bioguider 0.2.52__py3-none-any.whl

bioguider/utils/utils.py

@@ -0,0 +1,163 @@
+import logging
+from pathlib import Path
+import re
+import subprocess
+from typing import Optional
+from enum import Enum
+from pydantic import BaseModel
+import tiktoken
+from bs4 import BeautifulSoup
+
+from bioguider.utils.constants import DEFAULT_TOKEN_USAGE
+logger = logging.getLogger(__name__)
+
+def count_tokens(text: str, local_ollama: bool = False) -> int:
+    """
+    Count the number of tokens in a text string using tiktoken.
+
+    Args:
+        text (str): The text to count tokens for.
+        local_ollama (bool, optional): Whether using local Ollama embeddings. Default is False.
+
+    Returns:
+        int: The number of tokens in the text.
+    """
+    try:
+        if local_ollama:
+            encoding = tiktoken.get_encoding("cl100k_base")
+        else:
+            encoding = tiktoken.encoding_for_model("text-embedding-3-small")
+
+        return len(encoding.encode(text))
+    except Exception as e:
+        # Fallback to a simple approximation if tiktoken fails
+        logger.warning(f"Error counting tokens with tiktoken: {e}")
+        # Rough approximation: 4 characters per token
+        return len(text) // 4
+
+
+def run_command(command: list, cwd: str = None, timeout: int = None):
+    """
+    Run a shell command with optional timeout and return stdout, stderr, and return code.
+    """
+    try:
+        result = subprocess.run(
+            command,
+            cwd=cwd,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            text=True,
+            timeout=timeout
+        )
+        return result.stdout, result.stderr, result.returncode
+    except subprocess.TimeoutExpired as e:
+        return e.stdout or "", e.stderr or f"Command timed out after {timeout} seconds", -1
+
+def escape_braces(text: str) -> str:
+    def fix_braces(m):
+        s = m.group(0)
+        # If odd number of braces, double the last one
+        if len(s) % 2 == 1:
+            return s + s[-1]
+        return s
+    # Handle both { and } sequences
+    text = re.sub(r'{+|}+', fix_braces, text)
+    return text
+
+def increase_token_usage(
+    token_usage: Optional[dict] = None,
+    incremental: dict = {**DEFAULT_TOKEN_USAGE},
+):
+    if token_usage is None:
+        token_usage = {**DEFAULT_TOKEN_USAGE}
+    token_usage["total_tokens"] += incremental["total_tokens"]
+    token_usage["completion_tokens"] += incremental["completion_tokens"]
+    token_usage["prompt_tokens"] += incremental["prompt_tokens"]
+
+    return token_usage
+
+def clean_action_input(action_input: str) -> str:
+    replaced_input = ""
+
+    while (True):
+        replaced_input = action_input.strip()
+        replaced_input = replaced_input.strip("`")
+        replaced_input = replaced_input.strip('"')
+        replaced_input = replaced_input.strip()
+        replaced_input = replaced_input.strip("`")
+        replaced_input = replaced_input.strip('"')
+        replaced_input = replaced_input.strip()
+        if (replaced_input == action_input):
+            break
+        action_input = replaced_input
+    
+    action_input = action_input.replace("'", '"')
+    action_input = action_input.replace("`", '"')
+    return action_input
+
+# Convert BaseModel objects to dictionaries for JSON serialization
+def convert_to_serializable(obj):
+    if isinstance(obj, BaseModel):
+        return obj.model_dump()
+    elif hasattr(obj, 'model_dump'):
+        return obj.model_dump()
+    elif isinstance(obj, Enum):
+        return obj.value
+    elif isinstance(obj, dict):
+        return {k: convert_to_serializable(v) for k, v in obj.items()}
+    elif isinstance(obj, list):
+        return [convert_to_serializable(item) for item in obj]
+    elif isinstance(obj, tuple):
+        return [convert_to_serializable(item) for item in obj]
+    elif hasattr(obj, '__dict__') and not isinstance(obj, (str, int, float, bool, type(None))):
+        # Handle regular class instances by converting their __dict__ to a dictionary
+        # Exclude built-in types that might have __dict__ but shouldn't be converted
+        return {k: convert_to_serializable(v) for k, v in vars(obj).items()}
+    else:
+        return obj
+
+def convert_html_to_text(html_path: str | Path, exclude_tags: list[str] = ["script", "style", "img", "svg", "meta", "link"]) -> str:
+    """
+    This function is used to convert html string to text, that is,
+    extract text from html content, including tables.
+    """
+    html_path = Path(html_path)
+    if not html_path.exists():
+        raise FileNotFoundError(f"File {html_path} does not exist")
+    with html_path.open("r", encoding="utf-8") as f:
+        html_content = f.read()
+    soup = BeautifulSoup(html_content, "html.parser")
+    if exclude_tags is not None:
+        for tag in exclude_tags:
+            for element in soup.find_all(tag):
+                element.decompose()
+    text = soup.get_text(separator="\n", strip=True)
+    return text
+
+def get_overall_score(grade_levels: list[int | bool | float | str | None], weights: list[int]) -> int:
+    max_score = 100
+    min_score = 0
+    def get_grade_level_score(grade_level: int | bool | float | str | None) -> int:
+        if grade_level is None:
+            return 0
+        if isinstance(grade_level, bool):
+            if grade_level:
+                return max_score
+            else:
+                return min_score
+        try:
+            return int(float(grade_level))
+        except Exception:
+            logger.warning(f"Failed to convert grade level {grade_level} to int")
+            return 0
+    if len(grade_levels) != len(weights):
+        raise ValueError("The length of grade_levels and weights must be the same")
+    score = round(sum(
+        get_grade_level_score(grade_level) * weight for grade_level, weight in zip(grade_levels, weights)
+    ) / sum(weight * max_score for weight in weights), 2)
+        
+    return int(score*max_score) if score > 0 else min_score
+
+    
+
+

bioguider-0.2.52.dist-info/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 OSU_BMBL
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

bioguider-0.2.52.dist-info/METADATA

@@ -0,0 +1,51 @@
+Metadata-Version: 2.3
+Name: bioguider
+Version: 0.2.52
+Summary: An AI-Powered package to help biomedical developers to generate clear documentation
+License: MIT
+Author: Cankun Wang
+Author-email: Cankun.Wang@osumc.edu
+Requires-Python: >=3.11,<4.0
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: adalflow (>=1.0.4,<2.0.0)
+Requires-Dist: azure-ai-formrecognizer (>=3.3.3,<4.0.0)
+Requires-Dist: azure-ai-textanalytics (>=5.3.0,<6.0.0)
+Requires-Dist: azure-core (>=1.36.0,<2.0.0)
+Requires-Dist: azure-identity (>=1.25.1,<2.0.0)
+Requires-Dist: beautifulsoup4 (>=4.13.3,<5.0.0)
+Requires-Dist: binaryornot (>=0.4.4,<0.5.0)
+Requires-Dist: faiss-cpu (>=1.11.0,<2.0.0)
+Requires-Dist: grandalf (>=0.8,<0.9)
+Requires-Dist: langchain (>=0.3.20,<0.4.0)
+Requires-Dist: langchain-anthropic (>=0.3.10,<0.4.0)
+Requires-Dist: langchain-deepseek (>=0.1.2,<0.2.0)
+Requires-Dist: langchain-experimental (>=0.3.4,<0.4.0)
+Requires-Dist: langchain-google-genai (>=2.1.4,<3.0.0)
+Requires-Dist: langchain-openai (>=0.3.8,<0.4.0)
+Requires-Dist: langgraph (>=0.3.11,<0.4.0)
+Requires-Dist: markdownify (>=1.1.0,<2.0.0)
+Requires-Dist: nanoid (>=2.0.0,<3.0.0)
+Requires-Dist: pydantic (>=2.10.6,<3.0.0)
+Requires-Dist: pydantic-settings (>=2.8.1,<3.0.0)
+Requires-Dist: pyphen (>=0.17.2,<0.18.0)
+Requires-Dist: pytest (>=8.3.5,<9.0.0)
+Requires-Dist: python-dotenv (>=1.0.1,<2.0.0)
+Requires-Dist: python-iso639 (>=2025.2.18,<2026.0.0)
+Requires-Dist: python-magic (>=0.4.27,<0.5.0)
+Requires-Dist: tenacity (>=9.1.2,<10.0.0)
+Requires-Dist: textstat (>=0.7.6,<0.8.0)
+Requires-Dist: tiktoken (>=0.9.0,<0.10.0)
+Requires-Dist: tqdm (>=4.67.1,<5.0.0)
+Description-Content-Type: text/markdown
+
+# bioguider

bioguider-0.2.52.dist-info/RECORD

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bioguider-0.2.52.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: poetry-core 2.1.3
+Root-Is-Purelib: true
+Tag: py3-none-any