pen-stack 7.1.7__tar.gz → 7.1.8__tar.gz

{pen_stack-7.1.7 → pen_stack-7.1.8}/CHANGELOG.md

@@ -3,6 +3,29 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/).
 
+## [7.1.8] - 2026-06-30 - Writer immunogenicity moves to the Writer Atlas; SpCas9 removed from the writer options
+
+### Changed
+- **The writer enzyme is no longer chosen in the Design Studio; its immunogenicity moves to the Writer Atlas, where
+  writers belong.** The Design Studio's writer dropdown existed only to feed the two writer-as-antigen immune axes
+  (MHC-II + ADA); that duplicated the dedicated Writer Atlas page. Now:
+  - The **Writer enzyme dropdown is removed** from `DesignForm` (and `DEFAULT_DESIGN`). The Design Studio's "Profile
+    immune & delivery" action correctly scopes to the **delivery/vehicle** axes (genotoxicity, CD8 capsid, innate,
+    pre-existing NAb, anti-PEG). `ImmuneProfileCard` hides the writer axes by default (`hideWriterAxes`).
+  - A new **Writer immunogenicity** card on the **Writer Atlas** surfaces each genome writer's MHC-II/CD4 epitope
+    load + ADA risk + human self-match, read from the **committed NetMHCIIpan-4.0 cache — not recomputed**
+    (`GET /api/writer/immune`, `immune_profile.writer_immunogenicity_table()`).
+  - **SpCas9 is removed** from the writer set: it is a nuclease/editor, not a large-cargo genome writer. The Writer
+    Atlas immunogenicity covers the actual writers — **Bxb1** (serine integrase) and **ISCro4** (bridge recombinase);
+    the Cas9 nuclease and the human self control are excluded. (The engine retains SpCas9 in its cache for other
+    uses; only the user-facing writer list drops it.)
+- The engine still returns the `mhc2_writer` / `ada_writer` axes from `immune_profile()` for API/MCP callers that
+  pass a `writer_family` — only the web UI moved the writer profiling to the Writer Atlas. No data was recomputed.
+
+### Added
+- `test_ws_profile.py`: `test_writer_immunogenicity_table_for_the_writer_atlas` (covers Bxb1 + ISCro4 from the
+  cache; SpCas9 and the self control excluded; grounded MHC-II + ADA values).
+
 ## [7.1.7] - 2026-06-30 - Administration context (in-vivo / ex-vivo) now drives the immune profile
 
 ### Fixed

{pen_stack-7.1.7 → pen_stack-7.1.8}/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: 7.1.7
+version: 7.1.8
 date-released: 2026-06-30
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-7.1.7 → pen_stack-7.1.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 7.1.7
+Version: 7.1.8
 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-7.1.7 → pen_stack-7.1.8}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "7.1.7"
+__version__ = "7.1.8"

{pen_stack-7.1.7 → pen_stack-7.1.8}/pen_stack/planner/immune_profile.py

@@ -186,6 +186,24 @@ def _writer_antigen_card(design: dict) -> dict | None:
                     "Population-level proxy; realized CD4 response / ADA titer is a known-unknown."}
 
 
+# Genome-WRITER families surfaced in the Writer Atlas immunogenicity view: the bundled writers that are actual
+# genome writers (integrase / recombinase), each with a committed real NetMHCIIpan-4.0 MHC-II load + ADA-risk cache.
+# The Cas9 nuclease (an editor, not a large-cargo writer) and the human self control are intentionally excluded.
+_WRITER_IMMUNE_FAMILIES = ("serine_integrase", "bridge_IS110")
+
+
+def writer_immunogenicity_table() -> list[dict]:
+    """Per-writer immunogenicity (MHC-II/CD4 epitope load + ADA risk) for the bundled genome-writer families, read
+    from the committed NetMHCIIpan-4.0 cache (no recomputation). Surfaced in the Writer Atlas as the writer's
+    antigen profile. Reuses the v6.9 writer-as-antigen card; excludes the Cas9 nuclease and the self control."""
+    out = []
+    for fam in _WRITER_IMMUNE_FAMILIES:
+        card = _writer_antigen_card({"writer_family": fam})
+        if card:
+            out.append({"writer_family": fam, **card})
+    return out
+
+
 def immune_profile(design: dict) -> dict:
     """Per-design immune-risk profile across all axes. ``design`` keys: ``delivery_vehicle`` (or ``vehicle``),
     ``serotype``, ``cargo_seq``, ``writer_output_form`` (or ``cargo_form``), ``pegylated``.

{pen_stack-7.1.7 → pen_stack-7.1.8}/pen_stack/server/api.py

@@ -244,6 +244,22 @@ def writer_variants_endpoint(integrase: str | None = None, system: str | None =
                     "(reported as a known limitation, never a manufactured positive)."}
 
 
+@app.get("/writer/immune", tags=["writer atlas"])
+def writer_immune_endpoint():
+    """The writer enzyme's immunogenicity as an antigen (v6.9 writer-as-antigen, surfaced in the Writer Atlas from
+    v7.1.8): per genome-writer family, the real NetMHCIIpan-4.0 MHC-II/CD4 epitope load + the ADA-risk axis
+    (MHC-II density x foreignness, self-tolerance filtered against the human proteome). Read from the committed
+    cache - NOT recomputed. Population-level proxy, never a patient-specific magnitude (a known-unknown). The Cas9
+    nuclease (an editor, not a large-cargo writer) and the human self control are excluded."""
+    from pen_stack.planner.immune_profile import writer_immunogenicity_table
+    return {"writers": writer_immunogenicity_table(),
+            "method": "NetMHCIIpan-4.0 MHC-II epitope load + ADA risk (MHC-II density x foreignness, self-tolerance "
+                      "filtered against the human proteome). Population-level proxy from the committed cache; the "
+                      "realized CD4 response / ADA titer is a known-unknown.",
+            "scale": "0-1, higher = lower risk (1 = least presentable / least ADA-driving)",
+            "no_fabrication": True}
+
+
 @app.get("/bridge/design")
 def bridge_design(target: str, donor: str, scaffold: str = "ISCro4_enhanced",
                   ct: str | None = None, scan: bool = False):

{pen_stack-7.1.7 → pen_stack-7.1.8}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 7.1.7
+Version: 7.1.8
 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-7.1.7 → pen_stack-7.1.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "7.1.7"
+version = "7.1.8"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"