scitex 2.10.3__py3-none-any.whl → 2.13.0__py3-none-any.whl

scitex/fts/_stats/_dataclasses/_Stats.py

@@ -1,423 +0,0 @@
-#!/usr/bin/env python3
-# Timestamp: 2025-12-20
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/fts/_stats/_dataclasses/_Stats.py
-
-"""
-Stats - Statistical analysis results with provenance and GUI support.
-
-This module provides the single source of truth for statistical result schemas,
-supporting both:
-1. Bundle storage (data provenance, test results)
-2. GUI annotation (positioning, styling for interactive editing)
-"""
-
-import json
-from dataclasses import dataclass, field, asdict
-from datetime import datetime
-from typing import Any, Dict, List, Literal, Optional, Union
-
-STATS_VERSION = "1.1.0"
-
-# Type aliases for GUI support
-PositionMode = Literal["absolute", "relative_to_plot", "above_whisker", "auto"]
-UnitType = Literal["mm", "px", "inch", "data"]
-SymbolStyle = Literal["asterisk", "text", "bracket", "compact", "detailed", "publication"]
-
-
-@dataclass
-class DataRef:
-    """Reference to data used in analysis."""
-
-    path: str
-    columns: Optional[List[str]] = None
-    filter: Optional[str] = None
-
-    def to_dict(self) -> Dict[str, Any]:
-        result = {"path": self.path}
-        if self.columns:
-            result["columns"] = self.columns
-        if self.filter:
-            result["filter"] = self.filter
-        return result
-
-    @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "DataRef":
-        return cls(
-            path=data.get("path", ""),
-            columns=data.get("columns"),
-            filter=data.get("filter"),
-        )
-
-
-# =============================================================================
-# GUI Position and Styling Classes (merged from scitex.schema._stats)
-# =============================================================================
-
-
-@dataclass
-class Position:
-    """
-    Position specification with unit support for GUI integration.
-
-    Supports multiple coordinate systems for flexibility across
-    matplotlib (mm), Fabric.js (px), and data coordinates.
-    """
-
-    x: float
-    y: float
-    unit: UnitType = "mm"
-    relative_to: Optional[str] = None  # Plot ID or "axes"
-    offset: Optional[Dict[str, float]] = None  # {"dx": 0, "dy": 0}
-
-    def to_dict(self) -> Dict[str, Any]:
-        return {
-            "x": self.x,
-            "y": self.y,
-            "unit": self.unit,
-            "relative_to": self.relative_to,
-            "offset": self.offset,
-        }
-
-    @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "Position":
-        return cls(**data)
-
-    def to_mm(self, dpi: float = 300.0) -> "Position":
-        """Convert position to mm (for matplotlib)."""
-        if self.unit == "mm":
-            return self
-        elif self.unit == "px":
-            mm_per_px = 25.4 / dpi
-            return Position(
-                x=self.x * mm_per_px,
-                y=self.y * mm_per_px,
-                unit="mm",
-                relative_to=self.relative_to,
-                offset=self.offset,
-            )
-        elif self.unit == "inch":
-            return Position(
-                x=self.x * 25.4,
-                y=self.y * 25.4,
-                unit="mm",
-                relative_to=self.relative_to,
-                offset=self.offset,
-            )
-        return self
-
-    def to_px(self, dpi: float = 300.0) -> "Position":
-        """Convert position to px (for Fabric.js canvas)."""
-        mm_pos = self.to_mm(dpi)
-        px_per_mm = dpi / 25.4
-        return Position(
-            x=mm_pos.x * px_per_mm,
-            y=mm_pos.y * px_per_mm,
-            unit="px",
-            relative_to=self.relative_to,
-            offset=self.offset,
-        )
-
-
-@dataclass
-class StatStyling:
-    """Styling configuration for statistical annotation display."""
-
-    font_size_pt: float = 7.0
-    font_family: str = "Arial"
-    color: str = "#000000"
-    symbol_style: SymbolStyle = "asterisk"
-    line_width_mm: Optional[float] = None
-    bracket_height_mm: Optional[float] = None
-    theme: Literal["light", "dark", "auto"] = "auto"
-
-    def to_dict(self) -> Dict[str, Any]:
-        return asdict(self)
-
-    @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "StatStyling":
-        return cls(**data)
-
-    def get_theme_color(self, is_dark: bool = False) -> str:
-        """Get appropriate color for theme."""
-        if self.theme == "auto":
-            return "#ffffff" if is_dark else "#000000"
-        elif self.theme == "dark":
-            return "#ffffff"
-        return "#000000"
-
-
-@dataclass
-class StatPositioning:
-    """Position configuration for GUI-ready annotation placement."""
-
-    mode: PositionMode = "auto"
-    position: Optional[Position] = None
-    preferred_corner: Optional[str] = None  # "top-right", "bottom-left", etc.
-    avoid_overlap: bool = True
-    min_distance_mm: float = 2.0
-    anchor_to: Optional[str] = None  # "plot_center", "whisker_top", etc.
-
-    def to_dict(self) -> Dict[str, Any]:
-        return {
-            "mode": self.mode,
-            "position": self.position.to_dict() if self.position else None,
-            "preferred_corner": self.preferred_corner,
-            "avoid_overlap": self.avoid_overlap,
-            "min_distance_mm": self.min_distance_mm,
-            "anchor_to": self.anchor_to,
-        }
-
-    @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "StatPositioning":
-        data_copy = data.copy()
-        if data_copy.get("position"):
-            data_copy["position"] = Position.from_dict(data_copy["position"])
-        return cls(**data_copy)
-
-
-@dataclass
-class EffectSize:
-    """Effect size with confidence interval."""
-
-    name: str  # cohens_d, hedges_g, eta_squared, r_squared, etc.
-    value: float
-    ci_lower: Optional[float] = None
-    ci_upper: Optional[float] = None
-    ci_level: float = 0.95
-
-    def to_dict(self) -> Dict[str, Any]:
-        result = {"name": self.name, "value": self.value}
-        if self.ci_lower is not None:
-            result["ci_lower"] = self.ci_lower
-        if self.ci_upper is not None:
-            result["ci_upper"] = self.ci_upper
-        if self.ci_level != 0.95:
-            result["ci_level"] = self.ci_level
-        return result
-
-    @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "EffectSize":
-        return cls(
-            name=data.get("name", ""),
-            value=data.get("value", 0.0),
-            ci_lower=data.get("ci_lower"),
-            ci_upper=data.get("ci_upper"),
-            ci_level=data.get("ci_level", 0.95),
-        )
-
-
-@dataclass
-class StatMethod:
-    """Statistical method specification."""
-
-    name: str  # t-test, anova, chi-squared, correlation, etc.
-    variant: Optional[str] = None  # independent, paired, one-way, etc.
-    parameters: Dict[str, Any] = field(default_factory=dict)
-
-    def to_dict(self) -> Dict[str, Any]:
-        result = {"name": self.name}
-        if self.variant:
-            result["variant"] = self.variant
-        if self.parameters:
-            result["parameters"] = self.parameters
-        return result
-
-    @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "StatMethod":
-        return cls(
-            name=data.get("name", ""),
-            variant=data.get("variant"),
-            parameters=data.get("parameters", {}),
-        )
-
-
-@dataclass
-class StatResult:
-    """Statistical test result."""
-
-    statistic: float
-    statistic_name: str  # t, F, chi2, r, etc.
-    p_value: float
-    df: Optional[float] = None
-    effect_size: Optional[EffectSize] = None
-    significant: Optional[bool] = None
-    alpha: float = 0.05
-
-    def to_dict(self) -> Dict[str, Any]:
-        result = {
-            "statistic": self.statistic,
-            "statistic_name": self.statistic_name,
-            "p_value": self.p_value,
-        }
-        if self.df is not None:
-            result["df"] = self.df
-        if self.effect_size:
-            result["effect_size"] = self.effect_size.to_dict()
-        if self.significant is not None:
-            result["significant"] = self.significant
-        if self.alpha != 0.05:
-            result["alpha"] = self.alpha
-        return result
-
-    @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "StatResult":
-        effect_size = None
-        if "effect_size" in data:
-            effect_size = EffectSize.from_dict(data["effect_size"])
-        return cls(
-            statistic=data.get("statistic", 0.0),
-            statistic_name=data.get("statistic_name", ""),
-            p_value=data.get("p_value", 1.0),
-            df=data.get("df"),
-            effect_size=effect_size,
-            significant=data.get("significant"),
-            alpha=data.get("alpha", 0.05),
-        )
-
-
-@dataclass
-class StatDisplay:
-    """How to display the statistical result (with GUI support)."""
-
-    show_stars: bool = True
-    show_p_value: bool = True
-    show_effect_size: bool = False
-    bracket_groups: Optional[List[str]] = None
-    # Enhanced GUI support
-    positioning: Optional[StatPositioning] = None
-    styling: Optional[StatStyling] = None
-    plot_id: Optional[str] = None  # Associated plot in TrackingMixin
-
-    def to_dict(self) -> Dict[str, Any]:
-        result = {
-            "show_stars": self.show_stars,
-            "show_p_value": self.show_p_value,
-            "show_effect_size": self.show_effect_size,
-        }
-        if self.bracket_groups:
-            result["bracket_groups"] = self.bracket_groups
-        if self.positioning:
-            result["positioning"] = self.positioning.to_dict()
-        if self.styling:
-            result["styling"] = self.styling.to_dict()
-        if self.plot_id:
-            result["plot_id"] = self.plot_id
-        return result
-
-    @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "StatDisplay":
-        positioning = None
-        if "positioning" in data and data["positioning"]:
-            positioning = StatPositioning.from_dict(data["positioning"])
-        styling = None
-        if "styling" in data and data["styling"]:
-            styling = StatStyling.from_dict(data["styling"])
-        return cls(
-            show_stars=data.get("show_stars", True),
-            show_p_value=data.get("show_p_value", True),
-            show_effect_size=data.get("show_effect_size", False),
-            bracket_groups=data.get("bracket_groups"),
-            positioning=positioning,
-            styling=styling,
-            plot_id=data.get("plot_id"),
-        )
-
-
-@dataclass
-class Analysis:
-    """Complete analysis record with provenance."""
-
-    result_id: str
-    method: StatMethod
-    results: StatResult
-    data_refs: List[DataRef] = field(default_factory=list)
-    inputs: Dict[str, Any] = field(default_factory=dict)
-    display: Optional[StatDisplay] = None
-
-    def to_dict(self) -> Dict[str, Any]:
-        result = {
-            "result_id": self.result_id,
-            "method": self.method.to_dict(),
-            "results": self.results.to_dict(),
-        }
-        if self.data_refs:
-            result["data_refs"] = [d.to_dict() for d in self.data_refs]
-        if self.inputs:
-            result["inputs"] = self.inputs
-        if self.display:
-            result["display"] = self.display.to_dict()
-        return result
-
-    @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "Analysis":
-        display = None
-        if "display" in data:
-            display = StatDisplay.from_dict(data["display"])
-        return cls(
-            result_id=data.get("result_id", ""),
-            method=StatMethod.from_dict(data.get("method", {})),
-            results=StatResult.from_dict(data.get("results", {})),
-            data_refs=[DataRef.from_dict(d) for d in data.get("data_refs", [])],
-            inputs=data.get("inputs", {}),
-            display=display,
-        )
-
-
-@dataclass
-class Stats:
-    """Complete statistics specification for a bundle.
-
-    Stored in stats/stats.json.
-    """
-
-    analyses: List[Analysis] = field(default_factory=list)
-    software: Dict[str, str] = field(default_factory=dict)
-
-    # Schema metadata
-    schema_name: str = "fsb.stats"
-    schema_version: str = STATS_VERSION
-
-    def to_dict(self) -> Dict[str, Any]:
-        result = {"analyses": [a.to_dict() for a in self.analyses]}
-        if self.software:
-            result["software"] = self.software
-        return result
-
-    def to_json(self, indent: int = 2) -> str:
-        return json.dumps(self.to_dict(), indent=indent)
-
-    @classmethod
-    def from_dict(cls, data: Dict[str, Any]) -> "Stats":
-        return cls(
-            analyses=[Analysis.from_dict(a) for a in data.get("analyses", [])],
-            software=data.get("software", {}),
-        )
-
-    @classmethod
-    def from_json(cls, json_str: str) -> "Stats":
-        return cls.from_dict(json.loads(json_str))
-
-
-__all__ = [
-    # Version
-    "STATS_VERSION",
-    # Type aliases
-    "PositionMode",
-    "UnitType",
-    "SymbolStyle",
-    # Data reference
-    "DataRef",
-    # GUI classes (merged from scitex.schema._stats)
-    "Position",
-    "StatStyling",
-    "StatPositioning",
-    # Core stats classes
-    "EffectSize",
-    "StatMethod",
-    "StatResult",
-    "StatDisplay",
-    "Analysis",
-    "Stats",
-]
-
-# EOF

scitex/fts/_stats/_dataclasses/__init__.py

@@ -1,48 +0,0 @@
-#!/usr/bin/env python3
-# Timestamp: 2025-12-20
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/fts/_stats/_dataclasses/__init__.py
-
-"""Statistics-specific dataclasses for FTS with GUI support."""
-
-from ._Stats import (
-    STATS_VERSION,
-    # Type aliases
-    PositionMode,
-    UnitType,
-    SymbolStyle,
-    # GUI classes
-    Position,
-    StatStyling,
-    StatPositioning,
-    # Core classes
-    Analysis,
-    DataRef,
-    EffectSize,
-    StatDisplay,
-    StatMethod,
-    StatResult,
-    Stats,
-)
-
-__all__ = [
-    # Version
-    "STATS_VERSION",
-    # Type aliases
-    "PositionMode",
-    "UnitType",
-    "SymbolStyle",
-    # GUI classes
-    "Position",
-    "StatStyling",
-    "StatPositioning",
-    # Core classes
-    "DataRef",
-    "EffectSize",
-    "StatMethod",
-    "StatResult",
-    "StatDisplay",
-    "Analysis",
-    "Stats",
-]
-
-# EOF

scitex/fts/_tables/__init__.py

@@ -1,65 +0,0 @@
-#!/usr/bin/env python3
-# Timestamp: 2025-12-20
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/fsb/_tables/__init__.py
-
-"""Table handling and LaTeX export for FTS bundles.
-
-This module provides:
-- LaTeX export for figures and tables (booktabs style)
-- Statistical result formatting
-- LaTeX validation and error editor
-"""
-
-from ._latex import (
-    ColumnDef,
-    ErrorSeverity,
-    FigureExportOptions,
-    FormattedStat,
-    LaTeXError,
-    LaTeXExportOptions,
-    LaTeXResult,
-    TableExportOptions,
-    ValidationResult,
-    export_figure_to_latex,
-    export_multiple,
-    export_table_to_latex,
-    export_to_latex,
-    format_inline_stat,
-    format_stat_note,
-    format_stats_for_latex,
-    generate_figure_preamble,
-    generate_table_preamble,
-    launch_editor,
-    validate_latex,
-)
-
-__all__ = [
-    # Main export API
-    "export_to_latex",
-    "export_multiple",
-    "LaTeXExportOptions",
-    "LaTeXResult",
-    # Figure export
-    "export_figure_to_latex",
-    "FigureExportOptions",
-    "generate_figure_preamble",
-    # Table export
-    "export_table_to_latex",
-    "TableExportOptions",
-    "ColumnDef",
-    "generate_table_preamble",
-    # Stats formatting
-    "format_stats_for_latex",
-    "format_inline_stat",
-    "format_stat_note",
-    "FormattedStat",
-    # Validation
-    "validate_latex",
-    "ValidationResult",
-    "LaTeXError",
-    "ErrorSeverity",
-    # Editor
-    "launch_editor",
-]
-
-# EOF

scitex/fts/_tables/_latex/__init__.py

@@ -1,93 +0,0 @@
-#!/usr/bin/env python3
-# Timestamp: 2025-12-20
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/fsb/_tables/_latex/__init__.py
-
-"""LaTeX export for FTS bundles.
-
-This module provides LaTeX export capabilities for FTS figure and table bundles.
-
-Usage:
-    from scitex.fts._tables._latex import export_to_latex, launch_editor
-
-    # Export a bundle to LaTeX
-    result = export_to_latex(bundle)
-    print(result.latex_code)
-
-    # Open editor for manual fixes
-    launch_editor(result.latex_code, bundle=bundle)
-"""
-
-from ._editor import launch_editor
-from ._export import LaTeXExportOptions, LaTeXResult, export_multiple, export_to_latex
-from ._figure_exporter import FigureExportOptions, export_figure_to_latex, generate_figure_preamble
-from ._stats_formatter import (
-    FormattedStat,
-    format_inline_stat,
-    format_stat_note,
-    format_stats_for_latex,
-    format_stats_paragraph,
-)
-from ._table_exporter import (
-    ColumnDef,
-    TableExportOptions,
-    export_table_to_latex,
-    generate_table_preamble,
-)
-from ._utils import (
-    column_spec,
-    escape_latex,
-    escape_latex_minimal,
-    format_effect_size,
-    format_number,
-    format_p_value,
-    format_statistic,
-    format_unit,
-    sanitize_label,
-    significance_stars,
-    wrap_math,
-)
-from ._validator import ErrorSeverity, LaTeXError, ValidationResult, validate_latex
-
-__all__ = [
-    # Main export API
-    "export_to_latex",
-    "export_multiple",
-    "LaTeXExportOptions",
-    "LaTeXResult",
-    # Figure export
-    "export_figure_to_latex",
-    "FigureExportOptions",
-    "generate_figure_preamble",
-    # Table export
-    "export_table_to_latex",
-    "TableExportOptions",
-    "ColumnDef",
-    "generate_table_preamble",
-    # Stats formatting
-    "format_stats_for_latex",
-    "format_inline_stat",
-    "format_stat_note",
-    "format_stats_paragraph",
-    "FormattedStat",
-    # Validation
-    "validate_latex",
-    "ValidationResult",
-    "LaTeXError",
-    "ErrorSeverity",
-    # Editor
-    "launch_editor",
-    # Utilities
-    "escape_latex",
-    "escape_latex_minimal",
-    "format_unit",
-    "format_number",
-    "format_p_value",
-    "format_statistic",
-    "format_effect_size",
-    "significance_stars",
-    "sanitize_label",
-    "wrap_math",
-    "column_spec",
-]
-
-# EOF

scitex/fts/_tables/_latex/_editor/__init__.py

@@ -1,11 +0,0 @@
-#!/usr/bin/env python3
-# Timestamp: 2025-12-20
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/fsb/_tables/_latex/_editor/__init__.py
-
-"""Flask-based LaTeX error editor."""
-
-from ._app import launch_editor
-
-__all__ = ["launch_editor"]
-
-# EOF