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

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/cli/social.py

@@ -279,33 +279,74 @@ def thread(platform, file, delay, dry_run, as_json):
     sys.exit(_run_socialia(*args, json_output=as_json))
 
 
-@social.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=8086, type=int, help="Port for HTTP/SSE transport")
-def serve(transport, host, port):
+@social.group(invoke_without_command=True)
+@click.pass_context
+def mcp(ctx):
     """
-    Run socialia 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
+      installation - Show Claude Desktop configuration
 
     \b
     Examples:
-      scitex social serve                    # stdio for Claude Desktop
-      scitex social serve -t http --port 8086
+      scitex social mcp start
+      scitex social mcp doctor
+    """
+    if ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
+
+
+@mcp.command()
+def start():
+    """
+    Start the MCP server
+
+    \b
+    Example:
+      scitex social mcp start
+    """
+    sys.exit(_run_socialia("mcp", "start"))
+
+
+@mcp.command()
+def doctor():
+    """
+    Check MCP server health
+
+    \b
+    Example:
+      scitex social mcp doctor
+    """
+    sys.exit(_run_socialia("mcp", "doctor"))
+
+
+@mcp.command("list-tools")
+def list_tools():
+    """
+    List available MCP tools
+
+    \b
+    Example:
+      scitex social mcp list-tools
+    """
+    sys.exit(_run_socialia("mcp", "list-tools"))
+
+
+@mcp.command()
+def installation():
+    """
+    Show Claude Desktop configuration
+
+    \b
+    Example:
+      scitex social mcp installation
     """
-    args = ["mcp", "run", "--transport", transport]
-    if transport != "stdio":
-        args.extend(["--host", host, "--port", str(port)])
-        click.secho(f"Starting socialia MCP server ({transport})", fg="cyan")
-        click.echo(f"  Host: {host}")
-        click.echo(f"  Port: {port}")
-
-    sys.exit(_run_socialia(*args))
+    sys.exit(_run_socialia("mcp", "installation"))
 
 
 if __name__ == "__main__":

scitex/cli/stats.py

@@ -139,9 +139,9 @@ def recommend(
             output = {
                 "context": {
                     "n_groups": n_groups,
-                    "sample_sizes": list(sample_sizes)
-                    if sample_sizes
-                    else [30] * n_groups,
+                    "sample_sizes": (
+                        list(sample_sizes) if sample_sizes else [30] * n_groups
+                    ),
                     "outcome_type": outcome_type,
                     "design": design,
                     "paired": paired,
@@ -346,5 +346,123 @@ def tests():
         sys.exit(1)
 
 
+@stats.group(invoke_without_command=True)
+@click.pass_context
+def mcp(ctx):
+    """
+    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 stats mcp start
+      scitex stats 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=8095, type=int, help="Port for HTTP/SSE (default: 8095)"
+)
+def start(transport, host, port):
+    """
+    Start the stats MCP server
+
+    \b
+    Examples:
+      scitex stats mcp start
+      scitex stats mcp start -t http --port 8095
+    """
+    try:
+        from scitex.stats.mcp_server import main as run_server
+
+        if transport != "stdio":
+            click.secho(f"Starting stats MCP server ({transport})", fg="cyan")
+            click.echo(f"  Host: {host}")
+            click.echo(f"  Port: {port}")
+
+        run_server()
+
+    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():
+    """
+    Check MCP server health and dependencies
+
+    \b
+    Example:
+      scitex stats mcp doctor
+    """
+    click.secho("Stats 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 stats module... ", nl=False)
+    try:
+        from scitex import stats as _  # noqa: F401
+
+        click.secho("OK", fg="green")
+    except ImportError as e:
+        click.secho(f"FAIL ({e})", fg="red")
+
+
+@mcp.command("list-tools")
+def list_tools():
+    """
+    List available MCP tools
+
+    \b
+    Example:
+      scitex stats mcp list-tools
+    """
+    click.secho("Stats MCP Tools", fg="cyan", bold=True)
+    click.echo()
+    tools = [
+        ("stats_recommend_tests", "Recommend appropriate statistical tests"),
+        ("stats_run_test", "Execute a statistical test on data"),
+        ("stats_format_results", "Format results in journal style"),
+        ("stats_power_analysis", "Calculate power or sample size"),
+        ("stats_correct_pvalues", "Apply multiple comparison correction"),
+        ("stats_describe", "Calculate descriptive statistics"),
+        ("stats_effect_size", "Calculate effect size"),
+        ("stats_normality_test", "Test for normal distribution"),
+        ("stats_posthoc_test", "Run post-hoc pairwise comparisons"),
+        ("stats_p_to_stars", "Convert p-value to significance stars"),
+    ]
+    for name, desc in tools:
+        click.echo(f"  {name}: {desc}")
+
+
 if __name__ == "__main__":
     stats()