bioguider 0.2.27__tar.gz → 0.2.29__tar.gz

{bioguider-0.2.27 → bioguider-0.2.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioguider
-Version: 0.2.27
+Version: 0.2.29
 Summary: An AI-Powered package to help biomedical developers to generate clear documentation
 License: MIT
 Author: Cankun Wang

{bioguider-0.2.27 → bioguider-0.2.29}/bioguider/generation/output_manager.py

@@ -3,14 +3,14 @@ from __future__ import annotations
 import os
 import json
 from datetime import datetime
-from typing import Dict, List, Tuple
+from typing import Dict, List, Optional, Tuple
 
 from .models import OutputArtifact, GenerationManifest, PlannedEdit
 
 
 class OutputManager:
-    def __init__(self, base_outputs_dir: str = "outputs"):
-        self.base_outputs_dir = base_outputs_dir
+    def __init__(self, base_outputs_dir: Optional[str] = None):
+        self.base_outputs_dir = base_outputs_dir or "outputs"
 
     def prepare_output_dir(self, repo_url_or_name: str) -> str:
         repo_name = self._extract_repo_name(repo_url_or_name)

{bioguider-0.2.27 → bioguider-0.2.29}/bioguider/generation/report_loader.py

@@ -123,14 +123,17 @@ class EvaluationReportLoader:
         normalized = normalize(raw)
 
         # Special handling for stringified evaluation fields
-        inst_eval = normalized.get("installation_evaluation")
+        inst_eval = normalized.get("installation")
         if isinstance(inst_eval, str):
             normalized["installation_evaluation"] = {
-                "structured_evaluation": self._parse_structured_block(inst_eval, "structured_evaluation"),
+                "structured_evaluation": self._parse_structured_block(inst_eval["evaluation"], "structured_evaluation"),
             }
+        else:
+            normalized["installation_evaluation"] = inst_eval["evaluation"]
+            normalized["installation_files"] = inst_eval["files"]
 
-        readme_eval = normalized.get("readme_evaluation")
-        if isinstance(readme_eval, dict):
+        readme_eval = normalized.get("readme")
+        if isinstance(readme_eval["evaluations"], dict):
             fixed: Dict[str, Any] = {}
             for fname, val in readme_eval.items():
                 if isinstance(val, str):
@@ -140,10 +143,16 @@ class EvaluationReportLoader:
                 else:
                     fixed[fname] = val
             normalized["readme_evaluation"] = fixed
+            normalized["readme_files"] = readme_eval["files"]
 
-        submit_eval = normalized.get("submission_requirements_evaluation")
-        if isinstance(submit_eval, str):
-            normalized["submission_requirements_evaluation"] = self._parse_submission_eval_str(submit_eval)
+        userguide_eval = normalized.get("userguide")
+        if isinstance(userguide_eval["evaluation"], dict):
+            normalized["userguide_evaluation"] = userguide_eval["evaluation"]
+            normalized["userguide_files"] = userguide_eval["files"]
+
+        # userguide_eval = normalized.get("userguide")
+        # if isinstance(userguide_eval, str):
+        #     normalized["userguide_evaluation"] = self._parse_structured_block(userguide_eval["evaluation"], "structured_evaluation")
 
         report = EvaluationReport(**normalized)
         return report, report_path

{bioguider-0.2.27 → bioguider-0.2.29}/bioguider/managers/generation_manager.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 import os
 from pathlib import Path
-from typing import Tuple, Dict, List
+from typing import Optional, Tuple, Dict, List
 
 from bioguider.generation import (
     EvaluationReportLoader,
@@ -20,7 +20,7 @@ from bioguider.utils.file_utils import parse_repo_url
 
 
 class DocumentationGenerationManager:
-    def __init__(self, llm, step_callback):
+    def __init__(self, llm, step_callback, output_dir: Optional[str] = None):
         self.llm = llm
         self.step_callback = step_callback
         self.repo_url_or_path: str | None = None
@@ -30,7 +30,7 @@ class DocumentationGenerationManager:
         self.style_analyzer = StyleAnalyzer()
         self.planner = ChangePlanner()
         self.renderer = DocumentRenderer()
-        self.output = OutputManager()
+        self.output = OutputManager(base_outputs_dir=output_dir)
         self.llm_gen = LLMContentGenerator(llm)
         self.llm_cleaner = LLMCleaner(llm)
 

{bioguider-0.2.27 → bioguider-0.2.29}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bioguider"
-version = "0.2.27"
+version = "0.2.29"
 description = "An AI-Powered package to help biomedical developers to generate clear documentation"
 authors = [
     "Cankun Wang <Cankun.Wang@osumc.edu>",