scitex 2.7.0__py3-none-any.whl → 2.8.1__py3-none-any.whl

scitex/diagram/_diagram.py

@@ -0,0 +1,355 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: 2025-12-15
+# Author: ywatanabe / Claude
+# File: scitex/diagram/_diagram.py
+
+"""
+Main Diagram class - the user-facing API.
+"""
+
+from pathlib import Path
+from typing import Optional, Union, List
+import yaml
+import re
+
+from scitex.diagram._schema import DiagramSpec, DiagramType, NodeSpec, EdgeSpec, PaperMode
+from scitex.diagram._compile import compile_to_mermaid, compile_to_graphviz
+from scitex.diagram._presets import get_preset
+from scitex.diagram._split import split_diagram, SplitConfig, SplitStrategy, SplitResult
+
+
+class Diagram:
+    """
+    Paper-optimized diagram with semantic specification.
+
+    This class provides the main interface for creating diagrams
+    that compile to Mermaid or Graphviz with paper-appropriate
+    layout constraints.
+
+    Examples
+    --------
+    >>> # From YAML spec
+    >>> d = Diagram.from_yaml("workflow.diagram.yaml")
+    >>> d.to_mermaid("workflow.mmd")
+
+    >>> # From existing Mermaid (parse and enhance)
+    >>> d = Diagram.from_mermaid("existing.mmd", diagram_type="workflow")
+    >>> d.spec.paper.column = "double"
+    >>> d.to_mermaid("enhanced.mmd")
+
+    >>> # Programmatic creation
+    >>> d = Diagram(type="pipeline")
+    >>> d.add_node("input", "Raw Data")
+    >>> d.add_node("process", "Transform", emphasis="primary")
+    >>> d.add_node("output", "Results")
+    >>> d.add_edge("input", "process")
+    >>> d.add_edge("process", "output")
+    >>> print(d.to_mermaid())
+    """
+
+    def __init__(
+        self,
+        type: str = "workflow",
+        title: str = "",
+        column: str = "single",
+    ):
+        """
+        Initialize a new diagram.
+
+        Parameters
+        ----------
+        type : str
+            Diagram type: workflow, decision, pipeline, hierarchy.
+        title : str
+            Diagram title.
+        column : str
+            Paper column: single or double.
+        """
+        self.spec = DiagramSpec(
+            type=DiagramType(type),
+            title=title,
+        )
+        self.spec.paper.column = column
+
+    @classmethod
+    def from_yaml(cls, path: Union[str, Path]) -> "Diagram":
+        """
+        Load diagram from YAML specification file.
+
+        Parameters
+        ----------
+        path : str or Path
+            Path to YAML file.
+
+        Returns
+        -------
+        Diagram
+            Loaded diagram.
+        """
+        path = Path(path)
+        with open(path, "r", encoding="utf-8") as f:
+            data = yaml.safe_load(f)
+
+        diagram = cls.__new__(cls)
+        diagram.spec = DiagramSpec.from_dict(data)
+        return diagram
+
+    @classmethod
+    def from_mermaid(
+        cls,
+        path: Union[str, Path],
+        diagram_type: str = "workflow",
+    ) -> "Diagram":
+        """
+        Parse existing Mermaid file and create enhanced Diagram.
+
+        This allows upgrading existing Mermaid files with SciTeX
+        paper constraints while preserving the original structure.
+
+        Parameters
+        ----------
+        path : str or Path
+            Path to .mmd file.
+        diagram_type : str
+            Inferred diagram type.
+
+        Returns
+        -------
+        Diagram
+            Parsed diagram (can be enhanced and re-exported).
+        """
+        path = Path(path)
+        with open(path, "r", encoding="utf-8") as f:
+            content = f.read()
+
+        diagram = cls(type=diagram_type)
+        diagram._parse_mermaid(content)
+        return diagram
+
+    def _parse_mermaid(self, content: str):
+        """Parse Mermaid content to extract structure."""
+        # Extract nodes
+        # Pattern: ID["Label"] or ID("Label") etc.
+        node_pattern = r'(\w+)\s*[\[\(\{<][\"\']?([^"\'\]\)\}>]+)[\"\']?[\]\)\}>]'
+
+        for match in re.finditer(node_pattern, content):
+            node_id = match.group(1)
+            label = match.group(2).strip()
+            # Skip if it looks like a subgraph name
+            if node_id.lower() not in ["subgraph", "end", "style", "graph", "direction"]:
+                # Check for duplicates
+                existing = [n for n in self.spec.nodes if n.id == node_id]
+                if not existing:
+                    self.spec.nodes.append(NodeSpec(id=node_id, label=label))
+
+        # Extract edges
+        # Pattern: A --> B or A -->|label| B
+        edge_pattern = r'(\w+)\s*(-->|-.->|-----|---)\s*(?:\|["\']?([^|"\']+)["\']?\|)?\s*(\w+)'
+
+        for match in re.finditer(edge_pattern, content):
+            source = match.group(1)
+            arrow = match.group(2)
+            label = match.group(3)
+            target = match.group(4)
+
+            style = "solid"
+            if "-.->" in arrow or "-.." in arrow:
+                style = "dashed"
+
+            self.spec.edges.append(EdgeSpec(
+                source=source,
+                target=target,
+                label=label.strip() if label else None,
+                style=style,
+            ))
+
+        # Extract subgraphs as groups
+        subgraph_pattern = r'subgraph\s+(\w+)\s*\[?"?([^"\]]*)"?\]?'
+        for match in re.finditer(subgraph_pattern, content):
+            group_id = match.group(1)
+            group_name = match.group(2) or group_id
+            self.spec.layout.groups[group_name] = []
+
+    def add_node(
+        self,
+        id: str,
+        label: str,
+        shape: str = "box",
+        emphasis: str = "normal",
+    ):
+        """Add a node to the diagram."""
+        self.spec.nodes.append(NodeSpec(
+            id=id,
+            label=label,
+            shape=shape,
+            emphasis=emphasis,
+        ))
+
+    def add_edge(
+        self,
+        source: str,
+        target: str,
+        label: Optional[str] = None,
+        style: str = "solid",
+    ):
+        """Add an edge between nodes."""
+        self.spec.edges.append(EdgeSpec(
+            source=source,
+            target=target,
+            label=label,
+            style=style,
+        ))
+
+    def set_group(self, group_name: str, node_ids: list):
+        """Define a group of nodes (rendered as subgraph)."""
+        self.spec.layout.groups[group_name] = node_ids
+
+    def emphasize(self, *node_ids: str):
+        """Mark nodes as emphasized (primary styling)."""
+        self.spec.paper.emphasize.extend(node_ids)
+
+    def to_mermaid(self, path: Optional[Union[str, Path]] = None) -> str:
+        """
+        Compile to Mermaid format.
+
+        Parameters
+        ----------
+        path : str or Path, optional
+            If provided, write to file.
+
+        Returns
+        -------
+        str
+            Mermaid source code.
+        """
+        result = compile_to_mermaid(self.spec)
+
+        if path:
+            path = Path(path)
+            with open(path, "w", encoding="utf-8") as f:
+                f.write(result)
+
+        return result
+
+    def to_graphviz(self, path: Optional[Union[str, Path]] = None) -> str:
+        """
+        Compile to Graphviz DOT format.
+
+        Parameters
+        ----------
+        path : str or Path, optional
+            If provided, write to file.
+
+        Returns
+        -------
+        str
+            Graphviz DOT source code.
+        """
+        result = compile_to_graphviz(self.spec)
+
+        if path:
+            path = Path(path)
+            with open(path, "w", encoding="utf-8") as f:
+                f.write(result)
+
+        return result
+
+    def to_yaml(self, path: Optional[Union[str, Path]] = None) -> str:
+        """
+        Export specification as YAML.
+
+        Parameters
+        ----------
+        path : str or Path, optional
+            If provided, write to file.
+
+        Returns
+        -------
+        str
+            YAML specification.
+        """
+        data = {
+            "type": self.spec.type.value,
+            "title": self.spec.title,
+            "paper": {
+                "column": self.spec.paper.column.value if hasattr(self.spec.paper.column, 'value') else self.spec.paper.column,
+                "max_width_mm": self.spec.paper.max_width_mm,
+                "reading_direction": self.spec.paper.reading_direction,
+                "mode": self.spec.paper.mode.value if hasattr(self.spec.paper.mode, 'value') else self.spec.paper.mode,
+                "emphasize": self.spec.paper.emphasize,
+            },
+            "layout": {
+                "groups": self.spec.layout.groups,
+                "layers": self.spec.layout.layers,
+                "layer_gap": self.spec.layout.layer_gap.value,
+                "node_gap": self.spec.layout.node_gap.value,
+            },
+            "nodes": [
+                {"id": n.id, "label": n.label, "shape": n.shape, "emphasis": n.emphasis}
+                for n in self.spec.nodes
+            ],
+            "edges": [
+                {"from": e.source, "to": e.target, "label": e.label, "style": e.style}
+                for e in self.spec.edges
+            ],
+        }
+
+        result = yaml.dump(data, default_flow_style=False, allow_unicode=True)
+
+        if path:
+            path = Path(path)
+            with open(path, "w", encoding="utf-8") as f:
+                f.write(result)
+
+        return result
+
+    def split(
+        self,
+        max_nodes: int = 12,
+        strategy: str = "by_groups",
+        keep_hubs: bool = True,
+    ) -> List["Diagram"]:
+        """
+        Split diagram into multiple figures if too large.
+
+        Parameters
+        ----------
+        max_nodes : int
+            Maximum nodes per figure before splitting.
+        strategy : str
+            Split strategy: "by_groups" or "by_articulation".
+        keep_hubs : bool
+            Show hub nodes as ghosts in both parts.
+
+        Returns
+        -------
+        List[Diagram]
+            List of split diagrams (or single diagram if no split needed).
+
+        Examples
+        --------
+        >>> d = Diagram.from_yaml("large_workflow.yaml")
+        >>> parts = d.split(max_nodes=8)
+        >>> for i, part in enumerate(parts):
+        ...     part.to_mermaid(f"workflow_part_{i+1}.mmd")
+        """
+        config = SplitConfig(
+            enabled=True,
+            max_nodes=max_nodes,
+            strategy=SplitStrategy(strategy),
+            keep_hubs=keep_hubs,
+        )
+
+        result = split_diagram(self.spec, config)
+
+        # Wrap each spec in a Diagram object
+        diagrams = []
+        for fig_spec, label in zip(result.figures, result.labels):
+            d = Diagram.__new__(Diagram)
+            d.spec = fig_spec
+            if label:
+                d.spec.title = f"{self.spec.title} ({label})" if self.spec.title else f"Part {label}"
+            diagrams.append(d)
+
+        return diagrams

scitex/diagram/_presets.py

@@ -0,0 +1,173 @@
+#!/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)