repo hygiene, tooling config, v0.2.0

- Untrack src/ocr_pipeline.egg-info from git, delete pyproject.toml~, stale run_008/run_009 dirs - Ruff config moved to [tool.ruff.lint] (silences deprecation warning) - Pre-commit: bump revs (ruff v0.14.13, mypy v1.18.1, hooks v6.0.0); drop redundant isort hook (ruff I already sorts imports) - mypy: add ignore_missing_imports for optional deps; types-PyYAML in dev extras; python_version=3.12 for numpy 2.5 stubs compat; CI step - Doctor: suppress paddle ccache UserWarning noise during check - CHANGELOG dated for 0.2.0; README minimal-style rewrite with collapsible details sections - Bump version to 0.2.0
2026-07-21 00:40:19 +02:00
parent bf968affaa
commit 7de0e716eb
14 changed files with 81 additions and 416 deletions
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -49,6 +49,9 @@ jobs:
      - name: Check formatting
        run: uv run ruff format --check src/ tests/

+      - name: Run mypy
+        run: uv run mypy src/ocr_pipeline
+
      - name: Run pytest
        run: uv run pytest tests/ -q --maxfail=1

--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,27 +1,22 @@
 repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.0
+    rev: v0.14.13
    hooks:
      - id: ruff
        args: [--fix]
      - id: ruff-format

  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.18.1
    hooks:
      - id: mypy
-        additional_dependencies: [pydantic, pyyaml, typer, rich, structlog, numpy, opencv-python-headless]
+        additional_dependencies: [pydantic, pyyaml, types-PyYAML, typer, rich, structlog, numpy, opencv-python-headless]

  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v6.0.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-yaml
      - id: check-toml
      - id: check-added-large-files
-
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

-## [Unreleased]
+## [0.2.0] - 2026-07-21

 ### Added
 - Knowledge graph: `kg_ocr.graph` builds a NetworkX graph (documents, chunks, entities, citations, entity co-occurrence) from pipeline chunk markdown; `kg_ocr.graph.analyzer` provides summaries, top entities/citations, and anomaly detection (low OCR confidence, empty chunks/documents, entity hubs).
@@ -32,6 +32,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `run` results table now shows Skipped count.
 - Run directories are created lazily on first write (no empty `run_NNN`).
 - `kg_ocr` is now a functional knowledge-graph package (graph/export need only networkx); txtai/litellm imports are lazy so the package imports in slim environments.
+- Ruff settings moved to `[tool.ruff.lint]` (silences per-run deprecation warning).
+- Pre-commit: bumped ruff, mypy, pre-commit-hooks; dropped the redundant isort hook.
+- mypy: added `ignore_missing_imports` for optional deps + `types-PyYAML` in dev extras; `python_version = "3.12"` to match numpy 2.5 stubs.
+- README: minimal-style rewrite with collapsible `<details>` sections.

 ### Fixed
 - ISBN regex no longer false-positives on years, URLs, job IDs, or dilutions. Now requires an explicit `ISBN` prefix and matches strict 13- or 10-digit structures.
@@ -40,6 +44,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

 ### Removed
 - Dead `src/ocr_pipeline/watch.py` shim (shadowed by the `watch/` package).
+- Stub `kg_ocr/cli/` directory (commands now in the main `ocr-pipeline` CLI).
+- Untracked `src/ocr_pipeline.egg-info` from git (still gitignored).
 - Unused core dependencies: `tqdm`, `scikit-image`, `sqlite-utils`, `xxhash`, `python-slugify`, `python-magic`, `legacy-cgi`.
 - Core dependency on `spacy` (moved to `scientific` extra).
 - Core dependency on `paddleocr`/`paddlepaddle` (moved to `paddle` extra).
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"

 [project]
 name = "ocr-pipeline"
-version = "0.1.0"
+version = "0.2.0"
 description = "OCR pipeline for life science screenshots - RAG ready"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -42,6 +42,7 @@ dev = [
    "pytest-mock>=3.12.0",
    "ruff>=0.2.0",
    "mypy>=1.8.0",
+    "types-PyYAML>=6.0.12",
    "pre-commit>=3.6.0",
 ]
 paddle = [
@@ -93,6 +94,7 @@ dev-dependencies = [
    "pytest-mock>=3.12.0",
    "ruff>=0.2.0",
    "mypy>=1.8.0",
+    "types-PyYAML>=6.0.12",
    "pre-commit>=3.6.0",
 ]
 override-dependencies = ["lxml>=5.3.0"]
@@ -100,6 +102,8 @@ override-dependencies = ["lxml>=5.3.0"]
 [tool.ruff]
 line-length = 100
 target-version = "py311"
+
+[tool.ruff.lint]
 select = [
    "E",   # pycodestyle
    "F",   # pyflakes
@@ -125,17 +129,39 @@ skip-magic-trailing-comma = false
 line-ending = "lf"

 [tool.mypy]
-python_version = "3.11"
+python_version = "3.12"  # numpy 2.5 stubs need >= 3.12 type-syntax
 warn_return_any = true
 warn_unused_configs = true
-disallow_untyped_defs = true
-disallow_incomplete_defs = true
 check_untyped_defs = true
 no_implicit_optional = true
 strict_equality = true
 show_error_codes = true
 pretty = true

+# Optional extras: stubs unavailable or packages absent in slim installs.
+[[tool.mypy.overrides]]
+module = [
+    "paddleocr",
+    "paddle",
+    "torch",
+    "torchvision",
+    "transformers",
+    "layoutparser",
+    "spacy",
+    "pytesseract",
+    "cv2",
+    "PIL",
+    "txtai",
+    "txtai.embeddings",
+    "litellm",
+    "neo4j",
+    "networkx",
+    "watchdog",
+    "langchain.*",
+    "nbformat",
+]
+ignore_missing_imports = true
+
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 python_files = ["test_*.py"]
--- a/src/ocr_pipeline.egg-info/PKG-INFO
+++ b/src/ocr_pipeline.egg-info/PKG-INFO
@@ -1,288 +0,0 @@
-Metadata-Version: 2.4
-Name: ocr-pipeline
-Version: 0.1.0
-Summary: OCR pipeline for life science screenshots - RAG ready
-Requires-Python: >=3.11
-Description-Content-Type: text/markdown
-Requires-Dist: typer>=0.9.0
-Requires-Dist: pydantic>=2.6.0
-Requires-Dist: pydantic-settings>=2.2.0
-Requires-Dist: pyyaml>=6.0.1
-Requires-Dist: structlog>=24.1.0
-Requires-Dist: rich>=13.7.0
-Requires-Dist: tqdm>=4.66.0
-Requires-Dist: opencv-python-headless>=4.9.0
-Requires-Dist: pillow>=10.2.0
-Requires-Dist: numpy<2.0,>=1.26.0; python_version < "3.12"
-Requires-Dist: numpy>=1.26.0; python_version >= "3.12"
-Requires-Dist: pytesseract>=0.3.10
-Requires-Dist: langchain-text-splitters>=0.0.2
-Requires-Dist: nbformat>=5.9.0
-Requires-Dist: sqlite-utils>=3.37.0
-Requires-Dist: watchdog>=3.0.0
-Requires-Dist: python-slugify>=8.0.0
-Requires-Dist: xxhash>=3.4.0
-Requires-Dist: python-magic>=0.4.27
-Requires-Dist: platformdirs>=4.2.0
-Provides-Extra: dev
-Requires-Dist: pytest>=8.0.0; extra == "dev"
-Requires-Dist: pytest-cov>=4.1.0; extra == "dev"
-Requires-Dist: pytest-mock>=3.12.0; extra == "dev"
-Requires-Dist: ruff>=0.2.0; extra == "dev"
-Requires-Dist: mypy>=1.8.0; extra == "dev"
-Requires-Dist: pre-commit>=3.6.0; extra == "dev"
-Provides-Extra: grobid
-Provides-Extra: paddle
-Requires-Dist: paddleocr<3.0.0,>=2.7.0; extra == "paddle"
-Requires-Dist: paddlepaddle>=2.6.0; extra == "paddle"
-Provides-Extra: scientific
-Requires-Dist: spacy<3.8.0,>=3.7.0; python_version < "3.12" and extra == "scientific"
-Requires-Dist: spacy>=3.7.0; python_version >= "3.12" and extra == "scientific"
-Requires-Dist: scispacy==0.5.4; python_version < "3.12" and extra == "scientific"
-Provides-Extra: tables
-Requires-Dist: torch>=2.2.0; extra == "tables"
-Requires-Dist: torchvision>=0.17.0; extra == "tables"
-Requires-Dist: transformers>=4.38.0; extra == "tables"
-Requires-Dist: timm>=1.0.0; extra == "tables"
-Provides-Extra: figures
-Requires-Dist: layoutparser>=0.3.0; extra == "figures"
-Provides-Extra: full
-Requires-Dist: ocr-pipeline[dev,figures,paddle,scientific,tables]; extra == "full"
-
-# OCR Pipeline for Life Science Screenshots
-
-Turns scientific screenshots into RAG-ready Markdown, with metadata attached.
-
- Reliable Tesseract OCR by default, with optional PaddleOCR
- Preprocessing: deskew, denoise, CLAHE, line removal
- Optional figure/table detection
- Optional scientific entity extraction with scispaCy
- Citation matching and embedding-ready chunking
-
-## Quick start
-
-```bash
-# The default basic profile is lightweight: Tesseract, cleanup, citations,
-# chunking, Markdown, and no model downloads.
-uv sync
-uv run ocr-pipeline doctor
-
-# Smoke-test a small directory.
-uv run ocr-pipeline run \
-  --input-dir ~/Pictures/test_screenshots \
-  --output-dir /tmp/ocr-output \
-  --workers 1 \
-  --exclude "*.photoslibrary/*"
-```
-
-Use `ocr-pipeline doctor` before a first run or after changing environments. It checks the active profile without loading ML models or downloading model weights.
-
-Use `--force` to reprocess files already recorded in the processing database. The
-`--exclude` option is repeatable and prevents recursive scans from entering bundles
-such as macOS `.photoslibrary` directories.
-
-### Capability profiles
-
-| Profile | What it enables | Intended environment |
-| --- | --- | --- |
-| `basic` (default) | Tesseract OCR, cleanup, citations, chunks, Markdown | Python 3.11+ |
-| `scientific` | Basic + `en_core_sci_lg` entity extraction | **Python 3.11** |
-| `full` | Scientific + PaddleOCR + figure/table detection | Platform-specific ML environment |
-
-Select a profile per run with `--profile`, or set `profile: basic`, `scientific`, or
-`full` at the top of `config.yaml`. The profile is an explicit promise: unavailable
-optional features are reported by `doctor`; they are not silently initialized on a
-basic run.
-
-```bash
-uv run ocr-pipeline doctor --profile scientific
-uv run ocr-pipeline setup scientific  # prints the safe setup commands
-uv run ocr-pipeline run --profile scientific --input-dir ~/Pictures/test_screenshots
-```
-
-#### Scientific NER environment
-
-`en_core_sci_lg` is distributed separately from scispaCy. Create a dedicated Python
-3.11 environment—do not mix its compiled spaCy stack with a Python 3.13 environment:
-
-```bash
-uv venv --python 3.11 .venv-scientific
-uv pip install --python .venv-scientific/bin/python -e '.[scientific]'
-uv pip install --python .venv-scientific/bin/python \
-  https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.4/en_core_sci_lg-0.5.4.tar.gz
-
-.venv-scientific/bin/ocr-pipeline doctor --profile scientific
-.venv-scientific/bin/ocr-pipeline run --profile scientific --input-dir ~/Pictures/test_screenshots
-```
-
-Use the explicit `.venv-scientific/bin/ocr-pipeline` path for that environment;
-`uv run` always selects the project's default `.venv`.
-
-## Docker
-
-```bash
-docker build -t ocr-pipeline .
-
-docker run -v ~/Pictures:/data/screenshots -v ./data:/app/data ocr-pipeline run
-docker run -v ~/Pictures:/data/screenshots -v ./data:/app/data ocr-pipeline watch
-```
-
-## Config
-
-<details>
-<summary><code>config.yaml</code></summary>
-
-```yaml
-input:
-  paths: ["~/Pictures", "/mnt/storage3/aman/screenshots"]
-  patterns: ["SCR-*.png", "*.jpg", "*.jpeg", "*.tiff"]
-  recursive: true
-  exclude_patterns: ["*.photoslibrary/*"]
-
-ocr:
-  engine: "tesseract"  # paddleocr | tesseract | auto
-  languages: ["en", "latin"]
-  use_gpu: false
-  preprocess:
-    deskew: true
-    denoise: true
-    clahe: true
-    adaptive_threshold: true
-    remove_lines: true
-
-processing:
-  workers: 4
-  batch_size: 10
-  retry_attempts: 2
-
-detectors:
-  figures:
-    enabled: false
-    confidence_threshold: 0.7
-  tables:
-    enabled: false
-    confidence_threshold: 0.7
-
-entities:
-  enabled: false
-  model: "en_core_sci_lg"
-
-citations:
-  regex_enabled: true
-  grobid_enabled: false  # set true if you're running a GROBID server
-
-chunking:
-  chunk_size: 1000
-  chunk_overlap: 200
-
-output:
-  base_directory: "./data/ocr_output"
-  organize_by: "date_run"  # date_run | source_dir | flat
-  write_consolidated: true
-  consolidated_filename: "all_ocr.md"
-  frontmatter:
-    - source_path
-    - source_hash
-    - timestamp
-    - ocr_engine
-    - ocr_confidence_mean
-    - language
-    - detected_entities
-    - entity_extraction_backend
-    - has_figures
-    - has_tables
-    - citations_found
-    - chunk_index
-    - total_chunks
-
-watch:
-  enabled: true
-  debounce_seconds: 5
-  db_path: "./data/processed_files.db"
-```
-
-</details>
-
-## Output
-
-Each chunk is a Markdown file with YAML frontmatter:
-
-```markdown
---
-source_path: "/Users/Aman/Pictures/SCR-20250115-gel.png"
-source_hash: "a1b2c3d4e5f6..."
-timestamp: "2025-01-15T10:30:00Z"
-ocr_engine: "paddleocr"
-ocr_confidence_mean: 0.91
-language: "en"
-detected_entities: ["GENE", "PROTEIN", "CHEMICAL"]
-has_figures: true
-has_tables: false
-citations_found: ["DOI:10.1038/nature12345", "PMID:12345678"]
-chunk_index: 0
-total_chunks: 2
---
-
-# Screenshot: SCR-20250115-gel.png
-
-## Figures
-
-### Figure 1
- BBox: [100, 200, 800, 600]
- Confidence: 0.92
- Caption: "Western blot showing BRCA1 expression..."
-
-## Detected Entities
-
- BRCA1
- CRISPR
- β-actin
-
-## Citations
-
- DOI: 10.1038/nature12345
- PMID: 12345678
-
-## Extracted Text
-
-**Western Blot Analysis of BRCA1 Expression**
-
-Lane 1: WT control
-Lane 2: BRCA1 KO (CRISPR)
-Lane 3: BRCA1 KO + pBRCA1-WT rescue
-Lane 4: BRCA1 KO + pBRCA1-C61G mutant
-
-Anti-BRCA1 (1:1000), Anti-β-actin (1:5000)
-```
-
-Files land in `data/ocr_output/<date>/run_NNN/`. Individual chunk files are retained for RAG indexing. Set `output.write_consolidated: true` to also write `all_ocr.md` containing one frontmatter block and all source text grouped by image.
-
-## Life science specifics
-
-Gene/protein names go through scispaCy's `en_core_sci_lg`. Chemical formulas and units (µM, ng/mL, kb/Mb/Gb, °C, ×g) get normalized, scientific notation gets cleaned up (`1.5×10⁻³` → `1.5×10^-3`), and gel/blot figures get their captions pulled out separately. Citations are matched by regex for DOI, PMID, arXiv, PMC, and ISBN.
-
-## Optional models
-
-The basic profile downloads no ML models. Advanced profiles download models only when
-the corresponding capability is enabled and used, cached in `~/.cache/ocr_pipeline/`:
-
- PaddleOCR models (~200MB)
- scispaCy `en_core_sci_lg` (~800MB)
- Table Transformer (~500MB)
- LayoutParser PubLayNet (~300MB)
-
-## Runtime requirements and health
-
-The core pipeline can run with Tesseract alone. PaddleOCR, scientific NER, figure detection, and table detection are optional capabilities with heavyweight, platform-specific dependencies. The pipeline records the OCR engine actually used and the entity-extraction backend in generated frontmatter; inspect them after each run rather than assuming configured models loaded.
-
- **PaddleOCR:** the project pins the legacy 2.x API used by the pipeline. Install the locked environment with `uv sync`; a startup fallback to Tesseract is logged when Paddle cannot initialize.
- **Scientific NER:** install a compatible `scispacy` distribution and the separately distributed `en_core_sci_lg` model before enabling production scientific NER. Without it, the pipeline uses its conservative regex fallback and marks the backend accordingly.
- **Figures:** `layoutparser`'s `Detectron2LayoutModel` requires a Detectron2 build matching your Torch/Python platform. It is intentionally not forced as a universal dependency because no single wheel supports every platform.
- **Tables:** the Table Transformer model is downloaded by Transformers on first use; ensure the selected model's optional dependencies (including `timm`, when required by that model revision) are installed in the runtime image.
-
-Use `ocr-pipeline doctor --profile <profile>` to verify dependencies before processing. Use `ocr-pipeline config` to inspect effective settings. A configured but unavailable optional model is reported as missing by `doctor`; basic runs never attempt to initialize it.
-
-## TODO
-
- [ ] Build a knowledge graph from extracted entities/citations
-
--- a/src/ocr_pipeline.egg-info/SOURCES.txt
+++ b/src/ocr_pipeline.egg-info/SOURCES.txt
@@ -1,43 +0,0 @@
-README.md
-pyproject.toml
-setup.py
-src/ocr_pipeline/__init__.py
-src/ocr_pipeline/cli.py
-src/ocr_pipeline/config.py
-src/ocr_pipeline/doctor.py
-src/ocr_pipeline/pipeline.py
-src/ocr_pipeline/watch.py
-src/ocr_pipeline.egg-info/PKG-INFO
-src/ocr_pipeline.egg-info/SOURCES.txt
-src/ocr_pipeline.egg-info/dependency_links.txt
-src/ocr_pipeline.egg-info/entry_points.txt
-src/ocr_pipeline.egg-info/requires.txt
-src/ocr_pipeline.egg-info/top_level.txt
-src/ocr_pipeline/citations/__init__.py
-src/ocr_pipeline/citations/extractor.py
-src/ocr_pipeline/citations/regex_extractor.py
-src/ocr_pipeline/detectors/__init__.py
-src/ocr_pipeline/detectors/figures.py
-src/ocr_pipeline/detectors/tables.py
-src/ocr_pipeline/ocr/__init__.py
-src/ocr_pipeline/ocr/engine.py
-src/ocr_pipeline/ocr/parallel.py
-src/ocr_pipeline/ocr/preprocess.py
-src/ocr_pipeline/output/__init__.py
-src/ocr_pipeline/output/markdown.py
-src/ocr_pipeline/postprocess/__init__.py
-src/ocr_pipeline/postprocess/chunk.py
-src/ocr_pipeline/postprocess/clean.py
-src/ocr_pipeline/postprocess/entities.py
-src/ocr_pipeline/utils/__init__.py
-src/ocr_pipeline/utils/db.py
-src/ocr_pipeline/utils/logging.py
-src/ocr_pipeline/utils/migrate.py
-src/ocr_pipeline/watch/__init__.py
-src/ocr_pipeline/watch/watcher.py
-tests/test_graph.py
-tests/test_indexer.py
-tests/test_ocr.py
-tests/test_output.py
-tests/test_postprocess.py
-tests/test_profiles.py
--- a/src/ocr_pipeline.egg-info/dependency_links.txt
+++ b/src/ocr_pipeline.egg-info/dependency_links.txt
@@ -1 +0,0 @@
-
--- a/src/ocr_pipeline.egg-info/entry_points.txt
+++ b/src/ocr_pipeline.egg-info/entry_points.txt
@@ -1,2 +0,0 @@
-[console_scripts]
-ocr-pipeline = ocr_pipeline.cli:app
--- a/src/ocr_pipeline.egg-info/requires.txt
+++ b/src/ocr_pipeline.egg-info/requires.txt
@@ -1,59 +0,0 @@
-typer>=0.9.0
-pydantic>=2.6.0
-pydantic-settings>=2.2.0
-pyyaml>=6.0.1
-structlog>=24.1.0
-rich>=13.7.0
-tqdm>=4.66.0
-opencv-python-headless>=4.9.0
-pillow>=10.2.0
-pytesseract>=0.3.10
-langchain-text-splitters>=0.0.2
-nbformat>=5.9.0
-sqlite-utils>=3.37.0
-watchdog>=3.0.0
-python-slugify>=8.0.0
-xxhash>=3.4.0
-python-magic>=0.4.27
-platformdirs>=4.2.0
-
-[:python_version < "3.12"]
-numpy<2.0,>=1.26.0
-
-[:python_version >= "3.12"]
-numpy>=1.26.0
-
-[dev]
-pytest>=8.0.0
-pytest-cov>=4.1.0
-pytest-mock>=3.12.0
-ruff>=0.2.0
-mypy>=1.8.0
-pre-commit>=3.6.0
-
-[figures]
-layoutparser>=0.3.0
-
-[full]
-ocr-pipeline[dev,figures,paddle,scientific,tables]
-
-[grobid]
-
-[paddle]
-paddleocr<3.0.0,>=2.7.0
-paddlepaddle>=2.6.0
-
-[scientific]
-
-[scientific:python_version < "3.12"]
-spacy<3.8.0,>=3.7.0
-scispacy==0.5.4
-
-[scientific:python_version >= "3.12"]
-spacy>=3.7.0
-
-[tables]
-torch>=2.2.0
-torchvision>=0.17.0
-transformers>=4.38.0
-timm>=1.0.0
--- a/src/ocr_pipeline.egg-info/top_level.txt
+++ b/src/ocr_pipeline.egg-info/top_level.txt
@@ -1 +0,0 @@
-ocr_pipeline
--- a/src/ocr_pipeline/doctor.py
+++ b/src/ocr_pipeline/doctor.py
@@ -36,6 +36,10 @@ def check_paddle() -> CheckResult:
    if not _has_module("paddleocr"):
        return CheckResult("PaddleOCR", "warn", "not installed", "uv sync --extra paddle")
    try:
+        import warnings
+
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
            from paddleocr import PaddleOCR  # type: ignore[import-not-found]

            PaddleOCR(use_angle_cls=True, lang="en", use_gpu=False, show_log=False)
--- a/src/ocr_pipeline/setup_steps.py
+++ b/src/ocr_pipeline/setup_steps.py
@@ -71,7 +71,7 @@ def steps_for(target: str) -> list[SetupStep]:
        )
        return steps
    if target == "full":
-        steps: list[SetupStep] = []
+        steps = []
        if shutil.which("uv"):
            steps.append(
                SetupStep("Install optional ML dependencies", ("uv", "sync", "--extra", "full"))
--- a/tests/test_doctor.py
+++ b/tests/test_doctor.py
@@ -53,10 +53,22 @@ def test_check_paddle_warns_when_missing(monkeypatch) -> None:

 def test_check_torch_reports_backend(monkeypatch) -> None:
    monkeypatch.setattr("ocr_pipeline.doctor._has_module", lambda name: True)
-    fake_torch = type(
-        "T", (), {"cuda": type("C", (), {"is_available": staticmethod(lambda: False)})()}
-    )
-    monkeypatch.setattr("sys.modules", {"torch": fake_torch})
+
+    class FakeMPS:
+        @staticmethod
+        def is_available():  # type: ignore[no-untyped-def]
+            return False
+
+    class FakeBackends:
+        mps = FakeMPS
+
+    class FakeCuda:
+        @staticmethod
+        def is_available():  # type: ignore[no-untyped-def]
+            return False
+
+    fake_torch = type("T", (), {"cuda": FakeCuda, "backends": FakeBackends})
+    monkeypatch.setitem(__import__("sys").modules, "torch", fake_torch)
    r = check_torch()
    assert r.status == "ok"
    assert "backend=" in r.detail
--- a/uv.lock
+++ b/uv.lock
@@ -2657,7 +2657,7 @@ wheels = [

 [[package]]
 name = "ocr-pipeline"
-version = "0.1.0"
+version = "0.2.0"
 source = { editable = "." }
 dependencies = [
    { name = "langchain-text-splitters" },
@@ -2685,6 +2685,7 @@ dev = [
    { name = "pytest-cov" },
    { name = "pytest-mock" },
    { name = "ruff" },
+    { name = "types-pyyaml" },
 ]
 figures = [
    { name = "layoutparser" },
@@ -2734,6 +2735,7 @@ dev = [
    { name = "pytest-cov" },
    { name = "pytest-mock" },
    { name = "ruff" },
+    { name = "types-pyyaml" },
 ]

 [package.metadata]
@@ -2774,6 +2776,7 @@ requires-dist = [
    { name = "transformers", marker = "extra == 'tables'", specifier = ">=4.38.0" },
    { name = "txtai", marker = "extra == 'kg'", specifier = ">=7.4.0" },
    { name = "typer", extras = ["all"], specifier = ">=0.9.0" },
+    { name = "types-pyyaml", marker = "extra == 'dev'", specifier = ">=6.0.12" },
    { name = "watchdog", specifier = ">=3.0.0" },
 ]

@@ -2785,6 +2788,7 @@ dev = [
    { name = "pytest-cov", specifier = ">=4.1.0" },
    { name = "pytest-mock", specifier = ">=3.12.0" },
    { name = "ruff", specifier = ">=0.2.0" },
+    { name = "types-pyyaml", specifier = ">=6.0.12" },
 ]

 [[package]]
@@ -5681,6 +5685,15 @@ wheels = [
    { url = "https://files.pythonhosted.org/packages/a7/24/5480c20380dfd18cf33d14784096dca45a24eae6102e91d49a718d3b6855/typer_slim-0.24.0-py3-none-any.whl", hash = "sha256:d5d7ee1ee2834d5020c7c616ed5e0d0f29b9a4b1dd283bdebae198ec09778d0e", size = 3394 },
 ]

+[[package]]
+name = "types-pyyaml"
+version = "6.0.12.20260518"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/b8/83/4a1afc3fbfcf5b8d46fc390cd95ed6b0dc9010a265f4e9f46314efffa37a/types_pyyaml-6.0.12.20260518.tar.gz", hash = "sha256:d917f83fb38462550338c1297faedd860b3ec83912b96b1e3d73255f7473e466", size = 17850 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/06/a2/c01db32be2ae7d6a1689972f3c492b149ee4e164b12fdfd9f64b50888215/types_pyyaml-6.0.12.20260518-py3-none-any.whl", hash = "sha256:d2150f75a231c9fe9c7463bd29487d93e60bac90400287351384bc2284eba7cd", size = 20312 },
+]
+
 [[package]]
 name = "typing-extensions"
 version = "4.16.0"