academia-mcp 1.8.1__py3-none-any.whl → 1.9.0__py3-none-any.whl

academia_mcp/files.py

@@ -1,7 +1,8 @@
-import os
 from typing import Optional
 from pathlib import Path
 
+from academia_mcp.settings import settings
+
 DIR_PATH = Path(__file__).parent
 ROOT_PATH = DIR_PATH.parent
 DEFAULT_WORKSPACE_DIR_PATH: Path = DIR_PATH / "workdir"
@@ -14,7 +15,7 @@ class WorkspaceDirectory:
     @classmethod
     def get_dir(cls) -> Path:
         if cls.workspace_dir is None:
-            return Path(os.getenv("WORKSPACE_DIR", DEFAULT_WORKSPACE_DIR_PATH))
+            return Path(settings.WORKSPACE_DIR)
         return cls.workspace_dir
 
     @classmethod

academia_mcp/llm.py

@@ -1,10 +1,11 @@
-import os
 from typing import List, Dict, Any
 
 from pydantic import BaseModel
 from openai import AsyncOpenAI
 from openai.types.chat.chat_completion_message import ChatCompletionMessage
 
+from academia_mcp.settings import settings
+
 
 class ChatMessage(BaseModel):  # type: ignore
     role: str
@@ -15,9 +16,9 @@ ChatMessages = List[ChatMessage]
 
 
 async def llm_acall(model_name: str, messages: ChatMessages, **kwargs: Any) -> str:
-    key = os.getenv("OPENROUTER_API_KEY", "")
+    key = settings.OPENROUTER_API_KEY
     assert key, "Please set OPENROUTER_API_KEY in the environment variables"
-    base_url = os.getenv("BASE_URL", "https://openrouter.ai/api/v1")
+    base_url = settings.BASE_URL
 
     client = AsyncOpenAI(base_url=base_url, api_key=key)
     response: ChatCompletionMessage = (

academia_mcp/server.py

@@ -1,34 +1,45 @@
-import os
 import socket
+import logging
+from logging.config import dictConfig
 from typing import Optional, Literal
 
 import fire  # type: ignore
 from mcp.server.fastmcp import FastMCP
-from dotenv import load_dotenv
+from uvicorn.config import LOGGING_CONFIG as UVICORN_LOGGING_CONFIG
 
-from .tools.arxiv_search import arxiv_search
-from .tools.arxiv_download import arxiv_download
-from .tools.s2_citations import s2_get_citations, s2_get_references
-from .tools.hf_datasets_search import hf_datasets_search
-from .tools.anthology_search import anthology_search
-from .tools.document_qa import document_qa
-from .tools.latex import (
+from academia_mcp.settings import settings
+from academia_mcp.tools.arxiv_search import arxiv_search
+from academia_mcp.tools.arxiv_download import arxiv_download
+from academia_mcp.tools.s2_citations import s2_get_citations, s2_get_references
+from academia_mcp.tools.hf_datasets_search import hf_datasets_search
+from academia_mcp.tools.anthology_search import anthology_search
+from academia_mcp.tools.document_qa import document_qa
+from academia_mcp.tools.latex import (
     compile_latex,
     get_latex_template,
     get_latex_templates_list,
     read_pdf,
 )
-from .tools.web_search import web_search, tavily_web_search, exa_web_search, brave_web_search
-from .tools.visit_webpage import visit_webpage
-from .tools.bitflip import (
+from academia_mcp.tools.web_search import (
+    web_search,
+    tavily_web_search,
+    exa_web_search,
+    brave_web_search,
+)
+from academia_mcp.tools.visit_webpage import visit_webpage
+from academia_mcp.tools.bitflip import (
     extract_bitflip_info,
     generate_research_proposals,
     score_research_proposals,
 )
-from .tools.review import review_pdf_paper, download_pdf_paper
+from academia_mcp.tools.review import review_pdf_paper, download_pdf_paper
 
 
-load_dotenv()
+def configure_uvicorn_style_logging(level: int = logging.INFO) -> None:
+    config = {**UVICORN_LOGGING_CONFIG}
+    config["disable_existing_loggers"] = False
+    config["root"] = {"handlers": ["default"], "level": logging.getLevelName(level)}
+    dictConfig(config)
 
 
 def find_free_port() -> int:
@@ -51,12 +62,14 @@ def run(
     disable_web_search_tools: bool = False,
     disable_llm_tools: bool = False,
 ) -> None:
+    configure_uvicorn_style_logging()
     server = FastMCP(
         "Academia MCP",
         stateless_http=True,
         streamable_http_path=streamable_http_path,
         mount_path=mount_path,
     )
+    logger = logging.getLogger(__name__)
 
     server.add_tool(arxiv_search)
     server.add_tool(arxiv_download)
@@ -64,33 +77,45 @@ def run(
     server.add_tool(s2_get_references)
     server.add_tool(hf_datasets_search)
     server.add_tool(anthology_search)
-    server.add_tool(compile_latex)
     server.add_tool(get_latex_template)
     server.add_tool(get_latex_templates_list)
     server.add_tool(visit_webpage)
-    server.add_tool(download_pdf_paper)
-    server.add_tool(read_pdf)
+
+    if settings.WORKSPACE_DIR:
+        server.add_tool(compile_latex)
+        server.add_tool(download_pdf_paper)
+        server.add_tool(read_pdf)
+    else:
+        logger.warning(
+            "WORKSPACE_DIR is not set, compile_latex/download_pdf_paper/read_pdf will not be available!"
+        )
 
     if not disable_web_search_tools:
-        if os.getenv("TAVILY_API_KEY"):
+        if settings.TAVILY_API_KEY:
             server.add_tool(tavily_web_search)
-        if os.getenv("EXA_API_KEY"):
+        if settings.EXA_API_KEY:
             server.add_tool(exa_web_search)
-        if os.getenv("BRAVE_API_KEY"):
+        if settings.BRAVE_API_KEY:
             server.add_tool(brave_web_search)
-        if os.getenv("EXA_API_KEY") or os.getenv("BRAVE_API_KEY") or os.getenv("TAVILY_API_KEY"):
+        if settings.EXA_API_KEY or settings.BRAVE_API_KEY or settings.TAVILY_API_KEY:
             server.add_tool(web_search)
+        else:
+            logger.warning("No web search tools keys are set, web_search will not be available!")
 
-    if not disable_llm_tools and os.getenv("OPENROUTER_API_KEY"):
+    if not disable_llm_tools and settings.OPENROUTER_API_KEY:
         server.add_tool(extract_bitflip_info)
         server.add_tool(generate_research_proposals)
         server.add_tool(score_research_proposals)
         server.add_tool(document_qa)
-        server.add_tool(review_pdf_paper)
+        if settings.WORKSPACE_DIR:
+            server.add_tool(review_pdf_paper)
+    else:
+        logger.warning("No OpenRouter API key is set, LLM-related tools will not be available!")
 
     if port is None:
-        port = int(os.environ.get("PORT", -1))
-        if port == -1:
+        if settings.PORT is not None:
+            port = int(settings.PORT)
+        else:
             port = find_free_port()
     server.settings.port = port
     server.settings.host = host

academia_mcp/settings.py

@@ -0,0 +1,33 @@
+from pathlib import Path
+from typing import Optional
+
+from pydantic_settings import BaseSettings, SettingsConfigDict
+
+
+class Settings(BaseSettings):
+    BASE_URL: str = "https://openrouter.ai/api/v1"
+
+    OPENROUTER_API_KEY: str = ""
+    TAVILY_API_KEY: Optional[str] = None
+    EXA_API_KEY: Optional[str] = None
+    BRAVE_API_KEY: Optional[str] = None
+
+    REVIEW_MODEL_NAME: str = "gpt-5"
+    BITFLIP_MODEL_NAME: str = "deepseek/deepseek-chat-v3-0324"
+    BITFLIP_MAX_COMPLETION_TOKENS: int = 16384
+    DOCUMENT_QA_MODEL_NAME: str = "deepseek/deepseek-chat-v3-0324"
+    DOCUMENT_QA_QUESTION_MAX_LENGTH: int = 10000
+    DOCUMENT_QA_DOCUMENT_MAX_LENGTH: int = 200000
+
+    PORT: int = 5056
+    WORKSPACE_DIR: Optional[Path] = None
+
+    model_config = SettingsConfigDict(
+        env_file=".env",
+        env_file_encoding="utf-8",
+        env_prefix="",
+        extra="ignore",
+    )
+
+
+settings = Settings()

academia_mcp/tools/__init__.py

@@ -13,7 +13,7 @@ from .latex import (
 from .web_search import web_search, tavily_web_search, exa_web_search, brave_web_search
 from .visit_webpage import visit_webpage
 from .bitflip import extract_bitflip_info, generate_research_proposals, score_research_proposals
-from .review import review_pdf_paper, download_pdf_paper
+from .review import review_pdf_paper, download_pdf_paper, review_pdf_paper_by_url
 
 __all__ = [
     "arxiv_search",
@@ -35,6 +35,7 @@ __all__ = [
     "generate_research_proposals",
     "score_research_proposals",
     "review_pdf_paper",
+    "review_pdf_paper_by_url",
     "download_pdf_paper",
     "read_pdf",
 ]

academia_mcp/tools/bitflip.py

@@ -2,7 +2,6 @@
 # https://web.stanford.edu/class/cs197c/slides/02-literature-search.pdf
 
 import json
-import os
 import random
 from typing import List, Optional, Any, Dict
 
@@ -12,6 +11,7 @@ from datasets import load_dataset  # type: ignore
 from academia_mcp.tools.arxiv_download import arxiv_download
 from academia_mcp.utils import extract_json, encode_prompt
 from academia_mcp.llm import llm_acall, ChatMessage
+from academia_mcp.settings import settings
 
 
 class ProposalDataset:
@@ -201,7 +201,7 @@ async def extract_bitflip_info(arxiv_id: str) -> str:
     Args:
         arxiv_id: The arXiv ID of the paper to extract the Bit-Flip information from.
     """
-    model_name = os.getenv("BITFLIP_MODEL_NAME", "deepseek/deepseek-chat-v3-0324")
+    model_name = settings.BITFLIP_MODEL_NAME
     paper = arxiv_download(arxiv_id)
     abstract = json.loads(paper)["abstract"]
     prompt = encode_prompt(EXTRACT_PROMPT, abstract=abstract)
@@ -240,8 +240,8 @@ async def generate_research_proposals(
     ]
     Use `json.loads` to deserialize the result if you want to get specific items.
     """
-    model_name = os.getenv("BITFLIP_MODEL_NAME", "deepseek/deepseek-chat-v3-0324")
-    max_completion_tokens = int(os.getenv("BITFLIP_MAX_COMPLETION_TOKENS", 16384))
+    model_name = settings.BITFLIP_MODEL_NAME
+    max_completion_tokens = int(settings.BITFLIP_MAX_COMPLETION_TOKENS)
     examples = ProposalDataset.get_dataset()[:]
     examples = random.choices(examples, k=2)
 
@@ -293,7 +293,7 @@ async def score_research_proposals(proposals: str | List[str | Dict[str, Any] |
     Args:
         proposals: A list of JSON strings with research proposals.
     """
-    model_name = os.getenv("BITFLIP_MODEL_NAME", "deepseek/deepseek-chat-v3-0324")
+    model_name = settings.BITFLIP_MODEL_NAME
     if isinstance(proposals, str):
         proposals = json.loads(proposals)
         assert isinstance(proposals, list), "Proposals should be a list of JSON strings"

academia_mcp/tools/document_qa.py

@@ -1,14 +1,12 @@
-import os
 import json
 from typing import List, Any, Dict
-from dotenv import load_dotenv
 
 from pydantic import BaseModel
 
 from academia_mcp.llm import llm_acall
 from academia_mcp.utils import truncate_content
+from academia_mcp.settings import settings
 
-load_dotenv()
 
 PROMPT = """You are a helpful assistant that answers questions about documents accurately and concisely.
 Please answer the following questions based solely on the provided document.
@@ -65,10 +63,10 @@ async def document_qa(
         document = json.dumps(document)
     assert document and document.strip(), "Please provide non-empty 'document'"
 
-    question = truncate_content(question, 10000)
-    document = truncate_content(document, 200000)
+    question = truncate_content(question, settings.DOCUMENT_QA_QUESTION_MAX_LENGTH)
+    document = truncate_content(document, settings.DOCUMENT_QA_DOCUMENT_MAX_LENGTH)
 
-    model_name = os.getenv("DOCUMENT_QA_MODEL_NAME", "deepseek/deepseek-chat-v3-0324")
+    model_name = settings.DOCUMENT_QA_MODEL_NAME
     prompt = PROMPT.format(question=question, document=document)
     content = await llm_acall(
         model_name=model_name, messages=[ChatMessage(role="user", content=prompt)]

academia_mcp/tools/review.py

@@ -1,6 +1,6 @@
 import base64
-import os
 import uuid
+import tempfile
 from io import BytesIO
 from pathlib import Path
 from typing import List, Dict, Any
@@ -8,6 +8,7 @@ from typing import List, Dict, Any
 from academia_mcp.pdf import parse_pdf_file_to_images, parse_pdf_file, download_pdf
 from academia_mcp.llm import llm_acall, ChatMessage
 from academia_mcp.files import get_workspace_dir
+from academia_mcp.settings import settings
 
 
 PROMPT = """
@@ -138,6 +139,16 @@ Always produce a correct JSON object.
 """
 
 
+def _create_pdf_filename(pdf_url: str) -> str:
+    if "arxiv.org/pdf" in pdf_url:
+        pdf_filename = pdf_url.split("/")[-1]
+    else:
+        pdf_filename = str(uuid.uuid4())
+    if not pdf_filename.endswith(".pdf"):
+        pdf_filename += ".pdf"
+    return pdf_filename
+
+
 def download_pdf_paper(pdf_url: str) -> str:
     """
     Download a pdf file from a url to the workspace directory.
@@ -147,13 +158,7 @@ def download_pdf_paper(pdf_url: str) -> str:
     Args:
         pdf_url: The url of the pdf file.
     """
-    if "arxiv.org/pdf" in pdf_url:
-        pdf_filename = pdf_url.split("/")[-1]
-    else:
-        pdf_filename = str(uuid.uuid4())
-    if not pdf_filename.endswith(".pdf"):
-        pdf_filename += ".pdf"
-
+    pdf_filename = _create_pdf_filename(pdf_url)
     pdf_path = Path(get_workspace_dir()) / pdf_filename
     download_pdf(pdf_url, pdf_path)
     return pdf_filename
@@ -198,7 +203,7 @@ async def review_pdf_paper(pdf_filename: str) -> str:
             "text": "####\n\nInstructions:\n\n" + PROMPT,
         }
     )
-    model_name = os.getenv("REVIEW_MODEL_NAME", "gpt-5")
+    model_name = settings.REVIEW_MODEL_NAME
     llm_response = await llm_acall(
         model_name=model_name,
         messages=[
@@ -206,3 +211,21 @@ async def review_pdf_paper(pdf_filename: str) -> str:
         ],
     )
     return llm_response.strip()
+
+
+async def review_pdf_paper_by_url(pdf_url: str) -> str:
+    """
+    Review a pdf file with a paper by url.
+    It downloads the pdf file and then reviews it.
+    It parses the pdf file into images and then sends the images to the LLM for review.
+    It can detect different issues with the paper formatting.
+    Returns a proper NeurIPS-style review.
+
+    Args:
+        pdf_url: The url of the pdf file.
+    """
+    pdf_filename = _create_pdf_filename(pdf_url)
+    with tempfile.TemporaryDirectory(prefix="temp_pdf_") as temp_dir:
+        pdf_path = Path(temp_dir) / pdf_filename
+        download_pdf(pdf_url, pdf_path)
+        return await review_pdf_paper(str(pdf_path))

academia_mcp/tools/visit_webpage.py

@@ -1,18 +1,18 @@
 import re
-import os
 import json
 from typing import Optional
 
 from markdownify import markdownify  # type: ignore
 
 from academia_mcp.utils import get_with_retries, post_with_retries
+from academia_mcp.settings import settings
 
 EXA_CONTENTS_URL = "https://api.exa.ai/contents"
 AVAILABLE_PROVIDERS = ("basic", "exa")
 
 
 def _exa_visit_webpage(url: str) -> str:
-    key = os.getenv("EXA_API_KEY", "")
+    key = settings.EXA_API_KEY or ""
     assert key, "Error: EXA_API_KEY is not set and no api_key was provided"
     payload = {
         "urls": [url],
@@ -38,14 +38,14 @@ def visit_webpage(url: str, provider: Optional[str] = "basic") -> str:
         provider in AVAILABLE_PROVIDERS
     ), f"Invalid provider: {provider}. Available providers: {AVAILABLE_PROVIDERS}"
 
-    if provider == "exa":
+    if provider == "exa" and settings.EXA_API_KEY:
         return _exa_visit_webpage(url)
 
     assert provider == "basic"
     response = get_with_retries(url)
     content_type = response.headers.get("content-type", "").lower()
     if not content_type or (not content_type.startswith("text/") and "html" not in content_type):
-        if os.getenv("EXA_API_KEY"):
+        if settings.EXA_API_KEY:
             return _exa_visit_webpage(url)
         return json.dumps(
             {"id": url, "error": f"Unsupported content-type: {content_type or 'unknown'}"}

academia_mcp/tools/web_search.py

@@ -1,8 +1,8 @@
-import os
 import json
 from typing import Optional
 
 from academia_mcp.utils import post_with_retries, get_with_retries
+from academia_mcp.settings import settings
 
 
 EXA_SEARCH_URL = "https://api.exa.ai/search"
@@ -32,9 +32,9 @@ def web_search(
     providers = ("tavily", "brave", "exa")
     assert provider in providers, "Error: provider must be either 'exa', 'tavily' or 'brave'"
 
-    is_tavily_available = os.getenv("TAVILY_API_KEY") is not None
-    is_exa_available = os.getenv("EXA_API_KEY") is not None
-    is_brave_available = os.getenv("BRAVE_API_KEY") is not None
+    is_tavily_available = bool(settings.TAVILY_API_KEY)
+    is_exa_available = bool(settings.EXA_API_KEY)
+    is_brave_available = bool(settings.BRAVE_API_KEY)
     assert is_tavily_available or is_exa_available or is_brave_available
     availability = {
         "tavily": is_tavily_available,
@@ -76,7 +76,7 @@ def tavily_web_search(query: str, limit: Optional[int] = 20) -> str:
     assert isinstance(limit, int), "Error: limit should be an integer"
     assert 0 < limit <= 25, "Error: limit should be between 1 and 25"
 
-    key = os.getenv("TAVILY_API_KEY", "")
+    key = settings.TAVILY_API_KEY or ""
     assert key, "Error: TAVILY_API_KEY is not set and no api_key was provided"
     payload = {
         "query": query,
@@ -112,7 +112,7 @@ def exa_web_search(query: str, limit: Optional[int] = 20) -> str:
     assert isinstance(limit, int), "Error: limit should be an integer"
     assert 0 < limit <= 25, "Error: limit should be between 1 and 25"
 
-    key = os.getenv("EXA_API_KEY", "")
+    key = settings.EXA_API_KEY or ""
     assert key, "Error: EXA_API_KEY is not set and no api_key was provided"
     payload = {
         "query": query,
@@ -151,7 +151,7 @@ def brave_web_search(query: str, limit: Optional[int] = 20) -> str:
     assert isinstance(limit, int), "Error: limit should be an integer"
     assert 0 < limit <= 20, "Error: limit should be between 1 and 20"
 
-    key = os.getenv("BRAVE_API_KEY", "")
+    key = settings.BRAVE_API_KEY or ""
     assert key, "Error: BRAVE_API_KEY is not set and no api_key was provided"
     payload = {
         "q": query,

{academia_mcp-1.8.1.dist-info → academia_mcp-1.9.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: academia-mcp
-Version: 1.8.1
+Version: 1.9.0
 Summary: MCP server that provides different tools to search for scientific publications
 Author-email: Ilya Gusev <phoenixilya@gmail.com>
 Project-URL: Homepage, https://github.com/IlyaGusev/academia_mcp
@@ -29,6 +29,7 @@ Requires-Dist: jinja2>=3.1.6
 Requires-Dist: datasets>=4.0.0
 Requires-Dist: pymupdf>=1.26.4
 Requires-Dist: pillow>=11.3.0
+Requires-Dist: pydantic-settings>=2.6.0
 Dynamic: license-file
 
 # Academia MCP

{academia_mcp-1.8.1.dist-info → academia_mcp-1.9.0.dist-info}/RECORD

@@ -1,29 +1,30 @@
 academia_mcp/__init__.py,sha256=2Ru2I5u4cE7DrkkAsibDUEF1K6sYtqppb9VyFrRoQKI,94
 academia_mcp/__main__.py,sha256=rcmsOtJd3SA82exjrcGBuxuptcoxF8AXI7jNjiVq2BY,59
-academia_mcp/files.py,sha256=tvt3OPr5q6pAPCZ0XvRHHL9ZWuTXINRZvqjeRFmx5YE,815
-academia_mcp/llm.py,sha256=E0TjWUCjo2q3lONyWMxdppX72m6BdCjsZk-vFLRvGyo,1003
+academia_mcp/files.py,sha256=ynIt0XbU1Z7EPWkv_hVX0pGKsLlmjYv-MVJLOfi6yzs,817
+academia_mcp/llm.py,sha256=zpGkuJFf58Ofgys_fi28-47_wJ1a7sIs_yZvI1Si6z0,993
 academia_mcp/pdf.py,sha256=9PlXzHGhb6ay3ldbTdxCcTWvH4TkET3bnb64mgoh9i0,1273
 academia_mcp/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-academia_mcp/server.py,sha256=3qeJaO2udhlFu7AOy7_g3P2DrY-ygYxYsMl-FtlfQFc,3147
+academia_mcp/server.py,sha256=ufNqg_C75ziQFXSZY7rYc41XA6LUBEAmCrX0RyMopjk,4198
+academia_mcp/settings.py,sha256=vkhCrglL_OI1W0Me_1vS0WoQwDhpzj_XTfcuOylweYA,907
 academia_mcp/utils.py,sha256=P9U3RjYzcztE0KxXvJSy5wSBaUg2CM9tpByljYrsrl4,4607
 academia_mcp/latex_templates/agents4science_2025/agents4science_2025.sty,sha256=hGcEPCYBJS4vdhWvN_yEaJC4GvT_yDroI94CfY2Oguk,12268
 academia_mcp/latex_templates/agents4science_2025/agents4science_2025.tex,sha256=Tl1QkHXHRopw9VEfWrD3Layr5JP_0gIzVQjL4KXIWqc,15814
-academia_mcp/tools/__init__.py,sha256=V2A8sG3c2OTf4VOKnntdKDq8Z5EiUrjgBJLLffILrR4,1197
+academia_mcp/tools/__init__.py,sha256=Bf76VHYQtRKXsHukdwmxhDVcaVdtlsnMlHe4nxbcUMI,1253
 academia_mcp/tools/anthology_search.py,sha256=rhFpJZqGLABgr0raDuH0CARBiAJNJtEI4dlMrKNHfDQ,7669
 academia_mcp/tools/arxiv_download.py,sha256=gBY0_Kz0yGtVkLMwn6GrAyfBjovZVgcSMuyy67p65Cw,10474
 academia_mcp/tools/arxiv_search.py,sha256=pzM18qrF3QL03A53w003kE7hQi3s3QKtjgw0m7K88UY,8355
-academia_mcp/tools/bitflip.py,sha256=eihmNk_C_8ZkBcjtJYH6MvZ0rItgIlvHHA0eGLxsvRs,12276
-academia_mcp/tools/document_qa.py,sha256=t9mygYQ7AFIAPiha1nZ-y043luQlkTCBdWb_SDnzEsE,2444
+academia_mcp/tools/bitflip.py,sha256=1B-EEcDnJjB9YmvVWsGv_Un19Bkeud9SZDw2TpGTCSg,12184
+academia_mcp/tools/document_qa.py,sha256=Wb2nEEVu9UyPp8ktHWeT9wS2JBle8fb9zRjTNVIDdBE,2463
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 academia_mcp/tools/latex.py,sha256=B1Leqt1FHY6H3DlUgeYse4LMFpf4-K1FQViXl5MKk8A,6144
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