psyclaw 0.27.23 → 0.28.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1069) hide show
  1. package/README.md +11 -5
  2. package/agents/recommended/catalog.json +99 -0
  3. package/dist/apps/panel/index.html +5 -5
  4. package/dist/src/adapters/pi/extension.js +339 -94
  5. package/dist/src/adapters/pi/extension.js.map +1 -1
  6. package/dist/src/adapters/pi/rpc.d.ts +2 -0
  7. package/dist/src/adapters/pi/rpc.js +9 -2
  8. package/dist/src/adapters/pi/rpc.js.map +1 -1
  9. package/dist/src/agents/import.js +44 -32
  10. package/dist/src/agents/import.js.map +1 -1
  11. package/dist/src/agents/recommended-personas.d.ts +42 -0
  12. package/dist/src/agents/recommended-personas.js +135 -0
  13. package/dist/src/agents/recommended-personas.js.map +1 -0
  14. package/dist/src/analysis/hooks.d.ts +1 -0
  15. package/dist/src/analysis/hooks.js +20 -1
  16. package/dist/src/analysis/hooks.js.map +1 -1
  17. package/dist/src/ars/bridge.d.ts +20 -0
  18. package/dist/src/ars/bridge.js +132 -0
  19. package/dist/src/ars/bridge.js.map +1 -0
  20. package/dist/src/ars/contracts.d.ts +55 -0
  21. package/dist/src/ars/contracts.js +2 -0
  22. package/dist/src/ars/contracts.js.map +1 -0
  23. package/dist/src/ars/panel-plan.d.ts +4 -0
  24. package/dist/src/ars/panel-plan.js +11 -0
  25. package/dist/src/ars/panel-plan.js.map +1 -0
  26. package/dist/src/ars/pi-panel-executor.d.ts +30 -0
  27. package/dist/src/ars/pi-panel-executor.js +140 -0
  28. package/dist/src/ars/pi-panel-executor.js.map +1 -0
  29. package/dist/src/ars/profile.d.ts +36 -0
  30. package/dist/src/ars/profile.js +119 -0
  31. package/dist/src/ars/profile.js.map +1 -0
  32. package/dist/src/ars/re-review.d.ts +22 -0
  33. package/dist/src/ars/re-review.js +172 -0
  34. package/dist/src/ars/re-review.js.map +1 -0
  35. package/dist/src/branding.d.ts +2 -4
  36. package/dist/src/branding.js +3 -5
  37. package/dist/src/branding.js.map +1 -1
  38. package/dist/src/bundled-tools.d.ts +3 -0
  39. package/dist/src/bundled-tools.js +21 -0
  40. package/dist/src/bundled-tools.js.map +1 -0
  41. package/dist/src/chat.js +6 -5
  42. package/dist/src/chat.js.map +1 -1
  43. package/dist/src/cli.js +6 -3
  44. package/dist/src/cli.js.map +1 -1
  45. package/dist/src/creation/contracts.d.ts +41 -0
  46. package/dist/src/creation/contracts.js +2 -0
  47. package/dist/src/creation/contracts.js.map +1 -0
  48. package/dist/src/creation/service.d.ts +7 -0
  49. package/dist/src/creation/service.js +208 -0
  50. package/dist/src/creation/service.js.map +1 -0
  51. package/dist/src/index.d.ts +11 -0
  52. package/dist/src/index.js +11 -0
  53. package/dist/src/index.js.map +1 -1
  54. package/dist/src/install/installer.js +32 -10
  55. package/dist/src/install/installer.js.map +1 -1
  56. package/dist/src/orchestration/bundled-personas.d.ts +16 -0
  57. package/dist/src/orchestration/bundled-personas.js +101 -0
  58. package/dist/src/orchestration/bundled-personas.js.map +1 -0
  59. package/dist/src/orchestration/effects.d.ts +8 -0
  60. package/dist/src/orchestration/effects.js +39 -0
  61. package/dist/src/orchestration/effects.js.map +1 -0
  62. package/dist/src/orchestration/personas.d.ts +16 -0
  63. package/dist/src/orchestration/personas.js +64 -0
  64. package/dist/src/orchestration/personas.js.map +1 -0
  65. package/dist/src/orchestration/pi-executor.d.ts +9 -4
  66. package/dist/src/orchestration/pi-executor.js +55 -22
  67. package/dist/src/orchestration/pi-executor.js.map +1 -1
  68. package/dist/src/orchestration/research-agents.d.ts +3 -7
  69. package/dist/src/orchestration/research-agents.js +5 -69
  70. package/dist/src/orchestration/research-agents.js.map +1 -1
  71. package/dist/src/panel/server.js +19 -4
  72. package/dist/src/panel/server.js.map +1 -1
  73. package/dist/src/project/paths.d.ts +3 -0
  74. package/dist/src/project/paths.js +7 -0
  75. package/dist/src/project/paths.js.map +1 -1
  76. package/dist/src/rules/user-rules.d.ts +8 -0
  77. package/dist/src/rules/user-rules.js +36 -0
  78. package/dist/src/rules/user-rules.js.map +1 -0
  79. package/dist/src/skills/contracts.d.ts +4 -4
  80. package/dist/src/skills/recommended.js +1 -1
  81. package/dist/src/skills/registry.js +49 -28
  82. package/dist/src/skills/registry.js.map +1 -1
  83. package/dist/src/style/cli-ui.d.ts +14 -0
  84. package/dist/src/style/cli-ui.js +45 -1
  85. package/dist/src/style/cli-ui.js.map +1 -1
  86. package/dist/src/tui/skill-manager.js +1 -1
  87. package/dist/src/tui/skill-manager.js.map +1 -1
  88. package/dist/src/updates/update.js +9 -3
  89. package/dist/src/updates/update.js.map +1 -1
  90. package/package.json +15 -3
  91. package/scripts/rebrand-pi.mjs +6 -0
  92. package/skills/recommended/catalog.json +2 -11
  93. package/vendor/ars/.claude/CLAUDE.md +371 -0
  94. package/vendor/ars/.command-invariants.toml +24 -0
  95. package/vendor/ars/CITATION.cff +35 -0
  96. package/vendor/ars/LICENSE +417 -0
  97. package/vendor/ars/MODE_REGISTRY.md +76 -0
  98. package/vendor/ars/NOTICE.md +26 -0
  99. package/vendor/ars/POSITIONING.md +99 -0
  100. package/vendor/ars/PSYCLAW_SOURCE.json +10 -0
  101. package/vendor/ars/README.md +751 -0
  102. package/vendor/ars/SECURITY.md +52 -0
  103. package/vendor/ars/THIRD_PARTY.md +70 -0
  104. package/vendor/ars/academic-paper/SKILL.md +542 -0
  105. package/vendor/ars/academic-paper/agents/abstract_bilingual_agent.md +171 -0
  106. package/vendor/ars/academic-paper/agents/argument_builder_agent.md +276 -0
  107. package/vendor/ars/academic-paper/agents/citation_compliance_agent.md +422 -0
  108. package/vendor/ars/academic-paper/agents/draft_writer_agent.md +656 -0
  109. package/vendor/ars/academic-paper/agents/formatter_agent.md +999 -0
  110. package/vendor/ars/academic-paper/agents/intake_agent.md +393 -0
  111. package/vendor/ars/academic-paper/agents/literature_strategist_agent.md +626 -0
  112. package/vendor/ars/academic-paper/agents/peer_reviewer_agent.md +516 -0
  113. package/vendor/ars/academic-paper/agents/revision_coach_agent.md +334 -0
  114. package/vendor/ars/academic-paper/agents/socratic_mentor_agent.md +527 -0
  115. package/vendor/ars/academic-paper/agents/structure_architect_agent.md +401 -0
  116. package/vendor/ars/academic-paper/agents/visualization_agent.md +441 -0
  117. package/vendor/ars/academic-paper/examples/chinese_paper_example.md +278 -0
  118. package/vendor/ars/academic-paper/examples/clinical_citation_verification_checklist.md +95 -0
  119. package/vendor/ars/academic-paper/examples/clinical_epistemic_status_example.md +100 -0
  120. package/vendor/ars/academic-paper/examples/commitment_ledger_example.md +147 -0
  121. package/vendor/ars/academic-paper/examples/imrad_hei_example.md +234 -0
  122. package/vendor/ars/academic-paper/examples/literature_review_example.md +260 -0
  123. package/vendor/ars/academic-paper/examples/plan_mode_guided_writing.md +600 -0
  124. package/vendor/ars/academic-paper/examples/revision_mode_example.md +344 -0
  125. package/vendor/ars/academic-paper/examples/revision_recovery_example.md +506 -0
  126. package/vendor/ars/academic-paper/examples/version_family_reconciliation_example.md +89 -0
  127. package/vendor/ars/academic-paper/references/abstract_writing_guide.md +169 -0
  128. package/vendor/ars/academic-paper/references/academic_writing_style.md +188 -0
  129. package/vendor/ars/academic-paper/references/anti_leakage_protocol.md +83 -0
  130. package/vendor/ars/academic-paper/references/apa7_chinese_citation_guide.md +364 -0
  131. package/vendor/ars/academic-paper/references/apa7_extended_guide.md +198 -0
  132. package/vendor/ars/academic-paper/references/changelog.md +11 -0
  133. package/vendor/ars/academic-paper/references/citation_format_switcher.md +228 -0
  134. package/vendor/ars/academic-paper/references/committee_correspondence_protocol.md +158 -0
  135. package/vendor/ars/academic-paper/references/credit_authorship_guide.md +308 -0
  136. package/vendor/ars/academic-paper/references/disclosure_mode_protocol.md +478 -0
  137. package/vendor/ars/academic-paper/references/domain_evidence_profiles.md +38 -0
  138. package/vendor/ars/academic-paper/references/failure_paths.md +349 -0
  139. package/vendor/ars/academic-paper/references/funding_statement_guide.md +319 -0
  140. package/vendor/ars/academic-paper/references/hei_domain_glossary.md +169 -0
  141. package/vendor/ars/academic-paper/references/intro_title_rhetoric_guide.md +114 -0
  142. package/vendor/ars/academic-paper/references/journal_submission_guide.md +249 -0
  143. package/vendor/ars/academic-paper/references/latex_template_reference.md +378 -0
  144. package/vendor/ars/academic-paper/references/mode_selection_guide.md +378 -0
  145. package/vendor/ars/academic-paper/references/paper_structure_patterns.md +330 -0
  146. package/vendor/ars/academic-paper/references/plan_mode_protocol.md +112 -0
  147. package/vendor/ars/academic-paper/references/policy_anchor_disclosure_protocol.md +200 -0
  148. package/vendor/ars/academic-paper/references/policy_anchor_table.md +157 -0
  149. package/vendor/ars/academic-paper/references/revision_patch_protocol.md +173 -0
  150. package/vendor/ars/academic-paper/references/statistical_visualization_standards.md +750 -0
  151. package/vendor/ars/academic-paper/references/venue_disclosure_policies.md +259 -0
  152. package/vendor/ars/academic-paper/references/vlm_figure_verification.md +126 -0
  153. package/vendor/ars/academic-paper/references/workflow_phase_details.md +135 -0
  154. package/vendor/ars/academic-paper/references/writing_judgment_framework.md +59 -0
  155. package/vendor/ars/academic-paper/references/writing_quality_check.md +173 -0
  156. package/vendor/ars/academic-paper/templates/bilingual_abstract_template.md +78 -0
  157. package/vendor/ars/academic-paper/templates/case_study_template.md +129 -0
  158. package/vendor/ars/academic-paper/templates/conference_paper_template.md +108 -0
  159. package/vendor/ars/academic-paper/templates/credit_statement_template.md +132 -0
  160. package/vendor/ars/academic-paper/templates/funding_statement_template.md +290 -0
  161. package/vendor/ars/academic-paper/templates/imrad_template.md +183 -0
  162. package/vendor/ars/academic-paper/templates/latex_article_template.tex +199 -0
  163. package/vendor/ars/academic-paper/templates/literature_review_template.md +135 -0
  164. package/vendor/ars/academic-paper/templates/policy_brief_template.md +139 -0
  165. package/vendor/ars/academic-paper/templates/revision_tracking_template.md +199 -0
  166. package/vendor/ars/academic-paper/templates/theoretical_paper_template.md +119 -0
  167. package/vendor/ars/academic-paper-reviewer/SKILL.md +491 -0
  168. package/vendor/ars/academic-paper-reviewer/agents/devils_advocate_reviewer_agent.md +443 -0
  169. package/vendor/ars/academic-paper-reviewer/agents/domain_reviewer_agent.md +412 -0
  170. package/vendor/ars/academic-paper-reviewer/agents/editorial_synthesizer_agent.md +478 -0
  171. package/vendor/ars/academic-paper-reviewer/agents/eic_agent.md +339 -0
  172. package/vendor/ars/academic-paper-reviewer/agents/field_analyst_agent.md +221 -0
  173. package/vendor/ars/academic-paper-reviewer/agents/methodology_reviewer_agent.md +449 -0
  174. package/vendor/ars/academic-paper-reviewer/agents/perspective_reviewer_agent.md +427 -0
  175. package/vendor/ars/academic-paper-reviewer/examples/hei_paper_review_example.md +391 -0
  176. package/vendor/ars/academic-paper-reviewer/examples/interdisciplinary_review_example.md +299 -0
  177. package/vendor/ars/academic-paper-reviewer/examples/subclaim_decomposition_example.md +80 -0
  178. package/vendor/ars/academic-paper-reviewer/references/calibration_mode_protocol.md +256 -0
  179. package/vendor/ars/academic-paper-reviewer/references/changelog.md +10 -0
  180. package/vendor/ars/academic-paper-reviewer/references/editorial_decision_standards.md +236 -0
  181. package/vendor/ars/academic-paper-reviewer/references/guided_mode_protocol.md +34 -0
  182. package/vendor/ars/academic-paper-reviewer/references/integration_guide.md +15 -0
  183. package/vendor/ars/academic-paper-reviewer/references/quality_rubrics.md +84 -0
  184. package/vendor/ars/academic-paper-reviewer/references/re_review_mode_protocol.md +340 -0
  185. package/vendor/ars/academic-paper-reviewer/references/review_criteria_framework.md +98 -0
  186. package/vendor/ars/academic-paper-reviewer/references/review_panel_provenance_protocol.md +197 -0
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  188. package/vendor/ars/academic-paper-reviewer/references/reviewer_sprint_prompt_source.md +324 -0
  189. package/vendor/ars/academic-paper-reviewer/references/sprint_contract_protocol.md +296 -0
  190. package/vendor/ars/academic-paper-reviewer/references/statistical_reporting_standards.md +505 -0
  191. package/vendor/ars/academic-paper-reviewer/references/top_journals_by_field.md +206 -0
  192. package/vendor/ars/academic-paper-reviewer/templates/editorial_decision_template.md +235 -0
  193. package/vendor/ars/academic-paper-reviewer/templates/peer_review_report_template.md +305 -0
  194. package/vendor/ars/academic-paper-reviewer/templates/revision_response_template.md +248 -0
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  196. package/vendor/ars/academic-pipeline/agents/claim_ref_alignment_audit_agent.md +382 -0
  197. package/vendor/ars/academic-pipeline/agents/collaboration_depth_agent.md +164 -0
  198. package/vendor/ars/academic-pipeline/agents/integrity_verification_agent.md +870 -0
  199. package/vendor/ars/academic-pipeline/agents/pipeline_orchestrator_agent.md +1379 -0
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  204. package/vendor/ars/academic-pipeline/references/adapters/.gitkeep +0 -0
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  225. package/vendor/ars/agents/report_compiler_agent.md +341 -0
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  229. package/vendor/ars/commands/ars-abstract.md +10 -0
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@@ -0,0 +1,609 @@
1
+ """Tests for the #678 canonical bibliographic-integrity signal carrier."""
2
+ from __future__ import annotations
3
+
4
+ import copy
5
+ import hashlib
6
+ import json
7
+ import shutil
8
+ import sys
9
+ from pathlib import Path
10
+
11
+ import pytest
12
+ import yaml
13
+ from jsonschema import Draft202012Validator
14
+
15
+
16
+ SCRIPTS = Path(__file__).resolve().parent
17
+ REPO_ROOT = SCRIPTS.parent
18
+ sys.path.insert(0, str(SCRIPTS))
19
+
20
+ import bibliographic_integrity_signals as signals # noqa: E402
21
+ import check_bibliographic_integrity_signals as checker # noqa: E402
22
+ import tortured_phrase_screening as screening # noqa: E402
23
+
24
+
25
+ def _fixture(name: str) -> dict:
26
+ path = SCRIPTS / "fixtures/bibliographic_integrity_signals" / name
27
+ return json.loads(path.read_text(encoding="utf-8"))
28
+
29
+
30
+ def _validator() -> Draft202012Validator:
31
+ return Draft202012Validator(
32
+ signals.load_schema(), format_checker=Draft202012Validator.FORMAT_CHECKER
33
+ )
34
+
35
+
36
+ def _screening_state() -> screening.SnapshotState:
37
+ fixture_root = SCRIPTS / "fixtures/tortured_phrase_screening"
38
+ bundle = screening.load_snapshot(
39
+ fixture_root / "snapshot.json", fixture_root / "snapshot_manifest.json"
40
+ )
41
+ return screening.SnapshotState(
42
+ status="loaded",
43
+ reason_code="CHECK_COMPLETED",
44
+ bundle=bundle,
45
+ snapshot_sha256=bundle.snapshot_sha256,
46
+ manifest_sha256=bundle.manifest_sha256,
47
+ detail=None,
48
+ )
49
+
50
+
51
+ def _rendered_row(signal: dict) -> dict[str, str]:
52
+ lines = signals.render_advisory_section([signal]).splitlines()
53
+ headings = lines[2].strip("|").split(" | ")
54
+ values = lines[4].strip("|").split(" | ")
55
+ assert len(values) == len(headings)
56
+ return dict(zip(headings, values, strict=True))
57
+
58
+
59
+ def test_all_epistemic_class_fixtures_round_trip() -> None:
60
+ for name in (
61
+ "retraction.json",
62
+ "retraction_check_attestation.json",
63
+ "tortured_phrase.json",
64
+ "tortured_phrase_v1_2_detected.json",
65
+ "tortured_phrase_v1_2_abstract_missing.json",
66
+ ):
67
+ fixture = _fixture(name)
68
+ assert not list(_validator().iter_errors(fixture))
69
+ assert json.loads(json.dumps(fixture)) == fixture
70
+
71
+
72
+ def test_v1_2_fixtures_replay_except_frozen_unicode_provenance() -> None:
73
+ corpus_path = SCRIPTS / "fixtures/tortured_phrase_screening/corpus_input.yaml"
74
+ corpus = yaml.safe_load(corpus_path.read_text(encoding="utf-8"))[
75
+ "literature_corpus"
76
+ ]
77
+ by_key = {entry["citation_key"]: entry for entry in corpus}
78
+ cases = (
79
+ (
80
+ "tortured_phrase_v1_2_detected.json",
81
+ "fixture_complete_2026",
82
+ "cited_title",
83
+ ),
84
+ (
85
+ "tortured_phrase_v1_2_abstract_missing.json",
86
+ "fixture_missing_2026",
87
+ "cited_abstract",
88
+ ),
89
+ )
90
+ state = _screening_state()
91
+ for fixture_name, citation_key, surface in cases:
92
+ expected = screening.build_cited_signal(
93
+ by_key[citation_key],
94
+ surface=surface,
95
+ state=state,
96
+ checked_at="2026-08-10T01:00:00Z",
97
+ recorded_at="2026-08-10T01:00:01Z",
98
+ )
99
+ fixture = _fixture(fixture_name)
100
+ runtime_version = expected["tortured_phrase_context"]["snapshot"][
101
+ "unicode_data_version"
102
+ ]
103
+ assert runtime_version == state.bundle.unicode_data_version
104
+ fixture_version = fixture["tortured_phrase_context"]["snapshot"][
105
+ "unicode_data_version"
106
+ ]
107
+ assert fixture_version == checker.V12_FIXTURE_UNICODE_DATA_VERSION
108
+ expected["tortured_phrase_context"]["snapshot"][
109
+ "unicode_data_version"
110
+ ] = fixture_version
111
+ assert fixture == expected
112
+ screening.validate_cited_signal_binding(fixture, by_key[citation_key])
113
+
114
+
115
+ def test_legacy_fixture_byte_identity_is_frozen() -> None:
116
+ fixture_root = SCRIPTS / "fixtures/bibliographic_integrity_signals"
117
+ for name, expected_sha256 in checker.LEGACY_FIXTURE_SHA256.items():
118
+ assert hashlib.sha256((fixture_root / name).read_bytes()).hexdigest() == expected_sha256
119
+
120
+
121
+ def test_closed_schema_rejects_undeclared_field() -> None:
122
+ fixture = _fixture("retraction.json")
123
+ fixture["undeclared"] = True
124
+ assert any("Additional properties" in err.message for err in _validator().iter_errors(fixture))
125
+
126
+
127
+ def test_heuristic_cannot_use_deterministic_label() -> None:
128
+ fixture = _fixture("tortured_phrase.json")
129
+ fixture["epistemic_label"] = "RESOLVER-OR-LIST-OBSERVATION"
130
+ assert list(_validator().iter_errors(fixture))
131
+
132
+
133
+ def test_unknown_or_degraded_can_never_be_clean() -> None:
134
+ fixture = _fixture("retraction.json")
135
+ fixture["check_status"] = "degraded"
136
+ fixture["finding"] = "not_detected"
137
+ assert list(_validator().iter_errors(fixture))
138
+
139
+
140
+ def test_legacy_migration_preserves_epistemic_boundaries() -> None:
141
+ entry = {
142
+ "citation_key": "legacy2024",
143
+ "source_pointer": "zotero://select/items/0_LEGACY",
144
+ "obtained_at": "2026-08-01T00:00:00Z",
145
+ "contamination_signals": {
146
+ "preprint_post_llm_inflection": True,
147
+ "semantic_scholar_unmatched": False,
148
+ },
149
+ "contamination_signal_omissions": {"openalex_unmatched": "api_degraded"},
150
+ "retraction_check": True,
151
+ }
152
+ migrated = signals.migrate_legacy_entry(
153
+ entry, recorded_at="2026-08-08T00:00:00Z"
154
+ )
155
+ by_type = {item["signal_type"]: item for item in migrated}
156
+ assert by_type["preprint_post_llm_inflection"]["epistemic_class"] == "heuristic_advisory"
157
+ assert by_type["semantic_scholar_unmatched"]["epistemic_class"] == "deterministic_fact"
158
+ assert by_type["openalex_unmatched"]["check_status"] == "degraded"
159
+ assert by_type["openalex_unmatched"]["finding"] == "unresolved"
160
+ assert by_type["retraction_status"]["epistemic_class"] == "process_attestation"
161
+ assert by_type["retraction_status"]["finding"] == "unresolved"
162
+ assert all(not signals.validation_errors(item) for item in migrated)
163
+ assert "contamination_signals" in entry
164
+ assert "retraction_check" in entry
165
+
166
+
167
+ def test_multiple_signals_compose_in_one_section_without_marker_token() -> None:
168
+ fixtures = [_fixture("retraction.json"), _fixture("tortured_phrase.json")]
169
+ rendered = signals.render_advisory_section(fixtures)
170
+ assert rendered.count("## Bibliographic Integrity Advisories") == 1
171
+ assert "CONTAMINATED-" not in rendered
172
+ assert "<!--ref:" not in rendered
173
+ assert rendered.index("bis:jones2025") < rendered.index("bis:smith2024")
174
+ for heading in (
175
+ "signal type",
176
+ "source version",
177
+ "source sha256",
178
+ "checked at",
179
+ "recorded at",
180
+ "stale after",
181
+ "source pointer",
182
+ ):
183
+ assert heading in rendered
184
+
185
+
186
+ def test_v1_2_renderer_projects_complete_neutral_metadata_for_all_states() -> None:
187
+ corpus = yaml.safe_load(
188
+ (SCRIPTS / "fixtures/tortured_phrase_screening/corpus_input.yaml").read_text(
189
+ encoding="utf-8"
190
+ )
191
+ )["literature_corpus"]
192
+ by_key = {entry["citation_key"]: entry for entry in corpus}
193
+ loaded = _screening_state()
194
+ detected = _fixture("tortured_phrase_v1_2_detected.json")
195
+ zero = screening.build_cited_signal(
196
+ by_key["fixture_negative_2026"],
197
+ surface="cited_title",
198
+ state=loaded,
199
+ checked_at="2026-08-10T01:00:00Z",
200
+ recorded_at="2026-08-10T01:00:01Z",
201
+ )
202
+ missing = _fixture("tortured_phrase_v1_2_abstract_missing.json")
203
+ degraded = screening.build_cited_signal(
204
+ by_key["fixture_negative_2026"],
205
+ surface="cited_title",
206
+ state=screening.SnapshotState(
207
+ status="degraded",
208
+ reason_code="SNAPSHOT_HASH_MISMATCH",
209
+ bundle=None,
210
+ snapshot_sha256="0" * 64,
211
+ manifest_sha256="1" * 64,
212
+ detail="synthetic degraded renderer probe",
213
+ ),
214
+ checked_at="2026-08-10T01:00:00Z",
215
+ recorded_at="2026-08-10T01:00:01Z",
216
+ )
217
+
218
+ loaded_manifest = "34bfa9f92a612cd7e794024dded98ed96b0968dbc0f2c924d68cafbe3f280924"
219
+ shared = {
220
+ "summary label": "Phrase-list screening advisory",
221
+ "layer": "HEURISTIC-ADVISORY",
222
+ "evaluation status": "UNMEASURED",
223
+ }
224
+ expectations = (
225
+ (
226
+ detected,
227
+ {
228
+ **shared,
229
+ "status": "checked",
230
+ "finding": "detected",
231
+ "reason code": "CHECK_COMPLETED",
232
+ "snapshot as of": "2026-08-10",
233
+ "manifest sha256": loaded_manifest,
234
+ },
235
+ ),
236
+ (
237
+ zero,
238
+ {
239
+ **shared,
240
+ "status": "checked",
241
+ "finding": "not_detected",
242
+ "reason code": "CHECK_COMPLETED",
243
+ "snapshot as of": "2026-08-10",
244
+ "manifest sha256": loaded_manifest,
245
+ },
246
+ ),
247
+ (
248
+ missing,
249
+ {
250
+ **shared,
251
+ "status": "not_checked",
252
+ "finding": "NOT CLEAN — UNRESOLVED",
253
+ "reason code": "ABSTRACT_MISSING",
254
+ "snapshot as of": "2026-08-10",
255
+ "manifest sha256": loaded_manifest,
256
+ },
257
+ ),
258
+ (
259
+ degraded,
260
+ {
261
+ **shared,
262
+ "status": "degraded",
263
+ "finding": "NOT CLEAN — UNRESOLVED",
264
+ "reason code": "SNAPSHOT_HASH_MISMATCH",
265
+ "snapshot as of": "—",
266
+ "manifest sha256": "1" * 64,
267
+ },
268
+ ),
269
+ )
270
+ for signal, expected in expectations:
271
+ row = _rendered_row(signal)
272
+ assert {key: row[key] for key in expected} == expected
273
+
274
+ for signal in (zero, missing, degraded):
275
+ assert "phrase-list match requiring review" not in signals.render_advisory_section(
276
+ [signal]
277
+ )
278
+
279
+ legacy = _rendered_row(_fixture("retraction.json"))
280
+ for heading in (
281
+ "summary label",
282
+ "layer",
283
+ "evaluation status",
284
+ "reason code",
285
+ "snapshot as of",
286
+ "manifest sha256",
287
+ ):
288
+ assert legacy[heading] == "—"
289
+
290
+
291
+ def test_renderer_is_complete_injection_safe_and_bounds_match_projection() -> None:
292
+ malicious = "fixture://safe|`[link](https://invalid)\n<!--ref:INJECTED-->"
293
+ rows = []
294
+ for index in range(26):
295
+ row = copy.deepcopy(_fixture("retraction.json"))
296
+ row["signal_id"] = f"bis:render{index:02d}:retraction_status"
297
+ row["subject"]["citation_key"] = f"render{index:02d}"
298
+ row["subject"]["source_pointer"] = malicious if index == 0 else None
299
+ rows.append(row)
300
+ rendered = signals.render_advisory_section(rows)
301
+ assert rendered.count("## Bibliographic Integrity Advisories") == 1
302
+ assert "bis:render25:retraction_status" in rendered
303
+ assert "<!--ref:INJECTED-->" not in rendered
304
+ assert "[link](https://invalid)" not in rendered
305
+ assert "CONTAMINATED-" not in rendered
306
+
307
+ phrase = copy.deepcopy(_fixture("tortured_phrase_v1_2_detected.json"))
308
+ context = phrase["tortured_phrase_context"]
309
+ seed_match = context["matches"][0]
310
+ projected_matches = []
311
+ for index in range(4):
312
+ match = copy.deepcopy(seed_match)
313
+ match["pattern_id"] = f"render_pattern_{index}"
314
+ span = match["source_span"]
315
+ payload = {
316
+ "artifact_sha256": context["surface_binding"]["content_sha256"],
317
+ "snapshot_sha256": context["snapshot"]["snapshot_sha256"],
318
+ "surface": context["surface"],
319
+ "segment_id": match["segment_id"],
320
+ "context": match["context"],
321
+ "rule_id": match["pattern_id"],
322
+ "codepoint_start": span["codepoint_start"],
323
+ "codepoint_end": span["codepoint_end"],
324
+ }
325
+ match["match_id"] = "tpm-" + hashlib.sha256(
326
+ checker._canonical_json(payload).encode("utf-8")
327
+ ).hexdigest()[:24]
328
+ projected_matches.append(match)
329
+ context["matches"] = projected_matches
330
+ context["counts"]["rule_match_count"] = 4
331
+ context["counts"]["matched_rule_count"] = 4
332
+ context["counts"]["matches_by_context"]["cited_title"] = 4
333
+ phrase["evidence"][0]["observed_value"] = 4
334
+ phrase_rendered = signals.render_advisory_section([phrase])
335
+ assert phrase_rendered.count("render_pattern_") == 3
336
+ assert "+1 more machine rows" in phrase_rendered
337
+ assert "phrase-list match requiring review" in phrase_rendered
338
+
339
+ injected = copy.deepcopy(_fixture("tortured_phrase_v1_2_detected.json"))
340
+ injected_match = injected["tortured_phrase_context"]["matches"][0]
341
+ malicious_match = "![x](y)|`<tag>`!!!"
342
+ assert len(malicious_match) == len(injected_match["matched_text"])
343
+ injected_match["matched_text"] = malicious_match
344
+ injected_match["matched_text_sha256"] = hashlib.sha256(
345
+ malicious_match.encode("utf-8")
346
+ ).hexdigest()
347
+ injected_rendered = signals.render_advisory_section([injected])
348
+ assert malicious_match not in injected_rendered
349
+ assert "<tag>" not in injected_rendered
350
+ assert "&lt;tag&gt;" in injected_rendered
351
+ assert "\\|" in injected_rendered
352
+ assert "\\`" in injected_rendered
353
+ assert "\\[x\\]" in injected_rendered
354
+
355
+ corpus_path = SCRIPTS / "fixtures/tortured_phrase_screening/corpus_input.yaml"
356
+ negative_entry = yaml.safe_load(corpus_path.read_text(encoding="utf-8"))[
357
+ "literature_corpus"
358
+ ][2]
359
+ no_match = screening.build_cited_signal(
360
+ negative_entry,
361
+ surface="cited_title",
362
+ state=_screening_state(),
363
+ checked_at="2026-08-10T01:00:00Z",
364
+ recorded_at="2026-08-10T01:00:01Z",
365
+ )
366
+ no_match_rendered = signals.render_advisory_section([no_match])
367
+ assert "no phrase-list match observed on the checked surface" in no_match_rendered
368
+ assert "absence is not a clean certificate" in no_match_rendered
369
+
370
+ unresolved = _fixture("tortured_phrase_v1_2_abstract_missing.json")
371
+ unresolved_rendered = signals.render_advisory_section([unresolved])
372
+ assert "phrase-list screening unresolved; no clean conclusion" in unresolved_rendered
373
+
374
+
375
+ @pytest.mark.parametrize(
376
+ "mutation",
377
+ [
378
+ "reversed_codepoint",
379
+ "zero_utf8_span",
380
+ "codepoint_length",
381
+ "too_many_words",
382
+ "outside_surface",
383
+ "impossible_utf8_prefix",
384
+ "zero_surface_bytes",
385
+ "matched_rules_exceed_evaluated",
386
+ "submicrosecond_order",
387
+ ],
388
+ )
389
+ def test_source_independent_phrase_projection_mutations_fail(mutation: str) -> None:
390
+ phrase = copy.deepcopy(_fixture("tortured_phrase_v1_2_detected.json"))
391
+ context = phrase["tortured_phrase_context"]
392
+ match = context["matches"][0]
393
+ span = match["source_span"]
394
+ if mutation == "reversed_codepoint":
395
+ span["codepoint_end"] = span["codepoint_start"]
396
+ elif mutation == "zero_utf8_span":
397
+ span["utf8_end"] = span["utf8_start"]
398
+ elif mutation == "codepoint_length":
399
+ span["codepoint_end"] += 1
400
+ elif mutation == "too_many_words":
401
+ text = " ".join(["word"] * 26)
402
+ match["matched_text"] = text
403
+ match["matched_text_sha256"] = hashlib.sha256(text.encode()).hexdigest()
404
+ span["codepoint_start"] = 0
405
+ span["codepoint_end"] = len(text)
406
+ span["utf8_start"] = 0
407
+ span["utf8_end"] = len(text.encode())
408
+ elif mutation == "outside_surface":
409
+ width = span["codepoint_end"] - span["codepoint_start"]
410
+ start = context["surface_binding"]["content_utf8_bytes"] + 1
411
+ span["codepoint_start"] = start
412
+ span["codepoint_end"] = start + width
413
+ span["utf8_start"] = start
414
+ span["utf8_end"] = start + len(match["matched_text"].encode())
415
+ elif mutation == "impossible_utf8_prefix":
416
+ span["utf8_start"] += 1
417
+ span["utf8_end"] += 1
418
+ elif mutation == "zero_surface_bytes":
419
+ context["surface_binding"]["content_utf8_bytes"] = 0
420
+ elif mutation == "submicrosecond_order":
421
+ phrase["provenance"]["checked_at"] = "2026-08-10T01:00:00.0000009Z"
422
+ phrase["provenance"]["recorded_at"] = "2026-08-10T01:00:00.0000001Z"
423
+ else:
424
+ context["counts"]["rules_evaluated"] = 0
425
+ if mutation == "submicrosecond_order":
426
+ assert signals.validation_errors(phrase)
427
+ with pytest.raises(ValueError):
428
+ signals._validate_tortured_phrase_projection(phrase)
429
+
430
+
431
+ def test_checked_but_unresolved_attestation_is_visibly_not_clean() -> None:
432
+ rendered = signals.render_advisory_section(
433
+ [_fixture("retraction_check_attestation.json")]
434
+ )
435
+ assert "| checked | NOT CLEAN — UNRESOLVED |" in rendered
436
+
437
+
438
+ def _minimal_repo(tmp_path: Path) -> Path:
439
+ root = tmp_path / "repo"
440
+ paths = [
441
+ "shared/contracts/passport/bibliographic_integrity_signal.schema.json",
442
+ "shared/contracts/passport/literature_corpus_entry.schema.json",
443
+ "shared/bibliographic_integrity_signals.md",
444
+ "shared/handoff_schemas.md",
445
+ "academic-pipeline/agents/pipeline_orchestrator_agent.md",
446
+ "academic-paper/agents/formatter_agent.md",
447
+ "scripts/bibliographic_integrity_signals.py",
448
+ "scripts/fixtures/bibliographic_integrity_signals/retraction.json",
449
+ "scripts/fixtures/bibliographic_integrity_signals/retraction_check_attestation.json",
450
+ "scripts/fixtures/bibliographic_integrity_signals/tortured_phrase.json",
451
+ "scripts/fixtures/bibliographic_integrity_signals/tortured_phrase_v1_2_detected.json",
452
+ "scripts/fixtures/bibliographic_integrity_signals/tortured_phrase_v1_2_abstract_missing.json",
453
+ "scripts/fixtures/tortured_phrase_screening/corpus_input.yaml",
454
+ "scripts/fixtures/tortured_phrase_screening/snapshot.json",
455
+ "scripts/fixtures/tortured_phrase_screening/snapshot_manifest.json",
456
+ ]
457
+ for relative in paths:
458
+ source = REPO_ROOT / relative
459
+ destination = root / relative
460
+ destination.parent.mkdir(parents=True, exist_ok=True)
461
+ shutil.copy2(source, destination)
462
+ return root
463
+
464
+
465
+ def test_sync_checker_passes_current_repo() -> None:
466
+ assert checker.run_checks(REPO_ROOT) == []
467
+
468
+
469
+ def test_sync_checker_detects_formatter_drift(tmp_path: Path) -> None:
470
+ root = _minimal_repo(tmp_path)
471
+ path = root / "academic-paper/agents/formatter_agent.md"
472
+ text = path.read_text(encoding="utf-8").replace(
473
+ "**NOT CLEAN — UNRESOLVED**", "**CLEAN**"
474
+ )
475
+ path.write_text(text, encoding="utf-8")
476
+ found = checker.run_checks(root)
477
+ assert any("formatter_agent.md" in error for error in found)
478
+
479
+
480
+ def test_sync_checker_detects_legacy_fixture_byte_drift(tmp_path: Path) -> None:
481
+ root = _minimal_repo(tmp_path)
482
+ path = root / "scripts/fixtures/bibliographic_integrity_signals/retraction.json"
483
+ path.write_bytes(path.read_bytes() + b"\n")
484
+ found = checker.run_checks(root)
485
+ assert any("legacy fixture byte identity drifted" in error for error in found)
486
+
487
+
488
+ @pytest.mark.parametrize(
489
+ ("mutation", "expected_error"),
490
+ [
491
+ ("deterministic_fact", "v1.2 advisory lock epistemic_class drifted"),
492
+ ("terminal", "escaped the non-terminal lock"),
493
+ ("stale", "surface content_sha256 is stale"),
494
+ ("hash", "evidence_sha256 drifted"),
495
+ ("count", "rule_match_count does not equal the complete match array"),
496
+ ("provenance", "provenance stale_after drifted"),
497
+ ("unicode_version", "unicode_data_version does not replay fixture provenance"),
498
+ ("missing_abstract", "CHECK_COMPLETED cannot describe an absent cited surface"),
499
+ ],
500
+ )
501
+ def test_sync_checker_rejects_v1_2_mutations(
502
+ tmp_path: Path, mutation: str, expected_error: str
503
+ ) -> None:
504
+ root = _minimal_repo(tmp_path)
505
+ fixtures = root / "scripts/fixtures/bibliographic_integrity_signals"
506
+ detected_path = fixtures / "tortured_phrase_v1_2_detected.json"
507
+ missing_path = fixtures / "tortured_phrase_v1_2_abstract_missing.json"
508
+ if mutation == "stale":
509
+ corpus_path = root / "scripts/fixtures/tortured_phrase_screening/corpus_input.yaml"
510
+ corpus = yaml.safe_load(corpus_path.read_text(encoding="utf-8"))
511
+ corpus["literature_corpus"][0]["title"] += " stale"
512
+ corpus_path.write_text(
513
+ yaml.safe_dump(corpus, sort_keys=False, allow_unicode=True),
514
+ encoding="utf-8",
515
+ )
516
+ elif mutation == "missing_abstract":
517
+ fixture = json.loads(missing_path.read_text(encoding="utf-8"))
518
+ fixture["check_status"] = "checked"
519
+ fixture["finding"] = "not_detected"
520
+ fixture["provenance"]["checked_at"] = "2026-08-10T01:00:00Z"
521
+ fixture["evidence"][0]["evidence_type"] = "list_record"
522
+ fixture["evidence"][0]["observed_value"] = 0
523
+ fixture["tortured_phrase_context"]["reason_code"] = "CHECK_COMPLETED"
524
+ missing_path.write_text(
525
+ json.dumps(fixture, ensure_ascii=False, indent=2) + "\n",
526
+ encoding="utf-8",
527
+ )
528
+ else:
529
+ fixture = json.loads(detected_path.read_text(encoding="utf-8"))
530
+ if mutation == "deterministic_fact":
531
+ fixture["epistemic_class"] = "deterministic_fact"
532
+ fixture["epistemic_label"] = "RESOLVER-OR-LIST-OBSERVATION"
533
+ elif mutation == "terminal":
534
+ fixture["terminal_policy"] = {
535
+ "eligible": True,
536
+ "owner": "citation_finalizer",
537
+ "policy_key": "tortured_phrase",
538
+ "current_effect": "policy_gated",
539
+ }
540
+ elif mutation == "count":
541
+ fixture["tortured_phrase_context"]["counts"]["rule_match_count"] += 1
542
+ elif mutation == "provenance":
543
+ fixture["provenance"]["stale_after"] = "2026-08-11T01:00:00Z"
544
+ fixture["provenance"]["freshness"] = "stale"
545
+ elif mutation == "unicode_version":
546
+ fixture["tortured_phrase_context"]["snapshot"][
547
+ "unicode_data_version"
548
+ ] = "15.0.0"
549
+ else:
550
+ fixture["evidence"][0]["evidence_sha256"] = "0" * 64
551
+ detected_path.write_text(
552
+ json.dumps(fixture, ensure_ascii=False, indent=2) + "\n",
553
+ encoding="utf-8",
554
+ )
555
+ found = checker.run_checks(root)
556
+ assert any(expected_error in error for error in found), found
557
+
558
+
559
+ def test_existing_canonical_record_wins_idempotently() -> None:
560
+ fixture = _fixture("retraction.json")
561
+ entry = {
562
+ "citation_key": "smith2024",
563
+ "retraction_check": True,
564
+ "bibliographic_integrity_signals": [copy.deepcopy(fixture)],
565
+ }
566
+ migrated = signals.migrate_legacy_entry(
567
+ entry, recorded_at="2026-08-08T01:00:00Z"
568
+ )
569
+ assert migrated == [fixture]
570
+
571
+
572
+ @pytest.mark.parametrize(
573
+ "existing",
574
+ [
575
+ [{}],
576
+ [{"signal_id": ""}],
577
+ [
578
+ {"signal_id": "bis:smith2024:retraction_status"},
579
+ {"signal_id": "bis:smith2024:retraction_status"},
580
+ ],
581
+ ],
582
+ )
583
+ def test_lossy_existing_carrier_is_rejected(existing: list[dict]) -> None:
584
+ entry = {
585
+ "citation_key": "smith2024",
586
+ "bibliographic_integrity_signals": existing,
587
+ }
588
+ with pytest.raises(ValueError):
589
+ signals.migrate_legacy_entry(entry, recorded_at="2026-08-08T01:00:00Z")
590
+
591
+
592
+ def test_evidence_cannot_be_empty() -> None:
593
+ fixture = _fixture("retraction.json")
594
+ fixture["evidence"] = []
595
+ assert list(_validator().iter_errors(fixture))
596
+
597
+
598
+ def test_handoff_source_id_projects_to_a_schema_safe_stable_signal_id() -> None:
599
+ entry = {"id": "[S01]", "retraction_check": False}
600
+ first = signals.migrate_legacy_entry(
601
+ entry, recorded_at="2026-08-08T01:00:00Z"
602
+ )
603
+ second = signals.migrate_legacy_entry(
604
+ entry, recorded_at="2026-08-08T01:00:00Z"
605
+ )
606
+ assert first == second
607
+ assert first[0]["subject"]["citation_key"] == "[S01]"
608
+ assert first[0]["signal_id"].startswith("bis:source-")
609
+ assert not signals.validation_errors(first[0])