pen-stack 7.1.5__tar.gz → 7.1.6__tar.gz

{pen_stack-7.1.5 → pen_stack-7.1.6}/CHANGELOG.md

@@ -3,6 +3,38 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/).
 
+## [7.1.6] - 2026-06-30 - Immune axes wired end-to-end + Delivery folded into Design Studio
+
+### Fixed
+- **Four immune-risk axes were unreachable from the web UI and showed as out-of-scope** — innate sensing, anti-PEG,
+  and the writer-as-antigen MHC-II + ADA axes abstained on every web design because the design form never collected
+  their inputs (the engine computed them correctly when called directly; this was a wiring gap, not a model gap):
+  - **`innate`** needs a cargo sequence. The design form now has an optional **Cargo sequence** field; the cargo
+    nucleic-acid form (DNA -> CpG/TLR9, mRNA -> U-content + dsRNA, RNP -> transient) is derived from the vehicle's
+    defining cargo class (`immune_profile._vehicle_cargo_form`) so the axis computes for any caller (chat / MCP /
+    REST) once a sequence is supplied. Empty sequence still abstains; an explicit `cargo_form` still wins. No
+    fabrication: an unknown vehicle returns no form and the axis abstains.
+  - **`mhc2_writer` / `ada_writer`** need a writer protein. The design form now has a **Writer enzyme** selector
+    (the three grounded families with a bundled UniProt sequence + committed NetMHCIIpan-4.0 cache: serine integrase
+    Bxb1, bridge recombinase ISCro4, Cas9 SpCas9); `DEFAULT_DESIGN` ships a serine integrase so the two axes populate
+    out of the box. No writer selected -> the two axes abstain (never fabricated).
+  - **`anti_peg`** applies only to PEGylated vehicles; selecting `lnp_mrna` now surfaces it (with an inline hint),
+    and it correctly abstains for non-PEG vehicles.
+  - `ImmuneProfileCard` now shows the **writer-as-antigen** summary (representative writer, foreign/self, dominant
+    antigen) so the writer axes are self-explanatory.
+
+### Changed
+- **Delivery & Immunity folded into Design Studio.** The standalone Delivery page duplicated the same design form and
+  immune profile, so it is merged into Design Studio as a third action - **Profile immune & delivery** - with the
+  per-axis immune ScoreGuide, the vehicle quick-switch, the `ImmuneProfileCard` and the scope ledger. Design Studio is
+  now one design surface with three actions (Verify / Generate / Profile immune & delivery). `/delivery` redirects to
+  `/design`; the nav drops the separate item; old links keep working.
+
+### Added
+- `test_ws_profile.py`: tests for the vehicle-derived cargo form (innate computes for a DNA vehicle with a cargo
+  sequence; abstains without one; explicit form overrides) and for the writer axes computing when a grounded writer
+  is supplied (and abstaining otherwise).
+
 ## [7.1.5] - 2026-06-29 - Chromosome field: validation, gene concordance, context
 
 ### Added

{pen_stack-7.1.5 → pen_stack-7.1.6}/CITATION.cff

@@ -1,8 +1,8 @@
 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: 7.1.5
-date-released: 2026-06-29
+version: 7.1.6
+date-released: 2026-06-30
 authors:
   - family-names: "Mahaboob Ali"
     given-names: "Anees Ahmed"

{pen_stack-7.1.5 → pen_stack-7.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 7.1.5
+Version: 7.1.6
 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

{pen_stack-7.1.5 → pen_stack-7.1.6}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "7.1.5"
+__version__ = "7.1.6"

{pen_stack-7.1.5 → pen_stack-7.1.6}/pen_stack/planner/immune_profile.py

@@ -53,6 +53,34 @@ _SCORE_KEY = {"genotoxicity": "genotox_score", "cd8_epitope": "capsid_immune_sco
               "innate": "innate_score", "preexisting_nab": "preexisting_score",
               "anti_peg": "preexisting_antipeg_score"}
 
+# Canonical cargo nucleic-acid FORM per delivery vehicle, used to drive the innate-sensing pathway (DNA -> TLR9
+# CpG; mRNA -> TLR7/8 + RIG-I/MDA5; RNP -> transient) when a design does not state ``cargo_form`` explicitly.
+# This is the vehicle's defining cargo class, NOT a fabricated quantity: an LNP-mRNA vehicle delivers mRNA, a
+# DNA-virus / electroporated-plasmid vehicle delivers DNA, an (e)VLP delivers a transient ribonucleoprotein. A
+# lentivirus is packaged as RNA but the persistent, innate-relevant cassette is the integrated proviral DNA.
+# An unknown vehicle returns None so the innate axis ABSTAINS rather than guesses a form.
+_VEHICLE_CARGO_FORM = {
+    "lnp_mrna": "mRNA",
+    "aav_single": "DNA", "aav_dual": "DNA", "lentivirus": "DNA",
+    "helper_dependent_adenovirus": "DNA", "hsv_amplicon": "DNA", "electroporation": "DNA",
+    "evlp": "RNP", "vlp": "RNP",
+}
+
+
+def _vehicle_cargo_form(vehicle: str | None) -> str | None:
+    """Derive the cargo nucleic-acid form (DNA / mRNA / RNP) from the delivery vehicle, or None when unknown.
+    Used only when the design does not supply ``cargo_form`` / ``writer_output_form`` explicitly."""
+    if not vehicle:
+        return None
+    v = str(vehicle).strip().lower()
+    if v in _VEHICLE_CARGO_FORM:
+        return _VEHICLE_CARGO_FORM[v]
+    if "mrna" in v or "lnp" in v:
+        return "mRNA"
+    if "vlp" in v:
+        return "RNP"
+    return None
+
 
 def _axis(result, axis: str) -> dict:
     """One axis record: value (headline score or None when abstaining) + native uncertainty + scope + the
@@ -108,7 +136,11 @@ def immune_profile(design: dict) -> dict:
     veh = design.get("delivery_vehicle") or design.get("vehicle")
     sero = design.get("serotype")
     cargo_seq = design.get("cargo_seq") or ""
-    form = design.get("writer_output_form") or design.get("cargo_form") or ""
+    # cargo form: honour an explicit design field, else derive it from the vehicle's defining cargo class so the
+    # innate axis computes for any caller (chat / MCP / REST) once a cargo sequence is supplied. Still abstains
+    # with no sequence and for an unknown vehicle (form None) - never fabricates.
+    form = (design.get("writer_output_form") or design.get("cargo_form")
+            or _vehicle_cargo_form(veh) or "")
     peg = design.get("pegylated")
 
     capsid_cd8 = capsid_epitope_oracle(veh)

{pen_stack-7.1.5 → pen_stack-7.1.6}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 7.1.5
+Version: 7.1.6
 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

{pen_stack-7.1.5 → pen_stack-7.1.6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "7.1.5"
+version = "7.1.6"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"