ci: validate Issue #33 release candidate

skills/deeppapernote/references/user-configuration.md

@@ -2,6 +2,8 @@
 
 Use one device-local User Configuration at `~/.deeppapernote/config.json`:
 
+For isolated validation only, `DEEPPAPERNOTE_CONFIG_PATH` may relocate this one file for the current process. It is not a preference, does not create a second configuration layer, and must not be persisted into the configuration itself.
+
 - `output_language`: `zh-CN` or `en`
 - `save_mode`: `workspace` or `obsidian`
 - `obsidian_vault`: existing absolute directory, required only in Obsidian mode

skills/deeppapernote/scripts/common.py

@@ -1265,6 +1265,25 @@ def _is_unique_exact_zotero_title_observation(
     )
 
 
+def _is_unique_exact_arxiv_title_observation(
+    anchor: dict[str, Any],
+    item: dict[str, Any],
+    observation: dict[str, Any],
+) -> bool:
+    relation = item.get("relation")
+    if not isinstance(relation, dict):
+        return False
+    return bool(
+        _string_field(item, "provider").lower() == "arxiv"
+        and _string_field(relation, "kind") == "arxiv_lookup"
+        and _string_field(relation, "match_kind") == "title"
+        and _string_field(relation, "match_resolution") == "unique_exact"
+        and _record_arxiv_id(observation)
+        and normalize_identity_title(_string_field(anchor, "title"))
+        == normalize_identity_title(_string_field(observation, "title"))
+    )
+
+
 def adjudicate_identity_observations(
     anchor: dict[str, Any],
     observations: list[Any],
@@ -1336,6 +1355,11 @@ def adjudicate_identity_observations(
             item,
             observation,
         )
+        unique_exact_arxiv_title_match = _is_unique_exact_arxiv_title_observation(
+            anchor,
+            item,
+            observation,
+        )
         if not title_author_year_match and not shared_identifiers:
             observation_provider = (
                 _string_field(item, "provider")
@@ -1379,6 +1403,7 @@ def adjudicate_identity_observations(
             not shared_identifiers
             and not title_author_year_match
             and not unique_exact_zotero_title_match
+            and not unique_exact_arxiv_title_match
         ):
             rejected_observations.append(
                 _identity_observation_summary(
@@ -1393,6 +1418,8 @@ def adjudicate_identity_observations(
             acceptance_reason = "shared_identifier"
         elif unique_exact_zotero_title_match:
             acceptance_reason = "unique_exact_zotero_title"
+        elif unique_exact_arxiv_title_match:
+            acceptance_reason = "unique_exact_arxiv_title"
         else:
             acceptance_reason = "title_author_year"
         summary = _identity_observation_summary(
@@ -2346,14 +2373,22 @@ def collect_metadata_observations(record: dict[str, Any]) -> list[dict[str, Any]
     title = normalize_whitespace(str(base.get("title", "")))
     arxiv_id = normalize_whitespace(str(base.get("arxiv_id", "")))
 
-    def append(provider: str, kind: str, value: str, candidate: dict[str, Any] | None) -> None:
+    def append(
+        provider: str,
+        kind: str,
+        value: str,
+        candidate: dict[str, Any] | None,
+        relation: dict[str, str] | None = None,
+    ) -> None:
         if not candidate:
             return
         observation = {
             "provider": provider,
             "retrieved_by": {"kind": kind, "value": value},
             "record": deepcopy(candidate),
         }
+        if relation:
+            observation["relation"] = relation
         if observation not in observations:
             observations.append(observation)
 
@@ -2377,11 +2412,26 @@ def append(provider: str, kind: str, value: str, candidate: dict[str, Any] | Non
         append("openalex", "title", title, oa)
         cross = choose_best_title_match(title, search_crossref_by_title(title, limit=5))
         append("crossref", "title", title, cross)
-        arxiv = choose_best_title_match(
-            title,
-            safe_fetch_arxiv_entries(search_query=f'ti:"{title}"', max_results=5),
+        arxiv_candidates = safe_fetch_arxiv_entries(
+            search_query=f'ti:"{title}"', max_results=5
+        )
+        arxiv = choose_best_title_match(title, arxiv_candidates)
+        exact_matches = [
+            candidate
+            for candidate in arxiv_candidates
+            if normalize_identity_title(_string_field(candidate, "title"))
+            == normalize_identity_title(title)
+        ]
+        relation = (
+            {
+                "kind": "arxiv_lookup",
+                "match_kind": "title",
+                "match_resolution": "unique_exact",
+            }
+            if arxiv is not None and len(exact_matches) == 1 and arxiv == exact_matches[0]
+            else None
         )
-        append("arxiv", "title", title, arxiv)
+        append("arxiv", "title", title, arxiv, relation)
 
     return observations
 

skills/deeppapernote/scripts/run_pipeline.py

@@ -82,11 +82,13 @@ def main() -> None:
     identity_json = workdir / f"{args.prefix}_identity.json"
     identity_trace_json = workdir / f"{args.prefix}_identity_repair_trace.json"
     fetch_json = workdir / f"{args.prefix}_fetch.json"
+    pdf_dir = workdir / f"{args.prefix}_pdfs"
     source_manifest_json = workdir / f"{args.prefix}_source_manifest.json"
     raw_sections_jsonl = workdir / f"{args.prefix}_raw_sections.jsonl"
     full_text_md = workdir / f"{args.prefix}_full_text.md"
     evidence_json = workdir / f"{args.prefix}_evidence.json"
     assets_json = workdir / f"{args.prefix}_assets.json"
+    assets_dir = workdir / f"{args.prefix}_assets"
     figures_json = workdir / f"{args.prefix}_figures.json"
     figure_decisions_json = workdir / f"{args.prefix}_figure_table_decisions.json"
     bundle_json = workdir / f"{args.prefix}_bundle.json"
@@ -138,6 +140,8 @@ def main() -> None:
             str(metadata_json),
             "--identity",
             str(identity_json),
+            "--dest-dir",
+            str(pdf_dir),
             "--output",
             str(fetch_json),
         ],
@@ -177,6 +181,8 @@ def main() -> None:
             str(scripts_dir / "extract_pdf_assets.py"),
             "--input",
             str(fetch_json),
+            "--assets-dir",
+            str(assets_dir),
             "--output",
             str(assets_json),
         ],

skills/deeppapernote/scripts/user_configuration.py

@@ -42,6 +42,9 @@ def __init__(
 
 
 def user_config_path() -> Path:
+    override = os.environ.get("DEEPPAPERNOTE_CONFIG_PATH", "").strip()
+    if override:
+        return Path(override).expanduser()
     return Path.home() / ".deeppapernote" / "config.json"
 
 

skills/deeppapernote/scripts/write_obsidian_note.py

@@ -305,7 +305,7 @@ def main() -> None:
         if figure_decisions
         else []
     )
-    Path(target_path).write_text(note_text, encoding="utf-8")
+    Path(target_path).write_text(note_text, encoding="utf-8", newline="\n")
     require_reference_hygiene(Path(target_path).read_text(encoding="utf-8"), "after save")
     asset_dir.mkdir(parents=True, exist_ok=True)
 

tests/conftest.py

@@ -15,11 +15,24 @@
 
 @pytest.fixture(autouse=True)
 def configured_user_home(tmp_path: Path, monkeypatch) -> Path:
-    monkeypatch.setenv("HOME", str(tmp_path))
     config_path = tmp_path / ".deeppapernote" / "config.json"
     config_path.parent.mkdir(exist_ok=True)
+    for name in (
+        "DEEPPAPERNOTE_OUTPUT_LANGUAGE",
+        "DEEPPAPERNOTE_SAVE_MODE",
+        "DEEPPAPERNOTE_OBSIDIAN_VAULT",
+        "DEEPPAPERNOTE_PAPERS_DIR",
+    ):
+        monkeypatch.delenv(name, raising=False)
+    monkeypatch.setenv("DEEPPAPERNOTE_CONFIG_PATH", str(config_path))
     config_path.write_text(
-        json.dumps({"output_language": "zh-CN", "save_mode": "workspace"}),
+        json.dumps(
+            {
+                "output_language": "zh-CN",
+                "save_mode": "workspace",
+                "papers_dir": "Research/Papers",
+            }
+        ),
         encoding="utf-8",
     )
     return config_path

tests/test_acquisition_artifacts.py

@@ -1505,6 +1505,57 @@ def test_collect_metadata_preserves_provider_result_as_identity_observation(
     ]
 
 
+def test_exact_swe_bench_title_admits_one_unique_arxiv_match(
+    tmp_path: Path,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    title = "SWE-bench: Can Language Models Resolve Real-world Github Issues?"
+    resolve_payload = {
+        "status": "ok",
+        "script": "resolve_paper.py",
+        "paper_id": "title:2156776fbf55",
+        "source_type": "title_query",
+        "title": title,
+        "metadata_sources": ["title_query"],
+    }
+    monkeypatch.setattr(common, "search_semantic_scholar", lambda *args, **kwargs: [])
+    monkeypatch.setattr(common, "search_openalex_by_title", lambda *args, **kwargs: [])
+    monkeypatch.setattr(common, "search_crossref_by_title", lambda *args, **kwargs: [])
+    monkeypatch.setattr(
+        common,
+        "safe_fetch_arxiv_entries",
+        lambda **kwargs: [
+            {
+                "source": "arxiv",
+                "source_type": "arxiv",
+                "title": "SWE-bench: Can Language Models Resolve Real-World GitHub Issues?",
+                "authors": ["Carlos E. Jimenez"],
+                "published": "2023-10-10T16:47:29Z",
+                "arxiv_id": "2310.06770",
+                "pdf_url": "https://arxiv.org/pdf/2310.06770v3",
+            }
+        ],
+    )
+
+    observations = common.collect_metadata_observations(resolve_payload)
+    identity, _ = build_identity_from_payloads(
+        tmp_path,
+        monkeypatch,
+        resolve_payload=resolve_payload,
+        metadata_payload={
+            **resolve_payload,
+            "script": "collect_metadata.py",
+            "identity_observations": observations,
+        },
+    )
+
+    assert identity["identity_verdict"] == "accepted"
+    assert identity["accepted_metadata"]["arxiv_id"] == "2310.06770"
+    assert identity["accepted_observations"][0]["reason"] == (
+        "unique_exact_arxiv_title"
+    )
+
+
 @pytest.mark.parametrize(
     "module",
     [extract_source_text, extract_evidence, extract_pdf_assets],

tests/test_run_pipeline_manifest.py

@@ -253,12 +253,19 @@ def fake_run(cmd: list[str], check: bool = True, **kwargs) -> object:
     assert fetch_call[fetch_call.index("--identity") + 1] == str(
         (workdir / "paper_identity.json").resolve()
     )
+    assert fetch_call[fetch_call.index("--dest-dir") + 1] == str(
+        (workdir / "paper_pdfs").resolve()
+    )
 
     evidence_call = calls[5]
     assert "--source-manifest" in evidence_call
     assert evidence_call[evidence_call.index("--source-manifest") + 1] == str(
         (workdir / "paper_source_manifest.json").resolve()
     )
+    assets_call = calls[6]
+    assert assets_call[assets_call.index("--assets-dir") + 1] == str(
+        (workdir / "paper_assets").resolve()
+    )
 
 
 def test_run_pipeline_stops_at_configuration_before_identity(

tests/test_user_configuration.py

@@ -15,13 +15,23 @@
     inspect_configuration,
     persist_preferences,
     resolve_preferences,
+    user_config_path,
 )
 
 PROJECT_ROOT = Path(__file__).resolve().parents[1]
 CONFIG_SCRIPT = PROJECT_ROOT / "skills/deeppapernote/scripts/user_configuration.py"
 ENVIRONMENT_SCRIPT = PROJECT_ROOT / "skills/deeppapernote/scripts/check_environment.py"
 
 
+def test_user_config_path_honors_process_isolation_override(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    isolated_path = tmp_path / "isolated" / "config.json"
+    monkeypatch.setenv("DEEPPAPERNOTE_CONFIG_PATH", str(isolated_path))
+
+    assert user_config_path() == isolated_path
+
+
 def test_first_use_requests_one_workspace_prompt_batch(tmp_path: Path) -> None:
     result = inspect_configuration(config_path=tmp_path / "config.json", environ={})
 
@@ -500,6 +510,10 @@ def test_output_language_reference_matches_both_machine_schemas() -> None:
 def test_configuration_cli_keeps_semantic_failures_repairable(
     configured_user_home: Path,
 ) -> None:
+    configured_user_home.write_text(
+        json.dumps({"output_language": "zh-CN", "save_mode": "workspace"}),
+        encoding="utf-8",
+    )
     result = subprocess.run(
         [sys.executable, str(CONFIG_SCRIPT), "--set-save-mode", "obsidian"],
         env=os.environ.copy(),
@@ -520,7 +534,7 @@ def test_environment_report_survives_missing_user_configuration(
     home = tmp_path / "empty-home"
     home.mkdir()
     env = os.environ.copy()
-    env["HOME"] = str(home)
+    env["DEEPPAPERNOTE_CONFIG_PATH"] = str(home / ".deeppapernote" / "config.json")
     result = subprocess.run(
         [sys.executable, str(ENVIRONMENT_SCRIPT)],
         env=env,