bioguider 0.2.22__py3-none-any.whl → 0.2.24__py3-none-any.whl

bioguider/agents/consistency_query_step.py

@@ -45,14 +45,17 @@ class ConsistencyQueryStep(CommonStep):
             else:
                 if file_path is not None and parent is not None:
                     rows = self.code_structure_db.select_by_name_and_parent_and_path(name, parent, file_path)
+                    rows = rows if rows is None else [rows]
                     if rows is None or len(rows) == 0:
                         rows = self.code_structure_db.select_by_name_and_path(name, file_path)
+                        rows = rows if rows is None else [rows]
                     if rows is None or len(rows) == 0:
                         rows = self.code_structure_db.select_by_name_and_parent(name, parent)
                     if rows is None or len(rows) == 0:
                         rows = self.code_structure_db.select_by_name(name)
                 elif file_path is not None:
                     rows = self.code_structure_db.select_by_name_and_path(name, file_path)
+                    rows = rows if rows is None else [rows]
                     if rows is None or len(rows) == 0:
                         rows = self.code_structure_db.select_by_name(name)
                 elif parent is not None:

bioguider/agents/evaluation_tutorial_task.py

@@ -102,12 +102,13 @@ class EvaluationTutorialTask(EvaluationTask):
     def _evaluate_individual_tutorial(self, file: str) -> tuple[IndividualTutorialEvaluationResult | None, dict]:
         content = read_file(Path(self.repo_path, file))
         if content is None:
-            logger.error(f"Error in reading file {file}")
+            logger.error(f"Error in reading file {file} - {Path(self.repo_path, file).resolve()}")
             return None, {**DEFAULT_TOKEN_USAGE}
 
         if file.endswith(".ipynb"):
             readability_content = extract_markdown_from_notebook(Path(self.repo_path, file))
             content = json.dumps(strip_notebook_to_code_and_markdown(Path(self.repo_path, file)))
+            content = content.replace("{", "<<").replace("}", ">>")
         else:
             readability_content = content
         readability = PyphenReadability()

bioguider/managers/evaluation_manager.py

@@ -83,22 +83,6 @@ class EvaluationManager:
         results, readme_files = task.evaluate()
         return results, readme_files
     
-    def evaluate_tutorial(self):
-        pass
-        # task = CollectionTask(
-        #     llm=self.llm,
-        #     step_callback=self.step_callback,
-        # )
-        # task.compile(
-        #     repo_path=self.rag.repo_dir,
-        #     gitignore_path=Path(self.rag.repo_dir, ".gitignore"),
-        #     db=self.summary_file_db,
-        #     goal_item=CollectionGoalItemEnum.Tutorial.name,
-        # )
-        # s = task.collect()
-        # if s is None or 'final_answer' not in s:
-        #     return None
-        
     def evaluate_installation(self):
         evaluation_task = EvaluationInstallationTask(
             llm=self.llm,

{bioguider-0.2.22.dist-info → bioguider-0.2.24.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioguider
-Version: 0.2.22
+Version: 0.2.24
 Summary: An AI-Powered package to help biomedical developers to generate clear documentation
 License: MIT
 Author: Cankun Wang

{bioguider-0.2.22.dist-info → bioguider-0.2.24.dist-info}/RECORD

@@ -16,7 +16,7 @@ bioguider/agents/consistency_collection_step.py,sha256=evgb0W3PD5pXfViuP_0T5LqLn
 bioguider/agents/consistency_evaluation_task.py,sha256=_nYPEs3xhj1jraQWMRML_Y6vZJD_zydY4BstQYXmXJk,1908
 bioguider/agents/consistency_evaluation_task_utils.py,sha256=8PC4KS14ek9NJy3bLuhZNmpOUKFx3_06nKXzuTWb0tE,444
 bioguider/agents/consistency_observe_step.py,sha256=0FEtNpkaGcuL30wb2d43uTlSyHJ9Pxttn9r3NzPD0oo,4409
-bioguider/agents/consistency_query_step.py,sha256=uYE_V_e74kqoDSxmIkMpZpBjoZRKRsJPmiqs1xHhRF8,3674
+bioguider/agents/consistency_query_step.py,sha256=SRkw9UiLAhMnbPgexffHsAznrdLAQvIP4KD7S7N-P14,3858
 bioguider/agents/dockergeneration_execute_step.py,sha256=F92jDlkc6KjAvTkX7q1FsCYP8J15SCaNgmwh3YPqfDo,6500
 bioguider/agents/dockergeneration_observe_step.py,sha256=Bo5Td0fzMYLbLki0FvwamzqRFOy4eu3AvIUa8oFApE4,6131
 bioguider/agents/dockergeneration_plan_step.py,sha256=SB8tQM9PkIKsD2o1DFD7bedcxz6r6hSy8n_EVK60Fz0,7235
@@ -26,7 +26,7 @@ bioguider/agents/evaluation_installation_task.py,sha256=0RNH5NV7YKwn_we_d3IjnFf_
 bioguider/agents/evaluation_readme_task.py,sha256=pi3oAGJgZhJgJG1xLgiobrk3Uy2a_JIarD5QSPBkmHA,30647
 bioguider/agents/evaluation_submission_requirements_task.py,sha256=J_6C-M2AfYue2C-gWBHl7KqGrTBuFBn9zmMV5vSRk-U,7834
 bioguider/agents/evaluation_task.py,sha256=uu0BjalctF9hQjGtT53whbeJHv2RVvs8_2woVUmOLRE,8132
-bioguider/agents/evaluation_tutorial_task.py,sha256=n4eElsGEW38JV7pKtOyoATe1K-pSJZfMr8DdMIAhkyY,8332
+bioguider/agents/evaluation_tutorial_task.py,sha256=wRhHqvuOhGEICOhAlZrtshHJ8LkmnAYfjazFe090aeU,8441
 bioguider/agents/evaluation_tutorial_task_prompts.py,sha256=WTqIKBI3JErYaiQfLcPNj_hb3D-hSZrae50uJ7526zw,5996
 bioguider/agents/evaluation_userguide_prompts.py,sha256=eyJUx5nUr8v9k0B5GpKDaX2dBxSLVZGA0fwOWS4Uiow,7154
 bioguider/agents/evaluation_userguide_task.py,sha256=ONdempCOyn_N-LGV35diKciBbnjDSItXchcLV738XTw,6456
@@ -55,7 +55,7 @@ bioguider/generation/report_loader.py,sha256=KtJ6JHGPDL-PQoucU8hkVzMSz-B0bHbF2WS
 bioguider/generation/style_analyzer.py,sha256=Vn9FAK1qJBNLolLC1tz362k4UBaPl107BlvkQc8pV2I,983
 bioguider/generation/suggestion_extractor.py,sha256=tfkyWtdbAo-maLCF_wqwBXyh93yjulvDY17FuvTnTjk,7611
 bioguider/generation/test_metrics.py,sha256=fG6H1jVikHEx1YvN5Ds4QbVinudJ5OEYkzrV760oLLQ,3766
-bioguider/managers/evaluation_manager.py,sha256=2RRlVWu3kxBYrK0DRsX1k82LLFKJaNZ1i4HuCYxwJPw,6447
+bioguider/managers/evaluation_manager.py,sha256=EoZ8V4rmx16zk1J3N9cNjeo0aCa7i32fLEQ3b2UolEQ,5917
 bioguider/managers/generation_manager.py,sha256=EbAJSvUz-SIriVlozuJ6wa5_1aIbbFfpgg3c9Vcz34g,7615
 bioguider/managers/generation_test_manager.py,sha256=0ty8IibdfN90Oj6M6lkYbxASnQxHYb9I3w9eG7hvEsQ,3270
 bioguider/rag/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -74,7 +74,7 @@ bioguider/utils/pyphen_utils.py,sha256=cdZc3qphkvMDeL5NiZ8Xou13M_uVNP7ifJ-FwxO-0
 bioguider/utils/python_file_handler.py,sha256=BERiE2RHxpu3gAzv26jr8ZQetkrtnMZOv9SjpQ7WIdg,2650
 bioguider/utils/r_file_handler.py,sha256=8HpFaYKP8N1nItwr9tOx49m99pcLSt8EUtTNTJ7xNoE,19564
 bioguider/utils/utils.py,sha256=1N7Wv_i9spTBQ_FbZnlxsjC8mszbBzaegrmvuKGUISg,3531
-bioguider-0.2.22.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
-bioguider-0.2.22.dist-info/METADATA,sha256=khsXgvUKBtkO4HOo1dCqVsw8vgk7zwOh9KdZFP4DtSc,1868
-bioguider-0.2.22.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-bioguider-0.2.22.dist-info/RECORD,,
+bioguider-0.2.24.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
+bioguider-0.2.24.dist-info/METADATA,sha256=ExmR7sflPHuNCSyjnvl6B-hUpK9AFFU5zEaK8zqQdUY,1868
+bioguider-0.2.24.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+bioguider-0.2.24.dist-info/RECORD,,