sciwrite-lint 0.4.0__tar.gz → 0.5.1__tar.gz

{sciwrite_lint-0.4.0/sciwrite_lint.egg-info → sciwrite_lint-0.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciwrite-lint
-Version: 0.4.0
+Version: 0.5.1
 Summary: A linter for scientific manuscripts — reference verification, consistency checking, and structural validation.
 Author: Sergey Samsonau
 Maintainer-email: Authentic Research Partners LLC <info@arpconnect.com>
@@ -147,7 +147,7 @@ sciwrite-lint contributions paper.pdf --format json
 
 ### Optimizations
 
-Three models — a vision model (Qwen3-VL-2B default, or 8B FP8 via `--vision-backend vllm` for +15% accuracy), an embedding model (Arctic Embed), and an 8B reasoning LLM (Qwen3 via vLLM) — share a single consumer GPU. The pipeline runs each in its own stage and explicitly stops one before starting the next, so only one ever owns GPU memory at a time (same code path on WSL2 and native Linux). FP8 weights and KV cache (Ada Lovelace+) and per-paper SQLite caching with hash-based invalidation are baseline. On top of that:
+Three models — a vision model (Qwen3-VL-2B default, or 8B FP8 via `--vision-backend vllm` for +15% accuracy), an embedding model (Arctic Embed), and an 8B reasoning LLM (Qwen3 via vLLM) — share a single consumer GPU. The pipeline runs each in its own stage and explicitly stops one before starting the next, so only one ever owns GPU memory at a time (same code path on WSL2 and native Linux). FP8 weights and KV cache (Ada Lovelace+) and per-paper SQLite caching are baseline; every cache layer pins its inputs by hash so editing the paper, replacing a figure, or refreshing a reference recomputes only what's affected (see the *Iterative editing* subsection under Usage — `--fresh` is not part of the normal loop). On top of that:
 
 - **Cost-aware verify-claim ladder** — sentence chunk → paragraph chunk → whole section. Each level fans out top-N candidates in parallel; stops on a conclusive verdict. Most claims resolve at the cheap sentence level (~200-token prompts) instead of paying for whole sections (~5K tokens), with full-section escalation reserved for hard cases
 - **Prefix-first prompt structure** — shared context placed before variable content in all prompts, maximizing vLLM's automatic prefix caching
@@ -158,11 +158,11 @@ Three models — a vision model (Qwen3-VL-2B default, or 8B FP8 via `--vision-ba
 - **14-source full-text cascade** — early exit on first successful download across arXiv, Semantic Scholar, OpenAlex, PubMed Central, Europe PMC, Unpaywall, bioRxiv, NBER, RePEc/IDEAS, HAL, ERIC, NASA ADS, OSF Preprints, CORE
 - **Live monitoring** *(advanced)* — `sciwrite-lint containers monitor` shows service health, VRAM usage, and KV cache utilization in a terminal dashboard
 
-Full pipeline on a 50-reference paper: ~30 minutes initial (dominated by downloads and claim verification), minutes on cached reruns. The pipeline automatically swaps vLLM containers to free GPU for embedding and vision stages (~50× faster than CPU) — same code path on WSL2 and native Linux.
+The pipeline automatically swaps vLLM containers to free GPU for embedding and vision stages (~50× faster than CPU).
 
 ## Install
 
-**Assumed setup:** A workstation with an NVIDIA GPU (16+ GB VRAM). Tested on WSL2 with NVIDIA driver 546.01+. Native Linux is likely to work with GPU memory allocation tuning (see [docs/services.md](https://github.com/authentic-research-partners/sciwrite-lint/blob/main/docs/services.md#embedding-device)). Not tested on macOS.
+**Assumed setup:** A workstation with an NVIDIA GPU (16+ GB VRAM). Tested on WSL2 with NVIDIA driver 546.01+. Native Linux uses the same GPU-sequencing code path with no extra configuration (see [docs/services.md](https://github.com/authentic-research-partners/sciwrite-lint/blob/main/docs/services.md#embedding-device)), though it isn't actively tested. Not tested on macOS.
 
 Requires [uv](https://docs.astral.sh/uv/getting-started/installation/), a container runtime (podman or docker), CUDA drivers, and [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html).
 
@@ -207,6 +207,8 @@ sciwrite-lint containers start         # start GROBID + vLLM (needs GPU for vLLM
 sciwrite-lint containers monitor       # live dashboard: service health, VRAM, KV cache
 ```
 
+`init` detects `.tex` files and their `.bib` references and generates a `.sciwrite-lint.toml` config. Review to confirm the right files were detected.
+
 ### WSL2: disable CUDA Sysmem Fallback (recommended)
 
 By default Windows silently spills GPU overflow into system RAM via PCIe (30–100× slower than VRAM); you'll see this as a sudden throughput collapse during the heaviest pipeline stages with no error in the logs. Tell the NVIDIA driver to fail loudly instead:
@@ -217,8 +219,6 @@ Driver 546.01+. After this, WSL2 behaves like native Linux on overflow (CUDA OOM
 
 ![Monitor dashboard](https://github.com/authentic-research-partners/sciwrite-lint/raw/main/docs/monitor.png)
 
-`init` detects `.tex` files and their `.bib` references and generates a `.sciwrite-lint.toml` config. Review to confirm the right files were detected.
-
 **Providing references manually — two drop folders.** sciwrite-lint reads two local directories before going to the open-access waterfall, kept separate because the folder itself signals how much to trust the source:
 
 - `local_pdfs/` — **academic sources**. Accepts `.pdf` (primary) and `.md` summaries you've written yourself. Use this for paywalled papers, for OA papers whose publisher requires a browser (Cloudflare/JS walls, Cell, Springer, some PMC pages), and for anything you'd cite as peer-reviewed evidence.
@@ -280,9 +280,36 @@ sciwrite-lint contributions --paper my_paper    # add contribution axes to SciLi
 sciwrite-lint contributions paper.pdf           # standalone file scoring
 ```
 
+**Supported inputs.**
+
+*The manuscript you check:*
+
+| Format | Notes |
+|---|---|
+| `.tex` | LaTeX — hand-written, or pandoc-generated (e.g. from Markdown); pandoc's heading anchors are unwrapped automatically. |
+| `.pdf` | Parsed via GROBID (container required). |
+
+*Cited sources you optionally supply (drop folders — see [Setup](#setup)):*
+
+| Folder | Accepts | Trust level |
+|---|---|---|
+| `local_pdfs/` | `.pdf`, `.md` (your own summaries) | academic |
+| `local_web/` | `.mhtml` / `.mht`, `.md` | web capture |
+
 `check` runs the full pipeline in one command: text checks → figure analysis → LLM consistency → reference verification via APIs → download and parse cited papers → claim verification → consistency checks on cited papers → bibliography verification → aggregate reliability scores → SciLint Score. An initial run on a 50-reference paper takes up to 30 minutes (dominated by downloads and claim verification); subsequent cached runs complete in minutes.
 
-Use `--fresh` to start from scratch (backs up the existing workspace before recreating it).
+### Iterative editing — no `--fresh` needed
+
+`sciwrite-lint check` invalidates cached results whenever the inputs they were derived from change, so rerunning after an edit just works. Concretely:
+
+- **Edit a sentence or paragraph** → the manuscript-LLM checks (prose-quality, cross-section consistency, etc.) re-run only on the touched sentences and their paragraph siblings; untouched prose stays cached
+- **Edit a paragraph around a citation** → the claim verifier reruns on the edited prose
+- **Replace a figure** (overwrite the PNG/PDF in your tree) → the vision cache re-describes it
+- **Swap the local LLM model** (e.g. `qwen3` ↔ `gemma3` via `--model`) → manuscript-check rows and claim verdicts no longer count as cache hits
+- **Overwrite a reference PDF** in your drop folder, or **re-fetch** an open-access PDF that has new bytes → the parser, embeddings, and claim verifier all rerun against the new content
+- **Upgrade a summary `.md` to a real PDF** in your drop folder → claims are re-verified against the richer evidence
+
+Use `--fresh` only when you want to wipe the workspace deliberately (it backs up the existing workspace before recreating it). It is not the answer to "I edited the paper and a finding looks stale" — if you ever see that, file an issue; a cache invariant is wrong and we'll fix it.
 
 Use `--checks ID[,ID...]` to run only the listed checks (comma-separated), disabling the rest for this invocation. Useful for fast iteration during editing (`--checks prose-quality` runs just the prose review), for debugging a single check, or for scripting a two-pass workflow. Unknown check IDs fail loudly — run `sciwrite-lint checks` to list available IDs.
 

{sciwrite_lint-0.4.0 → sciwrite_lint-0.5.1}/README.md

@@ -81,7 +81,7 @@ sciwrite-lint contributions paper.pdf --format json
 
 ### Optimizations
 
-Three models — a vision model (Qwen3-VL-2B default, or 8B FP8 via `--vision-backend vllm` for +15% accuracy), an embedding model (Arctic Embed), and an 8B reasoning LLM (Qwen3 via vLLM) — share a single consumer GPU. The pipeline runs each in its own stage and explicitly stops one before starting the next, so only one ever owns GPU memory at a time (same code path on WSL2 and native Linux). FP8 weights and KV cache (Ada Lovelace+) and per-paper SQLite caching with hash-based invalidation are baseline. On top of that:
+Three models — a vision model (Qwen3-VL-2B default, or 8B FP8 via `--vision-backend vllm` for +15% accuracy), an embedding model (Arctic Embed), and an 8B reasoning LLM (Qwen3 via vLLM) — share a single consumer GPU. The pipeline runs each in its own stage and explicitly stops one before starting the next, so only one ever owns GPU memory at a time (same code path on WSL2 and native Linux). FP8 weights and KV cache (Ada Lovelace+) and per-paper SQLite caching are baseline; every cache layer pins its inputs by hash so editing the paper, replacing a figure, or refreshing a reference recomputes only what's affected (see the *Iterative editing* subsection under Usage — `--fresh` is not part of the normal loop). On top of that:
 
 - **Cost-aware verify-claim ladder** — sentence chunk → paragraph chunk → whole section. Each level fans out top-N candidates in parallel; stops on a conclusive verdict. Most claims resolve at the cheap sentence level (~200-token prompts) instead of paying for whole sections (~5K tokens), with full-section escalation reserved for hard cases
 - **Prefix-first prompt structure** — shared context placed before variable content in all prompts, maximizing vLLM's automatic prefix caching
@@ -92,11 +92,11 @@ Three models — a vision model (Qwen3-VL-2B default, or 8B FP8 via `--vision-ba
 - **14-source full-text cascade** — early exit on first successful download across arXiv, Semantic Scholar, OpenAlex, PubMed Central, Europe PMC, Unpaywall, bioRxiv, NBER, RePEc/IDEAS, HAL, ERIC, NASA ADS, OSF Preprints, CORE
 - **Live monitoring** *(advanced)* — `sciwrite-lint containers monitor` shows service health, VRAM usage, and KV cache utilization in a terminal dashboard
 
-Full pipeline on a 50-reference paper: ~30 minutes initial (dominated by downloads and claim verification), minutes on cached reruns. The pipeline automatically swaps vLLM containers to free GPU for embedding and vision stages (~50× faster than CPU) — same code path on WSL2 and native Linux.
+The pipeline automatically swaps vLLM containers to free GPU for embedding and vision stages (~50× faster than CPU).
 
 ## Install
 
-**Assumed setup:** A workstation with an NVIDIA GPU (16+ GB VRAM). Tested on WSL2 with NVIDIA driver 546.01+. Native Linux is likely to work with GPU memory allocation tuning (see [docs/services.md](https://github.com/authentic-research-partners/sciwrite-lint/blob/main/docs/services.md#embedding-device)). Not tested on macOS.
+**Assumed setup:** A workstation with an NVIDIA GPU (16+ GB VRAM). Tested on WSL2 with NVIDIA driver 546.01+. Native Linux uses the same GPU-sequencing code path with no extra configuration (see [docs/services.md](https://github.com/authentic-research-partners/sciwrite-lint/blob/main/docs/services.md#embedding-device)), though it isn't actively tested. Not tested on macOS.
 
 Requires [uv](https://docs.astral.sh/uv/getting-started/installation/), a container runtime (podman or docker), CUDA drivers, and [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html).
 
@@ -141,6 +141,8 @@ sciwrite-lint containers start         # start GROBID + vLLM (needs GPU for vLLM
 sciwrite-lint containers monitor       # live dashboard: service health, VRAM, KV cache
 ```
 
+`init` detects `.tex` files and their `.bib` references and generates a `.sciwrite-lint.toml` config. Review to confirm the right files were detected.
+
 ### WSL2: disable CUDA Sysmem Fallback (recommended)
 
 By default Windows silently spills GPU overflow into system RAM via PCIe (30–100× slower than VRAM); you'll see this as a sudden throughput collapse during the heaviest pipeline stages with no error in the logs. Tell the NVIDIA driver to fail loudly instead:
@@ -151,8 +153,6 @@ Driver 546.01+. After this, WSL2 behaves like native Linux on overflow (CUDA OOM
 
 ![Monitor dashboard](https://github.com/authentic-research-partners/sciwrite-lint/raw/main/docs/monitor.png)
 
-`init` detects `.tex` files and their `.bib` references and generates a `.sciwrite-lint.toml` config. Review to confirm the right files were detected.
-
 **Providing references manually — two drop folders.** sciwrite-lint reads two local directories before going to the open-access waterfall, kept separate because the folder itself signals how much to trust the source:
 
 - `local_pdfs/` — **academic sources**. Accepts `.pdf` (primary) and `.md` summaries you've written yourself. Use this for paywalled papers, for OA papers whose publisher requires a browser (Cloudflare/JS walls, Cell, Springer, some PMC pages), and for anything you'd cite as peer-reviewed evidence.
@@ -214,9 +214,36 @@ sciwrite-lint contributions --paper my_paper    # add contribution axes to SciLi
 sciwrite-lint contributions paper.pdf           # standalone file scoring
 ```
 
+**Supported inputs.**
+
+*The manuscript you check:*
+
+| Format | Notes |
+|---|---|
+| `.tex` | LaTeX — hand-written, or pandoc-generated (e.g. from Markdown); pandoc's heading anchors are unwrapped automatically. |
+| `.pdf` | Parsed via GROBID (container required). |
+
+*Cited sources you optionally supply (drop folders — see [Setup](#setup)):*
+
+| Folder | Accepts | Trust level |
+|---|---|---|
+| `local_pdfs/` | `.pdf`, `.md` (your own summaries) | academic |
+| `local_web/` | `.mhtml` / `.mht`, `.md` | web capture |
+
 `check` runs the full pipeline in one command: text checks → figure analysis → LLM consistency → reference verification via APIs → download and parse cited papers → claim verification → consistency checks on cited papers → bibliography verification → aggregate reliability scores → SciLint Score. An initial run on a 50-reference paper takes up to 30 minutes (dominated by downloads and claim verification); subsequent cached runs complete in minutes.
 
-Use `--fresh` to start from scratch (backs up the existing workspace before recreating it).
+### Iterative editing — no `--fresh` needed
+
+`sciwrite-lint check` invalidates cached results whenever the inputs they were derived from change, so rerunning after an edit just works. Concretely:
+
+- **Edit a sentence or paragraph** → the manuscript-LLM checks (prose-quality, cross-section consistency, etc.) re-run only on the touched sentences and their paragraph siblings; untouched prose stays cached
+- **Edit a paragraph around a citation** → the claim verifier reruns on the edited prose
+- **Replace a figure** (overwrite the PNG/PDF in your tree) → the vision cache re-describes it
+- **Swap the local LLM model** (e.g. `qwen3` ↔ `gemma3` via `--model`) → manuscript-check rows and claim verdicts no longer count as cache hits
+- **Overwrite a reference PDF** in your drop folder, or **re-fetch** an open-access PDF that has new bytes → the parser, embeddings, and claim verifier all rerun against the new content
+- **Upgrade a summary `.md` to a real PDF** in your drop folder → claims are re-verified against the richer evidence
+
+Use `--fresh` only when you want to wipe the workspace deliberately (it backs up the existing workspace before recreating it). It is not the answer to "I edited the paper and a finding looks stale" — if you ever see that, file an issue; a cache invariant is wrong and we'll fix it.
 
 Use `--checks ID[,ID...]` to run only the listed checks (comma-separated), disabling the rest for this invocation. Useful for fast iteration during editing (`--checks prose-quality` runs just the prose review), for debugging a single check, or for scripting a two-pass workflow. Unknown check IDs fail loudly — run `sciwrite-lint checks` to list available IDs.
 

{sciwrite_lint-0.4.0 → sciwrite_lint-0.5.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "sciwrite-lint"
-version = "0.4.0"
+version = "0.5.1"
 description = "A linter for scientific manuscripts — reference verification, consistency checking, and structural validation."
 requires-python = ">=3.13,<3.14"
 license = "MIT"
@@ -86,3 +86,5 @@ sciwrite-lint = "sciwrite_lint.__main__:main"
 [tool.setuptools.packages.find]
 include = ["sciwrite_lint*"]
 
+[tool.setuptools.package-data]
+

{sciwrite_lint-0.4.0 → sciwrite_lint-0.5.1}/sciwrite_lint/__init__.py

@@ -2,7 +2,7 @@
 
 from sciwrite_lint.exceptions import LLMConnectionError, SciWriteLintError
 
-__version__ = "0.4.0"
+__version__ = "0.5.1"
 
 from sciwrite_lint.oa import (
     DownloadResult,

{sciwrite_lint-0.4.0 → sciwrite_lint-0.5.1}/sciwrite_lint/__main__.py

@@ -14,8 +14,6 @@ import argparse
 import sys
 from pathlib import Path
 
-from loguru import logger
-
 from sciwrite_lint import __version__
 from sciwrite_lint.cli._common import (
     _classify_verify_issue as _classify_verify_issue,
@@ -42,6 +40,31 @@ _REPLACE_HELP = (
 # ---------------------------------------------------------------------------
 
 
+def _register_optional_extensions(
+    sub: argparse._SubParsersAction,  # type: ignore[type-arg]
+) -> None:
+    """Load CLI extensions discovered under ``sciwrite_lint``.
+
+    An underscore-prefixed subpackage is a CLI extension when its
+    ``__init__.py`` defines ``register_cli(sub)``. Discovery walks
+    ``sciwrite_lint.__path__`` via ``pkgutil``, so no extension package
+    names appear in this source — adding or removing one is a filesystem
+    change.
+    """
+    import importlib
+    import pkgutil
+
+    import sciwrite_lint as _pkg
+
+    for _finder, name, ispkg in pkgutil.iter_modules(_pkg.__path__):
+        if not ispkg or not name.startswith("_"):
+            continue
+        ext = importlib.import_module(f"{_pkg.__name__}.{name}")
+        register = getattr(ext, "register_cli", None)
+        if register is not None:
+            register(sub)
+
+
 def main(argv: list[str] | None = None) -> int:
     from sciwrite_lint.cli.check import run_check, run_checks_list
     from sciwrite_lint.cli.config import run_config
@@ -125,47 +148,8 @@ def main(argv: list[str] | None = None) -> int:
     p_checks = sub.add_parser("checks", help="List all registered checks")
     p_checks.set_defaults(func=run_checks_list)
 
-    # --- aicode-lint (optional — only registered when the WIP module is installed) ---
-    # ``sciwrite_lint.aicode_lint`` is excluded from the public release rsync
-    # while it stabilizes. Use ``importlib.util.find_spec`` to check whether
-    # the module is present rather than try/except ImportError (separately
-    # banned). Public installs (pip from PyPI) won't have it; dev installs
-    # do. Check the parent ``sciwrite_lint.aicode_lint`` first because
-    # ``find_spec`` raises ``ModuleNotFoundError`` on a missing intermediate
-    # path; once the parent is confirmed present, the child lookup is safe.
-    import importlib.util as _importlib_util
-
-    if _importlib_util.find_spec("sciwrite_lint.aicode_lint") is not None:
-        from sciwrite_lint.aicode_lint.cli import run_aicode_lint
-
-        p_aicode = sub.add_parser(
-            "aicode-lint",
-            help="LLM code review on Python sources via local vLLM (semantic antipatterns)",
-        )
-        p_aicode.add_argument(
-            "paths",
-            nargs="*",
-            help="Files, directories, or globs to scan (default: sciwrite_lint/**/*.py)",
-        )
-        p_aicode.add_argument(
-            "--rules",
-            default=None,
-            metavar="ID[,ID...]",
-            help="Run only the listed rule IDs (comma-separated). Default: all built-in rules.",
-        )
-        p_aicode.add_argument(
-            "--list-rules",
-            action="store_true",
-            help="Print the rule registry and exit.",
-        )
-        p_aicode.add_argument(
-            "--format",
-            choices=["terminal", "json"],
-            default=None,
-            help="Output format (default: terminal).",
-        )
-        p_aicode.add_argument("--config", help="Path to .sciwrite-lint.toml")
-        p_aicode.set_defaults(func=run_aicode_lint)
+    # Load optional underscore-prefixed CLI extension subpackages (if any).
+    _register_optional_extensions(sub)
 
     # --- init ---
     p_init = sub.add_parser(
@@ -270,12 +254,6 @@ def main(argv: list[str] | None = None) -> int:
     # --- verify-claims ---
     p_vc = sub.add_parser("verify-claims", help="Verify claims against cited sources")
     p_vc.add_argument("--paper", required=True, help="Paper to verify")
-    p_vc.add_argument(
-        "--backend",
-        choices=["vllm", "claude"],
-        default="vllm",
-        help="vllm (local LLM, fast) or claude (Claude CLI, deep)",
-    )
     p_vc.add_argument(
         "--model",
         choices=_TEXT_MODELS,
@@ -499,14 +477,32 @@ def main(argv: list[str] | None = None) -> int:
         p_vllm.print_help()
         return 0
 
-    # Set up file logging from config (stderr sink stays at INFO by default)
-    try:
-        config = load_config(
-            Path(args.config) if getattr(args, "config", None) else None
-        )
-    except Exception as e:
-        logger.debug("Config load failed, using defaults: {}", e)
+    # Set up file logging from config (stderr sink stays at INFO by default).
+    # ``load_config`` already returns ``LintConfig()`` when no config file is
+    # discovered; reaching the exception path means a file WAS found (or
+    # explicitly passed via --config) but failed to parse or validate.
+    # Surface that instead of silently substituting hardcoded defaults — a
+    # broken TOML otherwise produces results computed against the wrong
+    # workspace, paper list, or API keys.
+    #
+    # The ``init`` command is the one exception: its job is to scaffold a
+    # config, so it must run against a missing, broken, or sentinel TOML
+    # without aborting. Use ``LintConfig()`` for logging setup only and let
+    # init proceed to (over)write the file.
+    if args.command == "init":
         config = LintConfig()
+    else:
+        try:
+            config = load_config(
+                Path(args.config) if getattr(args, "config", None) else None
+            )
+        except Exception as e:
+            cfg_arg = getattr(args, "config", None)
+            cfg_hint = f" ({cfg_arg})" if cfg_arg else " (.sciwrite-lint.toml)"
+            raise SystemExit(
+                f"ERROR: failed to load configuration{cfg_hint}: {type(e).__name__}: {e}\n"
+                "  Fix the TOML or remove the file to use built-in defaults."
+            ) from e
     _setup_logging(config)
 
     return args.func(args)

{sciwrite_lint-0.4.0 → sciwrite_lint-0.5.1}/sciwrite_lint/cli/misc/parse.py

@@ -84,7 +84,7 @@ def run_parse(args: argparse.Namespace) -> int:
                         n = compute_and_store_embeddings(key, text, refs_dir)
                         print(f"    {key}: {n} chunks")
                     except Exception as e:
-                        print(f"    {key}: error — {e}")
+                        logger.warning("parse: embedding failed for {}: {}", key, e)
 
     print(f"\n  Summary: {cached} cached, {parsed} parsed, {failed} failed")
     if failed:

{sciwrite_lint-0.4.0 → sciwrite_lint-0.5.1}/sciwrite_lint/cli/verify.py

@@ -335,6 +335,7 @@ def run_ref_health(args: argparse.Namespace) -> int:
     academic_unmatched: list[Path] = []
     web_matched: dict[str, Path] = {}
     web_unmatched: list[Path] = []
+    local_match_error: str | None = None
     try:
         if tex_file:
             from sciwrite_lint.config import load_config as _load_cfg
@@ -356,8 +357,13 @@ def run_ref_health(args: argparse.Namespace) -> int:
             _cfg.local_web_dir, titles, WEB_SUFFIXES
         )
     except Exception as e:
-        logger.debug(
-            f"ref-health: local source matching skipped ({type(e).__name__}: {e})"
+        # Record the failure so the report renders a visible notice instead
+        # of silently producing a ref-health output with the local-source
+        # section missing. Log at WARNING (not DEBUG) so the operator sees
+        # it even when running with the default log level.
+        local_match_error = f"{type(e).__name__}: {e}"
+        logger.warning(
+            "ref-health: local source matching skipped ({})", local_match_error
         )
 
     # --- Output ---
@@ -398,7 +404,9 @@ def run_ref_health(args: argparse.Namespace) -> int:
     if web_count:
         print(f"    ({web_count} web resources)")
 
-    # Local sources — academic (PDFs + MD summaries) + web (MD + MHTML)
+    # Local sources — academic (PDFs + MD summaries) + web (MD + MHTML).
+    # Matching failures are surfaced via logger.warning (above) so they
+    # appear in the operator's terminal regardless of report formatting.
     if academic_matched or academic_unmatched:
         print("\n  LOCAL ACADEMIC SOURCES")
         if academic_matched:
@@ -425,7 +433,7 @@ def run_ref_health(args: argparse.Namespace) -> int:
 
 
 def run_verify_claims(args: argparse.Namespace) -> int:
-    """Verify claims against cited sources using local LLM or Claude Opus."""
+    """Verify claims against cited sources using local vLLM."""
     from sciwrite_lint.cli._common import _load_config, _resolve_paper
 
     config = _load_config(args)
@@ -446,7 +454,6 @@ def run_verify_claims(args: argparse.Namespace) -> int:
             refs_dir,
             config=config,
             bib_path=pc.bib,
-            backend=args.backend,
             model=args.model,
             key_filter=args.key,
             limit=args.limit,