scitex 2.15.3__py3-none-any.whl → 2.15.5__py3-none-any.whl

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)

scitex/cli/scholar/_crossref_scitex.py

@@ -1,142 +1,41 @@
 #!/usr/bin/env python3
-# Timestamp: 2026-01-24
+# Timestamp: 2026-01-29
 # File: src/scitex/cli/scholar/_crossref_scitex.py
-"""CrossRef-SciTeX CLI commands for scitex scholar.
+"""CrossRef-SciTeX CLI - Thin wrapper delegating to crossref-local.
 
-Provides access to the local CrossRef database (167M+ papers) via crossref-local.
-Branded as crossref-scitex to distinguish from official CrossRef API.
+This module provides access to the local CrossRef database (167M+ papers)
+by delegating directly to crossref-local CLI without any modifications.
 """
 
 from __future__ import annotations
 
-import json
 import sys
 
 import click
 
 
-@click.group("crossref-scitex")
-def crossref_scitex():
-    """
-    CrossRef-SciTeX database search (167M+ papers)
-
-    \b
-    Search and query the local CrossRef database via crossref-local.
-    Supports both direct DB access and HTTP API mode.
-
-    \b
-    Examples:
-        scitex scholar crossref-scitex search "deep learning"
-        scitex scholar crossref-scitex get 10.1038/nature12373
-        scitex scholar crossref-scitex count "epilepsy seizure"
-        scitex scholar crossref-scitex info
-    """
-    pass
-
-
-@crossref_scitex.command("search")
-@click.argument("query")
-@click.option("-n", "--limit", default=20, help="Maximum results (default: 20)")
-@click.option("--offset", default=0, help="Skip N results for pagination")
-@click.option("--year-min", type=int, help="Minimum publication year")
-@click.option("--year-max", type=int, help="Maximum publication year")
-@click.option("--enrich", is_flag=True, help="Add citation counts and references")
-@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
-def search_cmd(query, limit, offset, year_min, year_max, enrich, as_json):
-    """
-    Search for papers in CrossRef database.
+@click.command(
+    "crossref-scitex",
+    context_settings={"ignore_unknown_options": True, "allow_extra_args": True},
+)
+@click.option("--help-recursive", is_flag=True, help="Show help for all commands")
+@click.pass_context
+def crossref_scitex(ctx, help_recursive):
+    r"""CrossRef-SciTeX database search (167M+ papers).
 
     \b
-    Examples:
-        scitex scholar crossref-scitex search "hippocampal sharp wave ripples"
-        scitex scholar crossref search "deep learning" --limit 50
-        scitex scholar crossref search "CRISPR" --year-min 2020 --enrich
-    """
-    try:
-        from scitex.scholar import crossref_scitex as crossref
-    except ImportError:
-        click.secho(
-            "crossref-local not installed. Install with: pip install crossref-local",
-            fg="red",
-        )
-        sys.exit(1)
-
-    try:
-        results = crossref.search(query, limit=limit, offset=offset)
-
-        if enrich:
-            results = crossref.enrich(results)
-
-        papers = []
-        for work in results:
-            if year_min and work.year and work.year < year_min:
-                continue
-            if year_max and work.year and work.year > year_max:
-                continue
-            papers.append(work)
-            if len(papers) >= limit:
-                break
-
-        if as_json:
-            output = {
-                "query": query,
-                "total": results.total,
-                "count": len(papers),
-                "papers": [
-                    {
-                        "doi": p.doi,
-                        "title": p.title,
-                        "authors": p.authors,
-                        "year": p.year,
-                        "journal": p.journal,
-                        "citation_count": p.citation_count,
-                    }
-                    for p in papers
-                ],
-            }
-            click.echo(json.dumps(output, indent=2))
-        else:
-            click.secho(
-                f"Found {results.total} papers for: {query}", fg="green", bold=True
-            )
-            click.echo()
-
-            for i, paper in enumerate(papers, 1):
-                authors = ", ".join(paper.authors[:3]) if paper.authors else "Unknown"
-                if paper.authors and len(paper.authors) > 3:
-                    authors += " et al."
-
-                click.secho(f"{i}. {paper.title}", fg="cyan", bold=True)
-                click.echo(f"   Authors: {authors}")
-                click.echo(
-                    f"   Year: {paper.year or 'N/A'} | Journal: {paper.journal or 'N/A'}"
-                )
-                click.echo(f"   DOI: {paper.doi}")
-                if paper.citation_count:
-                    click.echo(f"   Citations: {paper.citation_count}")
-                click.echo()
-
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red")
-        sys.exit(1)
-
-
-@crossref_scitex.command("get")
-@click.argument("doi")
-@click.option("--citations", is_flag=True, help="Include citing papers")
-@click.option("--references", is_flag=True, help="Include referenced papers")
-@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
-def get_cmd(doi, citations, references, as_json):
-    """
-    Get paper details by DOI.
+    Thin wrapper for crossref-local. All arguments passed directly.
+    Run 'crossref-local --help' for full options.
 
     \b
     Examples:
-        scitex scholar crossref get 10.1038/nature12373
-        scitex scholar crossref get 10.1126/science.aax0758 --citations
+        scitex scholar crossref-scitex search "deep learning" --abstracts
+        scitex scholar crossref-scitex search-by-doi 10.1038/nature12373
+        scitex scholar crossref-scitex status
+        scitex scholar crossref-scitex cache query "neural networks"
     """
     try:
-        from scitex.scholar import crossref_scitex as crossref
+        from crossref_local.cli import cli as crossref_cli
     except ImportError:
         click.secho(
             "crossref-local not installed. Install with: pip install crossref-local",
@@ -144,153 +43,13 @@ def get_cmd(doi, citations, references, as_json):
         )
         sys.exit(1)
 
-    try:
-        work = crossref.get(doi)
-
-        if work is None:
-            click.secho(f"DOI not found: {doi}", fg="red")
-            sys.exit(1)
-
-        if as_json:
-            output = {
-                "doi": work.doi,
-                "title": work.title,
-                "authors": work.authors,
-                "year": work.year,
-                "journal": work.journal,
-                "abstract": work.abstract,
-                "citation_count": work.citation_count,
-                "reference_count": work.reference_count,
-                "type": work.type,
-                "publisher": work.publisher,
-            }
-            if citations:
-                output["citing_dois"] = crossref.get_citing(doi)
-            if references:
-                output["referenced_dois"] = crossref.get_cited(doi)
-            click.echo(json.dumps(output, indent=2))
-        else:
-            click.secho(work.title, fg="cyan", bold=True)
-            click.echo()
-
-            if work.authors:
-                click.echo(f"Authors: {', '.join(work.authors)}")
-            click.echo(f"Year: {work.year or 'N/A'}")
-            click.echo(f"Journal: {work.journal or 'N/A'}")
-            click.echo(f"DOI: {work.doi}")
-            click.echo(f"Type: {work.type or 'N/A'}")
-            click.echo(f"Publisher: {work.publisher or 'N/A'}")
-            click.echo(f"Citations: {work.citation_count or 0}")
-            click.echo(f"References: {work.reference_count or 0}")
-
-            if work.abstract:
-                click.echo()
-                click.secho("Abstract:", bold=True)
-                click.echo(
-                    work.abstract[:500] + "..."
-                    if len(work.abstract) > 500
-                    else work.abstract
-                )
-
-            if citations:
-                citing = crossref.get_citing(doi)
-                click.echo()
-                click.secho(f"Citing papers ({len(citing)}):", bold=True)
-                for c_doi in citing[:10]:
-                    click.echo(f"  - {c_doi}")
-                if len(citing) > 10:
-                    click.echo(f"  ... and {len(citing) - 10} more")
-
-            if references:
-                cited = crossref.get_cited(doi)
-                click.echo()
-                click.secho(f"References ({len(cited)}):", bold=True)
-                for r_doi in cited[:10]:
-                    click.echo(f"  - {r_doi}")
-                if len(cited) > 10:
-                    click.echo(f"  ... and {len(cited) - 10} more")
-
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red")
-        sys.exit(1)
+    # Handle --help-recursive by delegating to crossref-local
+    args = ctx.args
+    if help_recursive:
+        args = ["--help-recursive"]
 
-
-@crossref_scitex.command("count")
-@click.argument("query")
-def count_cmd(query):
-    """
-    Count papers matching a query.
-
-    \b
-    Examples:
-        scitex scholar crossref count "machine learning"
-        scitex scholar crossref count "CRISPR gene editing"
-    """
-    try:
-        from scitex.scholar import crossref_scitex as crossref
-    except ImportError:
-        click.secho(
-            "crossref-local not installed. Install with: pip install crossref-local",
-            fg="red",
-        )
-        sys.exit(1)
-
-    try:
-        count = crossref.count(query)
-        click.echo(f"{count:,} papers match: {query}")
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red")
-        sys.exit(1)
-
-
-@crossref_scitex.command("info")
-@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
-def info_cmd(as_json):
-    """
-    Show CrossRef database configuration and status.
-
-    \b
-    Examples:
-        scitex scholar crossref info
-        scitex scholar crossref info --json
-    """
-    try:
-        from scitex.scholar import crossref_scitex as crossref
-    except ImportError:
-        click.secho(
-            "crossref-local not installed. Install with: pip install crossref-local",
-            fg="red",
-        )
-        sys.exit(1)
-
-    try:
-        info = crossref.info()
-        mode = crossref.get_mode()
-
-        if as_json:
-            info["mode"] = mode
-            click.echo(json.dumps(info, indent=2))
-        else:
-            click.secho("CrossRef Database Status", fg="cyan", bold=True)
-            click.echo()
-            click.echo(f"Mode: {mode}")
-            click.echo(f"Status: {info.get('status', 'unknown')}")
-
-            if "version" in info:
-                click.echo(f"Version: {info['version']}")
-
-            if "work_count" in info:
-                click.echo(f"Papers: {info['work_count']:,}")
-
-            if "db_path" in info:
-                click.echo(f"Database: {info['db_path']}")
-
-            if "api_url" in info:
-                click.echo(f"API URL: {info['api_url']}")
-
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red")
-        sys.exit(1)
+    # Delegate all arguments to crossref-local CLI
+    sys.exit(crossref_cli.main(args, standalone_mode=False))
 
 
 # EOF

scitex/cli/scholar/_openalex_scitex.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-29
+# File: src/scitex/cli/scholar/_openalex_scitex.py
+"""OpenAlex-SciTeX CLI - Thin wrapper delegating to openalex-local.
+
+This module provides access to the local OpenAlex database (284M+ works)
+by delegating directly to openalex-local CLI without any modifications.
+"""
+
+from __future__ import annotations
+
+import sys
+
+import click
+
+
+@click.command(
+    "openalex-scitex",
+    context_settings={"ignore_unknown_options": True, "allow_extra_args": True},
+)
+@click.option("--help-recursive", is_flag=True, help="Show help for all commands")
+@click.pass_context
+def openalex_scitex(ctx, help_recursive):
+    """
+    OpenAlex-SciTeX database search (284M+ works)
+
+    \b
+    Thin wrapper for openalex-local. All arguments passed directly.
+    Run 'openalex-local --help' for full options.
+
+    \b
+    Examples:
+        scitex scholar openalex-scitex search "machine learning"
+        scitex scholar openalex-scitex search-by-doi 10.1038/nature12373
+        scitex scholar openalex-scitex status
+    """
+    try:
+        from openalex_local.cli import cli as openalex_cli
+    except ImportError:
+        click.secho(
+            "openalex-local not installed. Install with: pip install openalex-local",
+            fg="red",
+        )
+        sys.exit(1)
+
+    # Handle --help-recursive by delegating to openalex-local
+    args = ctx.args
+    if help_recursive:
+        args = ["--help-recursive"]
+
+    # Delegate all arguments to openalex-local CLI
+    sys.exit(openalex_cli.main(args, standalone_mode=False))
+
+
+# EOF

scitex/scholar/__init__.py

@@ -1,5 +1,4 @@
-"""
-SciTeX Scholar - Scientific Literature Management Made Simple
+"""SciTeX Scholar - Scientific Literature Management Made Simple.
 
 This module provides a unified interface for:
 - Searching scientific literature across multiple sources
@@ -27,17 +26,17 @@ _missing = warn_module_deps("scholar")
 try:
     from scitex.scholar.auth import ScholarAuthManager
 except ImportError:
-    ScholarAuthManager = None
+    ScholarAuthManager = None  # type: ignore[misc,assignment]
 
 try:
     from scitex.scholar.browser import ScholarBrowserManager
 except ImportError:
-    ScholarBrowserManager = None
+    ScholarBrowserManager = None  # type: ignore[misc,assignment]
 
 try:
     from scitex.scholar.config import ScholarConfig
 except ImportError:
-    ScholarConfig = None
+    ScholarConfig = None  # type: ignore[misc,assignment]
 
 try:
     from scitex.scholar.core import Paper, Papers, Scholar
@@ -71,12 +70,17 @@ try:
 except ImportError:
     utils = None
 
-# CrossRef integration via crossref-local delegation (branded as crossref-scitex)
+# Local database integrations (crossref-local, openalex-local)
 try:
-    from . import crossref_scitex
+    from .local_dbs import crossref_scitex
 except ImportError:
     crossref_scitex = None
 
+try:
+    from .local_dbs import openalex_scitex
+except ImportError:
+    openalex_scitex = None
+
 __all__ = [
     "ScholarConfig",
     "ScholarEngine",
@@ -87,8 +91,9 @@ __all__ = [
     "Papers",
     "Scholar",
     "utils",
-    # CrossRef integration (167M+ papers via crossref-local)
-    "crossref_scitex",
+    # Local database integrations
+    "crossref_scitex",  # CrossRef (167M+ papers via crossref-local)
+    "openalex_scitex",  # OpenAlex (284M+ works via openalex-local)
 ]
 
 # # Import core classes for advanced users