scitex 2.15.2__py3-none-any.whl → 2.15.4__py3-none-any.whl

scitex/cli/introspect.py

@@ -11,6 +11,13 @@ import sys
 import click
 
 
+def _normalize_path(ctx, param, value):
+    """Normalize dotted path: convert hyphens to underscores for Python module names."""
+    if value:
+        return value.replace("-", "_")
+    return value
+
+
 @click.group(
     context_settings={"help_option_names": ["-h", "--help"]},
     invoke_without_command=True,
@@ -48,7 +55,7 @@ def introspect(ctx, help_recursive):
 
 
 @introspect.command()
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option("--no-defaults", is_flag=True, help="Exclude default values")
 @click.option("--no-annotations", is_flag=True, help="Exclude type annotations")
 @click.option("--json", "as_json", is_flag=True, help="Output as JSON")
@@ -90,7 +97,7 @@ def q(dotted_path, no_defaults, no_annotations, as_json):
 
 
 @introspect.command()
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option("--max-lines", "-n", type=int, help="Limit output to N lines")
 @click.option("--no-decorators", is_flag=True, help="Exclude decorator lines")
 @click.option("--json", "as_json", is_flag=True, help="Output as JSON")
@@ -125,7 +132,7 @@ def qq(dotted_path, max_lines, no_decorators, as_json):
 
 
 @introspect.command("dir")
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option(
     "--filter",
     "-f",
@@ -176,7 +183,7 @@ def dir_cmd(dotted_path, filter, kind, inherited, as_json):
 
 
 @introspect.command()
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option("--max-depth", "-d", type=int, default=5, help="Max recursion depth")
 @click.option("--docstring", is_flag=True, help="Include docstrings")
 @click.option("--root-only", is_flag=True, help="Show only root-level items")
@@ -214,7 +221,7 @@ def api(dotted_path, max_depth, docstring, root_only, as_json):
 
 
 @introspect.command()
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option(
     "--format",
     "-f",
@@ -259,7 +266,7 @@ def docstring(dotted_path, format, as_json):
 
 
 @introspect.command()
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option("--json", "as_json", is_flag=True, help="Output as JSON")
 def exports(dotted_path, as_json):
     """
@@ -289,7 +296,7 @@ def exports(dotted_path, as_json):
 
 
 @introspect.command()
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option("--search-paths", "-p", help="Comma-separated search paths")
 @click.option("--max-results", "-n", type=int, default=10, help="Max examples")
 @click.option("--json", "as_json", is_flag=True, help="Output as JSON")
@@ -332,7 +339,7 @@ def examples(dotted_path, search_paths, max_results, as_json):
 
 
 @introspect.command("hierarchy")
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option("--builtins", is_flag=True, help="Include builtin classes")
 @click.option("--max-depth", "-d", type=int, default=10, help="Max subclass depth")
 @click.option("--json", "as_json", is_flag=True, help="Output as JSON")
@@ -368,7 +375,7 @@ def _print_subclasses(subclasses, indent=0):
 
 
 @introspect.command("hints")
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option("--json", "as_json", is_flag=True, help="Output as JSON")
 def type_hints(dotted_path, as_json):
     """Get detailed type hint analysis"""
@@ -392,7 +399,7 @@ def type_hints(dotted_path, as_json):
 
 
 @introspect.command("imports")
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option("--no-categorize", is_flag=True, help="Don't group by category")
 @click.option("--json", "as_json", is_flag=True, help="Output as JSON")
 def imports(dotted_path, no_categorize, as_json):
@@ -421,7 +428,7 @@ def imports(dotted_path, no_categorize, as_json):
 
 
 @introspect.command("deps")
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option("--recursive", "-r", is_flag=True, help="Recursive analysis")
 @click.option("--max-depth", "-d", type=int, default=3, help="Max recursion depth")
 @click.option("--json", "as_json", is_flag=True, help="Output as JSON")
@@ -444,7 +451,7 @@ def dependencies(dotted_path, recursive, max_depth, as_json):
 
 
 @introspect.command("calls")
-@click.argument("dotted_path")
+@click.argument("dotted_path", callback=_normalize_path)
 @click.option("--timeout", "-t", type=int, default=10, help="Timeout in seconds")
 @click.option("--all", "all_calls", is_flag=True, help="Include external calls")
 @click.option("--json", "as_json", is_flag=True, help="Output as JSON")

scitex/cli/plt.py

@@ -322,33 +322,90 @@ def convert(input_file, output, fmt):
     sys.exit(_run_figrecipe(*args))
 
 
-@plt.command()
-@click.option(
-    "-t",
-    "--transport",
-    type=click.Choice(["stdio", "sse", "http"]),
-    default="stdio",
-    help="Transport protocol",
-)
-@click.option("--host", default="0.0.0.0", help="Host for HTTP/SSE transport")
-@click.option("--port", default=8087, type=int, help="Port for HTTP/SSE transport")
-def serve(transport, host, port):
+@plt.group(invoke_without_command=True)
+@click.pass_context
+def mcp(ctx):
     """
-    Run figrecipe MCP server
+    MCP (Model Context Protocol) server operations
+
+    \b
+    Commands:
+      start      - Start the MCP server
+      doctor     - Check MCP server health
+      list-tools - List available MCP tools
+      info       - Show MCP server information
+      install    - Show installation instructions
 
     \b
     Examples:
-      scitex plt serve                    # stdio for Claude Desktop
-      scitex plt serve -t http --port 8087
+      scitex plt mcp start
+      scitex plt mcp doctor
     """
-    args = ["mcp", "run", "--transport", transport]
-    if transport != "stdio":
-        args.extend(["--host", host, "--port", str(port)])
-        click.secho(f"Starting figrecipe MCP server ({transport})", fg="cyan")
-        click.echo(f"  Host: {host}")
-        click.echo(f"  Port: {port}")
+    if ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
 
-    sys.exit(_run_figrecipe(*args))
+
+@mcp.command()
+@click.option("--host", default="0.0.0.0", help="Host for HTTP transport")
+@click.option("--port", default=8087, type=int, help="Port for HTTP transport")
+def start(host, port):
+    """
+    Start the MCP server
+
+    \b
+    Example:
+      scitex plt mcp start
+      scitex plt mcp start --port 8087
+    """
+    sys.exit(_run_figrecipe("mcp", "run", "--host", host, "--port", str(port)))
+
+
+@mcp.command()
+def doctor():
+    """
+    Check MCP server health
+
+    \b
+    Example:
+      scitex plt mcp doctor
+    """
+    sys.exit(_run_figrecipe("mcp", "doctor"))
+
+
+@mcp.command("list-tools")
+def list_tools_mcp():
+    """
+    List available MCP tools
+
+    \b
+    Example:
+      scitex plt mcp list-tools
+    """
+    sys.exit(_run_figrecipe("mcp", "list-tools"))
+
+
+@mcp.command()
+def info():
+    """
+    Show MCP server information
+
+    \b
+    Example:
+      scitex plt mcp info
+    """
+    sys.exit(_run_figrecipe("mcp", "info"))
+
+
+@mcp.command()
+def install():
+    """
+    Show installation instructions
+
+    \b
+    Example:
+      scitex plt mcp install
+    """
+    sys.exit(_run_figrecipe("mcp", "install"))
 
 
 if __name__ == "__main__":

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.
@@ -93,7 +98,160 @@ def _print_help_recursive(ctx):
                         click.echo(sub_cmd.get_help(sub_sub_ctx))
 
 
+@scholar.group(invoke_without_command=True)
+@click.pass_context
+def mcp(ctx):
+    r"""MCP (Model Context Protocol) server operations.
+
+    \b
+    Commands:
+      start      - Start the MCP server
+      doctor     - Check MCP server health
+      list-tools - List available MCP tools
+
+    \b
+    Examples:
+      scitex scholar mcp start
+      scitex scholar mcp list-tools
+    """
+    if ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
+
+
+@mcp.command()
+@click.option(
+    "-t",
+    "--transport",
+    type=click.Choice(["stdio", "sse", "http"]),
+    default="stdio",
+    help="Transport protocol (default: stdio)",
+)
+@click.option("--host", default="0.0.0.0", help="Host for HTTP/SSE (default: 0.0.0.0)")
+@click.option(
+    "--port", default=8085, type=int, help="Port for HTTP/SSE (default: 8085)"
+)
+def start(transport, host, port):
+    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 8085
+
+    \b
+    Equivalent to: scitex serve -t <transport>
+    """
+    import sys
+
+    try:
+        from scitex.mcp_server import run_server
+
+        if transport != "stdio":
+            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(transport=transport, host=host, port=port)
+
+    except ImportError as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        click.echo("\nInstall dependencies: pip install fastmcp")
+        sys.exit(1)
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@mcp.command()
+def doctor():
+    r"""Check MCP server health and dependencies.
+
+    \b
+    Example:
+      scitex scholar mcp doctor
+    """
+    click.secho("Scholar MCP Server Health Check", fg="cyan", bold=True)
+    click.echo()
+
+    click.echo("Checking FastMCP... ", nl=False)
+    try:
+        import fastmcp  # noqa: F401
+
+        click.secho("OK", fg="green")
+    except ImportError:
+        click.secho("NOT INSTALLED", fg="red")
+        click.echo("  Install with: pip install fastmcp")
+
+    click.echo("Checking scholar module... ", nl=False)
+    try:
+        from scitex import scholar as _  # noqa: F401
+
+        click.secho("OK", fg="green")
+    except ImportError as e:
+        click.secho(f"FAIL ({e})", fg="red")
+
+    click.echo("Checking crossref-local... ", nl=False)
+    try:
+        import crossref_local  # noqa: F401
+
+        click.secho("OK", fg="green")
+    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():
+    r"""List available MCP tools.
+
+    \b
+    Example:
+      scitex scholar mcp list-tools
+    """
+    click.secho("Scholar MCP Tools", fg="cyan", bold=True)
+    click.echo()
+    tools = [
+        ("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)