From deab02610b79c5a67e2b1c9fb86f2381e4a3a5fd Mon Sep 17 00:00:00 2001 From: Aman Nalakath Date: Sun, 19 Jul 2026 20:01:32 +0200 Subject: [PATCH] update README pyproject & config --- README.md | 48 +++- config.yaml | 1 + pyproject.toml | 9 +- uv.lock | 654 +++++++++++++++++++++++++++++++++++++------------ 4 files changed, 547 insertions(+), 165 deletions(-) diff --git a/README.md b/README.md index 7d690d6..e4c055a 100644 --- a/README.md +++ b/README.md @@ -12,15 +12,49 @@ Turns scientific screenshots into RAG-ready Markdown, with metadata attached. ## Quick start ```bash -uv sync # or: pip install -e . +uv sync pre-commit install -ocr-pipeline run # process screenshots -ocr-pipeline watch # watch a folder -ocr-pipeline reprocess ocr_sc.ipynb # pull screenshots out of a notebook -ocr-pipeline status +# Smoke test a small directory with the lightweight OCR path +uv run ocr-pipeline run \ + --input-dir ~/Pictures/test_screenshots \ + --output-dir /tmp/ocr-output \ + --engine tesseract \ + --workers 1 \ + --exclude "*.photoslibrary/*" + +uv run ocr-pipeline watch +uv run ocr-pipeline reprocess ocr_sc.ipynb +uv run ocr-pipeline status ``` +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. + +### Scientific NER environment + +`en_core_sci_lg` is distributed separately from scispaCy and is not installed by +`uv sync`. The compatible scispaCy 0.5.4 release requires spaCy 3.7.x, so install it +in a dedicated Python 3.11 environment rather than mixing it with the main Python +3.13 environment: + +```bash +uv venv --python 3.11 .venv-scispacy +source .venv-scispacy/bin/activate +uv pip install "spacy>=3.7,<3.8" "scispacy==0.5.4" click +uv pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.4/en_core_sci_lg-0.5.4.tar.gz +uv pip install -e . +uv pip install timm + +# Confirm the model and command use this same environment +.venv-scispacy/bin/python -c "import spacy; spacy.load('en_core_sci_lg'); print('scispaCy OK')" +.venv-scispacy/bin/ocr-pipeline run --help +``` + +If the two environments are kept separate, invoke the pipeline with the explicit +`.venv-scispacy/bin/ocr-pipeline` path; `uv run` selects the project's default `.venv`. + ## Docker ```bash @@ -40,6 +74,7 @@ input: paths: ["~/Pictures", "/mnt/storage3/aman/screenshots"] patterns: ["SCR-*.png", "*.jpg", "*.jpeg", "*.tiff"] recursive: true + exclude_patterns: ["*.photoslibrary/*"] ocr: engine: "paddleocr" # paddleocr | tesseract | auto @@ -80,6 +115,8 @@ chunking: 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 @@ -88,6 +125,7 @@ output: - ocr_confidence_mean - language - detected_entities + - entity_extraction_backend - has_figures - has_tables - citations_found diff --git a/config.yaml b/config.yaml index 7b42b7f..bfac240 100644 --- a/config.yaml +++ b/config.yaml @@ -84,6 +84,7 @@ output: - "ocr_confidence_mean" - "language" - "detected_entities" + - "entity_extraction_backend" - "has_figures" - "has_tables" - "citations_found" diff --git a/pyproject.toml b/pyproject.toml index 3a1ba23..528cfd2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,8 +21,10 @@ dependencies = [ # Image processing "opencv-python-headless>=4.9.0", 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}, marker = "python_full_version >= '3.12'" }, { name = "pillow" }, { name = "torch" }, @@ -4414,7 +4754,7 @@ version = "5.14.1" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "huggingface-hub" }, - { name = "numpy", version = "2.4.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.12'" }, + { name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.12'" }, { name = "numpy", version = "2.5.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.12'" }, { name = "packaging" }, { name = "pyyaml" },