scitex 2.14.0__py3-none-any.whl → 2.15.3__py3-none-any.whl

scitex/cli/stats.py

@@ -11,8 +11,13 @@ from pathlib import Path
 import click
 
 
-@click.group(context_settings={"help_option_names": ["-h", "--help"]})
-def stats():
+@click.group(
+    context_settings={"help_option_names": ["-h", "--help"]},
+    invoke_without_command=True,
+)
+@click.option("--help-recursive", is_flag=True, help="Show help for all subcommands")
+@click.pass_context
+def stats(ctx, help_recursive):
     """
     Statistical analysis and testing utilities
 
@@ -29,20 +34,22 @@ def stats():
       scitex stats describe data.csv
       scitex stats save results.json --output analysis.stats
     """
-    pass
+    if help_recursive:
+        _print_help_recursive(ctx)
+        ctx.exit(0)
+    elif ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
 
 
-@stats.command("help-recursive")
-@click.pass_context
-def help_recursive(ctx):
-    """Show help for all commands recursively."""
+def _print_help_recursive(ctx):
+    """Print help for all commands recursively."""
     fake_parent = click.Context(click.Group(), info_name="scitex")
     parent_ctx = click.Context(stats, info_name="stats", parent=fake_parent)
     click.secho("━━━ scitex stats ━━━", fg="cyan", bold=True)
     click.echo(stats.get_help(parent_ctx))
     for name in sorted(stats.list_commands(ctx) or []):
         cmd = stats.get_command(ctx, name)
-        if cmd is None or name == "help-recursive":
+        if cmd is None:
             continue
         click.echo()
         click.secho(f"━━━ scitex stats {name} ━━━", fg="cyan", bold=True)
@@ -132,9 +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,
@@ -339,5 +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()

scitex/cli/template.py

@@ -11,38 +11,55 @@ from pathlib import Path
 import click
 
 
-@click.group(context_settings={"help_option_names": ["-h", "--help"]})
-def template():
+@click.group(
+    context_settings={"help_option_names": ["-h", "--help"]},
+    invoke_without_command=True,
+)
+@click.option("--help-recursive", is_flag=True, help="Show help for all subcommands")
+@click.pass_context
+def template(ctx, help_recursive):
     """
     Project template scaffolding
 
     \b
-    Available templates:
+    Project Templates (clone):
       research      - Full scientific workflow structure
       pip-project   - Pip-installable Python package
       singularity   - Container-based project
       paper         - Academic paper writing template
 
+    \b
+    Code Templates (get):
+      session       - @stx.session script with CONFIG docs (priority)
+      io            - stx.io save/load patterns (priority)
+      config        - YAML configuration file
+      session-minimal/plot/stats - Variants
+      module        - Standard Python module
+      all           - All templates combined
+
     \b
     Examples:
-      scitex template list                        # Show available templates
-      scitex template clone research ./my-project # Clone research template
-      scitex template clone pip-project ./my-pkg  # Clone package template
+      scitex template get session                 # Session script template
+      scitex template get io                      # I/O operations template
+      scitex template get all                     # All templates
+      scitex template get session -o script.py   # Save to file
     """
-    pass
+    if help_recursive:
+        _print_help_recursive(ctx)
+        ctx.exit(0)
+    elif ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
 
 
-@template.command("help-recursive")
-@click.pass_context
-def help_recursive(ctx):
-    """Show help for all commands recursively."""
+def _print_help_recursive(ctx):
+    """Print help for all commands recursively."""
     fake_parent = click.Context(click.Group(), info_name="scitex")
     parent_ctx = click.Context(template, info_name="template", parent=fake_parent)
     click.secho("━━━ scitex template ━━━", fg="cyan", bold=True)
     click.echo(template.get_help(parent_ctx))
     for name in sorted(template.list_commands(ctx) or []):
         cmd = template.get_command(ctx, name)
-        if cmd is None or name == "help-recursive":
+        if cmd is None:
             continue
         click.echo()
         click.secho(f"━━━ scitex template {name} ━━━", fg="cyan", bold=True)
@@ -198,6 +215,106 @@ def clone(template_type, destination, git_strategy, branch, tag):
         sys.exit(1)
 
 
+@template.command()
+@click.argument(
+    "template_id",
+    type=click.Choice(
+        [
+            # Core templates (priority 1-3)
+            "session",
+            "io",
+            "config",
+            # Session variants
+            "session-minimal",
+            "session-plot",
+            "session-stats",
+            # Module template
+            "module",
+            # Module usage templates
+            "plt",
+            "stats",
+            "scholar",
+            "audio",
+            "capture",
+            "diagram",
+            "canvas",
+            "writer",
+            # All templates
+            "all",
+        ]
+    ),
+)
+@click.option(
+    "--output", "-o", type=click.Path(), help="Save to file instead of printing"
+)
+@click.option("--docstring", "-d", help="Custom docstring for the template")
+def get(template_id, output, docstring):
+    """
+    Get a code template (print or save to file)
+
+    \b
+    Core Templates (priority 1-3):
+      session         - Full @stx.session script with CONFIG docs
+      io              - stx.io.save/load patterns (30+ formats)
+      config          - YAML configuration file
+
+    \b
+    Session Variants:
+      session-minimal - Minimal session script
+      session-plot    - Plotting-focused session script
+      session-stats   - Statistical analysis script
+      module          - Standard Python module
+
+    \b
+    Module Usage Templates:
+      plt             - stx.plt plotting usage
+      stats           - stx.stats statistical analysis
+      scholar         - stx.scholar literature management
+      audio           - stx.audio text-to-speech
+      capture         - stx.capture screenshots
+      diagram         - stx.diagram Mermaid/Graphviz
+      canvas          - stx.canvas figure composition
+      writer          - stx.writer LaTeX compilation
+
+    \b
+    All:
+      all             - All templates combined
+
+    \b
+    Examples:
+      scitex template get session              # Print to stdout
+      scitex template get io                   # I/O operations template
+      scitex template get all                  # All templates
+      scitex template get session -o script.py # Save to file
+    """
+    try:
+        if template_id == "all":
+            from scitex.template import get_all_templates
+
+            content = get_all_templates()
+        else:
+            from scitex.template import get_code_template
+
+            filepath = output if output else None
+            content = get_code_template(
+                template_id, filepath=filepath, docstring=docstring
+            )
+
+        if output:
+            # Save to file
+            out_path = Path(output)
+            out_path.parent.mkdir(parents=True, exist_ok=True)
+            out_path.write_text(content)
+            click.secho(f"Template saved: {out_path}", fg="green")
+        else:
+            # Print to stdout
+            click.echo(content)
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
 @template.command()
 @click.argument("template_id")
 def info(template_id):

scitex/cli/tex.py

@@ -11,8 +11,13 @@ from pathlib import Path
 import click
 
 
-@click.group(context_settings={"help_option_names": ["-h", "--help"]})
-def tex():
+@click.group(
+    context_settings={"help_option_names": ["-h", "--help"]},
+    invoke_without_command=True,
+)
+@click.option("--help-recursive", is_flag=True, help="Show help for all subcommands")
+@click.pass_context
+def tex(ctx, help_recursive):
     """
     LaTeX compilation and utilities
 
@@ -28,20 +33,22 @@ def tex():
       scitex tex preview paper.tex
       scitex tex to-vec figure.tex --format svg
     """
-    pass
+    if help_recursive:
+        _print_help_recursive(ctx)
+        ctx.exit(0)
+    elif ctx.invoked_subcommand is None:
+        click.echo(ctx.get_help())
 
 
-@tex.command("help-recursive")
-@click.pass_context
-def help_recursive(ctx):
-    """Show help for all commands recursively."""
+def _print_help_recursive(ctx):
+    """Print help for all commands recursively."""
     fake_parent = click.Context(click.Group(), info_name="scitex")
     parent_ctx = click.Context(tex, info_name="tex", parent=fake_parent)
     click.secho("━━━ scitex tex ━━━", fg="cyan", bold=True)
     click.echo(tex.get_help(parent_ctx))
     for name in sorted(tex.list_commands(ctx) or []):
         cmd = tex.get_command(ctx, name)
-        if cmd is None or name == "help-recursive":
+        if cmd is None:
             continue
         click.echo()
         click.secho(f"━━━ scitex tex {name} ━━━", fg="cyan", bold=True)