Record verified GitHub publication and preserved historical scientific payloads

wu_20261104_structure_function/publication_status.json

@@ -1,26 +1,29 @@
 {
-  "status": "HF_PUBLISHED_GITHUB_STATUS_RECORDED_SEPARATELY",
+  "status": "BASE_AND_CROSSBRAIN_CODE_DATA_PUBLISHED_AND_VERIFIED",
   "github": {
     "repository": "https://github.com/ydchen0806/bio_fly_cyber_lateralization",
     "branch": "research/wu-structure-function-20261104",
-    "uploaded": false,
-    "authenticated_account": "XiangchenYin",
-    "target_access_http_status": 404,
-    "reason": "Existing managed GitHub login cannot access the user-specified repository. Requires managed login with target-repository write access.",
-    "local_commit": "f6042fe34ec1f9fe454769aa49774171ded0c144",
+    "uploaded": true,
+    "authenticated_account": "ydchen0806",
+    "target_access_http_status": 200,
+    "reason": "Managed account switched and target branch pushed; remote SHA verified.",
     "push_attempted": true,
-    "push_returncode": 128
+    "push_returncode": 0,
+    "initial_verified_commit": "f6042fe34ec1f9fe454769aa49774171ded0c144",
+    "scientific_code_commit": "c8421d95d8ffcca9ff513bfa0aa94489e9ef052c"
   },
   "huggingface": {
     "dataset": "cyd0806/neuronmimic-data",
     "prefix": "wu_20261104_structure_function",
     "uploaded": true,
-    "authenticated_account": "joy4",
-    "write_http_status": null,
+    "authenticated_account": "cyd0806",
+    "write_http_status": 200,
     "previous_remote_commit": "b4143c83be3df42a95983d2be34af4354a25a84c",
-    "reason": "Published and checked against the frozen file manifest.",
+    "reason": "All base scientific data uploaded and checked against the frozen object manifest.",
     "payload_commit": "6f24982d0375d957c7c3906e81a2c2678c5c4667",
-    "verified_payload_files": 71
+    "verified_payload_files": 71,
+    "status_commit": "c90fa7da815e32c8d56c0829de48f9313b93b789",
+    "verified_payload_objects": 71
   },
   "git_identity": {
     "name": "ydchen0806",
@@ -40,16 +43,15 @@
   "complete_inventory_files": 8994,
   "source_retrieval_only_files": 144,
   "credentials_in_release": false,
-  "note": "Code commit is recorded in the external delivery status after creation; publication is not inferred from local files.",
+  "note": "Scientific code/data commits are immutable. Later receipt-only Git commits do not change the scientific implementation. Original source retrieval requirements and manuscript evidence limits remain explicit.",
   "local_code_worktree": "deliveries/wu_structure_function_code_20261105",
-  "local_git_bundle": "deliveries/wu_structure_function_code_20261105.bundle",
   "local_data_directory": "deliveries/wu_structure_function_data_20261105",
   "manuscript": {
     "pdf": "projects/wu_20261104_manuscript_release/exports/manuscript.pdf",
-    "pages": 21,
+    "pages": 23,
     "main_figures": 5,
-    "extended_data_figures": 6,
-    "verified_references": 8,
+    "extended_data_figures": 7,
+    "verified_references": 9,
     "status": "INTERNAL_DRAFT_NOT_SUBMITTED"
   },
   "validation": {
@@ -58,5 +60,45 @@
     "source_numeric_checks": "PASS: 7 checks",
     "source_code_syntax_and_secret_scan": "PASS",
     "restore_tool": "PASS: 5 cases"
-  }
+  },
+  "crossbrain_extension": {
+    "project": "projects/wu_20261105_crossbrain_transfer",
+    "dataset_prefix": "wu_20261105_crossbrain_transfer",
+    "status": "PUBLISHED_AND_VERIFIED",
+    "n_animals": 2,
+    "n_cells": 257,
+    "null_fits": 796,
+    "independent_reproduction": "PASS: all 20 prediction arrays and score tables exactly reproduced",
+    "payload_commit": "ffd770b32a11f850e122ab13d69bc71f100b45b4",
+    "status_commit": "a7f2f558584bc05709b858734b23e90faa98d7c3",
+    "scientific_code_commit": "c8421d95d8ffcca9ff513bfa0aa94489e9ef052c",
+    "archive_member_files": 106,
+    "verified_uploaded_objects": 7
+  },
+  "historical_dataset_verification": {
+    "status": "PASS_WITH_LFS_ATTRIBUTE_EXTENSION",
+    "original_revision": "b4143c83be3df42a95983d2be34af4354a25a84c",
+    "verified_revision": "a7f2f558584bc05709b858734b23e90faa98d7c3",
+    "original_files_checked": 593,
+    "current_files": 676,
+    "original_files_missing": [],
+    "original_files_changed": [
+      ".gitattributes"
+    ],
+    "root_README_unchanged": true,
+    "new_release_files_added": 83,
+    "all_original_payload_files_unchanged": true,
+    "original_payload_files_unchanged": 592,
+    "metadata_change_scope": "Only .gitattributes changed: Hugging Face appended new-file LFS rules; all original rules retained.",
+    "added_attribute_rules": [
+      "wu_20261104_structure_function/manuscript_release/exports/manuscript.pdf filter=lfs diff=lfs merge=lfs -text",
+      "wu_20261104_structure_function/manuscript_release/figures/ExtendedData1.pdf filter=lfs diff=lfs merge=lfs -text",
+      "wu_20261104_structure_function/manuscript_release/figures/ExtendedData5.pdf filter=lfs diff=lfs merge=lfs -text",
+      "wu_20261104_structure_function/manuscript_release/figures/ExtendedData6.pdf filter=lfs diff=lfs merge=lfs -text",
+      "wu_20261105_crossbrain_transfer/manuscript.pdf filter=lfs diff=lfs merge=lfs -text"
+    ]
+  },
+  "initial_git_bundle": "deliveries/wu_structure_function_code_20261105.bundle",
+  "local_git_bundle_latest": "deliveries/wu_structure_function_code_20261105_latest.bundle",
+  "local_crossbrain_data_directory": "deliveries/wu_crossbrain_release_20261105"
 }

wu_20261105_crossbrain_transfer/metadata/historical_preservation.json

@@ -0,0 +1,23 @@
+{
+  "status": "PASS_WITH_LFS_ATTRIBUTE_EXTENSION",
+  "original_revision": "b4143c83be3df42a95983d2be34af4354a25a84c",
+  "verified_revision": "a7f2f558584bc05709b858734b23e90faa98d7c3",
+  "original_files_checked": 593,
+  "current_files": 676,
+  "original_files_missing": [],
+  "original_files_changed": [
+    ".gitattributes"
+  ],
+  "root_README_unchanged": true,
+  "new_release_files_added": 83,
+  "all_original_payload_files_unchanged": true,
+  "original_payload_files_unchanged": 592,
+  "metadata_change_scope": "Only .gitattributes changed: Hugging Face appended new-file LFS rules; all original rules retained.",
+  "added_attribute_rules": [
+    "wu_20261104_structure_function/manuscript_release/exports/manuscript.pdf filter=lfs diff=lfs merge=lfs -text",
+    "wu_20261104_structure_function/manuscript_release/figures/ExtendedData1.pdf filter=lfs diff=lfs merge=lfs -text",
+    "wu_20261104_structure_function/manuscript_release/figures/ExtendedData5.pdf filter=lfs diff=lfs merge=lfs -text",
+    "wu_20261104_structure_function/manuscript_release/figures/ExtendedData6.pdf filter=lfs diff=lfs merge=lfs -text",
+    "wu_20261105_crossbrain_transfer/manuscript.pdf filter=lfs diff=lfs merge=lfs -text"
+  ]
+}

wu_20261105_crossbrain_transfer/publication_status.json

@@ -47,5 +47,9 @@
       "verified": true,
       "bytes": 986389
     }
-  ]
+  ],
+  "initial_status_commit": "a7f2f558584bc05709b858734b23e90faa98d7c3",
+  "base_release_payload_commit": "6f24982d0375d957c7c3906e81a2c2678c5c4667",
+  "original_dataset_payload_files_preserved": 592,
+  "original_LFS_rules_preserved": true
 }