.gitignore
.readthedocs.yaml
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.dev.md
README.md
pyproject.toml
sonar-project.properties
uv.lock
.github/workflows/build.yml
.github/workflows/cffconvert.yml
.github/workflows/documentation.yml
.github/workflows/publish.yml
.github/workflows/sonarcloud.yml
docs/Makefile
docs/conf.py
docs/index.rst
docs/make.bat
docs/_templates/.gitignore
src/aoptk/__init__.py
src/aoptk/chemical.py
src/aoptk/effect.py
src/aoptk/find_chemical.py
src/aoptk/relationship_type.py
src/aoptk/text_generation_api.py
src/aoptk/text_utils.py
src/aoptk.egg-info/PKG-INFO
src/aoptk.egg-info/SOURCES.txt
src/aoptk.egg-info/dependency_links.txt
src/aoptk.egg-info/entry_points.txt
src/aoptk.egg-info/requires.txt
src/aoptk.egg-info/top_level.txt
src/aoptk/literature/__init__.py
src/aoptk/literature/abstract.py
src/aoptk/literature/convert_image.py
src/aoptk/literature/convert_pdf_scan.py
src/aoptk/literature/find_relevant_publication.py
src/aoptk/literature/get_abstract.py
src/aoptk/literature/get_id.py
src/aoptk/literature/get_pdf.py
src/aoptk/literature/get_publication.py
src/aoptk/literature/get_publication_metadata.py
src/aoptk/literature/id.py
src/aoptk/literature/pdf.py
src/aoptk/literature/pdf_parser.py
src/aoptk/literature/publication.py
src/aoptk/literature/publication_metadata.py
src/aoptk/literature/pymupdf_parser.py
src/aoptk/literature/utils.py
src/aoptk/literature/databases/__init__.py
src/aoptk/literature/databases/europepmc.py
src/aoptk/literature/databases/pmc.py
src/aoptk/literature/databases/pubmed.py
src/aoptk/normalization/__init__.py
src/aoptk/normalization/mesh_terms.py
src/aoptk/normalization/normalize_chemical.py
src/aoptk/normalization/provide_mesh_term_dataframe_from_xml.py
src/aoptk/normalization/provide_normalization_dataframe.py
src/aoptk/normalization/pubchem_api.py
src/aoptk/normalization/pubchem_local.py
src/aoptk/prompts/chemical_prompt.txt
src/aoptk/prompts/convert_image_prompt.txt
src/aoptk/prompts/convert_pdf_scan_prompt.txt
src/aoptk/prompts/find_relevant_publications_prompt.txt
src/aoptk/prompts/normalization_prompt.txt
src/aoptk/prompts/relationship_text_images_prompt.txt
src/aoptk/prompts/relationship_text_prompt.txt
src/aoptk/prompts/relationships_table_prompt.txt
src/aoptk/relationships/__init__.py
src/aoptk/relationships/find_relationship.py
src/aoptk/relationships/relationship.py
tests/__init__.py
tests/conftest.py
tests/test_chemical.py
tests/test_europepmc.py
tests/test_europepmc_mocked.py
tests/test_id.py
tests/test_literature_utils.py
tests/test_mesh_terms.py
tests/test_pdf_parser.py
tests/test_pmc.py
tests/test_provide_mesh_term_dataframe_from_xml.py
tests/test_pubchem_api.py
tests/test_pubchem_local.py
tests/test_pubmed.py
tests/test_pubmed_mocked.py
tests/test_pymupdf_parser.py
tests/test_text_generation.py
tests/test_text_utils.py
tests/test-data/PMC12181427.txt
tests/test-data/PMC12231352.txt
tests/test-data/PMC12416454.txt
tests/test-data/test_mesh_term_database.xml
tests/test-data/test_pdf_base64_image.txt
tests/test_figures/gjic.jpeg
tests/test_pdfs/7835547_corrupted_pdf.pdf
tests/test_pdfs/test_pdf.pdf