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Functions4,061 in github.com/Imbad0202/academic-research-skills

↓ 1,211 callersMethodget
Return the cached response, or None on miss / expired entry. An entry whose verification_timestamp is older than the TTL is a miss (t
scripts/verification_cache.py:84
↓ 134 callersFunctionexpect_contains
(rel_path: str, needle: str)
scripts/check_spec_consistency.py:23
↓ 97 callersFunctionbuild_passport
Build a minimal passport JSON wrapping the seven aggregates the lint reads (six pre-v3.8.2 + uncited_audit_failures[]).
scripts/test_claim_audit_schema.py:202
↓ 78 callersMethodrun
(self)
scripts/check_v3_6_7_pattern_protection.py:279
↓ 70 callersMethodrun_pipeline
(self, **kwargs: Any)
scripts/test_claim_audit_pipeline.py:211
↓ 64 callersMethodassertLintFinds
Assert lint exits non-zero AND stdout contains `invariant` tag.
scripts/test_claim_audit_schema.py:321
↓ 64 callersFunctionload_yaml
Return a function that loads a YAML file into a Python dict.
scripts/adapters/tests/conftest.py:72
↓ 62 callersFunctionmake_valid_persisted_entry_minor
()
scripts/test_check_audit_artifact_consistency.py:122
↓ 60 callersFunctionrun_script
Invoke a script via subprocess, capturing stdout/stderr as text. extra_env values are merged into os.environ (not replaced).
tests/test_helpers.py:15
↓ 56 callersFunction_citation
( *, claim_id: str = "C-001", claim_text: str = "Sample preprints accounted for 67% of corpus.",
scripts/test_claim_audit_pipeline.py:88
↓ 51 callersMethodassert_mutation_fails
(self)
scripts/test_check_v3_6_7_pattern_protection.py:84
↓ 50 callersFunctionmake_valid_sidecar
(template_sha: str = "1" * 64)
scripts/test_check_audit_artifact_consistency.py:170
↓ 49 callersFunctionlint_file
Return a list of violation strings; empty list = PASS.
scripts/check_v3_7_3_three_layer_citation.py:140
↓ 49 callersFunctionparse_document
Parse a draft (or, with ``fragment=True``, a patch ``new_text``). Fragment mode differences: no YAML-frontmatter detection (frontmatter is ne
scripts/_block_parser.py:200
↓ 49 callersFunctionpayload
(tool_name, tool_input, cwd, agent_type=None, agent_id=None)
scripts/test_ars_write_scope_guard.py:74
↓ 48 callersFunction_valid_reviewer_full_contract
Returns a fresh fully-valid reviewer_full contract. Callers may mutate freely.
scripts/test_check_sprint_contract.py:32
↓ 47 callersFunctionwrite
(tmp_path: Path, content: str)
scripts/test_check_v3_7_3_three_layer_citation.py:23
↓ 46 callersFunction_load_schema
()
scripts/adapters/tests/test_literature_corpus_entry_schema.py:12
↓ 46 callersFunctionchecks_by_id
(report)
scripts/test_verify_submission_package.py:57
↓ 43 callersFunction_mutate
Apply a single replace mutation to `repo_dir/rel_path`. Asserts the `old` string is present (so a refactored prompt that no longer matches sur
scripts/test_check_v3_6_7_pattern_protection.py:55
↓ 43 callersFunction_validator
Validator with format_checker so format-keyword constraints (e.g. date-time on obtained_at) are actually enforced.
scripts/adapters/tests/test_literature_corpus_entry_schema.py:17
↓ 43 callersFunctionvalidate
Return list of schema violation messages. Empty list means pass.
scripts/check_sprint_contract.py:27
↓ 40 callersFunction_minimal_entry
Smallest valid v3.6.4 entry; tests overlay trust fields on top.
scripts/test_check_v3_6_8_frontmatter_trust_schema.py:43
↓ 40 callersFunctionmake_valid_verdict_file_minor
()
scripts/test_check_audit_artifact_consistency.py:74
↓ 39 callersFunction_run_jq
Run `jq [-r] [-e] -f <filter>` over a Python payload. Returns (returncode, stdout).
scripts/test_cross_model_verification_guards.py:65
↓ 38 callersFunction_check
(check_id: str, status: str, detail: str, *, signal_class: str = "deterministic", locati
scripts/verify_submission_package.py:350
↓ 38 callersFunctionrun_on
Copy a fixture package into tmp and run the CLI on the copy. Returns (exit_code, report_dict, package_dir). The copy keeps the repo fixture p
scripts/test_verify_submission_package.py:45
↓ 37 callersFunction_base_patch
(anchored: str, ops: list[dict], round_: int = 1)
scripts/test_ars_apply_revision_patch.py:60
↓ 37 callersMethodlookup
Return {"matched": bool, ...}. Raise SemanticScholarUnavailable on transient API failures (after the protocol's retry budget is exhaus
scripts/contamination_signals.py:102
↓ 36 callersFunction_run_lint
Run the v3.6.8 lint as a subprocess (so its sys.exit propagates).
scripts/test_check_v3_6_8_pattern_protection.py:43
↓ 36 callersMethod_write
(self, anchored: str, patch: dict)
scripts/test_ars_apply_revision_patch.py:80
↓ 35 callersFunction_inp
( *, ai_used=None, categories=None, policy_anchor="icmje", venue=None, slr_lineage=Fal
scripts/test_policy_anchor_disclosure.py:38
↓ 34 callersFunction_run
(root: Path)
scripts/test_check_version_consistency.py:15
↓ 34 callersFunctionfail
(message: str)
scripts/check_spec_consistency.py:19
↓ 34 callersFunctionrun
(argv: Optional[list[str]] = None)
scripts/verify_submission_package.py:1520
↓ 32 callersFunction_hash_of
(anchored: str, block_id: str)
scripts/test_ars_apply_revision_patch.py:56
↓ 31 callersMethod_run
(self, **kwargs)
scripts/test_ars_apply_revision_patch.py:84
↓ 31 callersMethod_v
(self, data: dict, manifest: dict | None = ...)
scripts/test_check_surface_form_parity.py:40
↓ 31 callersFunctionload_json_schema
Load a JSON Schema file and verify it parses as Draft 2020-12. Centralised so test files don't re-implement the same load + check_schema pair
tests/test_helpers.py:49
↓ 30 callersFunction_report
(task="citation_extraction", agg_value=0.95, agg_metric="accuracy", agg_direction="higher_is_bette
scripts/test_check_ranking_lift.py:50
↓ 30 callersMethodanchored_fixture
(self, with_frontmatter: bool = False)
scripts/test_ars_apply_revision_patch.py:99
↓ 30 callersFunctionrun_lint
Run the lint script in `cwd`. Returns CompletedProcess.
scripts/adapters/tests/test_check_corpus_consumer_protocol.py:21
↓ 29 callersFunctionsupported_entry
Minimal SUPPORTED row — INV-1 positive baseline.
scripts/test_claim_audit_schema.py:64
↓ 28 callersFunction_manifest
( *, claims: list[dict[str, Any]] | None = None, mncs: list[dict[str, str]] | None = None, man
scripts/test_claim_audit_pipeline.py:63
↓ 28 callersFunctionclean_timestamps
Return a function `_clean(doc, extra_blank=None)` that returns a copy of a dict/list with timestamp-like fields blanked to '<TIMESTAMP>'. By
scripts/adapters/tests/conftest.py:55
↓ 28 callersFunctionwarn_suspicious
Soft warnings per spec §4.3 (SC-1 baseline lag through SC-11 panel_size sanity). Non-blocking; printed to stderr by main().
scripts/check_sprint_contract.py:86
↓ 27 callersFunction_safe_get
Dotted-path get on a dict tree; returns None if any segment missing.
scripts/check_audit_artifact_consistency.py:195
↓ 26 callersFunction_baseline_text
Return template text and assert baseline anchors are present.
scripts/test_check_v3_6_8_audit_scope_block.py:95
↓ 26 callersFunction_run_lint
Run the v3.7.1 audit-scope lint as a subprocess (so sys.exit propagates).
scripts/test_check_v3_6_8_audit_scope_block.py:60
↓ 26 callersFunction_valid_sr_report
Returns a fresh fully-valid SR compliance report. Callers may mutate freely.
scripts/test_check_compliance_report.py:14
↓ 26 callersFunction_write_aligned_fixture
Everything lines up — baseline for PASS cases and drift mutations.
scripts/test_check_version_consistency.py:145
↓ 26 callersMethodassertInvalid
(self, doc: dict[str, Any])
scripts/test_audit_schemas.py:412
↓ 26 callersFunctionparse_ref_marker
Parse the FIRST <!--ref:...--> marker found in `text`. Returns None if no ref marker is present (e.g. a bare `HIGH-BLOCK` token in prose — which m
scripts/check_v3_10_policy.py:165
↓ 25 callersFunction_run_with
Write report to a temp file and run the validator against it.
scripts/test_check_compliance_report.py:99
↓ 25 callersFunctionbuild_passport
Minimal passport carrying the #260 aggregates the lint reads. A standard happy-path passport: one manifest with one experiment-backed claim,
scripts/test_experiment_provenance.py:183
↓ 25 callersFunctionbuild_schema_validator
Construct a Draft 2020-12 validator with format checking enabled. Without format_checker, format keywords (date-time on verified_at / acknowl
tests/test_helpers.py:64
↓ 24 callersFunction_entry
(**overrides)
scripts/test_verification_gate.py:27
↓ 24 callersFunction_write
(path: Path, content: str)
scripts/test_check_ci_pytest_manifest.py:53
↓ 24 callersFunctionmain
(argv: list[str] | None = None)
scripts/check_audit_artifact_consistency.py:2001
↓ 24 callersFunctionrun_lint
(cwd: Path)
scripts/test_check_domain_evidence_profile.py:35
↓ 23 callersFunction_base_entry
()
scripts/adapters/tests/test_literature_corpus_entry_schema.py:333
↓ 23 callersFunction_clone_repo
Copy the four lint-relevant files into a minimal repo tree under tmp_path.
scripts/test_check_domain_evidence_profile.py:48
↓ 23 callersFunction_copy_clean
Copy clean fixture to a tmp dir for mutation.
scripts/test_check_evals_gold_set.py:19
↓ 23 callersFunction_load_yaml
(path: Path)
scripts/test_pattern_eval_runtime.py:127
↓ 23 callersFunctionreduce_lookup_verified
Reduce per-resolver outcomes to a 3-class lookup_verified value. Each value in `resolver_outcomes` is a dict with at least `status`, and (for
scripts/citation_verification_summary.py:44
↓ 23 callersMethodtitle_search
Title search under the #431 exact-title-or-bust gate. A candidate matches iff it clears the 0.70 ratio AND is an exact normalized tit
scripts/arxiv_client.py:191
↓ 22 callersFunction_clients
Build a clients dict of MagicMocks. Pass a configured mock per resolver, or None to get a default (all lookups miss).
scripts/test_verification_gate.py:50
↓ 22 callersFunction_run
(args, cwd=None)
scripts/adapters/tests/test_check_literature_corpus_schema.py:20
↓ 22 callersMethoddecide
(self, p)
scripts/test_ars_write_scope_guard.py:112
↓ 21 callersFunction_agent_path
(rel: str)
scripts/test_check_v3_6_8_pattern_protection.py:619
↓ 21 callersMethodput
Store (or overwrite) the resolver response, stamping it now (UTC).
scripts/verification_cache.py:117
↓ 20 callersMethod_patch
(self, mutate)
scripts/test_check_216_surface_form.py:38
↓ 20 callersFunction_rx
(pattern: str)
scripts/check_rq_framing_patterns.py:35
↓ 20 callersFunctionmake_valid_jsonl_events_no_tool
()
scripts/test_check_audit_artifact_consistency.py:209
↓ 20 callersFunctionrun_lint
(args: list[str] | None = None)
scripts/test_check_v3_9_0_triangulation.py:16
↓ 20 callersFunctionuncited_audit_failure_entry
Minimal UAF-INV-* positive baseline (v3.8.2 / #118).
scripts/test_claim_audit_schema.py:181
↓ 19 callersFunction_entry
(**overrides)
scripts/test_citation_verification_summary.py:42
↓ 19 callersFunctionanchorize_text
Return the anchored document text (pure function; parser may raise).
scripts/ars_anchorize_draft.py:85
↓ 19 callersMethodassertLintClean
Assert lint exits 0 (no findings) on a passport that should pass.
scripts/test_claim_audit_schema.py:339
↓ 19 callersFunctionclaim
( *, claim_id: str = "C-001", kind: str = "empirical", planned_refs: list[str] | None = None,
scripts/test_experiment_provenance.py:141
↓ 18 callersFunction_load_schema
()
scripts/adapters/tests/test_rejection_log_schema.py:12
↓ 18 callersFunction_result
Build a synthetic claim_audit_result row for matrix-row tests.
scripts/test_claim_audit_finalizer.py:105
↓ 18 callersFunction_run
(*args)
scripts/adapters/tests/test_obsidian.py:13
↓ 18 callersMethoddecide_in_project
(self, p)
scripts/test_ars_write_scope_guard.py:577
↓ 18 callersFunctionmanifest
(claims: list[dict[str, Any]] | None = None)
scripts/test_experiment_provenance.py:159
↓ 17 callersFunction_run
(root: Path)
scripts/test_check_firm_rules_sync.py:32
↓ 17 callersFunction_run
(*args)
scripts/adapters/tests/test_zotero.py:13
↓ 17 callersFunction_run_launcher
Run the launcher with PATH = bin_dir + system dirs (bin_dir first, so injected interpreters shadow the real ones). Returns (exit_code, stdout, std
scripts/test_run_guard_launcher.py:74
↓ 17 callersFunction_validator
Validator with format_checker so format keywords (date-time on generated_at) are actually enforced. Same pattern as T2's test_literature_corpu
scripts/adapters/tests/test_rejection_log_schema.py:17
↓ 17 callersFunctiondetect_uncited
Return `(is_candidate, trigger_tokens)` for one sentence. Trigger tokens are returned in document order (left-to-right in the source sentence
scripts/uncited_assertion_detector.py:155
↓ 17 callersFunctionload_schema
()
scripts/test_verify_submission_package.py:30
↓ 17 callersFunctionrun_lint
Invoke the lint subprocess; returns (exit_code, stdout, stderr).
scripts/test_claim_audit_schema.py:230
↓ 17 callersFunctionverify_citation
Verify one citation's existence across the four resolvers. `entry` carries citation_key, title, authors, year, source_pointer, optional doi /
scripts/verification_gate/__init__.py:134
↓ 16 callersFunction_measured
(name, metric="accuracy", value=1.0, threshold=0.9, comparison=">=", passed=True, per_class=None
scripts/test_render_eval_comment.py:17
↓ 16 callersFunction_mutate
Remove the exact (case-sensitive) literal; assert it was present so a drifted probe fails loudly instead of exercising nothing.
scripts/test_check_390_revision_patch_discipline.py:90
↓ 16 callersFunction_run
(workdir: Path, *extra_args: str)
scripts/test_check_pipeline_integrity.py:13
↓ 16 callersFunctionprovenance_entry
A well-formed experiment_provenance[] entry.
scripts/test_experiment_provenance.py:97
↓ 16 callersFunctionrun_dir
Run the CLI on a package dir; returns (exit_code, report_dict).
scripts/test_verify_submission_package.py:34
↓ 16 callersFunctionwrite_passport
(tmp: Path, body: dict[str, Any])
scripts/test_claim_audit_schema.py:224
↓ 15 callersFunction_run_lint
Run the v3.6.8 cite-provenance pipeline lint.
scripts/test_check_v3_6_8_cite_provenance_pipeline.py:31
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