CHANGELOG.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
docs/README.md
docs/configuration.md
docs/doi_downloader.json
docs/doi_downloader.md
docs/index.md
docs/installation.md
docs/markdown_conver.md
docs/migration_guide.md
docs/overview.md
docs/pubmed_baseline_keywords_filter.md
docs/quickstart.md
docs/ricedatacn_gene_parser.md
docs/api/core/doi_downloader.md
docs/api/core/downloader.md
docs/api/llm_filter/config.md
docs/api/llm_filter/core.md
docs/api/llm_filter/llm_interface.md
docs/api/llm_filter/utils.md
docs/api/markdown/markdown.md
docs/api/pdf/cli.md
docs/api/pdf/validator.md
docs/api/pubmed/baseline.md
docs/api/pubmed/pubmed.md
docs/api/pubmed/search.md
docs/api/sites/base.md
docs/api/sites/google_scholar.md
docs/api/sites/ricedatacn.md
docs/development/changelog.md
docs/development/code-quality.md
docs/development/contributing.md
docs/examples/README.md
docs/examples/doi-download-examples.md
docs/examples/google-scholar-examples.md
docs/examples/llm-filter-examples.md
docs/examples/markdown-processing-examples.md
docs/examples/pdf-validator-examples.md
docs/examples/pubmed-examples.md
docs/examples/ricedatacn-examples.md
docs/guides/configuration.md
docs/guides/crossref-integration.md
docs/guides/doi-download.md
docs/guides/google-scholar-integration.md
docs/guides/llm-filtering.md
docs/guides/markdown-processing.md
docs/guides/pdf-validator.md
docs/guides/pubmed-integration.md
docs/guides/ricedatacn-integration.md
docs/guides/rss-integration.md
examples/create_test_data.py
examples/test_examples.py
examples/test_offline_examples.py
examples/marimo/pdf_information_analysis.py
examples/marimo/pubmed_search_save_query_localdatabase.py
examples/python_scripts/doi_download_by_using_pubmed_batch_example.py
examples/python_scripts/doi_download_example.py
examples/python_scripts/doi_download_single.py
examples/python_scripts/google_scholar_advanced_example.py
examples/python_scripts/google_scholar_basic_example.py
examples/python_scripts/google_scholar_batch_example.py
examples/python_scripts/litsense_example.py
examples/python_scripts/llm_filter_example.py
examples/python_scripts/markdown_converter.py
examples/python_scripts/markdown_filter_ref.py
examples/python_scripts/pdf_validator_example.py
examples/python_scripts/pubmed_analyzer_example.py
examples/python_scripts/pubmed_analyzer_integration_example.py
examples/python_scripts/pubmed_analyzer_ollama_example.py
examples/python_scripts/pubmed_analyzer_openai_example.py
examples/python_scripts/pubmed_cli_example.py
examples/python_scripts/pubmed_details_batch_example.py
examples/python_scripts/pubmed_details_example.py
examples/python_scripts/pubmed_journal_recent.py
examples/python_scripts/pubmed_keywords_filter_example.py
examples/python_scripts/pubmed_mul_journals_recent.py
examples/python_scripts/pubmed_query_pmid.py
examples/python_scripts/pubmed_uorf_genome_editing_analysis.py
examples/python_scripts/ricedatacn_gene_download_example.py
examples/python_scripts/ricedatacn_gene_example.py
examples/python_scripts/rss_basic_example.py
examples/python_scripts/rss_fetch_basic_example.py
examples/python_scripts/verify_analyzer.py
src/information_composer/__init__.py
src/information_composer.egg-info/PKG-INFO
src/information_composer.egg-info/SOURCES.txt
src/information_composer.egg-info/dependency_links.txt
src/information_composer.egg-info/entry_points.txt
src/information_composer.egg-info/requires.txt
src/information_composer.egg-info/top_level.txt
src/information_composer/core/__init__.py
src/information_composer/core/doi_downloader.py
src/information_composer/core/downloader.py
src/information_composer/core/utils/__init__.py
src/information_composer/crossref/__init__.py
src/information_composer/crossref/py.typed
src/information_composer/crossref/cli/__init__.py
src/information_composer/crossref/cli/main.py
src/information_composer/crossref/core/__init__.py
src/information_composer/crossref/core/client.py
src/information_composer/crossref/core/models.py
src/information_composer/llm_filter/__init__.py
src/information_composer/llm_filter/cli/__init__.py
src/information_composer/llm_filter/cli/main.py
src/information_composer/llm_filter/config/__init__.py
src/information_composer/llm_filter/config/settings.py
src/information_composer/llm_filter/core/__init__.py
src/information_composer/llm_filter/core/extractor.py
src/information_composer/llm_filter/core/filter.py
src/information_composer/llm_filter/core/parser.py
src/information_composer/llm_filter/llm/__init__.py
src/information_composer/llm_filter/llm/llm_interface.py
src/information_composer/llm_filter/llm/ollama_client.py
src/information_composer/llm_filter/llm/openai_client.py
src/information_composer/llm_filter/llm/pydantic_ai_client.py
src/information_composer/llm_filter/utils/__init__.py
src/information_composer/llm_filter/utils/markdown_utils.py
src/information_composer/llm_filter/utils/text_processing.py
src/information_composer/markdown/__init__.py
src/information_composer/markdown/markdown.py
src/information_composer/markdown/vendor/__init__.py
src/information_composer/markdown/vendor/CommonMark/CommonMark.py
src/information_composer/markdown/vendor/CommonMark/__init__.py
src/information_composer/markdown/vendor/CommonMark/entitytrans.py
src/information_composer/markdown/vendor/CommonMark/test/test-CommonMark.py
src/information_composer/markdown/vendor/docopt/__init__.py
src/information_composer/markdown/vendor/docopt/_version.py
src/information_composer/markdown/vendor/docopt/py.typed
src/information_composer/pdf/__init__.py
src/information_composer/pdf/validator.py
src/information_composer/pdf/cli/__init__.py
src/information_composer/pdf/cli/main.py
src/information_composer/pubmed/__init__.py
src/information_composer/pubmed/baseline.py
src/information_composer/pubmed/litsense.py
src/information_composer/pubmed/pubmed.py
src/information_composer/pubmed/py.typed
src/information_composer/pubmed/analyzer/__init__.py
src/information_composer/pubmed/analyzer/agents.py
src/information_composer/pubmed/analyzer/analyzer.py
src/information_composer/pubmed/analyzer/cache.py
src/information_composer/pubmed/analyzer/dependencies.py
src/information_composer/pubmed/analyzer/exceptions.py
src/information_composer/pubmed/analyzer/models.py
src/information_composer/pubmed/analyzer/validators.py
src/information_composer/pubmed/cli/__init__.py
src/information_composer/pubmed/cli/main.py
src/information_composer/pubmed/core/__init__.py
src/information_composer/pubmed/core/search.py
src/information_composer/pubmed/database/__init__.py
src/information_composer/pubmed/database/models.py
src/information_composer/pubmed/database/operations.py
src/information_composer/rss/__init__.py
src/information_composer/rss/cache.py
src/information_composer/rss/config.py
src/information_composer/rss/fetcher.py
src/information_composer/rss/models.py
src/information_composer/rss/parser.py
src/information_composer/rss/cli/__init__.py
src/information_composer/rss/cli/main.py
src/information_composer/sites/__init__.py
src/information_composer/sites/base.py
src/information_composer/sites/ricedatacn_gene_parser.py
src/information_composer/sites/google_scholar/__init__.py
src/information_composer/sites/google_scholar/crawler.py
src/information_composer/sites/google_scholar/models.py
src/information_composer/sites/google_scholar/core/__init__.py
src/information_composer/sites/google_scholar/core/data_extractor.py
src/information_composer/sites/google_scholar/core/result_processor.py
src/information_composer/sites/google_scholar/core/search_engine.py
src/information_composer/sites/google_scholar/utils/__init__.py
src/information_composer/sites/google_scholar/utils/cache_manager.py
src/information_composer/sites/google_scholar/utils/error_handling.py
src/information_composer/sites/google_scholar/utils/rate_limiter.py
src/information_composer/sites/google_scholar/utils/user_agents.py
tests/test_agents_pydantic.py
tests/test_crossref.py
tests/test_token_usage.py
tests/test_validators.py