fix: make governance freeze cross-platform

.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "celltypepilot",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "description": "Single-cell annotation review plugin — governed context, independent state evidence, conservative abstention, and critic checks.",
   "author": {
     "name": "HERRY423"

.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "celltypepilot",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "description": "Single-cell annotation review plugin — governed context, independent state evidence, conservative abstention, and critic checks.",
   "author": {
     "name": "HERRY423",

.github/workflows/release.yml

@@ -57,17 +57,28 @@ jobs:
         run: |
           python -m venv --system-site-packages .release-smoke
           .release-smoke/bin/python -m pip install --no-deps --force-reinstall dist/*.whl
-          .release-smoke/bin/python -c \
-            "import celltypepilot; assert celltypepilot.__version__ == '${GITHUB_REF_NAME#v}'"
-          .release-smoke/bin/celltypepilot --version
-          .release-smoke/bin/celltypepilot doctor --json
+          .release-smoke/bin/python -I -c \
+            "import pathlib, sys, celltypepilot; root=pathlib.Path(sys.prefix).resolve(); module=pathlib.Path(celltypepilot.__file__).resolve(); assert module.is_relative_to(root), (module, root); assert celltypepilot.__version__ == '${GITHUB_REF_NAME#v}'"
+
+          smoke_cwd="$(mktemp -d)"
+          smoke_cli="$GITHUB_WORKSPACE/.release-smoke/bin/celltypepilot"
+          (
+            cd "$smoke_cwd"
+            "$smoke_cli" --version
+            "$smoke_cli" doctor --json
+            "$smoke_cli" governance-freeze-verify
+          )
 
           mkdir plugin-smoke
           python -m zipfile -e release-assets/celltypepilot-plugin-*.zip plugin-smoke
           .release-smoke/bin/python -m pip install \
             --no-build-isolation --no-deps --force-reinstall \
             plugin-smoke/celltypepilot-plugin-*
-          .release-smoke/bin/celltypepilot --version
+          (
+            cd "$smoke_cwd"
+            "$smoke_cli" --version
+            "$smoke_cli" governance-freeze-verify
+          )
 
       - name: Upload Python distributions
         uses: actions/upload-artifact@v7

CHANGELOG.md

@@ -4,6 +4,20 @@ All notable changes to CellTypePilot are documented here. The project follows
 [Semantic Versioning](https://semver.org/). Release claims remain bounded by the
 validation scope recorded in the repository and generated manifests.
 
+## [0.4.1] - 2026-08-11
+
+### Fixed
+
+- Governance-freeze schema v2 hashes governed UTF-8 text after LF normalization, so the same
+  semantic release verifies across Windows source trees and Linux-built wheels.
+- Release smoke tests now assert that imports resolve inside the fresh release virtual environment
+  and run governance verification from outside the repository checkout.
+
+### Validation boundary
+
+- This patch changes cross-platform integrity verification only. It does not change candidate
+  selection, Atlas content, calibration evidence, benchmark results, or biological claims.
+
 ## [0.4.0] - 2026-08-11
 
 ### Added
@@ -79,6 +93,7 @@ validation scope recorded in the repository and generated manifests.
 - It does not establish biological superiority over CellTypist, SingleR, Azimuth, popV, or expert review.
 - A qualified human remains responsible for final annotations and biological claims.
 
+[0.4.1]: https://github.com/HERRY423/CellTypePilot/releases/tag/v0.4.1
 [0.4.0]: https://github.com/HERRY423/CellTypePilot/releases/tag/v0.4.0
 [0.3.1]: https://github.com/HERRY423/CellTypePilot/releases/tag/v0.3.1
 [0.3.0]: https://github.com/HERRY423/CellTypePilot/releases/tag/v0.3.0

README.md

@@ -108,7 +108,7 @@ output/
 ├── transitional_states.csv      # Clusters flagged as differentiation intermediates
 ├── disagreements.csv            # Marker vs reference disagreement analysis
 ├── report_draft.html            # Self-contained HTML report with all figures embedded
-├── methodology_draft.txt        # "We annotated N clusters using CellTypePilot v0.4.0..."
+├── methodology_draft.txt        # "We annotated N clusters using CellTypePilot v0.4.1..."
 ├── manifest.json                # Provenance: versions, params, data hash, output hashes
 └── figures/
     ├── umap_cluster.png         # UMAP by cluster (colorblind-friendly Wong palette)
@@ -385,9 +385,9 @@ reference, evidence, and provenance gates apply as the CLI.
 ```
 CellTypePilot/
 ├── .claude-plugin/
-│   └── plugin.json              ← Claude Code plugin manifest (v0.4.0)
+│   └── plugin.json              ← Claude Code plugin manifest (v0.4.1)
 ├── .codex-plugin/
-│   └── plugin.json              ← Codex plugin manifest (v0.4.0, with interface block)
+│   └── plugin.json              ← Codex plugin manifest (v0.4.1, with interface block)
 ├── skills/
 │   └── celltypepilot/
 │       ├── SKILL.md              ← Shared skill instructions (4-stage workflow)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "celltypepilot"
-version = "0.4.0"
+version = "0.4.1"
 description = "Deterministic single-cell annotation backend for Agent plugins"
 readme = "README.md"
 license = "MIT"

scripts/build_governance_freeze.py

@@ -17,7 +17,7 @@ def main() -> None:
     parser.add_argument("--release-id", required=True)
     parser.add_argument(
         "--output",
-        default="src/celltypepilot/data/governance_freeze_v1.json",
+        default="src/celltypepilot/data/governance_freeze_v2.json",
     )
     args = parser.parse_args()
     output = Path(args.output)

skills/celltypepilot/reference/outputs.md

@@ -83,7 +83,7 @@ does not contribute marker evidence.
 
 ```json
 {
-  "celltypepilot_version": "0.4.0",
+  "celltypepilot_version": "0.4.1",
   "mkg_version": "mkg-2026.08.1",
   "timestamp": "2026-08-06T12:00:00+00:00",
   "input": {
@@ -126,7 +126,7 @@ Self-contained HTML report with embedded CSS. Sections:
 
 A plain-text paragraph suitable for adaptation into a paper's Methods section. Example:
 
-> Cell type annotation was performed using CellTypePilot (v0.4.0), an evidence-driven
+> Cell type annotation was performed using CellTypePilot (v0.4.1), an evidence-driven
 > annotation pipeline with built-in critic review. Marker gene evidence was sourced from
 > the CellTypePilot Marker Knowledge Graph (MKG mkg-2026.08.1), a curated atlas integrating
 > PanglaoDB, CellMarker, and Cell Ontology resources. For each of the N clusters identified

src/celltypepilot/__init__.py

@@ -8,7 +8,7 @@
 
 from importlib import import_module
 
-__version__ = "0.4.0"
+__version__ = "0.4.1"
 MKG_VERSION = "mkg-2026.08.1"  # Marker Knowledge Graph version
 
 __all__ = [

src/celltypepilot/cli.py

@@ -1420,7 +1420,7 @@ def calibration_split(
 @app.command("governance-freeze-verify")
 def governance_freeze_verify(
     freeze: Path = typer.Option(
-        Path(__file__).parent / "data" / "governance_freeze_v1.json",
+        Path(__file__).parent / "data" / "governance_freeze_v2.json",
         "--freeze",
         help="Frozen governance manifest",
     ),

src/celltypepilot/data/governance_freeze_v1.json → src/celltypepilot/data/governance_freeze_v2.json

@@ -1,135 +1,136 @@
 {
-  "schema_version": "celltypepilot.governance-freeze.v1",
-  "release_id": "celltypepilot-v0.4.0",
+  "schema_version": "celltypepilot.governance-freeze.v2",
+  "hash_semantics": "utf8_text_lf_v1",
+  "release_id": "celltypepilot-v0.4.1",
   "files": [
     {
       "path": "src/celltypepilot/calibration.py",
-      "size": 13337,
+      "normalized_size": 13337,
       "sha256": "1cfa08da58c6b03ff1e6028c1b5d702b97b88578051519fb6b40b4ebfb2ef338"
     },
     {
       "path": "src/celltypepilot/calibration_split.py",
-      "size": 13601,
+      "normalized_size": 13601,
       "sha256": "3270edbb49f3660202a446f145bf2d4d51344c711be0e66ae1bdf1b8b526f5dc"
     },
     {
       "path": "src/celltypepilot/candidate_backends.py",
-      "size": 13127,
+      "normalized_size": 13127,
       "sha256": "5b6120dd9803dbe36ea28da0685253b11d0deb1d5151f864e992932b1db20233"
     },
     {
       "path": "src/celltypepilot/critic.py",
-      "size": 33266,
+      "normalized_size": 33266,
       "sha256": "13faf74d8d8c0373d4d845f2eb47fd9e3d4b23417b2b00a8b08c8e4991daca78"
     },
     {
       "path": "src/celltypepilot/data/marker_atlas.json",
-      "size": 834184,
-      "sha256": "2aaaab14fc15b5811332baf697a575ac41122d7fb9a4e6f32ea1ed12875449b3"
+      "normalized_size": 813538,
+      "sha256": "b1097382b669acdc81ffb9bed77df05d98acf977e1e2a99a14512b54063957ed"
     },
     {
       "path": "src/celltypepilot/data/packs/gut_ibd_depth_v1/ontology_map.json",
-      "size": 1018,
+      "normalized_size": 1018,
       "sha256": "0eb6c9762285f0f4f607953cb3c154d8b5e223c5cb1dff338d57f9dc285a80b5"
     },
     {
       "path": "src/celltypepilot/data/packs/gut_ibd_depth_v1/pack.json",
-      "size": 986,
+      "normalized_size": 986,
       "sha256": "89d712fbedb47cb3f141c319907811e3f5d758e83ed7d6c43ad1ab257a639858"
     },
     {
       "path": "src/celltypepilot/data/packs/gut_ibd_depth_v1/reference_manifest.json",
-      "size": 445,
+      "normalized_size": 445,
       "sha256": "e79bba8098ec1a9c6c86f72f97ac207007396d63e312596c050985e762d6a6fe"
     },
     {
       "path": "src/celltypepilot/data/packs/lung_evidence_v0_1/marker_atlas.json",
-      "size": 9852,
+      "normalized_size": 9852,
       "sha256": "f6539e227987d1faf10823e561bff10f290fa7c7e3ace4a21704df7558a212e6"
     },
     {
       "path": "src/celltypepilot/data/packs/lung_evidence_v0_1/ontology_map.json",
-      "size": 1131,
+      "normalized_size": 1131,
       "sha256": "233c8bf42f8611191ffc2ae67cc41a9ed86ee1eacad7b3a3480602eb243c8285"
     },
     {
       "path": "src/celltypepilot/data/packs/lung_evidence_v0_1/pack.json",
-      "size": 897,
+      "normalized_size": 897,
       "sha256": "64245fcc47560c6f0a88cb7512b37ecc40a01f49f93783e055ea40f06d11e75e"
     },
     {
       "path": "src/celltypepilot/data/packs/lung_evidence_v0_1/reference_manifest.json",
-      "size": 453,
+      "normalized_size": 453,
       "sha256": "b2c90292b4e984f0b322e20514afee72bc21c4250d78d27fbb0c9728e2c5cc11"
     },
     {
       "path": "src/celltypepilot/data/packs/premium/marker_atlas.json",
-      "size": 170227,
-      "sha256": "dc62461805dcc99aab257ba256e68e2b6034e5642d23bc7f12b4f124acadb81a"
+      "normalized_size": 165634,
+      "sha256": "94de0378d806a8462e1f870f0d129866b10870723e8e946776c0219691b131f9"
     },
     {
       "path": "src/celltypepilot/data/packs/premium/pack.json",
-      "size": 473,
-      "sha256": "f310fd5439297cbc033db72059d35e462e9c813d7bbfde3141eef6a001bad797"
+      "normalized_size": 452,
+      "sha256": "e392ecfaf7db4a85adf75d1b4d816423ac8530be8a6b9f3287c5287fbe57d2ef"
     },
     {
       "path": "src/celltypepilot/data/packs/tme_depth_v1/ontology_map.json",
-      "size": 793,
+      "normalized_size": 793,
       "sha256": "cd5cf521863ecae69d6af12edb166cf6be92b0212c2a67f5d847fb26cc2130d2"
     },
     {
       "path": "src/celltypepilot/data/packs/tme_depth_v1/pack.json",
-      "size": 982,
+      "normalized_size": 982,
       "sha256": "357b3d94e321eba2125aa7486111b90950c1f25b0903f8232aaf792bfa130884"
     },
     {
       "path": "src/celltypepilot/data/packs/tme_depth_v1/reference_manifest.json",
-      "size": 467,
+      "normalized_size": 467,
       "sha256": "97b99bb3966956c39b9ec57b9c11d07a89fbebee63f6cd5d5b20b4b4ae7810da"
     },
     {
       "path": "src/celltypepilot/data/state_atlas.json",
-      "size": 43503,
-      "sha256": "f3af1ae5a92dcb2e54bd09c0c50122dd16ad4959e8bcfd55cf8962428fd0c42d"
+      "normalized_size": 41814,
+      "sha256": "ecf8e00333c89cebba5db03afc03cea9c95a6e8970cb501b58ec0cbc951b4c61"
     },
     {
       "path": "src/celltypepilot/data/validation_domains.json",
-      "size": 4814,
+      "normalized_size": 4814,
       "sha256": "b5efb42cfc1d11b90f66614824027704da0587d61fdc35093a38b21d7cd8da79"
     },
     {
       "path": "src/celltypepilot/hierarchical_selector.py",
-      "size": 12051,
+      "normalized_size": 12051,
       "sha256": "5d14cead0f72769b2cf18cf208e922897c6c030c2cb11634e15392eae1b9e8fe"
     },
     {
       "path": "src/celltypepilot/identity_contract.py",
-      "size": 15979,
+      "normalized_size": 15979,
       "sha256": "53b252b12333ac82e85b0d425dead71eb90c2cd5b9cdff1737227b833846df5a"
     },
     {
       "path": "src/celltypepilot/lineage_coverage.py",
-      "size": 9756,
+      "normalized_size": 9756,
       "sha256": "c35fe5efccd4b9378c25f5e0dea29807be64e359b5bba711ca6260d9037348ae"
     },
     {
       "path": "src/celltypepilot/novelty_detector.py",
-      "size": 13038,
+      "normalized_size": 13038,
       "sha256": "a25856085ea7b5074160c36a2427dc6253ca769912e16eea5a77746fa6af2d6e"
     },
     {
       "path": "src/celltypepilot/pack_manager.py",
-      "size": 25322,
-      "sha256": "67eb877aa4a64b601f4332c6c0f75c9b47861c9ba699612f283f7522d65c8cf6"
+      "normalized_size": 24711,
+      "sha256": "6545260fd560a7e9a3a027c7cbdf98b5728fdc91cfff5dc8a9f301c93aaaae6e"
     },
     {
       "path": "src/celltypepilot/state_scorer.py",
-      "size": 16032,
+      "normalized_size": 16032,
       "sha256": "aef926461e52dfa43aa6117ebf75165f116bab55c84cde733bcbb614999987e4"
     },
     {
       "path": "src/celltypepilot/validation_domains.py",
-      "size": 4582,
+      "normalized_size": 4582,
       "sha256": "f1bc0a888328b9f4bb8a9567a82f5c3e6a4e6d9c45d91c5ad1b8f6585313cf7f"
     }
   ],
@@ -154,5 +155,5 @@
     "human_signoff": "required"
   },
   "claim_boundary": "This freezes software governance and content hashes. It does not freeze or establish biological accuracy, selective-risk calibration, or domain validation.",
-  "freeze_sha256": "398f5144ff66741595001b6ed265bef5726f1b93c81c442460f855a3f0813b24"
+  "freeze_sha256": "f6cec7b647bf4afcf0c5b1ed1247b9d4fb62adbd066a3f1bac22af284a47defc"
 }