scitex 2.15.3__py3-none-any.whl → 2.15.4__py3-none-any.whl

scitex/_mcp_resources/__init__.py

@@ -20,6 +20,7 @@ from ._cheatsheet import register_cheatsheet_resources
 from ._figrecipe import register_figrecipe_resources
 from ._formats import register_format_resources
 from ._modules import register_module_resources
+from ._scholar import register_scholar_resources
 from ._session import register_session_resources
 
 __all__ = ["register_resources"]
@@ -32,6 +33,7 @@ def register_resources(mcp) -> None:
     register_module_resources(mcp)
     register_format_resources(mcp)
     register_figrecipe_resources(mcp)
+    register_scholar_resources(mcp)
 
 
 # EOF

scitex/_mcp_resources/_scholar.py

@@ -0,0 +1,148 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-29
+# File: src/scitex/_mcp_resources/_scholar.py
+"""Scholar library resources for FastMCP unified server.
+
+Provides dynamic resources for:
+- scholar://library/{project} - Project paper listings
+- scholar://bibtex/{filename} - BibTeX file contents
+"""
+
+from __future__ import annotations
+
+import json
+import os
+from datetime import datetime
+from pathlib import Path
+
+__all__ = ["register_scholar_resources"]
+
+# Directory configuration
+SCITEX_BASE_DIR = Path(os.getenv("SCITEX_DIR", Path.home() / ".scitex"))
+SCITEX_SCHOLAR_DIR = SCITEX_BASE_DIR / "scholar"
+
+
+def _get_scholar_dir() -> Path:
+    """Get the scholar data directory."""
+    SCITEX_SCHOLAR_DIR.mkdir(parents=True, exist_ok=True)
+    return SCITEX_SCHOLAR_DIR
+
+
+def register_scholar_resources(mcp) -> None:
+    """Register scholar library resources with FastMCP server."""
+
+    @mcp.resource("scholar://library")
+    def list_library_projects() -> str:
+        """List all scholar library projects with paper counts."""
+        scholar_dir = _get_scholar_dir()
+        library_dir = scholar_dir / "library"
+
+        if not library_dir.exists():
+            return json.dumps({"projects": [], "total": 0}, indent=2)
+
+        projects = []
+        for project_dir in library_dir.iterdir():
+            if project_dir.is_dir() and not project_dir.name.startswith("."):
+                pdf_count = len(list(project_dir.rglob("*.pdf")))
+                metadata_count = len(list(project_dir.rglob("metadata.json")))
+                projects.append(
+                    {
+                        "name": project_dir.name,
+                        "pdf_count": pdf_count,
+                        "paper_count": metadata_count,
+                        "uri": f"scholar://library/{project_dir.name}",
+                    }
+                )
+
+        return json.dumps(
+            {
+                "projects": projects,
+                "total": len(projects),
+                "library_path": str(library_dir),
+            },
+            indent=2,
+        )
+
+    @mcp.resource("scholar://library/{project}")
+    def get_library_project(project: str) -> str:
+        """Get papers in a specific library project."""
+        library_dir = _get_scholar_dir() / "library" / project
+
+        if not library_dir.exists():
+            return json.dumps({"error": f"Project not found: {project}"}, indent=2)
+
+        metadata_files = list(library_dir.rglob("metadata.json"))
+        papers = []
+
+        for meta_file in metadata_files[:100]:
+            try:
+                with open(meta_file) as f:
+                    meta = json.load(f)
+                pdf_exists = any(meta_file.parent.glob("*.pdf"))
+                papers.append(
+                    {
+                        "id": meta_file.parent.name,
+                        "title": meta.get("title"),
+                        "doi": meta.get("doi"),
+                        "authors": meta.get("authors", [])[:3],
+                        "year": meta.get("year"),
+                        "has_pdf": pdf_exists,
+                    }
+                )
+            except Exception:
+                pass
+
+        return json.dumps(
+            {
+                "project": project,
+                "paper_count": len(papers),
+                "papers": papers,
+            },
+            indent=2,
+        )
+
+    @mcp.resource("scholar://bibtex")
+    def list_bibtex_files() -> str:
+        """List recent BibTeX files in scholar directory."""
+        scholar_dir = _get_scholar_dir()
+        bib_files = []
+
+        for bib_file in sorted(
+            scholar_dir.rglob("*.bib"),
+            key=lambda p: p.stat().st_mtime,
+            reverse=True,
+        )[:20]:
+            mtime = datetime.fromtimestamp(bib_file.stat().st_mtime)
+            bib_files.append(
+                {
+                    "name": bib_file.name,
+                    "path": str(bib_file),
+                    "modified": mtime.isoformat(),
+                    "uri": f"scholar://bibtex/{bib_file.name}",
+                }
+            )
+
+        return json.dumps(
+            {
+                "bibtex_files": bib_files,
+                "total": len(bib_files),
+            },
+            indent=2,
+        )
+
+    @mcp.resource("scholar://bibtex/{filename}")
+    def get_bibtex_file(filename: str) -> str:
+        """Read a BibTeX file by name."""
+        scholar_dir = _get_scholar_dir()
+        bib_files = list(scholar_dir.rglob(filename))
+
+        if not bib_files:
+            return json.dumps({"error": f"BibTeX file not found: {filename}"}, indent=2)
+
+        with open(bib_files[0]) as f:
+            content = f.read()
+
+        return content
+
+
+# EOF

scitex/_mcp_tools/scholar.py

@@ -6,7 +6,6 @@
 from __future__ import annotations
 
 import json
-from typing import List, Optional
 
 
 def _json(data: dict) -> str:
@@ -20,10 +19,10 @@ def register_scholar_tools(mcp) -> None:
     async def scholar_search_papers(
         query: str,
         limit: int = 20,
-        year_min: Optional[int] = None,
-        year_max: Optional[int] = None,
+        year_min: int | None = None,
+        year_max: int | None = None,
         search_mode: str = "local",
-        sources: Optional[List[str]] = None,
+        sources: list[str] | None = None,
     ) -> str:
         """[scholar] Search for scientific papers. Supports local library search and external databases (CrossRef, Semantic Scholar, PubMed, arXiv, OpenAlex)."""
         from scitex.scholar._mcp.handlers import search_papers_handler
@@ -40,9 +39,9 @@ def register_scholar_tools(mcp) -> None:
 
     @mcp.tool()
     async def scholar_resolve_dois(
-        titles: Optional[List[str]] = None,
-        bibtex_path: Optional[str] = None,
-        project: Optional[str] = None,
+        titles: list[str] | None = None,
+        bibtex_path: str | None = None,
+        project: str | None = None,
         resume: bool = True,
     ) -> str:
         """[scholar] Resolve DOIs from paper titles using Crossref API. Supports resumable operation for large batches."""
@@ -59,7 +58,7 @@ def register_scholar_tools(mcp) -> None:
     @mcp.tool()
     async def scholar_enrich_bibtex(
         bibtex_path: str,
-        output_path: Optional[str] = None,
+        output_path: str | None = None,
         add_abstracts: bool = True,
         add_citations: bool = True,
         add_impact_factors: bool = True,
@@ -94,10 +93,10 @@ def register_scholar_tools(mcp) -> None:
 
     @mcp.tool()
     async def scholar_download_pdfs_batch(
-        dois: Optional[List[str]] = None,
-        bibtex_path: Optional[str] = None,
-        project: Optional[str] = None,
-        output_dir: Optional[str] = None,
+        dois: list[str] | None = None,
+        bibtex_path: str | None = None,
+        project: str | None = None,
+        output_dir: str | None = None,
         max_concurrent: int = 3,
         resume: bool = True,
     ) -> str:
@@ -116,7 +115,7 @@ def register_scholar_tools(mcp) -> None:
 
     @mcp.tool()
     async def scholar_get_library_status(
-        project: Optional[str] = None,
+        project: str | None = None,
         include_details: bool = False,
     ) -> str:
         """[scholar] Get status of the paper library: download progress, missing PDFs, validation status."""
@@ -138,8 +137,8 @@ def register_scholar_tools(mcp) -> None:
 
     @mcp.tool()
     async def scholar_validate_pdfs(
-        project: Optional[str] = None,
-        pdf_paths: Optional[List[str]] = None,
+        project: str | None = None,
+        pdf_paths: list[str] | None = None,
     ) -> str:
         """[scholar] Validate PDF files in library for completeness and readability."""
         from scitex.scholar._mcp.handlers import validate_pdfs_handler
@@ -152,8 +151,8 @@ def register_scholar_tools(mcp) -> None:
 
     @mcp.tool()
     async def scholar_resolve_openurls(
-        dois: List[str],
-        resolver_url: Optional[str] = None,
+        dois: list[str],
+        resolver_url: str | None = None,
         resume: bool = True,
     ) -> str:
         """[scholar] Resolve publisher URLs via OpenURL resolver for institutional access."""
@@ -169,7 +168,7 @@ def register_scholar_tools(mcp) -> None:
     @mcp.tool()
     async def scholar_authenticate(
         method: str,
-        institution: Optional[str] = None,
+        institution: str | None = None,
         force: bool = False,
         confirm: bool = False,
     ) -> str:
@@ -215,7 +214,7 @@ def register_scholar_tools(mcp) -> None:
     @mcp.tool()
     async def scholar_export_papers(
         output_path: str,
-        project: Optional[str] = None,
+        project: str | None = None,
         format: str = "bibtex",
         filter_has_pdf: bool = False,
     ) -> str:
@@ -233,7 +232,7 @@ def register_scholar_tools(mcp) -> None:
     @mcp.tool()
     async def scholar_create_project(
         project_name: str,
-        description: Optional[str] = None,
+        description: str | None = None,
     ) -> str:
         """[scholar] Create a new scholar project for organizing papers."""
         from scitex.scholar._mcp.handlers import create_project_handler
@@ -255,8 +254,8 @@ def register_scholar_tools(mcp) -> None:
     @mcp.tool()
     async def scholar_add_papers_to_project(
         project: str,
-        dois: Optional[List[str]] = None,
-        bibtex_path: Optional[str] = None,
+        dois: list[str] | None = None,
+        bibtex_path: str | None = None,
     ) -> str:
         """[scholar] Add papers to a project by DOI or from BibTeX file."""
         from scitex.scholar._mcp.handlers import add_papers_to_project_handler
@@ -270,14 +269,14 @@ def register_scholar_tools(mcp) -> None:
 
     @mcp.tool()
     async def scholar_parse_pdf_content(
-        pdf_path: Optional[str] = None,
-        doi: Optional[str] = None,
-        project: Optional[str] = None,
+        pdf_path: str | None = None,
+        doi: str | None = None,
+        project: str | None = None,
         mode: str = "scientific",
         extract_sections: bool = True,
         extract_tables: bool = False,
         extract_images: bool = False,
-        max_pages: Optional[int] = None,
+        max_pages: int | None = None,
     ) -> str:
         """[scholar] Parse PDF content to extract text, sections (IMRaD), tables, images, and metadata."""
         from scitex.scholar._mcp.handlers import parse_pdf_content_handler
@@ -297,14 +296,14 @@ def register_scholar_tools(mcp) -> None:
     # Job management tools (from job_handlers.py)
     @mcp.tool()
     async def scholar_fetch_papers(
-        papers: Optional[List[str]] = None,
-        bibtex_path: Optional[str] = None,
-        project: Optional[str] = None,
-        workers: Optional[int] = None,
+        papers: list[str] | None = None,
+        bibtex_path: str | None = None,
+        project: str | None = None,
+        workers: int | None = None,
         browser_mode: str = "stealth",
         chrome_profile: str = "system",
         force: bool = False,
-        output: Optional[str] = None,
+        output: str | None = None,
         async_mode: bool = True,
     ) -> str:
         """[scholar] Fetch papers to your library. Supports async mode (default) which returns immediately with a job_id for tracking."""
@@ -325,7 +324,7 @@ def register_scholar_tools(mcp) -> None:
 
     @mcp.tool()
     async def scholar_list_jobs(
-        status: Optional[str] = None,
+        status: str | None = None,
         limit: int = 20,
     ) -> str:
         """[scholar] List all background jobs with their status."""
@@ -369,79 +368,31 @@ def register_scholar_tools(mcp) -> None:
         result = await get_job_result_handler(job_id=job_id)
         return _json(result)
 
-    # =========================================================================
-    # CrossRef Tools (via crossref-local delegation - 167M+ papers)
-    # =========================================================================
+    # Import crossref-local and openalex-local MCP servers
+    _import_local_db_servers(mcp)
 
-    @mcp.tool()
-    async def scholar_crossref_search(
-        query: str,
-        limit: int = 20,
-        offset: int = 0,
-        year_min: Optional[int] = None,
-        year_max: Optional[int] = None,
-        enrich: bool = False,
-    ) -> str:
-        """[scholar] Search CrossRef database (167M+ papers) via crossref-local. Fast full-text search with optional citation enrichment."""
-        from scitex.scholar._mcp.crossref_handlers import crossref_search_handler
 
-        result = await crossref_search_handler(
-            query=query,
-            limit=limit,
-            offset=offset,
-            year_min=year_min,
-            year_max=year_max,
-            enrich=enrich,
-        )
-        return _json(result)
+def _import_local_db_servers(mcp) -> None:
+    """Mount crossref-local and openalex-local MCP servers if available.
 
-    @mcp.tool()
-    async def scholar_crossref_get(
-        doi: str,
-        include_citations: bool = False,
-        include_references: bool = False,
-    ) -> str:
-        """[scholar] Get paper metadata by DOI from CrossRef database."""
-        from scitex.scholar._mcp.crossref_handlers import crossref_get_handler
+    Uses fastmcp's mount() for automatic tool delegation.
+    Tools are prefixed: crossref_search, openalex_search, etc.
+    """
+    # Mount crossref-local MCP server (167M+ papers)
+    try:
+        from crossref_local.mcp_server import mcp as crossref_mcp
 
-        result = await crossref_get_handler(
-            doi=doi,
-            include_citations=include_citations,
-            include_references=include_references,
-        )
-        return _json(result)
+        mcp.mount(crossref_mcp, prefix="crossref")
+    except ImportError:
+        pass  # crossref-local not installed
 
-    @mcp.tool()
-    async def scholar_crossref_count(query: str) -> str:
-        """[scholar] Count papers matching a query in CrossRef database."""
-        from scitex.scholar._mcp.crossref_handlers import crossref_count_handler
-
-        result = await crossref_count_handler(query=query)
-        return _json(result)
-
-    @mcp.tool()
-    async def scholar_crossref_citations(
-        doi: str,
-        direction: str = "citing",
-        limit: int = 100,
-    ) -> str:
-        """[scholar] Get citation relationships (citing/cited papers) for a DOI."""
-        from scitex.scholar._mcp.crossref_handlers import crossref_citations_handler
+    # Mount openalex-local MCP server (250M+ papers)
+    try:
+        from openalex_local._cli.mcp_server import mcp as openalex_mcp
 
-        result = await crossref_citations_handler(
-            doi=doi,
-            direction=direction,
-            limit=limit,
-        )
-        return _json(result)
-
-    @mcp.tool()
-    async def scholar_crossref_info() -> str:
-        """[scholar] Get CrossRef database configuration and status info."""
-        from scitex.scholar._mcp.crossref_handlers import crossref_info_handler
-
-        result = await crossref_info_handler()
-        return _json(result)
+        mcp.mount(openalex_mcp, prefix="openalex")
+    except ImportError:
+        pass  # openalex-local not installed
 
 
 # EOF

scitex/canvas/mcp_server.py

@@ -3,8 +3,12 @@
 # File: src/scitex/canvas/mcp_server.py
 # ----------------------------------------
 
-"""
-MCP Server for SciTeX canvas - Multi-panel figure composition.
+"""MCP Server for SciTeX canvas - Multi-panel figure composition.
+
+.. deprecated::
+    This standalone server is deprecated. Use the unified scitex MCP server:
+    CLI: scitex serve
+    Python: from scitex.mcp_server import run_server
 
 Provides tools for:
 - Creating canvas workspaces
@@ -15,6 +19,15 @@ Provides tools for:
 
 from __future__ import annotations
 
+import warnings
+
+warnings.warn(
+    "scitex.canvas.mcp_server is deprecated. Use 'scitex serve' or "
+    "'from scitex.mcp_server import run_server' for the unified MCP server.",
+    DeprecationWarning,
+    stacklevel=2,
+)
+
 import asyncio
 
 # Graceful MCP dependency handling
@@ -126,7 +139,7 @@ async def _run_server():
 
 
 def main():
-    """Main entry point for the MCP server."""
+    """Run the MCP server."""
     if not MCP_AVAILABLE:
         import sys
 

scitex/capture/mcp_server.py

@@ -10,11 +10,25 @@ __FILE__ = "./src/scitex/capture/mcp_server.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
-"""
-MCP Server for SciTeX Capture - Screen Capture for Python
+"""MCP Server for SciTeX Capture - Screen Capture for Python.
+
+.. deprecated::
+    This standalone server is deprecated. Use the unified scitex MCP server:
+    CLI: scitex serve
+    Python: from scitex.mcp_server import run_server
+
 Provides screenshot capture capabilities via Model Context Protocol.
 """
 
+import warnings
+
+warnings.warn(
+    "scitex.capture.mcp_server is deprecated. Use 'scitex serve' or "
+    "'from scitex.mcp_server import run_server' for the unified MCP server.",
+    DeprecationWarning,
+    stacklevel=2,
+)
+
 import asyncio
 import base64
 from datetime import datetime

scitex/cli/scholar/__init__.py

@@ -21,6 +21,11 @@ CrossRef database (167M+ papers via crossref-local):
     scitex scholar crossref-scitex get 10.1038/nature12373
     scitex scholar crossref-scitex count "epilepsy seizure"
     scitex scholar crossref-scitex info
+
+OpenAlex database (284M+ works via openalex-local):
+    scitex scholar openalex-scitex search "neural networks"
+    scitex scholar openalex-scitex search-by-doi 10.1038/nature12373
+    scitex scholar openalex-scitex status
 """
 
 from __future__ import annotations
@@ -31,6 +36,7 @@ from ._crossref_scitex import crossref_scitex
 from ._fetch import fetch
 from ._jobs import jobs
 from ._library import config, library
+from ._openalex_scitex import openalex_scitex
 
 
 @click.group(
@@ -40,8 +46,7 @@ from ._library import config, library
 @click.option("--help-recursive", is_flag=True, help="Show help for all subcommands")
 @click.pass_context
 def scholar(ctx, help_recursive):
-    """
-    Scientific paper management
+    r"""Scientific paper management.
 
     \b
     Fetch papers, manage your library, and track background jobs.
@@ -96,8 +101,7 @@ def _print_help_recursive(ctx):
 @scholar.group(invoke_without_command=True)
 @click.pass_context
 def mcp(ctx):
-    """
-    MCP (Model Context Protocol) server operations
+    r"""MCP (Model Context Protocol) server operations.
 
     \b
     Commands:
@@ -124,28 +128,35 @@ def mcp(ctx):
 )
 @click.option("--host", default="0.0.0.0", help="Host for HTTP/SSE (default: 0.0.0.0)")
 @click.option(
-    "--port", default=8097, type=int, help="Port for HTTP/SSE (default: 8097)"
+    "--port", default=8085, type=int, help="Port for HTTP/SSE (default: 8085)"
 )
 def start(transport, host, port):
-    """
-    Start the scholar MCP server
+    r"""Start the MCP server with scholar tools.
+
+    \b
+    NOTE: This now uses the unified scitex MCP server which includes
+    all scholar tools plus other scitex tools (plt, stats, etc.)
 
     \b
     Examples:
       scitex scholar mcp start
-      scitex scholar mcp start -t http --port 8097
+      scitex scholar mcp start -t http --port 8085
+
+    \b
+    Equivalent to: scitex serve -t <transport>
     """
     import sys
 
     try:
-        from scitex.scholar.mcp_server import main as run_server
+        from scitex.mcp_server import run_server
 
         if transport != "stdio":
-            click.secho(f"Starting scholar MCP server ({transport})", fg="cyan")
+            click.secho(f"Starting unified scitex MCP server ({transport})", fg="cyan")
             click.echo(f"  Host: {host}")
             click.echo(f"  Port: {port}")
+            click.echo("  Includes: scholar, plt, stats, audio, and more")
 
-        run_server()
+        run_server(transport=transport, host=host, port=port)
 
     except ImportError as e:
         click.secho(f"Error: {e}", fg="red", err=True)
@@ -158,8 +169,7 @@ def start(transport, host, port):
 
 @mcp.command()
 def doctor():
-    """
-    Check MCP server health and dependencies
+    r"""Check MCP server health and dependencies.
 
     \b
     Example:
@@ -193,11 +203,18 @@ def doctor():
     except ImportError:
         click.secho("NOT INSTALLED (optional)", fg="yellow")
 
+    click.echo("Checking openalex-local... ", nl=False)
+    try:
+        import openalex_local  # noqa: F401
+
+        click.secho("OK", fg="green")
+    except ImportError:
+        click.secho("NOT INSTALLED (optional)", fg="yellow")
+
 
 @mcp.command("list-tools")
 def list_tools():
-    """
-    List available MCP tools
+    r"""List available MCP tools.
 
     \b
     Example:
@@ -206,25 +223,35 @@ def list_tools():
     click.secho("Scholar MCP Tools", fg="cyan", bold=True)
     click.echo()
     tools = [
-        ("scholar_search_papers", "Search for papers by query"),
-        ("scholar_resolve_dois", "Resolve DOIs to metadata"),
-        ("scholar_enrich_bibtex", "Enrich BibTeX with abstracts/DOIs"),
-        ("scholar_download_pdf", "Download PDF for a paper"),
-        ("scholar_download_pdfs_batch", "Batch download PDFs"),
-        ("scholar_get_library_status", "Get library status"),
-        ("scholar_parse_bibtex", "Parse BibTeX file"),
-        ("scholar_validate_pdfs", "Validate downloaded PDFs"),
-        ("scholar_authenticate", "Authenticate with institution"),
-        ("scholar_check_auth_status", "Check authentication status"),
-        ("scholar_fetch_papers", "Fetch papers by DOIs"),
-        ("scholar_crossref_search", "Search CrossRef database"),
-        ("scholar_crossref_get", "Get paper by DOI from CrossRef"),
+        ("search_papers", "Search for papers by query"),
+        ("resolve_dois", "Resolve DOIs to metadata"),
+        ("enrich_bibtex", "Enrich BibTeX with abstracts/DOIs"),
+        ("download_pdf", "Download PDF for a paper"),
+        ("download_pdfs_batch", "Batch download PDFs"),
+        ("get_library_status", "Get library status"),
+        ("parse_bibtex", "Parse BibTeX file"),
+        ("validate_pdfs", "Validate downloaded PDFs"),
+        ("authenticate", "Authenticate with institution"),
+        ("check_auth_status", "Check authentication status"),
+        ("fetch_papers", "Fetch papers by DOIs (async)"),
+        # CrossRef-Local (167M+ papers)
+        ("crossref_search", "Search CrossRef database (167M+ papers)"),
+        ("crossref_get", "Get paper by DOI from CrossRef"),
+        ("crossref_count", "Count papers matching query"),
+        ("crossref_citations", "Get citation relationships"),
+        ("crossref_info", "Get CrossRef database status"),
+        # OpenAlex-Local (284M+ works)
+        ("openalex_search", "Search OpenAlex database (284M+ works)"),
+        ("openalex_get", "Get paper by DOI/ID from OpenAlex"),
+        ("openalex_count", "Count papers matching query"),
+        ("openalex_info", "Get OpenAlex database status"),
     ]
     for name, desc in tools:
         click.echo(f"  {name}: {desc}")
 
 
 scholar.add_command(crossref_scitex)
+scholar.add_command(openalex_scitex)
 scholar.add_command(fetch)
 scholar.add_command(library)
 scholar.add_command(config)