bioguider 0.2.4__py3-none-any.whl → 0.2.5__py3-none-any.whl

bioguider/agents/evaluation_task.py

@@ -71,8 +71,22 @@ For each criterion below, provide a brief assessment followed by specific, actio
  * **Assessment**: Based on these scores, evaluate the overall readability and technical complexity of the language used.
 
 **Final Answer**
- * Project-Level README: Yes / No
- * Provide a final, overall assessment of the README file's quality, summarizing the key strengths and areas for improvement.
+ The final answer **must exactly match** the following format:
+```
+  * Project-Level README: Yes / No
+  * **Score:** <number from 0 to 100>  
+  * **Key Strengths**: <brief summary of the README's strongest points in 2-3 sentences> 
+  * **Improvement Suggestions:**
+    - "Original text snippet 1" - Improving comment 1  
+    - "Original text snippet 2" - Improving comment 2  
+    - ...
+```
+
+  * **Project-Level README**: Indicate “Yes” if the README is project-level, otherwise “No.”
+  * **Score**: Provide an overall quality score (100 = perfect).
+  * **Key Strengths**: Provide the README's strongest points in 2-3 sentences
+  * **Overall Improvement Suggestions**:
+    * List each original text snippet that needs improvement, followed by your suggestion.
 
 ---
 
@@ -108,8 +122,9 @@ For each criterion below, provide a brief assessment followed by specific, actio
  * **Assessment**: Based on these scores, evaluate the overall readability and technical complexity of the language used.
 
 **Final Answer**
+  The final answer **must exactly match** the following format:
  * Project-Level README: Yes / No
- * Provide a final, overall assessment of the README file's quality, summarizing the key strengths and areas for improvement.
+ * Overall Assessment: provide a final, overall assessment of the README file's quality, summarizing the key strengths and areas for improvement.
 ---
 
 ### **README path:**
@@ -167,8 +182,38 @@ class EvaluationTask(ABC):
         pass
 
 class EvaluationREADMEResult(BaseModel):
-    project_level: Optional[bool]=Field(description="a boolean value specifying if the README file is **project-level** README. TRUE: project-level, FALSE, folder-level")
-    overall_assessment: Optional[str]=Field(description="an overall assessment")
+    project_level: Optional[bool]=Field(description="A boolean value specifying if the README file is **project-level** README. TRUE: project-level, FALSE, folder-level")
+    score: Optional[float]=Field(description="An overall score")
+    key_strengths: Optional[str]=Field(description="A string specifying the key strengths of README file.")
+    overall_improvement_suggestions: Optional[list[str]]=Field(description="A list of overall improvement suggestions")
+
+EvaluationREADMEResultSchema = {
+    "title": "EvaluationREADMEResult",
+    "type": "object",
+    "properties": {
+        "project_level": {
+            "anyOf": [{"type": "boolean"}, {"type": "null"}],
+            "description": "A boolean value specifying if the README file is **project-level** README. TRUE: project-level, FALSE: folder-level.",
+            "title": "Project Level"
+        },
+        "score": {
+            "anyOf": [{"type": "number"}, {"type": "null"}],
+            "description": "An overall score",
+            "title": "Score"
+        },
+        "key_strengths": {
+            "anyOf": [{"type": "string"}, {"type": "null"}],
+            "description": "A string specifying the key strengths of README file.",
+            "title": "Key Strengths",
+        },
+        "overall_improvement_suggestions": {
+            "anyOf": [{"items": {"type": "string"}, "type": "array"}, {"type": "null"}],
+            "description": "A list of improvement suggestions",
+            "title": "Overall Improvement Suggestions"
+        }
+    },
+    "required": ["project_level", "score", "key_strengths", "overall_improvement_suggestions"]
+}
 
 class EvaluationREADMETask(EvaluationTask):
     def __init__(
@@ -195,7 +240,14 @@ class EvaluationREADMETask(EvaluationTask):
                 logger.error(f"Error in reading file {readme_file}")
                 continue
             if len(readme_content.strip()) == 0:
-                readme_content = "empty file"
+                readme_evaluations[readme_file] = {
+                    "evaluation": {
+                        "project_level": "/" in readme_file,
+                        "overall_assessment": f"{readme_file} is an empty file."
+                    },
+                    "reasoning_process": f"{readme_file} is an empty file.",
+                }
+                continue
 
             readability = PyphenReadability()
             flesch_reading_ease, flesch_kincaid_grade, gunning_fog_index, smog_index, \
@@ -215,14 +267,17 @@ class EvaluationREADMETask(EvaluationTask):
             response, _, token_usage, reasoning_process = agent.go(
                 system_prompt=system_prompt,
                 instruction_prompt="Before arriving at the conclusion, clearly explain your reasoning step by step. Now, let's begin the evaluation.",
-                schema=EvaluationREADMEResult,
+                schema=EvaluationREADMEResultSchema,
             )
+            response = EvaluationREADMEResult(**response)
             self.print_step(step_output=f"README: {readme_file}")
             self.print_step(step_output=reasoning_process)
             readme_evaluations[readme_file] = {
                 "evaluation": {
                     "project_level": response.project_level,
-                    "overall_assessment": response.overall_assessment,
+                    "score": response.score,
+                    "key_strengths": response.key_strengths,
+                    "overall_assessment": response.overall_improvement_suggestions,
                 }, 
                 "reasoning_process": reasoning_process
             }

{bioguider-0.2.4.dist-info → bioguider-0.2.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioguider
-Version: 0.2.4
+Version: 0.2.5
 Summary: An AI-Powered package to help biomedical developers to generate clear documentation
 License: MIT
 Author: Cankun Wang

{bioguider-0.2.4.dist-info → bioguider-0.2.5.dist-info}/RECORD

@@ -16,7 +16,7 @@ bioguider/agents/dockergeneration_observe_step.py,sha256=93PO_Y4YyUShVTKRt0nErcj
 bioguider/agents/dockergeneration_plan_step.py,sha256=SB8tQM9PkIKsD2o1DFD7bedcxz6r6hSy8n_EVK60Fz0,7235
 bioguider/agents/dockergeneration_task.py,sha256=ezsweVHJsFpOyOI6rYMt1DZ3PE19dcq4J3Lm-d0IA8M,6220
 bioguider/agents/dockergeneration_task_utils.py,sha256=v7emqrJlVW-A5ZdLmPSdiaMSKCR8uzy9UYzx_1cgzyo,9041
-bioguider/agents/evaluation_task.py,sha256=RRcbw4qTUPElZuiBAMj7heGsDV3t93l_IrioudMTGpc,14316
+bioguider/agents/evaluation_task.py,sha256=khUSDTcuBTbCDdLQ1uHkzumsWDGevdXhzKM11XtPXRs,16884
 bioguider/agents/identification_execute_step.py,sha256=_9x_KITVtNJjQlgjfq-LazoUl46Tctaj_W_AVxz5q-w,5488
 bioguider/agents/identification_observe_step.py,sha256=OENwf9XyOSIHvJMp7eoyQOYGjjtPnPT2S29xf1rCATk,3667
 bioguider/agents/identification_plan_step.py,sha256=p0BKziXdB4ph4D_T9FU5bH8CbHD5Gv0YuszMds_xh-Y,5224
@@ -41,7 +41,7 @@ bioguider/utils/file_utils.py,sha256=9VfAHsz1UkFPtzAmvWZvPl1TMaKIYNjNlLgsfB8tNjg
 bioguider/utils/gitignore_checker.py,sha256=pOYUwsS9D5014LxcZb0cj3s2CAYaD2uF_pYJpaNKcho,6532
 bioguider/utils/pyphen_utils.py,sha256=cdZc3qphkvMDeL5NiZ8Xou13M_uVNP7ifJ-FwxO-0BE,2680
 bioguider/utils/utils.py,sha256=YP3HXgU_rvYDWkEcTzWGiYZw-mlfVrqGhUGSc0_4Pms,900
-bioguider-0.2.4.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
-bioguider-0.2.4.dist-info/METADATA,sha256=VD_LpYetLIYKw2y-JH7_OZZT8D5oIbmzSCx8t5kgyJY,1823
-bioguider-0.2.4.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-bioguider-0.2.4.dist-info/RECORD,,
+bioguider-0.2.5.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
+bioguider-0.2.5.dist-info/METADATA,sha256=QQTOJ7Zj3RdXKBtcJwWtyWC51V_hgqJ-HovctZiegOo,1823
+bioguider-0.2.5.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+bioguider-0.2.5.dist-info/RECORD,,