scitex 2.11.0__py3-none-any.whl → 2.13.0__py3-none-any.whl

scitex/cli/resource.py

@@ -0,0 +1,240 @@
+#!/usr/bin/env python3
+"""
+SciTeX CLI - Resource Commands (System Monitoring)
+
+Provides system resource monitoring and specifications.
+"""
+
+import sys
+
+import click
+
+
+@click.group(context_settings={"help_option_names": ["-h", "--help"]})
+def resource():
+    """
+    System resource monitoring
+
+    \b
+    Commands:
+      specs     Show system specifications
+      usage     Show current resource usage
+      monitor   Continuously monitor resource usage
+
+    \b
+    Examples:
+      scitex resource specs              # Show system specs
+      scitex resource usage              # Current CPU/memory/GPU usage
+      scitex resource monitor --interval 5
+    """
+    pass
+
+
+@resource.command()
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+@click.option(
+    "--category",
+    "-c",
+    multiple=True,
+    type=click.Choice(["cpu", "memory", "disk", "network", "gpu", "os", "python"]),
+    help="Specific category to show",
+)
+def specs(as_json, category):
+    """
+    Show system specifications
+
+    \b
+    Categories:
+      cpu     - Processor information
+      memory  - RAM information
+      disk    - Storage information
+      network - Network interfaces
+      gpu     - GPU/CUDA information
+      os      - Operating system details
+      python  - Python environment
+
+    \b
+    Examples:
+      scitex resource specs
+      scitex resource specs --json
+      scitex resource specs --category cpu --category gpu
+    """
+    try:
+        from scitex.resource import get_specs
+
+        specs_data = get_specs()
+
+        # Filter categories if specified
+        if category:
+            category_map = {
+                "cpu": "_cpu_info",
+                "memory": "_memory_info",
+                "disk": "_disk_info",
+                "network": "_network_info",
+                "gpu": "_supple_nvidia_info",
+                "os": "_supple_os_info",
+                "python": "_supple_python_info",
+            }
+            filtered = {}
+            for cat in category:
+                key = category_map.get(cat, cat)
+                if key in specs_data:
+                    filtered[key] = specs_data[key]
+                elif cat in specs_data:
+                    filtered[cat] = specs_data[cat]
+            specs_data = filtered
+
+        if as_json:
+            import json
+
+            click.echo(json.dumps(specs_data, indent=2, default=str))
+        else:
+            click.secho("System Specifications", fg="cyan", bold=True)
+            click.echo("=" * 50)
+
+            for section, data in specs_data.items():
+                section_name = (
+                    section.replace("_info", "").replace("_supple_", "").upper()
+                )
+                click.secho(f"\n{section_name}:", fg="yellow")
+                if isinstance(data, dict):
+                    for key, value in data.items():
+                        click.echo(f"  {key}: {value}")
+                else:
+                    click.echo(f"  {data}")
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@resource.command()
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def usage(as_json):
+    """
+    Show current resource usage (CPU, memory, GPU)
+
+    \b
+    Examples:
+      scitex resource usage
+      scitex resource usage --json
+    """
+    try:
+        from scitex.resource import get_processor_usages
+
+        usage_data = get_processor_usages()
+
+        if as_json:
+            import json
+
+            click.echo(json.dumps(usage_data, indent=2, default=str))
+        else:
+            click.secho("Resource Usage", fg="cyan", bold=True)
+            click.echo("=" * 50)
+
+            # CPU
+            cpu = usage_data.get("cpu", {})
+            click.secho("\nCPU:", fg="yellow")
+            click.echo(f"  Usage: {cpu.get('percent', 'N/A')}%")
+            click.echo(f"  Cores: {cpu.get('count', 'N/A')}")
+
+            # Memory
+            mem = usage_data.get("memory", {})
+            click.secho("\nMemory:", fg="yellow")
+            click.echo(f"  Used: {mem.get('percent', 'N/A')}%")
+            click.echo(f"  Total: {mem.get('total_gb', 'N/A')} GB")
+            click.echo(f"  Available: {mem.get('available_gb', 'N/A')} GB")
+
+            # GPU (if available)
+            gpu = usage_data.get("gpu", {})
+            if gpu:
+                click.secho("\nGPU:", fg="yellow")
+                for i, g in enumerate(gpu.get("devices", [])):
+                    click.echo(f"  [{i}] {g.get('name', 'Unknown')}")
+                    click.echo(
+                        f"      Memory: {g.get('memory_used', 'N/A')} / {g.get('memory_total', 'N/A')} MB"
+                    )
+                    click.echo(f"      Utilization: {g.get('utilization', 'N/A')}%")
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@resource.command()
+@click.option(
+    "--interval",
+    "-i",
+    type=float,
+    default=2.0,
+    help="Update interval in seconds (default: 2.0)",
+)
+@click.option("--count", "-n", type=int, help="Number of updates (default: continuous)")
+@click.option("--log", "-l", type=click.Path(), help="Log to file")
+def monitor(interval, count, log):
+    """
+    Continuously monitor resource usage
+
+    \b
+    Examples:
+      scitex resource monitor
+      scitex resource monitor --interval 5
+      scitex resource monitor --count 10 --log usage.log
+    """
+    try:
+        import time
+
+        from scitex.resource import get_processor_usages
+
+        click.echo(f"Monitoring resources (interval: {interval}s)")
+        click.echo("Press Ctrl+C to stop")
+        click.echo()
+
+        log_file = None
+        if log:
+            log_file = open(log, "w")
+            log_file.write("timestamp,cpu_percent,memory_percent,gpu_percent\n")
+
+        iteration = 0
+        try:
+            while True:
+                if count and iteration >= count:
+                    break
+
+                usage_data = get_processor_usages()
+                cpu_pct = usage_data.get("cpu", {}).get("percent", 0)
+                mem_pct = usage_data.get("memory", {}).get("percent", 0)
+                gpu_pct = 0
+                gpu_info = usage_data.get("gpu", {})
+                if gpu_info and gpu_info.get("devices"):
+                    gpu_pct = gpu_info["devices"][0].get("utilization", 0)
+
+                # Display
+                from datetime import datetime
+
+                ts = datetime.now().strftime("%H:%M:%S")
+                line = f"[{ts}] CPU: {cpu_pct:5.1f}%  MEM: {mem_pct:5.1f}%  GPU: {gpu_pct:5.1f}%"
+                click.echo(line)
+
+                # Log
+                if log_file:
+                    log_file.write(f"{ts},{cpu_pct},{mem_pct},{gpu_pct}\n")
+                    log_file.flush()
+
+                iteration += 1
+                time.sleep(interval)
+
+        except KeyboardInterrupt:
+            click.echo("\nMonitoring stopped")
+        finally:
+            if log_file:
+                log_file.close()
+                click.echo(f"Log saved: {log}")
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    resource()

scitex/cli/stats.py

@@ -0,0 +1,325 @@
+#!/usr/bin/env python3
+"""
+SciTeX CLI - Stats Commands (Statistical Analysis)
+
+Provides statistical testing, test recommendation, and result management.
+"""
+
+import sys
+from pathlib import Path
+
+import click
+
+
+@click.group(context_settings={"help_option_names": ["-h", "--help"]})
+def stats():
+    """
+    Statistical analysis and testing utilities
+
+    \b
+    Commands:
+      recommend     Get recommended statistical tests for your data
+      describe      Compute descriptive statistics
+      save          Save statistical results to bundle
+      load          Load statistical results from bundle
+
+    \b
+    Examples:
+      scitex stats recommend --n-groups 2 --design between
+      scitex stats describe data.csv
+      scitex stats save results.json --output analysis.stats
+    """
+    pass
+
+
+@stats.command()
+@click.option(
+    "--n-groups", "-n", type=int, required=True, help="Number of groups to compare"
+)
+@click.option(
+    "--sample-sizes",
+    "-s",
+    multiple=True,
+    type=int,
+    help="Sample size for each group (can specify multiple times)",
+)
+@click.option(
+    "--outcome-type",
+    "-o",
+    type=click.Choice(["continuous", "binary", "ordinal", "count", "time_to_event"]),
+    default="continuous",
+    help="Type of outcome variable (default: continuous)",
+)
+@click.option(
+    "--design",
+    "-d",
+    type=click.Choice(["between", "within", "mixed"]),
+    default="between",
+    help="Study design (default: between)",
+)
+@click.option("--paired", is_flag=True, help="Whether measurements are paired")
+@click.option("--has-control", is_flag=True, help="Whether there is a control group")
+@click.option("--n-factors", type=int, default=1, help="Number of factors (default: 1)")
+@click.option(
+    "--top-k", "-k", type=int, default=3, help="Number of recommendations (default: 3)"
+)
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def recommend(
+    n_groups,
+    sample_sizes,
+    outcome_type,
+    design,
+    paired,
+    has_control,
+    n_factors,
+    top_k,
+    as_json,
+):
+    """
+    Get recommended statistical tests for your experimental design
+
+    \b
+    Examples:
+      # Two-group comparison
+      scitex stats recommend --n-groups 2 --sample-sizes 30 --sample-sizes 32
+
+      # Three-group ANOVA
+      scitex stats recommend --n-groups 3 --design between
+
+      # Paired t-test scenario
+      scitex stats recommend --n-groups 2 --paired --design within
+
+      # Binary outcome (chi-square)
+      scitex stats recommend --n-groups 2 --outcome-type binary
+    """
+    try:
+        from scitex.stats import StatContext, recommend_tests
+
+        # Build context
+        ctx = StatContext(
+            n_groups=n_groups,
+            sample_sizes=list(sample_sizes) if sample_sizes else [30] * n_groups,
+            outcome_type=outcome_type,
+            design=design,
+            paired=paired,
+            has_control_group=has_control,
+            n_factors=n_factors,
+        )
+
+        tests = recommend_tests(ctx, top_k=top_k)
+
+        if as_json:
+            import json
+
+            output = {
+                "context": {
+                    "n_groups": n_groups,
+                    "sample_sizes": list(sample_sizes)
+                    if sample_sizes
+                    else [30] * n_groups,
+                    "outcome_type": outcome_type,
+                    "design": design,
+                    "paired": paired,
+                    "has_control_group": has_control,
+                    "n_factors": n_factors,
+                },
+                "recommended_tests": tests,
+            }
+            click.echo(json.dumps(output, indent=2))
+        else:
+            click.secho("Recommended Statistical Tests", fg="cyan", bold=True)
+            click.echo("=" * 40)
+            click.echo("\nContext:")
+            click.echo(f"  Groups: {n_groups}")
+            click.echo(f"  Design: {design}")
+            click.echo(f"  Outcome: {outcome_type}")
+            click.echo(f"  Paired: {paired}")
+            click.echo(f"\nTop {top_k} Recommendations:")
+            for i, test in enumerate(tests, 1):
+                click.secho(f"  {i}. {test}", fg="green")
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@stats.command()
+@click.argument("data_path", type=click.Path(exists=True))
+@click.option("--column", "-c", multiple=True, help="Specific column(s) to describe")
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def describe(data_path, column, as_json):
+    """
+    Compute descriptive statistics for data
+
+    \b
+    Examples:
+      scitex stats describe data.csv
+      scitex stats describe data.csv --column age --column score
+      scitex stats describe data.csv --json
+    """
+    try:
+        import pandas as pd
+
+        from scitex.stats import describe as describe_data
+
+        # Load data
+        path = Path(data_path)
+        if path.suffix == ".csv":
+            df = pd.read_csv(path)
+        elif path.suffix in (".xls", ".xlsx"):
+            df = pd.read_excel(path)
+        elif path.suffix == ".json":
+            df = pd.read_json(path)
+        else:
+            click.secho(f"Unsupported file format: {path.suffix}", fg="red", err=True)
+            sys.exit(1)
+
+        # Filter columns if specified
+        if column:
+            df = df[list(column)]
+
+        # Get descriptive stats
+        result = describe_data(df)
+
+        if as_json:
+            import json
+
+            # Convert to JSON-serializable format
+            if hasattr(result, "to_dict"):
+                click.echo(json.dumps(result.to_dict(), indent=2, default=str))
+            else:
+                click.echo(json.dumps(result, indent=2, default=str))
+        else:
+            click.secho(f"Descriptive Statistics: {path.name}", fg="cyan", bold=True)
+            click.echo("=" * 50)
+            click.echo(result)
+
+    except ImportError:
+        click.secho(
+            "Error: pandas required. Install: pip install pandas", fg="red", err=True
+        )
+        sys.exit(1)
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@stats.command()
+@click.argument("input_path", type=click.Path(exists=True))
+@click.option(
+    "--output",
+    "-o",
+    type=click.Path(),
+    required=True,
+    help="Output bundle path (.stats)",
+)
+@click.option("--as-zip", is_flag=True, help="Save as ZIP archive")
+def save(input_path, output, as_zip):
+    """
+    Save statistical results to a SciTeX bundle
+
+    \b
+    Examples:
+      scitex stats save results.json --output analysis.stats
+      scitex stats save comparisons.json --output analysis.stats --as-zip
+    """
+    try:
+        import json
+
+        from scitex.stats import save_stats
+
+        # Load input
+        with open(input_path) as f:
+            data = json.load(f)
+
+        # Handle different input formats
+        if isinstance(data, list):
+            comparisons = data
+        elif isinstance(data, dict) and "comparisons" in data:
+            comparisons = data["comparisons"]
+        else:
+            comparisons = [data]
+
+        # Save bundle
+        result_path = save_stats(comparisons, output, as_zip=as_zip)
+        click.secho(f"Stats bundle saved: {result_path}", fg="green")
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@stats.command()
+@click.argument("bundle_path", type=click.Path(exists=True))
+@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
+def load(bundle_path, as_json):
+    """
+    Load statistical results from a SciTeX bundle
+
+    \b
+    Examples:
+      scitex stats load analysis.stats
+      scitex stats load analysis.stats --json
+    """
+    try:
+        from scitex.stats import load_stats
+
+        data = load_stats(bundle_path)
+
+        if as_json:
+            import json
+
+            click.echo(json.dumps(data, indent=2, default=str))
+        else:
+            click.secho(f"Statistics Bundle: {bundle_path}", fg="cyan", bold=True)
+            click.echo("=" * 50)
+
+            comparisons = data.get("comparisons", [])
+            click.echo(f"\nComparisons ({len(comparisons)}):")
+            for comp in comparisons:
+                name = comp.get("name", "unnamed")
+                method = comp.get("method", "unknown")
+                p_val = comp.get("p_value", "N/A")
+                formatted = comp.get("formatted", "")
+                click.echo(f"  - {name}: {method}, p={p_val} {formatted}")
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+@stats.command()
+def tests():
+    """
+    List available statistical tests
+
+    \b
+    Example:
+      scitex stats tests
+    """
+    try:
+        from scitex.stats import TEST_RULES
+
+        click.secho("Available Statistical Tests", fg="cyan", bold=True)
+        click.echo("=" * 50)
+
+        # Group by category
+        categories = {}
+        for rule in TEST_RULES:
+            cat = getattr(rule, "category", "other")
+            if cat not in categories:
+                categories[cat] = []
+            categories[cat].append(rule.name)
+
+        for cat, tests_list in sorted(categories.items()):
+            click.secho(f"\n{cat.title()}:", fg="yellow")
+            for test in sorted(tests_list):
+                click.echo(f"  - {test}")
+
+    except Exception as e:
+        click.secho(f"Error: {e}", fg="red", err=True)
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    stats()