bioguider 0.2.17__py3-none-any.whl → 0.2.19__py3-none-any.whl

bioguider/agents/common_conversation.py

@@ -20,7 +20,7 @@ class CommonConversation:
         )
         response = result.generations[0][0].text
         token_usage = result.llm_output.get("token_usage")
-        return response, token_usage
+        return response, vars(token_usage)
     
     def generate_with_schema(self, system_prompt: str, instruction_prompt: str, schema: any):
         system_prompt = escape_braces(system_prompt)

bioguider/agents/evaluation_installation_task.py

@@ -90,11 +90,39 @@ You will be given:
 4. Your improvement suggestions must also include the original text snippet and the improving comments.
 5. Your improvement suggestions must also include suggestions to improve readability.
 6. If you think the it is good enough, you can say so.
+7. In each section output, please first give a detailed explanation of the assessment, and then provide the detailed suggestion for improvement. If you think the it is good enough, you can say so.
+  The following is an example of the output format:
+  **Ease of Access:**
+    Detailed explanation of the assessment. Such as: The INSTALLATION file is present in the repository. The content of the file has been shared completely and is accessible. This confirms the availability of the installation documentation for evaluation. There's no issue with availability.
+    Detailed suggestion for improvement. Such as: No need to improve accessibility of the installation documentation.
+  **Clarity of Dependency Specification:**
+    Detailed explanation of the assessment. Such as: The installation section provides a clear list of dependencies. No need to improve.
+    Detailed suggestion for improvement. Such as: No need to improve.
+  **Hardware Requirements:**
+    Detailed explanation of the assessment. Such as: No hardware requirements are provided in the installation section.
+    Detailed suggestion for improvement. Such as: Add a section to describe the hardware requirements for the installation.
+  **Installation Guide:**
+    Detailed explanation of the assessment. Such as: The installation guide is present in the INSTALLATION file, but lacks a clear and concise guide for the installation process.
+    Detailed suggestion for improvement. Such as: 
+    - Add a clear and concise guide for the installation process.
+    - Improve the readability of the installation guide, like:
+      - <original text snippet> - <improving comments>
+      - <original text snippet> - <improving comments>
+      - ...
+  **Compatible Operating System:**
+    Detailed explanation of the assessment. Such as: No compatible operating system is provided in the installation section.
+    Detailed suggestion for improvement. Such as: 
+    - Add a section to describe the compatible operating systems for the installation.
+    - For example, Ubuntu 22.04 LTS+, CentOS 7+, Mac OS X 10.15+, Windows 10+ are supported.
+    - ...
+  **Overall Score:**
+    Detailed explanation of the assessment. Such as: The installation section provides a clear list of installation steps. No need to improve.
+    Detailed suggestion for improvement. Such as: Add a section to describe the compatible operating systems for the installation.
 
 ---
 
 ### **Output Format**
-Your output must **exactly match** the following format. Do not add or omit any sections.
+Your output must **exactly match** the following format. Do not add or omit any sections. In the output, your detailed assessment and detailed suggestion must include the original text snippet and the improving comments, and include the analysis and explanation.
 
 **FinalAnswer**
 **Ease of Access:** 
@@ -107,6 +135,8 @@ Your output must **exactly match** the following format. Do not add or omit any
   <Your assessment and suggestion here>  
 **Compatible Operating System:**
   <Your assessment and suggestion here>
+**Overall Score:**
+  <Your assessment and suggestion here>
 
 ---
 
@@ -194,7 +224,7 @@ class EvaluationInstallationTask(EvaluationTask):
             installation_files_content=files_content,
             structured_evaluation_and_reasoning_process=structured_evaluation_and_reasoning_process,
         )
-        agent = CommonAgentTwoChainSteps(llm=self.llm)
+        agent = CommonAgentTwoSteps(llm=self.llm)
         res, _, token_usage, reasoning_process = agent.go(
             system_prompt=system_prompt,
             instruction_prompt=EVALUATION_INSTRUCTION,

bioguider/agents/evaluation_readme_task.py

@@ -13,7 +13,10 @@ from bioguider.agents.agent_utils import (
     read_file, read_license_file, 
     summarize_file
 )
-from bioguider.agents.common_agent_2step import CommonAgentTwoChainSteps
+from bioguider.agents.common_agent_2step import (
+    CommonAgentTwoChainSteps, 
+    CommonAgentTwoSteps,
+)
 from bioguider.agents.evaluation_task import EvaluationTask
 from bioguider.utils.constants import (
     DEFAULT_TOKEN_USAGE, 
@@ -168,19 +171,8 @@ You will be given:
 
 ---
 
-### **Instructions**
-1. Based on the provided structured evaluation and its reasoning process, generate a free evaluation of the README file.
-2. Focus on the explanation of assessment in structured evaluation and how to improve the README file based on the structured evaluation and its reasoning process.
-   * For each suggestion to improve the README file, you **must provide some examples** of the original text snippet and the improving comments.
-3. For each item in the structured evaluation, provide a detailed assessment followed by specific, actionable comments for improvement.
-4. Your improvement suggestions must also include the original text snippet and the improving comments.
-5. Your improvement suggestions must also include suggestions to improve readability.
-6. If you think the it is good enough, you can say so.
-
----
-
 ### **Output Format**
-Your output must **exactly match** the following format. Do not add or omit any sections.
+Your output must **exactly match** the following format. Do not add or omit any sections. 
 
 **FinalAnswer**
 **Available:**
@@ -195,8 +187,67 @@ Your output must **exactly match** the following format. Do not add or omit any
   <Your assessment and suggestion here>
 **License Information Included:** 
   <Your assessment and suggestion here>
-** Code contributor / Author information included
+**Code contributor / Author information included
+  <Your assessment and suggestion here>
+**Overall Score:**
   <Your assessment and suggestion here>
+---
+
+### **Instructions**
+1. Based on the provided structured evaluation and its reasoning process, generate a free evaluation of the README file.
+2. Focus on the explanation of assessment in structured evaluation and how to improve the README file based on the structured evaluation and its reasoning process.
+   * For each suggestion to improve the README file, you **must provide some examples** of the original text snippet and the improving comments.
+3. For each item in the structured evaluation, provide a detailed assessment followed by specific, actionable comments for improvement.
+4. Your improvement suggestions must also include the original text snippet and the improving comments.
+5. Your improvement suggestions must also include suggestions to improve readability.
+6. In the **FinalAnswer** of output, in each section output, please first give a detailed explanation of the assessment, and then provide the detailed suggestion for improvement. If you think the it is good enough, you can say so.
+  The following is an example of the output format:
+  **FinalAnswer**
+  **Available:**
+    Detailed explanation of the assessment. Such as: The README file is present in the repository. The content of the file has been shared completely and is accessible. This confirms the availability of the README documentation for evaluation. There's no issue with availability.
+    Detailed suggestion for improvement. Such as: Add a brief introductory section summarizing the project and its main purpose would help orient readers.
+  **Readability:**
+    Detailed explanation of the assessment. Such as: The README is relatively easy to read for someone around the sixth-grade level. While the technical details provided are moderately easy to understand for those familiar with programming and command-line tools, newbies or non-technical users might face challenges due to jargon and lack of introductory explanations.
+    Detailed suggestion for improvement. Such as: 
+    - Add a brief introductory section summarizing the project and its main purpose would help orient readers.
+    - <original text snippet> - <improving comments>
+    - <original text snippet> - <improving comments>
+    - ...
+    - Break down long instructions into smaller bullet points.
+  **Project Purpose:**
+    Detailed explanation of the assessment. Such as: The README indirectly describes project activities like benchmarking and assessing functionalities using LLMs and tools like Poetry. However, it lacks a direct statement that defines the overarching project goals or explains who the intended audience is.
+    Detailed suggestion for improvement. Such as: 
+    - Including a clear project purpose at the beginning, such as: "This project provides a framework for evaluating tabular data models using large language model (LLM)-based assessments. Developers and researchers interested in benchmarking data model performance will find this repository particularly useful."
+    - <original text snippet> - <improving comments>
+    - <original text snippet> - <improving comments>
+    - ...
+  **Hardware and software spec and compatibility description:**
+    Detailed explanation of the assessment. Such as: The README provides partial information about software requirements, emphasizing tools like Poetry. Instructions regarding the setup of `.env` files and API keys are also provided. However, it doesn't specify hardware considerations like memory requirements or explain whether the software is compatible with particular operating systems. This omission can limit usability for certain users.
+    Detailed suggestion for improvement. Such as: 
+    - Adding a subsection titled "Hardware Requirements" to outline memory, processor, or other computational dependencies for running benchmarks effectively.
+    - <original text snippet> - <improving comments>
+    - <original text snippet> - <improving comments>
+    - ...
+  **Dependencies clearly stated:**
+    Detailed explanation of the assessment. Such as: Dependencies are referenced sporadically throughout the README (e.g., using Poetry to install certain tools). However, there isn't a dedicated section that consolidates these into a simple and easy-to-follow format. This could hinder understanding, especially for users looking to quickly identify and install necessary dependencies.
+    Detailed suggestion for improvement. Such as: 
+    - The dependencies are listed in the README and requirements.txt file. No need to improve.
+  **License Information Included:**
+    Detailed explanation of the assessment. Such as: The README mentions the MIT license, which is known for its permissive nature and widespread acceptance. The license information is clear and understandable. No improvements are necessary here.
+    Detailed suggestion for improvement. Such as: No need to improve.
+  **Code contributor / Author information included:**
+    Detailed explanation of the assessment. Such as: The README does not contain a section that credits contributors or maintains lines of communication for potential users or collaborators. This is an important omission, as it fails to acknowledge authors' efforts or encourage interaction.
+    Detailed suggestion for improvement. Such as: 
+    - Including a new "Contributors" section to credit the developers, provide contact information (e.g., email or GitHub profiles), or invite collaboration.
+    - <original text snippet> - <improving comments>
+  **Overall Score:**
+    Detailed explanation of the assessment. Such as: The README is relatively easy to read for someone around the sixth-grade level. While the technical details provided are moderately easy to understand for those familiar with programming and command-line tools, newbies or non-technical users might face challenges due to jargon and lack of introductory explanations.
+    Detailed suggestion for improvement. Such as: 
+    - Add a brief introductory section summarizing the project and its main purpose would help orient readers.
+    - <original text snippet> - <improving comments>
+    - <original text snippet> - <improving comments>
+    - ...
+    - Break down long instructions into smaller bullet points.
 
 ---
 
@@ -446,7 +497,7 @@ class EvaluationREADMETask(EvaluationTask):
             readme_content=readme_content,
             structured_evaluation=structured_reasoning_process,
         )
-        agent = CommonAgentTwoChainSteps(llm=self.llm)
+        agent = CommonAgentTwoSteps(llm=self.llm)
         response, _, token_usage, reasoning_process = agent.go(
             system_prompt=system_prompt,
             instruction_prompt=EVALUATION_INSTRUCTION,

bioguider/utils/constants.py

@@ -63,13 +63,14 @@ class StructuredEvaluationREADMEResult(BaseModel):
     overall_score: str=Field(description="A overall scroll for the README quality, could be `Poor`, `Fair`, `Good`, or `Excellent`")
 
 class FreeProjectLevelEvaluationREADMEResult(BaseModel):
-    available: Optional[str]=Field(description="A string including assessment and suggestion for the availability of the README file")
-    readability: Optional[str]=Field(description="A string including assessment and suggestion for the readability of the README file")
-    project_purpose: Optional[str]=Field(description="A string including assessment and suggestion for the project purpose of the README file")
-    hardware_and_software_spec: Optional[str]=Field(description="A string including assessment and suggestion for the hardware and software spec and compatibility description of the README file")
-    dependency: Optional[str]=Field(description="A string including assessment and suggestion for the dependencies of the README file")
-    license: Optional[str]=Field(description="A string including assessment and suggestion for the license information of the README file")
-    contributor_author: Optional[str]=Field(description="A string including assessment and suggestion for the contributor and author information of the README file")
+    available: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestion for the availability of the README file")
+    readability: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestion for the readability of the README file")
+    project_purpose: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestion for the project purpose of the README file")
+    hardware_and_software_spec: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestion for the hardware and software spec and compatibility description of the README file")
+    dependency: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestion for the dependencies of the README file")
+    license: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestion for the license information of the README file")
+    contributor_author: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestion for the contributor and author information of the README file")
+    overall_score: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestion for the overall score of the README file")
 
 class FreeFolderLevelEvaluationREADMEResult(BaseModel):
     score: Optional[str]=Field(description="An overall score")
@@ -94,11 +95,12 @@ class StructuredEvaluationInstallationResult(BaseModel):
     hardware_requirements: Optional[bool]=Field(description="A boolean value. Is the hardware requirements described?")
 
 class FreeEvaluationInstallationResult(BaseModel):
-    ease_of_access: Optional[str]=Field(description="A string including assessment and suggestions for the ease of access of the installation information")
-    clarity_of_dependency: Optional[str]=Field(description="A string including assessment and suggestions for the clarity of dependency specification")
-    hardware_requirements: Optional[str]=Field(description="A string including assessment and suggestions for the hardware requirements")
-    installation_guide: Optional[str]=Field(description="A string including assessment and suggestions for the installation guide")
-    compatible_os: Optional[str]=Field(description="A string including assessment and suggestions for the compatible operating system")
+    ease_of_access: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestions for the ease of access of the installation information")
+    clarity_of_dependency: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestions for the clarity of dependency specification")
+    hardware_requirements: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestions for the hardware requirements")
+    installation_guide: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestions for the installation guide")
+    compatible_os: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestions for the compatible operating system")
+    overall_score: Optional[list[str]]=Field(description="markdown texts including newlines that contains detailed assessment and detailed suggestions for the overall score of the installation")
 
 class EvaluationInstallationResult(BaseModel):
     structured_evaluation: StructuredEvaluationInstallationResult | None

{bioguider-0.2.17.dist-info → bioguider-0.2.19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioguider
-Version: 0.2.17
+Version: 0.2.19
 Summary: An AI-Powered package to help biomedical developers to generate clear documentation
 License: MIT
 Author: Cankun Wang

{bioguider-0.2.17.dist-info → bioguider-0.2.19.dist-info}/RECORD

@@ -10,15 +10,15 @@ bioguider/agents/collection_task.py,sha256=MjpTYiQQYUpmQf2UOn-dOCZU3kxypc4uOnzd1
 bioguider/agents/collection_task_utils.py,sha256=_e2EebYhl-UYjZ0rHNf2-p32YlstBSffv32suiuT9LI,5386
 bioguider/agents/common_agent.py,sha256=TpfxbYskwuwWrjs1g9RaG7sdA5rOLdiVac7If7uK2sg,4558
 bioguider/agents/common_agent_2step.py,sha256=rGiDzUkmmUIFnmJJxzXK5M5BfIyINHXLZ0pmPRUVqQg,7911
-bioguider/agents/common_conversation.py,sha256=zSRiIbUlif8VMC5ZuFfDTyyf1olg3YyWSnYj_E0_SXg,1649
+bioguider/agents/common_conversation.py,sha256=VrnQoPXXK3xeFjeP4-HH-yD9qmw-o9v93LFtNbYey6E,1655
 bioguider/agents/common_step.py,sha256=GdOCbmj1pwh4etg-futVFYVDQuoUG89DnIrw-B6QbzM,2594
 bioguider/agents/dockergeneration_execute_step.py,sha256=F92jDlkc6KjAvTkX7q1FsCYP8J15SCaNgmwh3YPqfDo,6500
 bioguider/agents/dockergeneration_observe_step.py,sha256=Bo5Td0fzMYLbLki0FvwamzqRFOy4eu3AvIUa8oFApE4,6131
 bioguider/agents/dockergeneration_plan_step.py,sha256=SB8tQM9PkIKsD2o1DFD7bedcxz6r6hSy8n_EVK60Fz0,7235
 bioguider/agents/dockergeneration_task.py,sha256=mYmorLKnJ-Jku3Qq_Y_kcSTsbYIo3RiVdD0puxqXY5Q,6221
 bioguider/agents/dockergeneration_task_utils.py,sha256=v7emqrJlVW-A5ZdLmPSdiaMSKCR8uzy9UYzx_1cgzyo,9041
-bioguider/agents/evaluation_installation_task.py,sha256=mbPRZK6gVEPt-XjDl76_Q71meqFkofFnGPDMq5csL7I,9496
-bioguider/agents/evaluation_readme_task.py,sha256=l0QJAFEE0eBcF2WTDO3S4qPHCJujHPPkfi29tTZf9nI,25223
+bioguider/agents/evaluation_installation_task.py,sha256=0RNH5NV7YKwn_we_d3IjnFf_ee9IPCEQ_olebq2y8Ng,12130
+bioguider/agents/evaluation_readme_task.py,sha256=pi3oAGJgZhJgJG1xLgiobrk3Uy2a_JIarD5QSPBkmHA,30647
 bioguider/agents/evaluation_submission_requirements_task.py,sha256=J_6C-M2AfYue2C-gWBHl7KqGrTBuFBn9zmMV5vSRk-U,7834
 bioguider/agents/evaluation_task.py,sha256=4UrcUCy8UIVLd1NpBpqGgmudqeSK3wWI3Jm8LEYySbY,12661
 bioguider/agents/identification_execute_step.py,sha256=w3IjL8f2WiHCyiLjVSoySnIAXpi1-hK1DLKCnXbAN2Y,5587
@@ -39,13 +39,13 @@ bioguider/rag/data_pipeline.py,sha256=bkJ2IUCgPx_OL2uZtPd6cIBor2VFZEIfGd5kVlmiPj
 bioguider/rag/embedder.py,sha256=jofR8hOj3Aj2IyBQ9y6FeAc84tgq5agbIfCGyFxYpJ8,650
 bioguider/rag/rag.py,sha256=JFPwrJlKDSyd3U3Gce_NSxI5343eNUbqPG9Fs5Pfoq0,4696
 bioguider/settings.py,sha256=BD_iz9aYarxmWUl0XaKl4-D4oTXMhFzljsXLNn2phis,3143
-bioguider/utils/constants.py,sha256=ZZqNsW59P1c2-vm5VP-IhWRNrVdYvWmvfa537oEVl3A,7904
+bioguider/utils/constants.py,sha256=Yzo9oFG4P4C83vKl22RsWkIDa4dcitvcCIceusNPIRQ,8928
 bioguider/utils/default.gitignore,sha256=XjPdyO2KV8z8iyuqluaNR_70tBQftMpyKL8HboVNyeI,1605
 bioguider/utils/file_utils.py,sha256=9VfAHsz1UkFPtzAmvWZvPl1TMaKIYNjNlLgsfB8tNjg,3683
 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=aWtgdvB04gEiJTfQNK4aQPO1mxv2zRZTbDaGUBy9DFc,2275
-bioguider-0.2.17.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
-bioguider-0.2.17.dist-info/METADATA,sha256=aUDhIK7X_YRYTp12m_MX1EDphsKaZDcQlnaGR_h34AM,1868
-bioguider-0.2.17.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-bioguider-0.2.17.dist-info/RECORD,,
+bioguider-0.2.19.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
+bioguider-0.2.19.dist-info/METADATA,sha256=YvAwNzOyncowyrbKcoKBSEeIVLPk8UiRK-Y4vihrUUY,1868
+bioguider-0.2.19.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+bioguider-0.2.19.dist-info/RECORD,,