structflo-ner 0.2.3__tar.gz → 0.4.0__tar.gz

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Files changed (45) hide show
  1. structflo_ner-0.4.0/.claude/settings.local.json +13 -0
  2. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/.gitignore +4 -0
  3. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/PKG-INFO +3 -3
  4. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/README.md +2 -2
  5. structflo_ner-0.4.0/images/ner_visualization.gif +0 -0
  6. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/notebooks/01_quickstart.ipynb +201 -300
  7. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/__init__.py +1 -1
  8. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/_examples.py +88 -14
  9. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/_prompts.py +11 -4
  10. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/extractor.py +55 -17
  11. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/tests/test_extractor.py +68 -0
  12. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/.github/workflows/ci.yml +0 -0
  13. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/.github/workflows/publish.yml +0 -0
  14. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/Makefile +0 -0
  15. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/coverage.xml +0 -0
  16. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/images/fast-viz.png +0 -0
  17. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/images/local-gen-pandas.png +0 -0
  18. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/images/local-gen-viz.png +0 -0
  19. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/images/local-tb-viz.png +0 -0
  20. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/images/struct-flo-ner.png +0 -0
  21. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/notebooks/02_fast_ner.ipynb +0 -0
  22. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/pyproject.toml +0 -0
  23. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/_display.py +0 -0
  24. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/_entities.py +0 -0
  25. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/_mapping.py +0 -0
  26. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/README.md +0 -0
  27. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/__init__.py +0 -0
  28. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/_loader.py +0 -0
  29. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/_matcher.py +0 -0
  30. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/_normalize.py +0 -0
  31. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/extractor.py +0 -0
  32. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/gazetteers/accession_number.yml +0 -0
  33. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/gazetteers/compound_name.yml +0 -0
  34. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/gazetteers/disease.yml +0 -0
  35. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/gazetteers/functional_category.yml +0 -0
  36. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/gazetteers/gene_name.yml +0 -0
  37. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/gazetteers/product.yml +0 -0
  38. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/gazetteers/screening_method.yml +0 -0
  39. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/gazetteers/strain.yml +0 -0
  40. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/fast/gazetteers/target.yml +0 -0
  41. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/structflo/ner/profiles.py +0 -0
  42. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/tests/__init__.py +0 -0
  43. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/tests/test_entities.py +0 -0
  44. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/tests/test_fast.py +0 -0
  45. {structflo_ner-0.2.3 → structflo_ner-0.4.0}/uv.lock +0 -0
@@ -0,0 +1,13 @@
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+ {
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+ "permissions": {
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+ "allow": [
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+ "Bash(uv sync:*)",
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+ "Bash(uv run pytest:*)",
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+ "Bash(uv run ruff check:*)",
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+ "Bash(uv run ruff format:*)",
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+ "Bash(uv run ruff:*)",
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+ "Bash(python -m pytest:*)",
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+ "Bash(uv run python:*)"
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+ ]
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+ }
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+ }
@@ -32,3 +32,7 @@ Thumbs.db
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  # Environment variables
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  .env
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  .env.*
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+
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+
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+ notebooks/.virtual_documents/
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+ notebooks/.ipynb_checkpoints/
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: structflo-ner
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- Version: 0.2.3
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+ Version: 0.4.0
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  Summary: Drug discovery NER wrapper around LangExtract — zero-config entity extraction for chemistry and biology.
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  License: Apache-2.0
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  Requires-Python: >=3.10
@@ -43,7 +43,7 @@ Description-Content-Type: text/markdown
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  ---
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- **structflo.ner** is a lightweight NER library specialized for pharmaceutical and biological sciences. It uses [LangExtract](https://github.com/langextract/langextract) and fuzzy based tools to deliver **zero-configuration** entity extraction.
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+ **structflo.ner** is a lightweight NER library specialized for pharmaceutical and biological sciences. It uses [LangExtract](https://github.com/google/langextract) and fuzzy based tools to deliver **zero-configuration** entity extraction.
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  It ships with two extraction engines:
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@@ -111,7 +111,7 @@ Any model served by [Ollama](https://ollama.com/) works gemma, llama, mistral,
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  Render results as color-coded, interactive HTML directly in Jupyter notebooks:
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- ![Results](images/local-gen-viz.png)
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+ ![Results](images/ner_visualization.gif)
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  To get a PANDAS dataframe.
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  ---
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- **structflo.ner** is a lightweight NER library specialized for pharmaceutical and biological sciences. It uses [LangExtract](https://github.com/langextract/langextract) and fuzzy based tools to deliver **zero-configuration** entity extraction.
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+ **structflo.ner** is a lightweight NER library specialized for pharmaceutical and biological sciences. It uses [LangExtract](https://github.com/google/langextract) and fuzzy based tools to deliver **zero-configuration** entity extraction.
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  It ships with two extraction engines:
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@@ -98,7 +98,7 @@ Any model served by [Ollama](https://ollama.com/) works gemma, llama, mistral,
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  Render results as color-coded, interactive HTML directly in Jupyter notebooks:
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- ![Results](images/local-gen-viz.png)
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+ ![Results](images/ner_visualization.gif)
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  To get a PANDAS dataframe.