scitex 2.14.0__py3-none-any.whl → 2.15.1__py3-none-any.whl

scitex/cli/writer.py

@@ -280,6 +280,123 @@ def info(dir):
         sys.exit(1)
 
 
+@writer.group()
+def mcp():
+    """
+    MCP (Model Context Protocol) tools for writer module.
+
+    \b
+    Examples:
+      scitex writer mcp list-tools      # List available MCP tools
+      scitex writer mcp usage           # Show tool usage and parameters
+    """
+    pass
+
+
+@mcp.command("list-tools")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def list_tools(as_json: bool):
+    """
+    List available MCP tools for writer module.
+
+    \b
+    Examples:
+      scitex writer mcp list-tools
+      scitex writer mcp list-tools --json
+    """
+    from scitex.writer._mcp.tool_schemas import get_tool_schemas
+
+    tools = get_tool_schemas()
+
+    if as_json:
+        import json
+
+        output = {
+            "module": "writer",
+            "count": len(tools),
+            "tools": [
+                {
+                    "name": t.name,
+                    "description": t.description,
+                    "parameters": list(t.inputSchema.get("properties", {}).keys()),
+                    "required": t.inputSchema.get("required", []),
+                }
+                for t in tools
+            ],
+        }
+        click.echo(json.dumps(output, indent=2))
+    else:
+        click.secho(
+            f"SciTeX Writer MCP Tools ({len(tools)} total)", fg="cyan", bold=True
+        )
+        click.echo()
+
+        for tool in tools:
+            click.secho(f"  {tool.name}", fg="green", bold=True)
+            # First line of description
+            desc = tool.description.split("\n")[0] if tool.description else ""
+            click.echo(f"    {desc}")
+
+            # Parameters
+            props = tool.inputSchema.get("properties", {})
+            required = tool.inputSchema.get("required", [])
+            if props:
+                params = []
+                for pname, pinfo in props.items():
+                    req_marker = "*" if pname in required else ""
+                    params.append(f"{pname}{req_marker}")
+                click.echo(f"    Parameters: {', '.join(params)}")
+            click.echo()
+
+
+@mcp.command("usage")
+@click.argument("tool_name", required=False)
+def usage(tool_name: str):
+    """
+    Show detailed usage for writer MCP tools.
+
+    \b
+    Examples:
+      scitex writer mcp usage                    # Show all tools
+      scitex writer mcp usage compile_manuscript # Show specific tool
+    """
+    from scitex.writer._mcp.tool_schemas import get_tool_schemas
+
+    tools = get_tool_schemas()
+
+    if tool_name:
+        # Find specific tool
+        tool = next((t for t in tools if t.name == tool_name), None)
+        if not tool:
+            click.secho(f"Tool '{tool_name}' not found", fg="red", err=True)
+            click.echo(f"Available tools: {', '.join(t.name for t in tools)}")
+            raise SystemExit(1)
+        tools = [tool]
+
+    for tool in tools:
+        click.secho(f"━━━ {tool.name} ━━━", fg="cyan", bold=True)
+        click.echo()
+        click.echo(f"Description: {tool.description}")
+        click.echo()
+
+        props = tool.inputSchema.get("properties", {})
+        required = tool.inputSchema.get("required", [])
+
+        if props:
+            click.secho("Parameters:", bold=True)
+            for pname, pinfo in props.items():
+                req = " (required)" if pname in required else ""
+                ptype = pinfo.get("type", "any")
+                pdesc = pinfo.get("description", "")
+                default = pinfo.get("default")
+                default_str = f" [default: {default}]" if default is not None else ""
+
+                click.echo(f"  {pname}: {ptype}{req}{default_str}")
+                if pdesc:
+                    click.echo(f"    {pdesc}")
+        click.echo()
+
+
 @writer.command()
 @click.option(
     "--dir",

scitex/config/README.md

@@ -1,7 +1,7 @@
 <!-- ---
 !-- Timestamp: 2025-12-09
 !-- Author: ywatanabe
-!-- File: /home/ywatanabe/proj/scitex-code/src/scitex/config/README.md
+!-- File: /home/ywatanabe/proj/scitex-python/src/scitex/config/README.md
 !-- --- -->
 
 # SciTeX Configuration Module

scitex/config/__init__.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # Timestamp: "2025-12-09 (ywatanabe)"
 # File: ./src/scitex/config/__init__.py
 
@@ -34,8 +33,16 @@ Usage:
     cache_dir = paths.resolve("cache", user_provided_path)
 """
 
-from ._PriorityConfig import PriorityConfig, get_scitex_dir, load_dotenv
+from ._env_registry import (
+    ENV_REGISTRY,
+    EnvVar,
+    generate_template,
+    get_all_modules,
+    get_env_by_module,
+    get_env_docs,
+)
 from ._paths import ScitexPaths, get_paths
+from ._PriorityConfig import PriorityConfig, get_scitex_dir, load_dotenv
 from ._ScitexConfig import ScitexConfig, get_config, load_yaml
 
 __all__ = [
@@ -50,6 +57,13 @@ __all__ = [
     "PriorityConfig",
     "get_scitex_dir",
     "load_dotenv",
+    # Environment variable registry
+    "ENV_REGISTRY",
+    "EnvVar",
+    "generate_template",
+    "get_all_modules",
+    "get_env_by_module",
+    "get_env_docs",
 ]
 
 

scitex/config/_env_registry.py

@@ -0,0 +1,191 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-24
+# File: src/scitex/config/_env_registry.py
+
+"""
+Registry of all SCITEX environment variables.
+
+Provides documentation and template generation for environment configuration.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import Dict, List, Optional
+
+
+@dataclass
+class EnvVar:
+    """Environment variable definition."""
+
+    name: str
+    description: str
+    module: str
+    default: Optional[str] = None
+    required: bool = False
+    sensitive: bool = False
+
+
+# Registry of all SCITEX environment variables
+ENV_REGISTRY: List[EnvVar] = [
+    # Core
+    EnvVar("SCITEX_DIR", "Base directory for scitex data", "core", "~/.scitex"),
+    EnvVar("SCITEX_ENV_SRC", "Path to env source file/directory", "core"),
+    EnvVar("SCITEX_LOGGING_LEVEL", "Logging level", "logging", "INFO"),
+    EnvVar("SCITEX_LOG_FORMAT", "Log format style", "logging", "default"),
+    EnvVar("SCITEX_FORCE_COLOR", "Force colored output", "logging", "false"),
+    # Audio
+    EnvVar("SCITEX_AUDIO_MODE", "Audio mode: local/remote/auto", "audio", "auto"),
+    EnvVar("SCITEX_AUDIO_RELAY_URL", "Relay server URL for remote audio", "audio"),
+    EnvVar("SCITEX_AUDIO_RELAY_HOST", "Relay server host", "audio"),
+    EnvVar("SCITEX_AUDIO_RELAY_PORT", "Relay server port", "audio", "31293"),
+    EnvVar("SCITEX_AUDIO_PORT", "Audio server port", "audio", "31293"),
+    EnvVar("ELEVENLABS_API_KEY", "ElevenLabs API key", "audio", sensitive=True),
+    # Scholar
+    EnvVar("SCITEX_SCHOLAR_DIR", "Scholar library directory", "scholar"),
+    EnvVar("SCITEX_CROSSREF_EMAIL", "Email for Crossref API", "scholar"),
+    EnvVar("SCITEX_PUBMED_EMAIL", "Email for PubMed API", "scholar"),
+    EnvVar("SCITEX_SCHOLAR_CROSSREF_DB", "Local Crossref database path", "scholar"),
+    EnvVar("SCITEX_SCHOLAR_CROSSREF_API_URL", "Crossref API URL", "scholar"),
+    EnvVar(
+        "SCITEX_SCHOLAR_CROSSREF_MODE", "Crossref mode: local/api/hybrid", "scholar"
+    ),
+    EnvVar("SCITEX_SCHOLAR_OPENATHENS_EMAIL", "OpenAthens login email", "scholar"),
+    EnvVar(
+        "SCITEX_SCHOLAR_OPENATHENS_ENABLED",
+        "Enable OpenAthens auth",
+        "scholar",
+        "false",
+    ),
+    EnvVar(
+        "SCITEX_SCHOLAR_EZPROXY_URL", "EZProxy URL for institutional access", "scholar"
+    ),
+    EnvVar("SCITEX_SCHOLAR_OPENURL_RESOLVER_URL", "OpenURL resolver URL", "scholar"),
+    EnvVar(
+        "SCITEX_SCHOLAR_ZENROWS_API_KEY",
+        "ZenRows API key for scraping",
+        "scholar",
+        sensitive=True,
+    ),
+    # Social
+    EnvVar("SCITEX_X_CONSUMER_KEY", "Twitter/X consumer key", "social", sensitive=True),
+    EnvVar(
+        "SCITEX_X_CONSUMER_SECRET",
+        "Twitter/X consumer secret",
+        "social",
+        sensitive=True,
+    ),
+    EnvVar("SCITEX_X_ACCESS_TOKEN", "Twitter/X access token", "social", sensitive=True),
+    EnvVar(
+        "SCITEX_X_ACCESS_TOKEN_SECRET",
+        "Twitter/X access token secret",
+        "social",
+        sensitive=True,
+    ),
+    EnvVar(
+        "SCITEX_LINKEDIN_ACCESS_TOKEN",
+        "LinkedIn access token",
+        "social",
+        sensitive=True,
+    ),
+    EnvVar("SCITEX_REDDIT_CLIENT_ID", "Reddit client ID", "social", sensitive=True),
+    EnvVar(
+        "SCITEX_REDDIT_CLIENT_SECRET",
+        "Reddit client secret",
+        "social",
+        sensitive=True,
+    ),
+    EnvVar("SCITEX_YOUTUBE_API_KEY", "YouTube API key", "social", sensitive=True),
+    EnvVar("SCITEX_GA_PROPERTY_ID", "Google Analytics property ID", "social"),
+    # Cloud
+    EnvVar("SCITEX_CLOUD_USERNAME", "Cloud username", "cloud", sensitive=True),
+    EnvVar("SCITEX_CLOUD_PASSWORD", "Cloud password", "cloud", sensitive=True),
+    EnvVar(
+        "SCITEX_CLOUD_CODE_WORKSPACE", "Running in cloud workspace", "cloud", "false"
+    ),
+    EnvVar("SCITEX_CLOUD_CODE_PROJECT_ROOT", "Cloud project root", "cloud"),
+    EnvVar("SCITEX_CLOUD_CODE_BACKEND", "Cloud backend type", "cloud"),
+    # UI/Notification
+    EnvVar("SCITEX_UI_DEFAULT_BACKEND", "Default notification backend", "ui"),
+    EnvVar(
+        "SCITEX_UI_BACKEND_PRIORITY",
+        "Notification backend priority (comma-sep)",
+        "ui",
+    ),
+    EnvVar("SCITEX_UI_INFO_BACKENDS", "Backends for info notifications", "ui"),
+    EnvVar("SCITEX_UI_WARNING_BACKENDS", "Backends for warning notifications", "ui"),
+    EnvVar("SCITEX_UI_ERROR_BACKENDS", "Backends for error notifications", "ui"),
+    EnvVar("SCITEX_UI_CRITICAL_BACKENDS", "Backends for critical notifications", "ui"),
+    EnvVar("SCITEX_NOTIFY_EMAIL_FROM", "Email notification sender", "ui"),
+    EnvVar("SCITEX_NOTIFY_EMAIL_TO", "Email notification recipient", "ui"),
+    EnvVar("SCITEX_NOTIFY_WEBHOOK_URL", "Webhook URL for notifications", "ui"),
+    # Capture
+    EnvVar("SCITEX_CAPTURE_DIR", "Screenshot capture directory", "capture"),
+    # Web
+    EnvVar("SCITEX_WEB_DOWNLOADS_DIR", "Web downloads directory", "web"),
+    # PLT
+    EnvVar("SCITEX_PLT_AXES_WIDTH_MM", "Default axes width in mm", "plt"),
+    EnvVar("SCITEX_PLT_LINES_TRACE_MM", "Default line trace width in mm", "plt"),
+    EnvVar("SCITEX_STYLE", "Default plot style", "plt"),
+    EnvVar("SCITEX_COLORS", "Color palette to use", "plt"),
+]
+
+
+def get_env_by_module(module: str) -> List[EnvVar]:
+    """Get all environment variables for a module."""
+    return [e for e in ENV_REGISTRY if e.module == module]
+
+
+def get_all_modules() -> List[str]:
+    """Get list of all modules with env vars."""
+    return sorted(set(e.module for e in ENV_REGISTRY))
+
+
+def generate_template(
+    include_sensitive: bool = True, include_defaults: bool = True
+) -> str:
+    """Generate a template .src file with all environment variables."""
+    lines = [
+        "#!/bin/bash",
+        "# SciTeX Environment Variables Template",
+        "# Generated by scitex.config.generate_template()",
+        "#",
+        "# Usage: source this file or set SCITEX_ENV_SRC to this path",
+        "",
+    ]
+
+    for module in get_all_modules():
+        lines.append(f"# === {module.upper()} ===")
+        for env in get_env_by_module(module):
+            if env.sensitive and not include_sensitive:
+                continue
+
+            if env.description:
+                lines.append(f"# {env.description}")
+
+            if env.default and include_defaults:
+                lines.append(f'export {env.name}="{env.default}"')
+            elif env.sensitive:
+                lines.append(f'# export {env.name}="YOUR_{env.name}_HERE"')
+            else:
+                lines.append(f"# export {env.name}=")
+        lines.append("")
+
+    return "\n".join(lines)
+
+
+def get_env_docs() -> Dict[str, Dict]:
+    """Get documentation for all environment variables."""
+    return {
+        e.name: {
+            "description": e.description,
+            "module": e.module,
+            "default": e.default,
+            "required": e.required,
+            "sensitive": e.sensitive,
+        }
+        for e in ENV_REGISTRY
+    }
+
+
+# EOF

scitex/diagram/__init__.py

@@ -1,38 +1,59 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: 2025-12-15
+# Timestamp: 2026-01-24
 # Author: ywatanabe / Claude
 # File: scitex/diagram/__init__.py
 
 """
 SciTeX Diagram - Paper-optimized diagram generation.
 
-This module provides a semantic layer above Mermaid/Graphviz/D2 that
-understands paper constraints (column width, reading direction, emphasis)
-and compiles to backend formats with appropriate layout hints.
-
-Key insight: LLMs are good at generating CONSTRAINTS, not pixel layouts.
-SciTeX Diagram defines "what this diagram means for a paper" and compiles
-that to backend-specific layout directives.
+This module delegates entirely to figrecipe._diagram.
+figrecipe is the single source of truth for diagram functionality.
 
 Example
 -------
->>> from scitex.diagram import Diagram
+>>> import scitex as stx
+>>>
+>>> # Recommended: Use stx.Diagram directly
+>>> d = stx.Diagram(type="pipeline")
+>>> d.add_node("input", "Raw Data")
+>>> d.add_node("process", "Transform", emphasis="primary")
+>>> d.add_edge("input", "process")
+>>> d.to_mermaid("pipeline.mmd")
 >>>
->>> diagram = Diagram.from_yaml("workflow.diagram.yaml")
->>> diagram.to_mermaid("workflow.mmd")
->>> diagram.to_graphviz("workflow.dot")
+>>> # From YAML spec
+>>> d = stx.Diagram.from_yaml("workflow.diagram.yaml")
+>>> d.to_mermaid("workflow.mmd")
+>>> d.to_graphviz("workflow.dot")
 """
 
-from scitex.diagram._schema import DiagramSpec, PaperConstraints, LayoutHints, PaperMode
-from scitex.diagram._diagram import Diagram
-from scitex.diagram._compile import compile_to_mermaid, compile_to_graphviz
-from scitex.diagram._presets import WORKFLOW_PRESET, DECISION_PRESET, PIPELINE_PRESET
-from scitex.diagram._split import split_diagram, SplitConfig, SplitStrategy, SplitResult
+# Import everything from figrecipe._diagram (single source of truth)
+from figrecipe._diagram import (
+    DECISION_PRESET,
+    PIPELINE_PRESET,
+    SCIENTIFIC_PRESET,
+    WORKFLOW_PRESET,
+    Diagram,
+    DiagramSpec,
+    DiagramType,
+    EdgeSpec,
+    LayoutHints,
+    NodeSpec,
+    PaperConstraints,
+    PaperMode,
+    SplitConfig,
+    SplitResult,
+    SplitStrategy,
+    get_preset,
+    list_presets,
+)
+from figrecipe._diagram._compile import compile_to_graphviz, compile_to_mermaid
 
 __all__ = [
     "Diagram",
     "DiagramSpec",
+    "DiagramType",
+    "NodeSpec",
+    "EdgeSpec",
     "PaperConstraints",
     "LayoutHints",
     "PaperMode",
@@ -41,7 +62,9 @@ __all__ = [
     "WORKFLOW_PRESET",
     "DECISION_PRESET",
     "PIPELINE_PRESET",
-    "split_diagram",
+    "SCIENTIFIC_PRESET",
+    "get_preset",
+    "list_presets",
     "SplitConfig",
     "SplitStrategy",
     "SplitResult",

scitex/diagram/mcp_server.py

@@ -1,148 +1,36 @@
 #!/usr/bin/env python3
-# Timestamp: 2026-01-08
+# Timestamp: 2026-01-24
 # File: src/scitex/diagram/mcp_server.py
-# ----------------------------------------
 
 """
-MCP Server for SciTeX diagram - Paper-optimized diagram generation.
+MCP Server for SciTeX diagram - delegates to figrecipe.
 
-Provides tools for:
-- Creating diagrams from YAML specs
-- Compiling to Mermaid/Graphviz formats
-- Using workflow/decision/pipeline presets
-- Splitting large diagrams for publication layouts
+This is a thin wrapper that redirects to figrecipe's MCP server.
+figrecipe is the single source of truth for diagram functionality.
 """
 
 from __future__ import annotations
 
-import asyncio
-
-# Graceful MCP dependency handling
-try:
-    import mcp.types as types
-    from mcp.server import NotificationOptions, Server
-    from mcp.server.models import InitializationOptions
-    from mcp.server.stdio import stdio_server
-
-    MCP_AVAILABLE = True
-except ImportError:
-    MCP_AVAILABLE = False
-    types = None  # type: ignore
-    Server = None  # type: ignore
-    NotificationOptions = None  # type: ignore
-    InitializationOptions = None  # type: ignore
-    stdio_server = None  # type: ignore
-
-__all__ = ["DiagramServer", "main", "MCP_AVAILABLE"]
-
-
-class DiagramServer:
-    """MCP Server for Paper-Optimized Diagram Generation."""
-
-    def __init__(self):
-        self.server = Server("scitex-diagram")
-        self.setup_handlers()
-
-    def setup_handlers(self):
-        """Set up MCP server handlers."""
-        from ._mcp.handlers import (
-            compile_graphviz_handler,
-            compile_mermaid_handler,
-            create_diagram_handler,
-            get_paper_modes_handler,
-            get_preset_handler,
-            list_presets_handler,
-            split_diagram_handler,
-        )
-        from ._mcp.tool_schemas import get_tool_schemas
-
-        @self.server.list_tools()
-        async def handle_list_tools():
-            return get_tool_schemas()
-
-        @self.server.call_tool()
-        async def handle_call_tool(name: str, arguments: dict):
-            if name == "create_diagram":
-                return await self._wrap_result(create_diagram_handler(**arguments))
-
-            elif name == "compile_mermaid":
-                return await self._wrap_result(compile_mermaid_handler(**arguments))
-
-            elif name == "compile_graphviz":
-                return await self._wrap_result(compile_graphviz_handler(**arguments))
-
-            elif name == "list_presets":
-                return await self._wrap_result(list_presets_handler())
-
-            elif name == "get_preset":
-                return await self._wrap_result(get_preset_handler(**arguments))
-
-            elif name == "split_diagram":
-                return await self._wrap_result(split_diagram_handler(**arguments))
-
-            elif name == "get_paper_modes":
-                return await self._wrap_result(get_paper_modes_handler())
-
-            else:
-                raise ValueError(f"Unknown tool: {name}")
-
-    async def _wrap_result(self, coro):
-        """Wrap handler result as MCP TextContent."""
-        import json
-
-        try:
-            result = await coro
-            return [
-                types.TextContent(
-                    type="text",
-                    text=json.dumps(result, indent=2, default=str),
-                )
-            ]
-        except Exception as e:
-            return [
-                types.TextContent(
-                    type="text",
-                    text=json.dumps({"success": False, "error": str(e)}, indent=2),
-                )
-            ]
-
-
-async def _run_server():
-    """Run the MCP server (internal)."""
-    server = DiagramServer()
-    async with stdio_server() as (read_stream, write_stream):
-        await server.server.run(
-            read_stream,
-            write_stream,
-            InitializationOptions(
-                server_name="scitex-diagram",
-                server_version="0.1.0",
-                capabilities=server.server.get_capabilities(
-                    notification_options=NotificationOptions(),
-                    experimental_capabilities={},
-                ),
-            ),
-        )
-
 
 def main():
-    """Main entry point for the MCP server."""
-    if not MCP_AVAILABLE:
+    """Main entry point - delegates to figrecipe's MCP server."""
+    try:
+        from figrecipe._mcp.server import mcp
+
+        mcp.run()
+    except ImportError as e:
         import sys
 
         print("=" * 60)
-        print("MCP Server 'scitex-diagram' requires the 'mcp' package.")
+        print("scitex-diagram requires figrecipe with MCP support.")
         print()
         print("Install with:")
-        print("  pip install mcp")
+        print("  pip install figrecipe[mcp]")
         print()
-        print("Or install scitex with MCP support:")
-        print("  pip install scitex[mcp]")
+        print(f"Error: {e}")
         print("=" * 60)
         sys.exit(1)
 
-    asyncio.run(_run_server())
-
 
 if __name__ == "__main__":
     main()

scitex/introspect/__init__.py

@@ -0,0 +1,75 @@
+#!/usr/bin/env python3
+# Timestamp: 2025-01-20
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/introspect/__init__.py
+
+"""
+Introspection utilities for Python packages.
+
+Provides IPython-like introspection capabilities for any Python package.
+
+Basic Introspection:
+- get_signature: Function/class signature with type hints (like `func?`)
+- get_docstring: Docstring extraction with parsing
+- get_source: Full source code (like `func??`)
+- list_members: List attributes/methods (like `dir()`)
+- get_exports: Module's __all__ contents
+- find_examples: Find usage examples in tests/examples
+
+Advanced Introspection:
+- get_class_hierarchy: Inheritance tree (MRO + subclasses)
+- get_mro: Method Resolution Order only
+- get_type_hints_detailed: Detailed type annotation analysis
+- get_class_annotations: Class variable and method annotations
+- get_imports: Static import analysis using AST
+- get_dependencies: Module dependency analysis
+- get_call_graph: Function call graph (with timeout protection)
+- get_function_calls: Simple outgoing calls list
+"""
+
+from ._core import (
+    # Basic
+    find_examples,
+    # Advanced - Call graph
+    get_call_graph,
+    # Advanced - Type hints
+    get_class_annotations,
+    # Advanced - Class hierarchy
+    get_class_hierarchy,
+    # Advanced - Imports
+    get_dependencies,
+    get_docstring,
+    get_exports,
+    get_function_calls,
+    get_imports,
+    get_mro,
+    get_signature,
+    get_source,
+    get_type_hints_detailed,
+    get_type_info,
+    list_members,
+    resolve_object,
+)
+
+__all__ = [
+    # Basic
+    "get_signature",
+    "get_docstring",
+    "get_source",
+    "list_members",
+    "get_exports",
+    "find_examples",
+    "resolve_object",
+    "get_type_info",
+    # Advanced - Class hierarchy
+    "get_class_hierarchy",
+    "get_mro",
+    # Advanced - Type hints
+    "get_type_hints_detailed",
+    "get_class_annotations",
+    # Advanced - Imports
+    "get_imports",
+    "get_dependencies",
+    # Advanced - Call graph
+    "get_call_graph",
+    "get_function_calls",
+]