bioguider 0.2.31__tar.gz → 0.2.32__tar.gz

{bioguider-0.2.31 → bioguider-0.2.32}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioguider
-Version: 0.2.31
+Version: 0.2.32
 Summary: An AI-Powered package to help biomedical developers to generate clear documentation
 License: MIT
 Author: Cankun Wang

{bioguider-0.2.31 → bioguider-0.2.32}/bioguider/agents/agent_utils.py

@@ -27,6 +27,7 @@ from bioguider.utils.utils import clean_action_input
 from ..utils.gitignore_checker import GitignoreChecker
 from ..database.summarized_file_db import SummarizedFilesDb
 from bioguider.agents.common_conversation import CommonConversation
+from bioguider.rag.config import configs
 
 logger = logging.getLogger(__name__)
 
@@ -153,7 +154,9 @@ def read_directory(
         return None
     gitignore_checker = GitignoreChecker(
         directory=dir_path,
-        gitignore_path=gitignore_path
+        gitignore_path=gitignore_path,
+        exclude_dir_patterns=configs["file_filters"]["excluded_dirs"],
+        exclude_file_patterns=configs["file_filters"]["excluded_files"],
     )
     files = gitignore_checker.check_files_and_folders(level=level)
     return files

{bioguider-0.2.31 → bioguider-0.2.32}/bioguider/agents/evaluation_readme_task.py

@@ -28,6 +28,7 @@ from bioguider.utils.constants import (
     EvaluationREADMEResult,
 )
 from bioguider.utils.utils import increase_token_usage
+from bioguider.rag.config import configs
 
 logger = logging.getLogger(__name__)
 
@@ -638,7 +639,9 @@ class EvaluationREADMETask(EvaluationTask):
         repo_path = self.repo_path
         gitignore_path = Path(repo_path, ".gitignore")
         gitignore_checker = GitignoreChecker(
-            directory=repo_path, gitignore_path=gitignore_path
+            directory=repo_path, gitignore_path=gitignore_path,
+            exclude_dir_patterns=configs["file_filters"]["excluded_dirs"],
+            exclude_file_patterns=configs["file_filters"]["excluded_files"],
         )
         found_readme_files = gitignore_checker.check_files_and_folders(
             check_file_cb=lambda root_dir, relative_path: Path(relative_path).name.lower() in possible_readme_files,

{bioguider-0.2.31 → bioguider-0.2.32}/bioguider/managers/evaluation_manager.py

@@ -3,10 +3,8 @@ from pathlib import Path
 
 from bioguider.agents.evaluation_tutorial_task import EvaluationTutorialTask
 from bioguider.agents.evaluation_userguide_task import EvaluationUserGuideTask
-from bioguider.agents.prompt_utils import CollectionGoalItemEnum
 from bioguider.database.code_structure_db import CodeStructureDb
 from bioguider.utils.constants import ProjectMetadata
-from bioguider.utils.gitignore_checker import GitignoreChecker
 
 from ..agents.identification_task import IdentificationTask
 from ..rag.rag import RAG

{bioguider-0.2.31 → bioguider-0.2.32}/bioguider/utils/code_structure_builder.py

@@ -6,6 +6,7 @@ from bioguider.utils.r_file_handler import RFileHandler
 from .gitignore_checker import GitignoreChecker
 from .python_file_handler import PythonFileHandler
 from ..database.code_structure_db import CodeStructureDb
+from ..rag.config import configs
 
 logger = logging.getLogger(__name__)
 
@@ -17,7 +18,12 @@ class CodeStructureBuilder:
         code_structure_db: CodeStructureDb,
     ):
         self.repo_path = str(repo_path)
-        self.gitignore_checker = GitignoreChecker(repo_path, str(gitignore_path))
+        self.gitignore_checker = GitignoreChecker(
+            directory=repo_path,
+            gitignore_path=str(gitignore_path),
+            exclude_dir_patterns=configs["file_filters"]["excluded_dirs"],
+            exclude_file_patterns=configs["file_filters"]["excluded_files"],
+        )
         self.file_handler = PythonFileHandler(repo_path)
         self.code_structure_db = code_structure_db
 

{bioguider-0.2.31 → bioguider-0.2.32}/bioguider/utils/r_file_handler.py

@@ -348,10 +348,12 @@ class RFileHandler:
             s = line.lstrip()
             if s.startswith("#'"):
                 buf.append(s[2:].lstrip())
-                line_idx -= 1
-                continue
-            # stop at first non-roxygen line (don’t cross blank + NULL padding blocks)
-            break
+            elif s.strip() == "":
+                pass
+            else:
+                # stop at first non-roxygen line (don’t cross blank + NULL padding blocks)
+                break
+            line_idx -= 1
         if not buf:
             return None
         buf.reverse()

{bioguider-0.2.31 → bioguider-0.2.32}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bioguider"
-version = "0.2.31"
+version = "0.2.32"
 description = "An AI-Powered package to help biomedical developers to generate clear documentation"
 authors = [
     "Cankun Wang <Cankun.Wang@osumc.edu>",