bioguider 0.2.8__py3-none-any.whl → 0.2.9__py3-none-any.whl

bioguider/agents/agent_tools.py

@@ -51,13 +51,22 @@ Returns:
         return content
 
 class summarize_file_tool(agent_tool):
-    """ read and summarize the file
-Args:
-    file_path str [required]: the file path
-    summarize_prompt str [required]: a prompt to guide how to summarize the file, if no prompt needed, please set "N/A"
-Returns:
-    A string of summarized file content, if the file does not exist, return None.         
-        """
+    """ Read a file and generate a summary according to a specified prompt.
+
+Arguments
+----------
+    file_path : str, required
+        Path to the file to read.
+    summarize_prompt : str, optional
+        Instruction guiding the summarization focus (default is "N/A").
+        Use this to emphasize specific aspects of the content.
+
+Returns
+-------
+    str or None
+        A summarized version of the file content.
+        Returns None if the file does not exist or cannot be read.     
+    """
     def __init__(
         self, 
         llm: BaseChatOpenAI,
@@ -96,7 +105,7 @@ Returns:
             summarized_text=summarized_text,
             token_usage=token_usage,
         )
-    def run(self, file_path: str, summarize_prompt: str) -> str | None:
+    def run(self, file_path: str, summarize_prompt: str = "N/A") -> str | None:
         if file_path is None:
             return None
         if summarize_prompt is None or len(summarize_prompt) == 0:

bioguider/agents/evaluation_installation_task.py

@@ -52,14 +52,12 @@ Please assess the installation information using the following criteria. For eac
 
 Your response **must exactly follow** the structure below:
 
-```
 **FinalAnswer**
 **Overall Score:** [Poor / Fair / Good / Excellent]  
 **Ease of Access:** <your comments>  
 **Clarity of Dependency Specification:** <your comments>  
 **Hardware Requirements:** <your comments>  
 **Installation Guide:** <your comments>  
-```
 
 ---
 
@@ -149,6 +147,7 @@ class EvaluationInstallationTask(EvaluationTask):
             schema=EvaluationInstallationResultSchema,
         )
         res = EvaluationInstallationResult(**res)
+        self.print_step(step_output=reasoning_process)
         evaluation = {
             "score": res.score,
             "ease_of_access": res.ease_of_access,

bioguider/agents/evaluation_task.py

@@ -18,7 +18,8 @@ from ..utils.gitignore_checker import GitignoreChecker
 logger = logging.getLogger(__name__)
 
 EVALUATION_README_SYSTEM_PROMPT = """
-You are an expert in evaluating the quality of README files in software repositories. Your task is to analyze the provided README file and generate a comprehensive quality report.
+You are an expert in evaluating the quality of README files in software repositories. 
+Your task is to analyze the provided README file and generate a comprehensive quality report.
 
 ---
 
@@ -28,9 +29,10 @@ First, determine whether the provided README is a **project-level README** (typi
 
 ---
 
-### **Project-level README Evaluation**
+### **Evaluation Criteria**
+
+#### If the README is a **project-level** file, evaluate it using the following criteria.
 
-If the README is a **project-level** file, evaluate it using the following criteria.
 For each criterion below, provide a brief assessment followed by specific, actionable comments for improvement.
 
 **1. Project Clarity & Purpose**
@@ -38,30 +40,45 @@ For each criterion below, provide a brief assessment followed by specific, actio
  * **Improvement Suggestions**:
     * **Original text:** [Quote a specific line/section from the README.]
     * **Improving comments:** [Provide your suggestions to improve clarity.]
+    * **Original text:** [Quote a specific line/section from the README.]
+    * **Improving comments:** [Provide your suggestions to improve clarity.]
+    ...
 
 **2. Installation Instructions**
  * **Assessment**: [Your evaluation of the installation instructions.]
  * **Improvement Suggestions**:
     * **Original text:** [Quote text related to installation.]
     * **Improving comments:** [Provide your suggestions.]
+    * **Original text:** [Quote text related to installation.]
+    * **Improving comments:** [Provide your suggestions.]
+    ...
 
 **3. Usage Instructions**
  * **Assessment**: [Your evaluation of the usage instructions.]
  * **Improvement Suggestions**:
     * **Original text:** [Quote text related to usage.]
     * **Improving comments:** [Provide your suggestions.]
+    * **Original text:** [Quote text related to usage.]
+    * **Improving comments:** [Provide your suggestions.]
+    ...
 
 **4. Contributing Guidelines**
  * **Assessment**: [Your evaluation of the contributing guidelines.]
  * **Improvement Suggestions**:
     * **Original text:** [Quote text related to contributions.]
     * **Improving comments:** [Provide your suggestions.]
+    * **Original text:** [Quote text related to contributions.]
+    * **Improving comments:** [Provide your suggestions.]
+    ...
 
 **5. License Information**
  * **Assessment**: [Your evaluation of the license information.]
  * **Improvement Suggestions**:
     * **Original text:** [Quote text related to the license.]
     * **Improving comments:** [Provide your suggestions.]
+    * **Original text:** [Quote text related to the license.]
+    * **Improving comments:** [Provide your suggestions.]
+    ...
 
 **6. Readability Analysis**
  * **Flesch Reading Ease**: `{flesch_reading_ease}` (A higher score is better, with 60-70 being easily understood by most adults).
@@ -70,29 +87,9 @@ For each criterion below, provide a brief assessment followed by specific, actio
  * **SMOG Index**: `{smog_index}` (Estimates the years of education needed to understand the text).
  * **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
-  * **Score:** <number from 0 to 100>  
-  * **Key Strengths**: <brief summary of the README's strongest points in 2-3 sentences> 
-  * **Overall 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.
-
 ---
 
-### **Folder-Level README Evaluation**
-
-If the README is a **folder-level** file, use the following criteria instead.
+#### If if is a **folder-level** file, use the following criteria instead.
 
 For each criterion below, provide a brief assessment followed by specific, actionable comments for improvement.
 
@@ -121,15 +118,30 @@ For each criterion below, provide a brief assessment followed by specific, actio
  * **SMOG Index**: `{smog_index}` (Estimates the years of education needed to understand the text).
  * **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:
+---
+
+### Final Report Format
+
+#### Your output **must exactly match**  the following template:
+
+**FinalAnswer**
+
  * Project-Level README: Yes / No
- * **Score:** <number from 0 to 100>  
+ * **Score:** [Poor / Fair / Good / Excellent]
   * **Key Strengths**: <brief summary of the README's strongest points in 2-3 sentences> 
   * **Overall Improvement Suggestions:**
     - "Original text snippet 1" - Improving comment 1  
     - "Original text snippet 2" - Improving comment 2  
     - ...
+
+#### Notes
+
+* **Project-Level README**: "Yes" if root-level; "No" if folder-level.
+* **Score**: Overall quality rating, could be Poor / Fair / Good / Excellent.
+* **Key Strengths**: Briefly highlight the README's strongest aspects.
+* **Improvement Suggestions**: Provide concrete snippets and suggested improvements.
+
+
 ---
 
 ### **README path:**

{bioguider-0.2.8.dist-info → bioguider-0.2.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioguider
-Version: 0.2.8
+Version: 0.2.9
 Summary: An AI-Powered package to help biomedical developers to generate clear documentation
 License: MIT
 Author: Cankun Wang

{bioguider-0.2.8.dist-info → bioguider-0.2.9.dist-info}/RECORD

@@ -1,7 +1,7 @@
 bioguider/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bioguider/agents/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bioguider/agents/agent_task.py,sha256=SX4iLdGqQttT39qvr-RtXiSpQEzm7Z3ECVw8IGQzpDc,2828
-bioguider/agents/agent_tools.py,sha256=tl78zCdeWInv5DtwPEKKI4-7CLzfKlr646Sr3hjxo5g,6827
+bioguider/agents/agent_tools.py,sha256=YWF44vGjTzK0H9dxfdZyJ5K2H4z2j1bz-Q0bVw1UoE8,7014
 bioguider/agents/agent_utils.py,sha256=GASgM8pwGcbs3xQ8RaryBtWCim19rAcd3_c4EDranmU,12843
 bioguider/agents/collection_execute_step.py,sha256=Ev4BLjjmBdsc52M1zrq7QK8g7fsffDkSxu-jN2rvedw,5614
 bioguider/agents/collection_observe_step.py,sha256=iNeV6f16Emk1LMStSR4FXBPZ6Sc0eTjwxEfmoeegV-U,4554
@@ -16,8 +16,8 @@ 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_installation_task.py,sha256=Qrn5f-YpqAfaInTgErprDi54Lnufm8geZAhxmNhCqmE,6451
-bioguider/agents/evaluation_task.py,sha256=8tjRPGsRQ9qDxVgYYDo-GhhEiwW71zSS-iyLZUPRbBA,17178
+bioguider/agents/evaluation_installation_task.py,sha256=G8oFpyiT99bGyHGgqE6eCW6_i5le64i3Hd7hSQkrndE,6498
+bioguider/agents/evaluation_task.py,sha256=0kwUkKixljs15VpasMCUdDjQH-xJwXzHV4GyNkGrmPc,17364
 bioguider/agents/identification_execute_step.py,sha256=w3IjL8f2WiHCyiLjVSoySnIAXpi1-hK1DLKCnXbAN2Y,5587
 bioguider/agents/identification_observe_step.py,sha256=OENwf9XyOSIHvJMp7eoyQOYGjjtPnPT2S29xf1rCATk,3667
 bioguider/agents/identification_plan_step.py,sha256=p0BKziXdB4ph4D_T9FU5bH8CbHD5Gv0YuszMds_xh-Y,5224
@@ -42,7 +42,7 @@ 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-0.2.8.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
-bioguider-0.2.8.dist-info/METADATA,sha256=KgszAjfuux0wkXcAbcfchBJiBgwbuhm61YIMsBRJoWQ,1867
-bioguider-0.2.8.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-bioguider-0.2.8.dist-info/RECORD,,
+bioguider-0.2.9.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
+bioguider-0.2.9.dist-info/METADATA,sha256=kctbCb5iK21lTibqx01l7hnLYUz10Be66afv61LwuJA,1867
+bioguider-0.2.9.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+bioguider-0.2.9.dist-info/RECORD,,