bioguider 0.2.25__tar.gz → 0.2.26__tar.gz

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  1. {bioguider-0.2.25 → bioguider-0.2.26}/PKG-INFO +1 -1
  2. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/utils/utils.py +9 -5
  3. {bioguider-0.2.25 → bioguider-0.2.26}/pyproject.toml +1 -1
  4. {bioguider-0.2.25 → bioguider-0.2.26}/LICENSE +0 -0
  5. {bioguider-0.2.25 → bioguider-0.2.26}/README.md +0 -0
  6. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/__init__.py +0 -0
  7. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/__init__.py +0 -0
  8. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/agent_task.py +0 -0
  9. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/agent_tools.py +0 -0
  10. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/agent_utils.py +0 -0
  11. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/collection_execute_step.py +0 -0
  12. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/collection_observe_step.py +0 -0
  13. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/collection_plan_step.py +0 -0
  14. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/collection_task.py +0 -0
  15. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/collection_task_utils.py +0 -0
  16. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/common_agent.py +0 -0
  17. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/common_agent_2step.py +0 -0
  18. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/common_conversation.py +0 -0
  19. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/common_step.py +0 -0
  20. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/consistency_collection_step.py +0 -0
  21. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/consistency_evaluation_task.py +0 -0
  22. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/consistency_evaluation_task_utils.py +0 -0
  23. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/consistency_observe_step.py +0 -0
  24. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/consistency_query_step.py +0 -0
  25. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/dockergeneration_execute_step.py +0 -0
  26. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/dockergeneration_observe_step.py +0 -0
  27. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/dockergeneration_plan_step.py +0 -0
  28. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/dockergeneration_task.py +0 -0
  29. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/dockergeneration_task_utils.py +0 -0
  30. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/evaluation_installation_task.py +0 -0
  31. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/evaluation_readme_task.py +0 -0
  32. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/evaluation_submission_requirements_task.py +0 -0
  33. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/evaluation_task.py +0 -0
  34. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/evaluation_tutorial_task.py +0 -0
  35. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/evaluation_tutorial_task_prompts.py +0 -0
  36. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/evaluation_userguide_prompts.py +0 -0
  37. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/evaluation_userguide_task.py +0 -0
  38. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/identification_execute_step.py +0 -0
  39. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/identification_observe_step.py +0 -0
  40. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/identification_plan_step.py +0 -0
  41. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/identification_task.py +0 -0
  42. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/identification_task_utils.py +0 -0
  43. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/peo_common_step.py +0 -0
  44. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/prompt_utils.py +0 -0
  45. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/python_ast_repl_tool.py +0 -0
  46. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/agents/rag_collection_task.py +0 -0
  47. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/conversation.py +0 -0
  48. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/database/code_structure_db.py +0 -0
  49. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/database/summarized_file_db.py +0 -0
  50. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/__init__.py +0 -0
  51. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/change_planner.py +0 -0
  52. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/document_renderer.py +0 -0
  53. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/llm_cleaner.py +0 -0
  54. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/llm_content_generator.py +0 -0
  55. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/llm_injector.py +0 -0
  56. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/models.py +0 -0
  57. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/output_manager.py +0 -0
  58. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/repo_reader.py +0 -0
  59. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/report_loader.py +0 -0
  60. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/style_analyzer.py +0 -0
  61. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/suggestion_extractor.py +0 -0
  62. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/generation/test_metrics.py +0 -0
  63. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/managers/evaluation_manager.py +0 -0
  64. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/managers/generation_manager.py +0 -0
  65. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/managers/generation_test_manager.py +0 -0
  66. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/rag/__init__.py +0 -0
  67. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/rag/config.py +0 -0
  68. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/rag/data_pipeline.py +0 -0
  69. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/rag/embedder.py +0 -0
  70. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/rag/rag.py +0 -0
  71. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/settings.py +0 -0
  72. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/utils/code_structure_builder.py +0 -0
  73. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/utils/constants.py +0 -0
  74. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/utils/default.gitignore +0 -0
  75. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/utils/file_utils.py +0 -0
  76. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/utils/gitignore_checker.py +0 -0
  77. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/utils/notebook_utils.py +0 -0
  78. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/utils/pyphen_utils.py +0 -0
  79. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/utils/python_file_handler.py +0 -0
  80. {bioguider-0.2.25 → bioguider-0.2.26}/bioguider/utils/r_file_handler.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: bioguider
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- Version: 0.2.25
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+ Version: 0.2.26
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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
@@ -53,10 +53,14 @@ def run_command(command: list, cwd: str = None, timeout: int = None):
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  return e.stdout or "", e.stderr or f"Command timed out after {timeout} seconds", -1
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  def escape_braces(text: str) -> str:
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- # First replace single } not part of }} with }}
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- text = re.sub(r'(?<!})}(?!})', '}}', text)
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- # Then replace single { not part of {{
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- text = re.sub(r'(?<!{){(?!{)', '{{', text)
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+ def fix_braces(m):
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+ s = m.group(0)
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+ # If odd number of braces, double the last one
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+ if len(s) % 2 == 1:
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+ return s + s[-1]
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+ return s
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+ # Handle both { and } sequences
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+ text = re.sub(r'{+|}+', fix_braces, text)
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  return text
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  def increase_token_usage(
@@ -105,7 +109,7 @@ def convert_to_serializable(obj):
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  else:
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  return obj
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- def convert_html_to_text(html_path: str | Path, exclude_tags: list[str] | None = None) -> str:
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+ def convert_html_to_text(html_path: str | Path, exclude_tags: list[str] = ["script", "style", "img", "svg", "meta", "link"]) -> str:
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  """
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  This function is used to convert html string to text, that is,
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  extract text from html content, including tables.
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "bioguider"
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- version = "0.2.25"
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+ version = "0.2.26"
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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>",
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