bioguider 0.2.22__tar.gz → 0.2.24__tar.gz

{bioguider-0.2.22 → bioguider-0.2.24}/PKG-INFO

@@ -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 → bioguider-0.2.24}/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-0.2.22 → bioguider-0.2.24}/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-0.2.22 → bioguider-0.2.24}/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 → bioguider-0.2.24}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bioguider"
-version = "0.2.22"
+version = "0.2.24"
 description = "An AI-Powered package to help biomedical developers to generate clear documentation"
 authors = [
     "Cankun Wang <Cankun.Wang@osumc.edu>",