bioguider 0.2.13__tar.gz → 0.2.14__tar.gz

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  1. {bioguider-0.2.13 → bioguider-0.2.14}/PKG-INFO +1 -1
  2. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/evaluation_installation_task.py +2 -0
  3. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/database/summarized_file_db.py +1 -1
  4. {bioguider-0.2.13 → bioguider-0.2.14}/pyproject.toml +1 -1
  5. {bioguider-0.2.13 → bioguider-0.2.14}/LICENSE +0 -0
  6. {bioguider-0.2.13 → bioguider-0.2.14}/README.md +0 -0
  7. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/__init__.py +0 -0
  8. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/__init__.py +0 -0
  9. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/agent_task.py +0 -0
  10. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/agent_tools.py +0 -0
  11. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/agent_utils.py +0 -0
  12. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/collection_execute_step.py +0 -0
  13. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/collection_observe_step.py +0 -0
  14. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/collection_plan_step.py +0 -0
  15. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/collection_task.py +0 -0
  16. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/collection_task_utils.py +0 -0
  17. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/common_agent.py +0 -0
  18. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/common_agent_2step.py +0 -0
  19. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/common_step.py +0 -0
  20. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/dockergeneration_execute_step.py +0 -0
  21. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/dockergeneration_observe_step.py +0 -0
  22. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/dockergeneration_plan_step.py +0 -0
  23. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/dockergeneration_task.py +0 -0
  24. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/dockergeneration_task_utils.py +0 -0
  25. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/evaluation_readme_task.py +0 -0
  26. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/evaluation_submission_requirements_task.py +0 -0
  27. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/evaluation_task.py +0 -0
  28. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/identification_execute_step.py +0 -0
  29. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/identification_observe_step.py +0 -0
  30. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/identification_plan_step.py +0 -0
  31. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/identification_task.py +0 -0
  32. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/identification_task_utils.py +0 -0
  33. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/peo_common_step.py +0 -0
  34. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/prompt_utils.py +0 -0
  35. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/python_ast_repl_tool.py +0 -0
  36. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/rag_collection_task.py +0 -0
  37. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/conversation.py +0 -0
  38. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/managers/evaluation_manager.py +0 -0
  39. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/rag/__init__.py +0 -0
  40. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/rag/config.py +0 -0
  41. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/rag/data_pipeline.py +0 -0
  42. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/rag/embedder.py +0 -0
  43. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/rag/rag.py +0 -0
  44. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/settings.py +0 -0
  45. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/utils/constants.py +0 -0
  46. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/utils/default.gitignore +0 -0
  47. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/utils/file_utils.py +0 -0
  48. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/utils/gitignore_checker.py +0 -0
  49. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/utils/pyphen_utils.py +0 -0
  50. {bioguider-0.2.13 → bioguider-0.2.14}/bioguider/utils/utils.py +0 -0
{bioguider-0.2.13 → bioguider-0.2.14}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: bioguider
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- Version: 0.2.13
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+ Version: 0.2.14
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  Summary: An AI-Powered package to help biomedical developers to generate clear documentation
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  License: MIT
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  Author: Cankun Wang
{bioguider-0.2.13 → bioguider-0.2.14}/bioguider/agents/evaluation_installation_task.py RENAMED
@@ -211,6 +211,8 @@ class EvaluationInstallationTask(EvaluationTask):
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  instruction_prompt=EVALUATION_INSTRUCTION,
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  schema=StructuredEvaluationInstallationResult,
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  )
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+ res: StructuredEvaluationInstallationResult = res
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+ res.dependency_number = 0 if res.dependency_number is None else res.dependency_number
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  self.print_step(step_output=reasoning_process)
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  self.print_step(token_usage=token_usage)
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{bioguider-0.2.13 → bioguider-0.2.14}/bioguider/database/summarized_file_db.py RENAMED
@@ -114,7 +114,7 @@ class SummarizedFilesDb:
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  file_path: str,
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  instruction: str,
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  summarize_level: int,
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- summarize_prompt: str,
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+ summarize_prompt: str = "N/A",
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  ) -> str | None:
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  self._connect_to_db()
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  self._ensure_tables()
{bioguider-0.2.13 → bioguider-0.2.14}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "bioguider"
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- version = "0.2.13"
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+ version = "0.2.14"
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  description = "An AI-Powered package to help biomedical developers to generate clear documentation"
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  authors = [
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  "Cankun Wang <Cankun.Wang@osumc.edu>",
{bioguider-0.2.13 → bioguider-0.2.14}/LICENSE RENAMED
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{bioguider-0.2.13 → bioguider-0.2.14}/README.md RENAMED
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