scitex 2.14.0__py3-none-any.whl → 2.16.0__py3-none-any.whl

scitex/diagram/_presets.py

@@ -1,173 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: 2025-12-15
-# Author: ywatanabe / Claude
-# File: scitex/diagram/_presets.py
-
-"""
-Presets for common diagram types in scientific papers.
-
-Each preset defines rules for compiling the semantic spec to backend formats.
-These encode domain knowledge about "what makes a good paper figure."
-"""
-
-from dataclasses import dataclass
-from typing import Dict, Any, List
-
-
-@dataclass
-class DiagramPreset:
-    """Rules for compiling a diagram type."""
-
-    # Mermaid settings
-    mermaid_direction: str  # TB, LR, RL, BT
-    mermaid_theme: Dict[str, str]
-
-    # Graphviz settings
-    graphviz_rankdir: str  # TB, LR, RL, BT
-    graphviz_ranksep: float
-    graphviz_nodesep: float
-
-    # Spacing mappings
-    spacing_map: Dict[str, Dict[str, float]]
-
-    # Shape mappings (semantic -> backend)
-    mermaid_shapes: Dict[str, str]
-    graphviz_shapes: Dict[str, str]
-
-    # Emphasis styles (colors, borders)
-    emphasis_styles: Dict[str, Dict[str, str]]
-
-
-# Workflow preset: sequential processes, emphasize flow
-WORKFLOW_PRESET = DiagramPreset(
-    mermaid_direction="LR",  # Left-to-right for workflows
-    mermaid_theme={
-        "primaryColor": "#1a2634",
-        "primaryTextColor": "#e0e0e0",
-        "primaryBorderColor": "#3a4a5a",
-        "lineColor": "#5a9fcf",
-    },
-    graphviz_rankdir="LR",
-    graphviz_ranksep=0.8,
-    graphviz_nodesep=0.5,
-    spacing_map={
-        "tight": {"ranksep": 0.3, "nodesep": 0.2},      # Publication: minimal
-        "compact": {"ranksep": 0.4, "nodesep": 0.3},
-        "medium": {"ranksep": 0.8, "nodesep": 0.5},
-        "large": {"ranksep": 1.2, "nodesep": 0.8},
-    },
-    mermaid_shapes={
-        "box": '["__LABEL__"]',
-        "rounded": '("__LABEL__")',
-        "diamond": '{"__LABEL__"}',
-        "circle": '(("__LABEL__"))',
-        "stadium": '(["__LABEL__"])',
-    },
-    graphviz_shapes={
-        "box": "box",
-        "rounded": "box",  # with style=rounded
-        "diamond": "diamond",
-        "circle": "circle",
-        "stadium": "box",  # with style=rounded
-    },
-    emphasis_styles={
-        "primary": {"fill": "#0d4a6b", "stroke": "#5a9fcf", "stroke-width": "2px"},
-        "success": {"fill": "#ccffcc", "stroke": "#00cc00"},
-        "warning": {"fill": "#ffcccc", "stroke": "#cc0000"},
-        "muted": {"fill": "#f0f0f0", "stroke": "#999999"},
-        "normal": {"fill": "#1a2634", "stroke": "#3a4a5a"},
-    },
-)
-
-# Decision tree preset: top-to-bottom with branches
-DECISION_PRESET = DiagramPreset(
-    mermaid_direction="TB",
-    mermaid_theme={
-        "primaryColor": "#f5f5f5",
-        "primaryTextColor": "#333333",
-        "primaryBorderColor": "#666666",
-        "lineColor": "#666666",
-    },
-    graphviz_rankdir="TB",
-    graphviz_ranksep=1.0,
-    graphviz_nodesep=0.6,
-    spacing_map={
-        "compact": {"ranksep": 0.6, "nodesep": 0.4},
-        "medium": {"ranksep": 1.0, "nodesep": 0.6},
-        "large": {"ranksep": 1.5, "nodesep": 1.0},
-    },
-    mermaid_shapes={
-        "box": '["__LABEL__"]',
-        "rounded": '("__LABEL__")',
-        "diamond": '{"__LABEL__"}',
-        "circle": '(("__LABEL__"))',
-        "stadium": '(["__LABEL__"])',
-    },
-    graphviz_shapes={
-        "box": "box",
-        "rounded": "box",
-        "diamond": "diamond",
-        "circle": "circle",
-        "stadium": "box",
-    },
-    emphasis_styles={
-        "primary": {"fill": "#e6f3ff", "stroke": "#0066cc", "stroke-width": "2px"},
-        "success": {"fill": "#e6ffe6", "stroke": "#00aa00"},
-        "warning": {"fill": "#ffe6e6", "stroke": "#cc0000"},
-        "muted": {"fill": "#f0f0f0", "stroke": "#aaaaaa"},
-        "normal": {"fill": "#ffffff", "stroke": "#666666"},
-    },
-)
-
-# Pipeline preset: strict horizontal stages
-PIPELINE_PRESET = DiagramPreset(
-    mermaid_direction="LR",
-    mermaid_theme={
-        "primaryColor": "#ffffff",
-        "primaryTextColor": "#333333",
-        "primaryBorderColor": "#0066cc",
-        "lineColor": "#0066cc",
-    },
-    graphviz_rankdir="LR",
-    graphviz_ranksep=1.2,
-    graphviz_nodesep=0.4,
-    spacing_map={
-        "compact": {"ranksep": 0.8, "nodesep": 0.3},
-        "medium": {"ranksep": 1.2, "nodesep": 0.4},
-        "large": {"ranksep": 1.8, "nodesep": 0.6},
-    },
-    mermaid_shapes={
-        "box": '["__LABEL__"]',
-        "rounded": '("__LABEL__")',
-        "diamond": '{"__LABEL__"}',
-        "circle": '(("__LABEL__"))',
-        "stadium": '(["__LABEL__"])',
-    },
-    graphviz_shapes={
-        "box": "box",
-        "rounded": "box",
-        "diamond": "diamond",
-        "circle": "circle",
-        "stadium": "box",
-    },
-    emphasis_styles={
-        "primary": {"fill": "#e6f0ff", "stroke": "#0044aa", "stroke-width": "2px"},
-        "success": {"fill": "#e6ffe6", "stroke": "#00aa00"},
-        "warning": {"fill": "#fff3e6", "stroke": "#ff8800"},
-        "muted": {"fill": "#f5f5f5", "stroke": "#cccccc"},
-        "normal": {"fill": "#ffffff", "stroke": "#0066cc"},
-    },
-)
-
-
-def get_preset(diagram_type: str) -> DiagramPreset:
-    """Get preset for diagram type."""
-    presets = {
-        "workflow": WORKFLOW_PRESET,
-        "decision": DECISION_PRESET,
-        "pipeline": PIPELINE_PRESET,
-        "hierarchy": DECISION_PRESET,  # Same as decision for now
-        "comparison": WORKFLOW_PRESET,  # Override direction in compiler
-    }
-    return presets.get(diagram_type.lower(), WORKFLOW_PRESET)

scitex/diagram/_schema.py

@@ -1,182 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: 2025-12-15
-# Author: ywatanabe / Claude
-# File: scitex/diagram/_schema.py
-
-"""
-Schema definitions for SciTeX Diagram.
-
-The schema defines paper-specific constraints that Mermaid/Graphviz don't know:
-- Paper layout (single/double column, max width)
-- Reading direction preferences
-- Node emphasis for scientific communication
-- Semantic layer grouping
-"""
-
-from dataclasses import dataclass, field
-from enum import Enum
-from typing import List, Dict, Optional, Literal
-
-
-class DiagramType(Enum):
-    """Semantic type of diagram - affects layout strategy."""
-    WORKFLOW = "workflow"       # Sequential process, prefer LR/TB flow
-    DECISION = "decision"       # Decision tree, prefer TB with branches
-    PIPELINE = "pipeline"       # Data pipeline, strict LR with stages
-    HIERARCHY = "hierarchy"     # Tree structure, TB with levels
-    COMPARISON = "comparison"   # Side-by-side, two columns
-
-
-class ColumnLayout(Enum):
-    """Paper column layout."""
-    SINGLE = "single"   # Full width (~170mm)
-    DOUBLE = "double"   # Half width (~85mm)
-
-
-class SpacingLevel(Enum):
-    """Abstract spacing levels - mapped to backend-specific values."""
-    TIGHT = "tight"       # Publication: minimal whitespace
-    COMPACT = "compact"
-    MEDIUM = "medium"
-    LARGE = "large"
-
-
-class PaperMode(Enum):
-    """Paper mode affects layout density and edge visibility."""
-    DRAFT = "draft"           # Full arrows, visible bidirectional, medium spacing
-    PUBLICATION = "publication"  # Compact, return edges hidden/dotted
-
-
-@dataclass
-class PaperConstraints:
-    """Paper-specific constraints that affect layout."""
-    column: ColumnLayout = ColumnLayout.SINGLE
-    max_width_mm: int = 170
-    reading_direction: Literal["left_to_right", "top_to_bottom"] = "left_to_right"
-    mode: PaperMode = PaperMode.DRAFT  # draft: full details, publication: compact
-    emphasize: List[str] = field(default_factory=list)  # Node IDs to highlight
-
-    # Scientific communication hints
-    main_flow: List[str] = field(default_factory=list)  # Critical path nodes
-    secondary_flow: List[str] = field(default_factory=list)  # Supporting elements
-    return_edges: List[tuple] = field(default_factory=list)  # Edges to hide in publication
-
-
-@dataclass
-class LayoutHints:
-    """Abstract layout hints - compiled to backend directives."""
-    layers: List[List[str]] = field(default_factory=list)  # Nodes grouped by rank
-    alignment: Dict[str, str] = field(default_factory=dict)  # Node alignment hints
-    layer_gap: SpacingLevel = SpacingLevel.MEDIUM
-    node_gap: SpacingLevel = SpacingLevel.MEDIUM
-
-    # Subgraph organization
-    groups: Dict[str, List[str]] = field(default_factory=dict)  # Named groups
-
-
-@dataclass
-class NodeSpec:
-    """Specification for a single node."""
-    id: str
-    label: str
-    shape: Literal["box", "rounded", "diamond", "circle", "stadium"] = "box"
-    emphasis: Literal["normal", "primary", "success", "warning", "muted"] = "normal"
-
-    def short_label(self, max_chars: int = 20) -> str:
-        """Return truncated label for compact layouts."""
-        if len(self.label) <= max_chars:
-            return self.label
-        return self.label[:max_chars-3] + "..."
-
-
-@dataclass
-class EdgeSpec:
-    """Specification for an edge between nodes."""
-    source: str
-    target: str
-    label: Optional[str] = None
-    style: Literal["solid", "dashed", "dotted"] = "solid"
-    arrow: Literal["normal", "none", "open"] = "normal"
-
-
-@dataclass
-class DiagramSpec:
-    """Complete diagram specification - the semantic layer."""
-
-    # Metadata
-    type: DiagramType = DiagramType.WORKFLOW
-    title: str = ""
-
-    # Paper constraints
-    paper: PaperConstraints = field(default_factory=PaperConstraints)
-
-    # Layout hints
-    layout: LayoutHints = field(default_factory=LayoutHints)
-
-    # Content
-    nodes: List[NodeSpec] = field(default_factory=list)
-    edges: List[EdgeSpec] = field(default_factory=list)
-
-    # Theme
-    theme: Dict[str, str] = field(default_factory=dict)
-
-    @classmethod
-    def from_dict(cls, data: dict) -> "DiagramSpec":
-        """Create DiagramSpec from dictionary (parsed YAML)."""
-        spec = cls()
-
-        # Parse type
-        if "type" in data:
-            spec.type = DiagramType(data["type"])
-
-        spec.title = data.get("title", "")
-
-        # Parse paper constraints
-        if "paper" in data:
-            p = data["paper"]
-            spec.paper = PaperConstraints(
-                column=ColumnLayout(p.get("column", "single")),
-                max_width_mm=p.get("max_width_mm", 170),
-                reading_direction=p.get("reading_direction", "left_to_right"),
-                mode=PaperMode(p.get("mode", "draft")),
-                emphasize=p.get("emphasize", []),
-                main_flow=p.get("main_flow", []),
-                secondary_flow=p.get("secondary_flow", []),
-                return_edges=[tuple(e) for e in p.get("return_edges", [])],
-            )
-
-        # Parse layout hints
-        if "layout" in data:
-            lt = data["layout"]
-            spec.layout = LayoutHints(
-                layers=lt.get("layers", []),
-                alignment=lt.get("alignment", {}),
-                layer_gap=SpacingLevel(lt.get("layer_gap", "medium")),
-                node_gap=SpacingLevel(lt.get("node_gap", "medium")),
-                groups=lt.get("groups", {}),
-            )
-
-        # Parse nodes
-        for n in data.get("nodes", []):
-            spec.nodes.append(NodeSpec(
-                id=n["id"],
-                label=n.get("label", n["id"]),
-                shape=n.get("shape", "box"),
-                emphasis=n.get("emphasis", "normal"),
-            ))
-
-        # Parse edges
-        for e in data.get("edges", []):
-            spec.edges.append(EdgeSpec(
-                source=e["from"] if "from" in e else e["source"],
-                target=e["to"] if "to" in e else e["target"],
-                label=e.get("label"),
-                style=e.get("style", "solid"),
-                arrow=e.get("arrow", "normal"),
-            ))
-
-        # Theme
-        spec.theme = data.get("theme", {})
-
-        return spec

scitex/diagram/_split.py

@@ -1,278 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: 2025-12-15
-# Author: ywatanabe / Claude
-# File: scitex/diagram/_split.py
-
-"""
-Auto-split large diagrams into multiple figures.
-
-Strategies:
-- by_groups: Split by existing layout.groups (deterministic, paper-friendly)
-- by_articulation: Split at hub nodes (graph-theoretic)
-
-The split preserves "ghost nodes" at boundaries for visual continuity.
-"""
-
-from dataclasses import dataclass, field
-from typing import List, Dict, Set, Optional, Tuple
-from copy import deepcopy
-from enum import Enum
-
-from scitex.diagram._schema import DiagramSpec, NodeSpec, EdgeSpec
-
-
-class SplitStrategy(Enum):
-    BY_GROUPS = "by_groups"           # Split by layout.groups
-    BY_ARTICULATION = "by_articulation"  # Split at hub nodes
-
-
-@dataclass
-class SplitConfig:
-    """Configuration for auto-splitting."""
-    enabled: bool = False
-    max_nodes: int = 12               # Split if more nodes than this
-    strategy: SplitStrategy = SplitStrategy.BY_GROUPS
-    keep_hubs: bool = True            # Show hub nodes in both parts
-    ghost_style: str = "muted"        # Style for ghost nodes
-
-
-@dataclass
-class SplitResult:
-    """Result of splitting a diagram."""
-    figures: List[DiagramSpec]
-    labels: List[str]                  # Figure labels (A, B, C, ...)
-    cut_nodes: Set[str]               # Nodes that appear in multiple figures
-
-
-def split_diagram(
-    spec: DiagramSpec,
-    config: Optional[SplitConfig] = None,
-    group_assignments: Optional[List[List[str]]] = None,
-) -> SplitResult:
-    """
-    Split a diagram into multiple figures.
-
-    Parameters
-    ----------
-    spec : DiagramSpec
-        Original diagram specification.
-    config : SplitConfig, optional
-        Split configuration.
-    group_assignments : List[List[str]], optional
-        Manual group assignments for splitting.
-        If provided, overrides automatic detection.
-
-    Returns
-    -------
-    SplitResult
-        List of split diagram specifications.
-    """
-    if config is None:
-        config = SplitConfig(enabled=True)
-
-    # Check if split is needed
-    if not config.enabled or len(spec.nodes) <= config.max_nodes:
-        return SplitResult(figures=[spec], labels=[""], cut_nodes=set())
-
-    # Determine groups to split by
-    if group_assignments:
-        groups = group_assignments
-    elif config.strategy == SplitStrategy.BY_GROUPS:
-        groups = _split_by_groups(spec, max_nodes=config.max_nodes)
-    else:  # BY_ARTICULATION
-        groups = _split_by_articulation(spec)
-
-    # Create split figures
-    figures = []
-    labels = []
-    cut_nodes = set()
-
-    for i, group_nodes in enumerate(groups):
-        fig, cuts = _create_split_figure(spec, group_nodes, config)
-        figures.append(fig)
-        labels.append(chr(ord('A') + i))
-        cut_nodes.update(cuts)
-
-    return SplitResult(figures=figures, labels=labels, cut_nodes=cut_nodes)
-
-
-def _split_by_groups(spec: DiagramSpec, max_nodes: int = 12) -> List[List[str]]:
-    """
-    Split by existing layout.groups using greedy packing.
-
-    Packs groups into figures until max_nodes is exceeded,
-    then starts a new figure.
-
-    Returns list of node ID lists, one per split figure.
-    """
-    if not spec.layout.groups:
-        # No groups defined - try to split in half
-        node_ids = [n.id for n in spec.nodes]
-        mid = len(node_ids) // 2
-        return [node_ids[:mid], node_ids[mid:]]
-
-    # Group keys in order
-    group_names = list(spec.layout.groups.keys())
-
-    # Greedy packing: add groups until max_nodes exceeded
-    figures = []
-    current_figure = []
-    current_count = 0
-
-    for group_name in group_names:
-        group_nodes = spec.layout.groups[group_name]
-        group_size = len(group_nodes)
-
-        # If adding this group exceeds max and we have something, start new figure
-        if current_count + group_size > max_nodes and current_figure:
-            figures.append(current_figure)
-            current_figure = []
-            current_count = 0
-
-        # Add group to current figure
-        current_figure.extend(group_nodes)
-        current_count += group_size
-
-    # Don't forget the last figure
-    if current_figure:
-        figures.append(current_figure)
-
-    # Add ungrouped nodes to first figure
-    grouped = set()
-    for fig in figures:
-        grouped.update(fig)
-    for n in spec.nodes:
-        if n.id not in grouped:
-            if figures:
-                figures[0].append(n.id)
-            else:
-                figures.append([n.id])
-
-    # Ensure at least 2 figures if we have enough nodes
-    if len(figures) == 1 and len(figures[0]) > max_nodes:
-        # Force split in half
-        nodes = figures[0]
-        mid = len(nodes) // 2
-        figures = [nodes[:mid], nodes[mid:]]
-
-    return figures
-
-
-def _split_by_articulation(spec: DiagramSpec) -> List[List[str]]:
-    """
-    Split at articulation points (hub nodes).
-
-    This finds nodes that, if removed, would disconnect the graph.
-    These are natural split points for large diagrams.
-    """
-    # Build adjacency
-    adj: Dict[str, Set[str]] = {n.id: set() for n in spec.nodes}
-    for e in spec.edges:
-        adj[e.source].add(e.target)
-        adj[e.target].add(e.source)
-
-    # Find node with most connections (hub)
-    hub = max(adj.keys(), key=lambda x: len(adj[x]))
-
-    # BFS from first node, stopping at hub
-    visited = {hub}  # Block the hub
-    node_ids = [n.id for n in spec.nodes if n.id != hub]
-
-    if not node_ids:
-        return [[hub]]
-
-    # Find components when hub is removed
-    components = []
-    for start in node_ids:
-        if start in visited:
-            continue
-        component = []
-        queue = [start]
-        while queue:
-            curr = queue.pop(0)
-            if curr in visited:
-                continue
-            visited.add(curr)
-            component.append(curr)
-            for neighbor in adj[curr]:
-                if neighbor not in visited:
-                    queue.append(neighbor)
-        if component:
-            components.append(component)
-
-    # Add hub to each component (as ghost)
-    for comp in components:
-        comp.append(hub)
-
-    return components if components else [[n.id for n in spec.nodes]]
-
-
-def _create_split_figure(
-    spec: DiagramSpec,
-    node_ids: List[str],
-    config: SplitConfig,
-) -> Tuple[DiagramSpec, Set[str]]:
-    """
-    Create a split figure containing specified nodes.
-
-    Returns (figure_spec, ghost_node_ids).
-    """
-    node_id_set = set(node_ids)
-
-    # Find edges that cross the boundary
-    boundary_nodes = set()
-    for edge in spec.edges:
-        src_in = edge.source in node_id_set
-        tgt_in = edge.target in node_id_set
-        if src_in and not tgt_in:
-            if config.keep_hubs:
-                boundary_nodes.add(edge.target)
-        elif tgt_in and not src_in:
-            if config.keep_hubs:
-                boundary_nodes.add(edge.source)
-
-    # Create new spec
-    new_spec = DiagramSpec(
-        type=spec.type,
-        title=spec.title,
-        paper=deepcopy(spec.paper),
-        layout=deepcopy(spec.layout),
-        theme=dict(spec.theme),
-    )
-
-    # Filter nodes
-    node_map = {n.id: n for n in spec.nodes}
-    for node_id in node_ids:
-        if node_id in node_map:
-            new_spec.nodes.append(deepcopy(node_map[node_id]))
-
-    # Add ghost nodes (boundary nodes not in this split)
-    for ghost_id in boundary_nodes:
-        if ghost_id in node_map and ghost_id not in node_id_set:
-            ghost = deepcopy(node_map[ghost_id])
-            ghost.emphasis = config.ghost_style
-            ghost.label = f"→ {ghost.label}"  # Mark as continuation
-            new_spec.nodes.append(ghost)
-
-    # Filter edges
-    all_ids = node_id_set | boundary_nodes
-    for edge in spec.edges:
-        if edge.source in all_ids and edge.target in all_ids:
-            new_spec.edges.append(deepcopy(edge))
-
-    # Filter groups
-    new_spec.layout.groups = {}
-    for group_name, group_nodes in spec.layout.groups.items():
-        filtered = [n for n in group_nodes if n in all_ids]
-        if filtered:
-            new_spec.layout.groups[group_name] = filtered
-
-    # Filter layers
-    new_spec.layout.layers = []
-    for layer in spec.layout.layers:
-        filtered = [n for n in layer if n in all_ids]
-        if filtered:
-            new_spec.layout.layers.append(filtered)
-
-    return new_spec, boundary_nodes

scitex/gen/_check_host.py

@@ -1,34 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Time-stamp: "2024-11-02 13:43:36 (ywatanabe)"
-# File: ./scitex_repo/src/scitex/gen/_check_host.py
-
-
-from scitex.sh import sh
-import sys
-
-
-def check_host(keyword):
-    return keyword in sh("echo $(hostname)", verbose=False)
-
-
-is_host = check_host
-
-
-def verify_host(keyword):
-    if is_host(keyword):
-        print(f"Host verification successed for keyword: {keyword}")
-        return
-    else:
-        print(f"Host verification failed for keyword: {keyword}")
-        sys.exit(1)
-
-
-if __name__ == "__main__":
-    # check_host("ywata")
-    verify_host("titan")
-    verify_host("ywata")
-    verify_host("crest")
-
-
-# EOF

scitex/gen/_ci.py

@@ -1,12 +0,0 @@
-#!./env/bin/python3
-# -*- coding: utf-8 -*-
-# Time-stamp: "2024-06-04 06:55:56 (ywatanabe)"
-# /home/ywatanabe/proj/scitex/src/scitex/gen/_ci.py
-
-
-import numpy as np
-
-
-def ci(xx, axis=None):
-    indi = ~np.isnan(xx)
-    return 1.96 * (xx[indi]).std(axis=axis) / np.sqrt(indi.sum())