene_coords) if gene_coords else gene_coords_path()
     gc = pd.read_parquet(gc_path)
-    g = gc[gc["gene"] == gene]
+    g = gc[gc["gene"] == resolve_gene(gene)]      # resolve safe-harbour nicknames (AAVS1 -> PPP1R12C)
     if g.empty:
         return pd.DataFrame()
     r = g.iloc[0]

{pen_stack-6.2.0 → pen_stack-6.2.2}/pen_stack/planner/optimize.py

@@ -209,9 +209,20 @@ def _gene_coords(path: str | None = None) -> pd.DataFrame:
     return pd.read_parquet(Path(path) if path else gene_coords_path())
 
 
+# Genomic safe-harbour *locus nicknames* are not HGNC gene symbols, so they are absent from gene_coords; map the
+# well-documented ones to their host gene so a user who types the common name still gets a plan. AAVS1 = intron 1
+# of PPP1R12C (19q13.42); H11/Hipp11 = an intron of EIF4ENIF1 (22q12). (CCR5, CLYBL, HPRT1 are real symbols.)
+_GSH_ALIASES = {"AAVS1": "PPP1R12C", "H11": "EIF4ENIF1", "HIPP11": "EIF4ENIF1"}
+
+
+def resolve_gene(gene: str) -> str:
+    """Map a safe-harbour locus nickname (e.g. AAVS1) to its HGNC host gene; pass real symbols through unchanged."""
+    return _GSH_ALIASES.get(str(gene).strip().upper(), gene)
+
+
 def gene_region(gene: str, flank_kb: int = 50) -> tuple[str, int, int] | None:
     gc = _gene_coords()
-    g = gc[gc["gene"] == gene]
+    g = gc[gc["gene"] == resolve_gene(gene)]
     if g.empty:
         return None
     r = g.iloc[0]
@@ -232,7 +243,7 @@ def plan(gene: str, intent: EditIntent | str, cargo_bp: int, writable_df: pd.Dat
         return pd.DataFrame()
     # on_target = bin overlaps the gene body (not just the flank)
     g = _gene_coords()
-    gr = g[g["gene"] == gene].iloc[0]
+    gr = g[g["gene"] == resolve_gene(gene)].iloc[0]
     sub["on_target"] = sub["bin"].between(int(gr["start"]) // BIN_BP, int(gr["end"]) // BIN_BP)
     scored = score_candidates(sub, intent, cargo_bp)
     cols = ["chrom", "bin", "writer", "safety", "p_durable", "writer_activity",

{pen_stack-6.2.0 → pen_stack-6.2.2}/pen_stack/server/api.py

@@ -8,6 +8,7 @@ Run: ``uvicorn pen_stack.server.api:app --host 0.0.0.0 --port 8000`` (needs the
 """
 from __future__ import annotations
 
+import json
 from pathlib import Path
 
 import pandas as pd
@@ -34,6 +35,12 @@ def _atlas_df() -> pd.DataFrame:
     return pd.read_parquet(_ATLAS)
 
 
+def _records(df: pd.DataFrame) -> list[dict]:
+    """JSON-safe records from a DataFrame: NaN/inf -> null and numpy scalars -> native (pandas `to_json`
+    handles both). Raw `to_dict('records')` leaks non-finite floats, which the JSON encoder rejects (500)."""
+    return json.loads(df.to_json(orient="records"))
+
+
 @app.get("/health")
 def health():
     return {"status": "ok", "version": __version__, "atlas_present": _ATLAS.exists()}
@@ -60,7 +67,7 @@ def atlas(family: str | None = None, limit: int = Query(50, le=500)):
     cols = [c for c in ["representative_system", "family", "confidence", "mechanism_bucket",
                         "deliv_class", "readiness", "cargo_capacity_bp", "reachability_tier",
                         "human_cell_activity"] if c in df.columns]
-    return {"n": int(len(df)), "rows": df[cols].head(limit).to_dict("records"), "disclaimer": _DISCLAIMER}
+    return {"n": int(len(df)), "rows": _records(df[cols].head(limit)), "disclaimer": _DISCLAIMER}
 
 
 @app.get("/crosslink/writers")
@@ -86,7 +93,7 @@ def crosslink_loci(family: str, ct: str = "k562", top: int = Query(20, le=200)):
         loci = cl.loci_for_writer(family, ct, top=top)
     except FileNotFoundError as e:
         raise HTTPException(503, str(e)) from e
-    return {"family": family, "ct": ct, "loci": loci.to_dict("records"), "disclaimer": _DISCLAIMER}
+    return {"family": family, "ct": ct, "loci": _records(loci), "disclaimer": _DISCLAIMER}
 
 
 @app.get("/writable")
@@ -99,7 +106,7 @@ def writable(gene: str, ct: str = "k562", top: int = Query(20, le=200)):
     if g.empty:
         return {"gene": gene, "ct": ct, "loci": [], "disclaimer": _DISCLAIMER}
     cols = ["chrom", "bin", "safety", "p_durable", "writability"]
-    return {"gene": gene, "ct": ct, "loci": g[cols].head(top).to_dict("records"), "disclaimer": _DISCLAIMER}
+    return {"gene": gene, "ct": ct, "loci": _records(g[cols].head(top)), "disclaimer": _DISCLAIMER}
 
 
 @app.get("/bridge/design")

{pen_stack-6.2.0 → pen_stack-6.2.2}/pen_stack/web/server.py

@@ -14,7 +14,7 @@ import json
 from pathlib import Path
 
 try:
-    from fastapi import FastAPI
+    from fastapi import FastAPI, HTTPException
     from fastapi.middleware.cors import CORSMiddleware
     from fastapi.responses import StreamingResponse
 except ImportError as e:  # pragma: no cover - server extra optional
@@ -23,6 +23,13 @@ except ImportError as e:  # pragma: no cover - server extra optional
 from pen_stack import __version__
 from pen_stack.server.api import app as _engine_app   # the v6.1 typed engine surface (reused verbatim)
 
+
+def _require_message(req: dict) -> str:
+    msg = (req or {}).get("message")
+    if not isinstance(msg, str) or not msg.strip():
+        raise HTTPException(422, "field 'message' is required and must be a non-empty string")
+    return msg
+
 app = FastAPI(
     title="PEN-STACK — Web Platform",
     version=__version__,
@@ -55,7 +62,7 @@ def chat_route(req: dict) -> dict:
     {reply, tool_results, grounded, backend}."""
     from pen_stack.web.llm import grounded_reply
 
-    return grounded_reply(req["message"], history=req.get("history", []),
+    return grounded_reply(_require_message(req), history=req.get("history", []),
                           allow_llm=bool(req.get("allow_llm", True)))
 
 
@@ -65,7 +72,7 @@ def chat_stream_route(req: dict) -> StreamingResponse:
     applied), then emitted word-by-word so the UI can render progressively; a final event carries the dossier."""
     from pen_stack.web.llm import grounded_reply
 
-    result = grounded_reply(req["message"], history=req.get("history", []),
+    result = grounded_reply(_require_message(req), history=req.get("history", []),
                             allow_llm=bool(req.get("allow_llm", True)))
 
     def _events():

{pen_stack-6.2.0 → pen_stack-6.2.2}/pen_stack/web/tools.py

@@ -48,7 +48,10 @@ def parse_goal(message: str) -> dict:
     return {"write_type": "insertion", "gene": gene, "chrom": "chr19",
             "edit_intent": _first(message, _INTENTS, "safe_harbour_insertion"),
             "delivery_vehicle": _first(message, _VEHICLES, "AAV_single"), "cargo_bp": cargo,
-            "cell_type": _first(message, _CELLS, "k562")}
+            "cell_type": _first(message, _CELLS, "k562"),
+            # the user's plain-language goal IS the cargo-function description the Guardian must screen — so a
+            # message like "express a ricin toxin" is biosecurity-screened, not silently passed as benign.
+            "cargo_function": message.strip()}
 
 
 def run_tools(message: str, history: list | None = None) -> dict[str, Any]:

{pen_stack-6.2.0 → pen_stack-6.2.2}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 6.2.0
+Version: 6.2.2
 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
@@ -90,9 +90,9 @@ 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-6.2.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.2.2-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-368%20passing-success.svg)](tests/)
+[![Tests](https://img.shields.io/badge/tests-370%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)
 [![Runtime: Docker](https://img.shields.io/badge/runtime-docker-2496ED.svg)](docker/)
 [![Validation: pre-registered](https://img.shields.io/badge/validation-pre--registered-critical.svg)](prereg/)

{pen_stack-6.2.0 → pen_stack-6.2.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "6.2.0"
+version = "6.2.2"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"