scitex 2.13.0__py3-none-any.whl → 2.15.1__py3-none-any.whl

scitex/cli/mcp.py

@@ -0,0 +1,362 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-15
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/cli/mcp.py
+"""
+SciTeX MCP CLI - Model Context Protocol server management commands.
+
+Commands:
+- scitex mcp list       List all available MCP tools
+- scitex mcp doctor     Check MCP server health and configuration
+- scitex mcp serve      Start the unified MCP server
+"""
+
+import click
+
+
+@click.group(invoke_without_command=True)
+@click.option("--help-recursive", is_flag=True, help="Show help for all subcommands")
+@click.pass_context
+def mcp(ctx, help_recursive):
+    """
+    MCP (Model Context Protocol) server management.
+
+    \b
+    Examples:
+      scitex mcp list-tools    # List all tools
+      scitex mcp start         # Start MCP server
+    """
+    if help_recursive:
+        _print_help_recursive(ctx)
+        ctx.exit(0)
+    elif ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
+
+
+@mcp.command("list-tools")
+@click.option(
+    "--module",
+    "-m",
+    type=str,
+    default=None,
+    help="Filter by module (audio, canvas, capture, diagram, plt, scholar, stats, template, ui, writer)",
+)
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def list_tools(module: str, as_json: bool):
+    """
+    List all available MCP tools.
+
+    \b
+    Examples:
+      scitex mcp list-tools
+      scitex mcp list-tools --module audio
+    """
+    try:
+        from scitex.mcp_server import FASTMCP_AVAILABLE
+        from scitex.mcp_server import mcp as mcp_server
+    except ImportError:
+        click.secho("ERROR: Could not import MCP server", fg="red", err=True)
+        raise SystemExit(1)
+
+    if not FASTMCP_AVAILABLE:
+        click.secho(
+            "ERROR: FastMCP not installed. Run: pip install fastmcp", fg="red", err=True
+        )
+        raise SystemExit(1)
+
+    if mcp_server is None:
+        click.secho("ERROR: MCP server not initialized", fg="red", err=True)
+        raise SystemExit(1)
+
+    # Get all tools
+    tools = list(mcp_server._tool_manager._tools.keys())
+
+    # Group by module
+    modules = {}
+    for tool in sorted(tools):
+        prefix = tool.split("_")[0]
+        if prefix not in modules:
+            modules[prefix] = []
+        modules[prefix].append(tool)
+
+    # Filter by module if specified
+    if module:
+        module = module.lower()
+        if module not in modules:
+            click.secho(f"ERROR: Unknown module '{module}'", fg="red", err=True)
+            click.echo(f"Available modules: {', '.join(sorted(modules.keys()))}")
+            raise SystemExit(1)
+        modules = {module: modules[module]}
+
+    if as_json:
+        import json
+
+        output = {
+            "total": sum(len(t) for t in modules.values()),
+            "modules": {m: {"count": len(t), "tools": t} for m, t in modules.items()},
+        }
+        click.echo(json.dumps(output, indent=2))
+    else:
+        total = sum(len(t) for t in modules.values())
+        click.secho(f"SciTeX MCP Tools ({total} total)", fg="cyan", bold=True)
+        click.echo()
+
+        for mod, tool_list in sorted(modules.items()):
+            # Calculate max tool name length for this module
+            max_name_len = max(len(t) for t in tool_list)
+
+            click.secho(f"{mod}: {len(tool_list)} tools", fg="green", bold=True)
+            for tool in tool_list:
+                # Get tool description if available
+                tool_obj = mcp_server._tool_manager._tools.get(tool)
+                desc = ""
+                if tool_obj and hasattr(tool_obj, "description"):
+                    desc = tool_obj.description
+                    if desc:
+                        # Truncate long descriptions
+                        desc = desc.split("\n")[0][:50]
+                        if len(desc) == 50:
+                            desc += "..."
+                # Use printf-style formatting for aligned columns
+                click.echo(f"  {tool:<{max_name_len}}  {desc}")
+            click.echo()
+
+
+@mcp.command("doctor")
+@click.option("--verbose", "-v", is_flag=True, help="Show detailed diagnostics")
+def doctor(verbose: bool):
+    """
+    Check MCP server health and configuration.
+
+    \b
+    Checks:
+      - FastMCP package installation
+      - Module imports
+      - Handler availability
+      - Tool registration
+    """
+    issues = []
+    warnings = []
+
+    click.secho("SciTeX MCP Doctor", fg="cyan", bold=True)
+    click.echo()
+
+    # Check 1: FastMCP installation
+    click.echo("Checking FastMCP installation... ", nl=False)
+    try:
+        from fastmcp import FastMCP
+
+        click.secho("OK", fg="green")
+        if verbose:
+            import fastmcp
+
+            click.echo(f"  Version: {getattr(fastmcp, '__version__', 'unknown')}")
+    except ImportError:
+        click.secho("FAIL", fg="red")
+        issues.append("FastMCP not installed. Run: pip install fastmcp")
+
+    # Check 2: MCP server import
+    click.echo("Checking MCP server module... ", nl=False)
+    try:
+        from scitex.mcp_server import FASTMCP_AVAILABLE
+        from scitex.mcp_server import mcp as mcp_server
+
+        if FASTMCP_AVAILABLE and mcp_server:
+            click.secho("OK", fg="green")
+        else:
+            click.secho("WARN", fg="yellow")
+            warnings.append("MCP server initialized but FastMCP not available")
+    except ImportError as e:
+        click.secho("FAIL", fg="red")
+        issues.append(f"Could not import MCP server: {e}")
+
+    # Check 3: _mcp_tools subpackage
+    click.echo("Checking _mcp_tools subpackage... ", nl=False)
+    try:
+        from scitex._mcp_tools import register_all_tools
+
+        click.secho("OK", fg="green")
+    except ImportError as e:
+        click.secho("FAIL", fg="red")
+        issues.append(f"Could not import _mcp_tools: {e}")
+
+    # Check 4: Individual module imports
+    modules = [
+        "audio",
+        "canvas",
+        "capture",
+        "diagram",
+        "plt",
+        "scholar",
+        "stats",
+        "template",
+        "ui",
+        "writer",
+    ]
+
+    click.echo("Checking module registrations... ", nl=False)
+    failed_modules = []
+    for mod in modules:
+        try:
+            exec(f"from scitex._mcp_tools.{mod} import register_{mod}_tools")
+        except ImportError as e:
+            failed_modules.append((mod, str(e)))
+
+    if failed_modules:
+        click.secho(f"FAIL ({len(failed_modules)} modules)", fg="red")
+        for mod, err in failed_modules:
+            issues.append(f"Module {mod}: {err}")
+    else:
+        click.secho("OK", fg="green")
+
+    # Check 5: Tool count
+    click.echo("Checking tool registration... ", nl=False)
+    try:
+        from scitex.mcp_server import mcp as mcp_server
+
+        if mcp_server:
+            tools = list(mcp_server._tool_manager._tools.keys())
+            if len(tools) >= 80:
+                click.secho(f"OK ({len(tools)} tools)", fg="green")
+            else:
+                click.secho(f"WARN ({len(tools)} tools, expected 80+)", fg="yellow")
+                warnings.append(f"Only {len(tools)} tools registered, expected 80+")
+        else:
+            click.secho("SKIP", fg="yellow")
+    except Exception as e:
+        click.secho("FAIL", fg="red")
+        issues.append(f"Tool registration check failed: {e}")
+
+    # Check 6: Handler imports (verbose only)
+    if verbose:
+        click.echo()
+        click.secho("Handler Import Checks:", bold=True)
+        handler_modules = [
+            ("scitex.audio._mcp.handlers", "speak_handler"),
+            ("scitex.capture._mcp.handlers", "capture_screenshot_handler"),
+            ("scitex.scholar._mcp.handlers", "search_papers_handler"),
+            ("scitex.stats._mcp.handlers", "run_test_handler"),
+            ("scitex.plt._mcp._handlers_figure", "create_figure_handler"),
+            ("scitex.canvas._mcp.handlers", "create_canvas_handler"),
+            ("scitex.diagram._mcp.handlers", "create_diagram_handler"),
+            ("scitex.template._mcp.handlers", "list_templates_handler"),
+            ("scitex.ui._mcp.handlers", "notify_handler"),
+            ("scitex.writer._mcp.handlers", "compile_manuscript_handler"),
+        ]
+
+        for mod_path, handler_name in handler_modules:
+            click.echo(f"  {mod_path}... ", nl=False)
+            try:
+                mod = __import__(mod_path, fromlist=[handler_name])
+                if hasattr(mod, handler_name):
+                    click.secho("OK", fg="green")
+                else:
+                    click.secho(f"WARN (missing {handler_name})", fg="yellow")
+            except ImportError as e:
+                click.secho(f"FAIL ({e})", fg="red")
+
+    # Summary
+    click.echo()
+    if issues:
+        click.secho(f"Issues Found: {len(issues)}", fg="red", bold=True)
+        for issue in issues:
+            click.echo(f"  ✗ {issue}")
+    if warnings:
+        click.secho(f"Warnings: {len(warnings)}", fg="yellow", bold=True)
+        for warning in warnings:
+            click.echo(f"  ⚠ {warning}")
+    if not issues and not warnings:
+        click.secho("All checks passed!", fg="green", bold=True)
+
+    raise SystemExit(1 if issues else 0)
+
+
+def _print_help_recursive(ctx):
+    """Print help for mcp and all its subcommands."""
+    fake_parent = click.Context(click.Group(), info_name="scitex")
+    parent_ctx = click.Context(mcp, info_name="mcp", parent=fake_parent)
+
+    click.secho("━━━ scitex mcp ━━━", fg="cyan", bold=True)
+    click.echo(mcp.get_help(parent_ctx))
+
+    for name in sorted(mcp.list_commands(ctx) or []):
+        cmd = mcp.get_command(ctx, name)
+        if cmd is None:
+            continue
+        click.echo()
+        click.secho(f"━━━ scitex mcp {name} ━━━", fg="cyan", bold=True)
+        with click.Context(cmd, info_name=name, parent=parent_ctx) as sub_ctx:
+            click.echo(cmd.get_help(sub_ctx))
+
+
+@mcp.command("start")
+@click.option(
+    "--transport",
+    "-t",
+    type=click.Choice(["stdio", "sse", "http"]),
+    default="stdio",
+    help="Transport type (default: stdio)",
+)
+@click.option("--host", "-h", default="0.0.0.0", help="Host to bind (default: 0.0.0.0)")
+@click.option(
+    "--port", "-p", default=8085, type=int, help="Port to bind (default: 8085)"
+)
+def start(transport: str, host: str, port: int):
+    """
+    Start the unified MCP server.
+
+    \b
+    Examples:
+      scitex mcp start
+      scitex mcp start -t sse -p 8085
+    """
+    try:
+        from scitex.mcp_server import run_server
+    except ImportError:
+        click.secho("ERROR: Could not import MCP server", fg="red", err=True)
+        click.echo("Run: pip install fastmcp")
+        raise SystemExit(1)
+
+    run_server(transport=transport, host=host, port=port)
+
+
+@mcp.command("installation")
+def installation():
+    """
+    Show Claude Desktop configuration for SciTeX MCP server.
+
+    \b
+    Examples:
+      scitex mcp installation
+    """
+    import shutil
+    import sys
+
+    from scitex import __version__
+
+    click.secho(f"SciTeX MCP Server v{__version__}", fg="cyan", bold=True)
+    click.echo()
+
+    # Get actual path
+    scitex_path = shutil.which("scitex")
+    python_path = sys.executable
+
+    if scitex_path:
+        click.echo(f"Your installation path: {scitex_path}")
+        click.echo(f"Your Python path: {python_path}")
+    click.echo()
+
+    click.secho("Claude Desktop Configuration:", fg="green", bold=True)
+    click.echo(
+        "Add to ~/Library/Application Support/Claude/claude_desktop_config.json (macOS)"
+    )
+    click.echo("or %APPDATA%\\Claude\\claude_desktop_config.json (Windows):")
+    click.echo()
+
+    config = f'''"scitex": {{
+  "command": "{scitex_path or "/path/to/.venv/bin/scitex"}",
+  "args": ["mcp", "start"]
+}}'''
+    click.secho(config, fg="yellow")
+
+
+# EOF

scitex/cli/repro.py

@@ -32,6 +32,24 @@ def repro():
     pass
 
 
+@repro.command("help-recursive")
+@click.pass_context
+def help_recursive(ctx):
+    """Show help for all commands recursively."""
+    fake_parent = click.Context(click.Group(), info_name="scitex")
+    parent_ctx = click.Context(repro, info_name="repro", parent=fake_parent)
+    click.secho("━━━ scitex repro ━━━", fg="cyan", bold=True)
+    click.echo(repro.get_help(parent_ctx))
+    for name in sorted(repro.list_commands(ctx) or []):
+        cmd = repro.get_command(ctx, name)
+        if cmd is None or name == "help-recursive":
+            continue
+        click.echo()
+        click.secho(f"━━━ scitex repro {name} ━━━", fg="cyan", bold=True)
+        with click.Context(cmd, info_name=name, parent=parent_ctx) as sub_ctx:
+            click.echo(cmd.get_help(sub_ctx))
+
+
 @repro.command("gen-id")
 @click.option("--length", "-l", type=int, default=8, help="ID length (default: 8)")
 @click.option("--prefix", "-p", default="", help="Prefix to add to ID")

scitex/cli/resource.py

@@ -30,6 +30,24 @@ def resource():
     pass
 
 
+@resource.command("help-recursive")
+@click.pass_context
+def help_recursive(ctx):
+    """Show help for all commands recursively."""
+    fake_parent = click.Context(click.Group(), info_name="scitex")
+    parent_ctx = click.Context(resource, info_name="resource", parent=fake_parent)
+    click.secho("━━━ scitex resource ━━━", fg="cyan", bold=True)
+    click.echo(resource.get_help(parent_ctx))
+    for name in sorted(resource.list_commands(ctx) or []):
+        cmd = resource.get_command(ctx, name)
+        if cmd is None or name == "help-recursive":
+            continue
+        click.echo()
+        click.secho(f"━━━ scitex resource {name} ━━━", fg="cyan", bold=True)
+        with click.Context(cmd, info_name=name, parent=parent_ctx) as sub_ctx:
+            click.echo(cmd.get_help(sub_ctx))
+
+
 @resource.command()
 @click.option("--json", "as_json", is_flag=True, help="Output as JSON")
 @click.option(

scitex/cli/scholar/__init__.py

@@ -0,0 +1,97 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-14
+# File: src/scitex/cli/scholar/__init__.py
+# ----------------------------------------
+
+"""Scholar CLI commands.
+
+This module provides the command-line interface for SciTeX Scholar.
+
+Usage:
+    scitex scholar fetch "10.1038/nature12373"
+    scitex scholar fetch --from-bibtex papers.bib --project myresearch
+    scitex scholar fetch "10.1038/nature12373" --async
+    scitex scholar library
+    scitex scholar config
+    scitex scholar jobs list
+    scitex scholar jobs status <job_id>
+
+CrossRef database (167M+ papers via crossref-local):
+    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
+"""
+
+from __future__ import annotations
+
+import click
+
+from ._crossref_scitex import crossref_scitex
+from ._fetch import fetch
+from ._jobs import jobs
+from ._library import config, library
+
+
+@click.group()
+def scholar():
+    """
+    Scientific paper management
+
+    \b
+    Fetch papers, manage your library, and track background jobs.
+
+    \b
+    Examples:
+        scitex scholar fetch "10.1038/nature12373"
+        scitex scholar fetch --from-bibtex refs.bib -p myproject
+        scitex scholar library
+        scitex scholar jobs list
+    """
+    pass
+
+
+@scholar.command("help-recursive")
+@click.pass_context
+def help_recursive(ctx):
+    """Show help for all commands recursively."""
+    fake_parent = click.Context(click.Group(), info_name="scitex")
+    parent_ctx = click.Context(scholar, info_name="scholar", parent=fake_parent)
+
+    click.secho("━━━ scitex scholar ━━━", fg="cyan", bold=True)
+    click.echo(scholar.get_help(parent_ctx))
+
+    for name in sorted(scholar.list_commands(ctx) or []):
+        cmd = scholar.get_command(ctx, name)
+        if cmd is None or name == "help-recursive":
+            continue
+        click.echo()
+        click.secho(f"━━━ scitex scholar {name} ━━━", fg="cyan", bold=True)
+        with click.Context(cmd, info_name=name, parent=parent_ctx) as sub_ctx:
+            click.echo(cmd.get_help(sub_ctx))
+            if isinstance(cmd, click.Group):
+                for sub_name in sorted(cmd.list_commands(sub_ctx) or []):
+                    sub_cmd = cmd.get_command(sub_ctx, sub_name)
+                    if sub_cmd is None:
+                        continue
+                    click.echo()
+                    click.secho(
+                        f"━━━ scitex scholar {name} {sub_name} ━━━",
+                        fg="cyan",
+                        bold=True,
+                    )
+                    with click.Context(
+                        sub_cmd, info_name=sub_name, parent=sub_ctx
+                    ) as sub_sub_ctx:
+                        click.echo(sub_cmd.get_help(sub_sub_ctx))
+
+
+scholar.add_command(crossref_scitex)
+scholar.add_command(fetch)
+scholar.add_command(library)
+scholar.add_command(config)
+scholar.add_command(jobs)
+
+__all__ = ["scholar"]
+
+# EOF