synkit 1.6.5__py3-none-win_amd64.whl

synkit/CRN/Visualize/palette.py

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+from __future__ import annotations
+
+from dataclasses import dataclass, replace
+
+
+@dataclass(frozen=True)
+class ColorPalette:
+    """
+    Muted publication-style palette for CRN visualization.
+
+    The defaults are intentionally restrained: muted species and rule colors,
+    light paper-like background, and neutral label text.
+    """
+
+    background: str
+    species_fill: str
+    species_edge: str
+    rule_fill: str
+    rule_edge: str
+    reactant_edge: str
+    product_edge: str
+    other_edge: str
+    highlight_node: str
+    highlight_edge: str
+    label_text: str
+    node_index_text: str
+    legend_text: str
+    title_text: str
+
+    def with_overrides(self, **kwargs) -> "ColorPalette":
+        return replace(self, **kwargs)
+
+
+_PALETTES: dict[str, ColorPalette] = {
+    "paper_sage": ColorPalette(
+        background="#FAF9F5",
+        species_fill="#D6E0D6",
+        species_edge="#5F7162",
+        rule_fill="#E8E2D8",
+        rule_edge="#847B6D",
+        reactant_edge="#748072",
+        product_edge="#8B8378",
+        other_edge="#A9A39A",
+        highlight_node="#EFE5C8",
+        highlight_edge="#9C8457",
+        label_text="#35352F",
+        node_index_text="#4B4A43",
+        legend_text="#35352F",
+        title_text="#2F2F2A",
+    ),
+    "stone_leaf": ColorPalette(
+        background="#FBFAF6",
+        species_fill="#D7E1D7",
+        species_edge="#627062",
+        rule_fill="#E6E0D7",
+        rule_edge="#82796C",
+        reactant_edge="#748074",
+        product_edge="#8B8276",
+        other_edge="#A7A097",
+        highlight_node="#EEE2C1",
+        highlight_edge="#9A8252",
+        label_text="#36352F",
+        node_index_text="#4B4A44",
+        legend_text="#36352F",
+        title_text="#302F2A",
+    ),
+    "soft_moss": ColorPalette(
+        background="#F8F8F3",
+        species_fill="#CFDDD2",
+        species_edge="#566A5D",
+        rule_fill="#E6E0D7",
+        rule_edge="#7B766D",
+        reactant_edge="#6C7B70",
+        product_edge="#837C72",
+        other_edge="#9FA097",
+        highlight_node="#E9DFC0",
+        highlight_edge="#8F7B50",
+        label_text="#34352F",
+        node_index_text="#474842",
+        legend_text="#34352F",
+        title_text="#2E2F2A",
+    ),
+    "linen_clay": ColorPalette(
+        background="#FCFAF7",
+        species_fill="#DCE1D9",
+        species_edge="#667167",
+        rule_fill="#E8DED2",
+        rule_edge="#837769",
+        reactant_edge="#7A8177",
+        product_edge="#907F73",
+        other_edge="#AAA194",
+        highlight_node="#F0E2C2",
+        highlight_edge="#9C8050",
+        label_text="#393730",
+        node_index_text="#4D4A43",
+        legend_text="#393730",
+        title_text="#322F29",
+    ),
+    "fog_olive": ColorPalette(
+        background="#F7F8F5",
+        species_fill="#D8DFD8",
+        species_edge="#616D64",
+        rule_fill="#E3E0D8",
+        rule_edge="#7D786E",
+        reactant_edge="#717B74",
+        product_edge="#867F76",
+        other_edge="#A3A097",
+        highlight_node="#E7E0C8",
+        highlight_edge="#8C7A53",
+        label_text="#33342F",
+        node_index_text="#484944",
+        legend_text="#33342F",
+        title_text="#2D2E29",
+    ),
+    "mineral_dust": ColorPalette(
+        background="#FAF9F7",
+        species_fill="#D9DDD8",
+        species_edge="#6A706A",
+        rule_fill="#E7E3DC",
+        rule_edge="#847D73",
+        reactant_edge="#787F79",
+        product_edge="#898178",
+        other_edge="#A7A39C",
+        highlight_node="#EDE3CB",
+        highlight_edge="#93815B",
+        label_text="#373732",
+        node_index_text="#4B4B46",
+        legend_text="#373732",
+        title_text="#31312C",
+    ),
+    "cedar_paper": ColorPalette(
+        background="#F9F8F4",
+        species_fill="#D2DED4",
+        species_edge="#55675A",
+        rule_fill="#E6DED4",
+        rule_edge="#7C7368",
+        reactant_edge="#69786C",
+        product_edge="#81796E",
+        other_edge="#9E9A92",
+        highlight_node="#ECDFBC",
+        highlight_edge="#8E7749",
+        label_text="#31322D",
+        node_index_text="#454640",
+        legend_text="#31322D",
+        title_text="#2B2C27",
+    ),
+    "ash_linen": ColorPalette(
+        background="#FBFBF9",
+        species_fill="#E0E3DE",
+        species_edge="#6F756E",
+        rule_fill="#E9E6E0",
+        rule_edge="#878075",
+        reactant_edge="#7B817B",
+        product_edge="#8B847C",
+        other_edge="#A9A49E",
+        highlight_node="#EEE5CF",
+        highlight_edge="#988562",
+        label_text="#383833",
+        node_index_text="#4C4C47",
+        legend_text="#383833",
+        title_text="#32322E",
+    ),
+    "quiet_forest": ColorPalette(
+        background="#F8F8F5",
+        species_fill="#D4DED3",
+        species_edge="#5D6E60",
+        rule_fill="#E4DED5",
+        rule_edge="#7E766B",
+        reactant_edge="#6E7B70",
+        product_edge="#857D73",
+        other_edge="#A09D95",
+        highlight_node="#EADFBE",
+        highlight_edge="#8E7B4F",
+        label_text="#34342F",
+        node_index_text="#484843",
+        legend_text="#34342F",
+        title_text="#2E2E29",
+    ),
+    "sandstone": ColorPalette(
+        background="#FCFAF5",
+        species_fill="#DCE1D8",
+        species_edge="#687266",
+        rule_fill="#E9DFD2",
+        rule_edge="#877A6C",
+        reactant_edge="#7B8378",
+        product_edge="#928477",
+        other_edge="#ADA397",
+        highlight_node="#F2E3BE",
+        highlight_edge="#A28450",
+        label_text="#3A3731",
+        node_index_text="#4E4B44",
+        legend_text="#3A3731",
+        title_text="#34312B",
+    ),
+    "slate_botanic": ColorPalette(
+        background="#F7F8F6",
+        species_fill="#D5DDD8",
+        species_edge="#5E6C67",
+        rule_fill="#E2DFD8",
+        rule_edge="#78756E",
+        reactant_edge="#6D7975",
+        product_edge="#817C74",
+        other_edge="#9FA09A",
+        highlight_node="#E7E0C7",
+        highlight_edge="#897754",
+        label_text="#333530",
+        node_index_text="#484A46",
+        legend_text="#333530",
+        title_text="#2D2F2B",
+    ),
+    "oak_stone": ColorPalette(
+        background="#FAF8F4",
+        species_fill="#D7E0D4",
+        species_edge="#61705F",
+        rule_fill="#E7DED3",
+        rule_edge="#817668",
+        reactant_edge="#738072",
+        product_edge="#8A7E72",
+        other_edge="#A39D93",
+        highlight_node="#EDE0BE",
+        highlight_edge="#927A49",
+        label_text="#35342E",
+        node_index_text="#494841",
+        legend_text="#35342E",
+        title_text="#2F2E28",
+    ),
+    "ivory_shale": ColorPalette(
+        background="#FBFAF8",
+        species_fill="#DDE1DD",
+        species_edge="#6A716B",
+        rule_fill="#E8E5E0",
+        rule_edge="#827C74",
+        reactant_edge="#797F7A",
+        product_edge="#88827B",
+        other_edge="#A8A39D",
+        highlight_node="#EDE4CE",
+        highlight_edge="#93825E",
+        label_text="#373733",
+        node_index_text="#4B4B47",
+        legend_text="#373733",
+        title_text="#31312D",
+    ),
+    "moss_quartz": ColorPalette(
+        background="#F8F8F4",
+        species_fill="#D1DDD5",
+        species_edge="#56685D",
+        rule_fill="#E5E0D8",
+        rule_edge="#79756C",
+        reactant_edge="#6A7870",
+        product_edge="#807B72",
+        other_edge="#9DA09A",
+        highlight_node="#E9E1C8",
+        highlight_edge="#887652",
+        label_text="#32332E",
+        node_index_text="#464741",
+        legend_text="#32332E",
+        title_text="#2C2D28",
+    ),
+    "graphite_sage": ColorPalette(
+        background="#F9F9F7",
+        species_fill="#D8DDD8",
+        species_edge="#626863",
+        rule_fill="#E3E1DB",
+        rule_edge="#77736C",
+        reactant_edge="#6F7671",
+        product_edge="#7E7972",
+        other_edge="#9A9A96",
+        highlight_node="#E6DEC6",
+        highlight_edge="#84724F",
+        label_text="#2F312D",
+        node_index_text="#434540",
+        legend_text="#2F312D",
+        title_text="#292B27",
+    ),
+}
+
+
+def palette_names() -> list[str]:
+    return sorted(_PALETTES)
+
+
+def get_palette(name: str = "paper_sage", **overrides) -> ColorPalette:
+    try:
+        palette = _PALETTES[name]
+    except KeyError as exc:
+        raise ValueError(
+            f"Unknown palette {name!r}. Available: {', '.join(palette_names())}"
+        ) from exc
+
+    if overrides:
+        return palette.with_overrides(**overrides)
+    return palette

synkit/CRN/Visualize/validation.py

@@ -0,0 +1,122 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import Hashable, List
+import logging
+
+import networkx as nx
+
+from ..kinds import ALL_KINDS, is_reaction_node, is_species_node
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass(frozen=True)
+class CRNGraphInfo:
+    species_nodes: List[Hashable]
+    rule_nodes: List[Hashable]
+    is_dag: bool
+
+
+def node_sort_key(graph: nx.DiGraph, node: Hashable):
+    """Order reaction nodes after species nodes, deterministically.
+
+    Reaction nodes are recognised through :func:`~synkit.CRN.kinds.is_reaction_node`,
+    so ``kind="reaction"`` and the legacy ``kind="rule"`` sort identically. A
+    direct ``kind == "rule"`` comparison here used to file ``kind="reaction"``
+    nodes under the species branch, giving two different drawings of the same
+    network.
+
+    :param graph:
+        Bipartite CRN graph.
+    :type graph: networkx.DiGraph
+
+    :param node:
+        Node to build a sort key for.
+    :type node: Hashable
+
+    :return:
+        Comparable sort key.
+    :rtype: tuple
+    """
+    data = graph.nodes[node]
+    if is_reaction_node(data):
+        return (
+            1,
+            data.get("step", 10**9),
+            data.get("rule_index", 10**9),
+            data.get("app_index", 10**9),
+            str(data.get("label", "")),
+            str(node),
+        )
+    return (
+        0,
+        data.get("step", -1),
+        str(data.get("label", "")),
+        str(data.get("smiles", "")),
+        str(node),
+    )
+
+
+def validate_crn_graph(graph: nx.DiGraph, *, strict: bool = True) -> CRNGraphInfo:
+    if not isinstance(graph, nx.DiGraph):
+        raise TypeError("CRNVis expects a networkx.DiGraph.")
+
+    invalid_kind_nodes = [
+        n
+        for n, d in graph.nodes(data=True)
+        if not (is_species_node(d) or is_reaction_node(d))
+    ]
+    if invalid_kind_nodes:
+        msg = (
+            "Found nodes with invalid or missing 'kind': "
+            f"{invalid_kind_nodes!r}. Expected one of {sorted(ALL_KINDS)!r}."
+        )
+        if strict:
+            raise ValueError(msg)
+        logger.warning(msg)
+
+    species_nodes = sorted(
+        [n for n, d in graph.nodes(data=True) if is_species_node(d)],
+        key=lambda n: node_sort_key(graph, n),
+    )
+    rule_nodes = sorted(
+        [n for n, d in graph.nodes(data=True) if is_reaction_node(d)],
+        key=lambda n: node_sort_key(graph, n),
+    )
+
+    invalid_edges = []
+    unknown_roles = []
+    for u, v, d in graph.edges(data=True):
+        role = d.get("role")
+        u_data = graph.nodes[u]
+        v_data = graph.nodes[v]
+        if role == "reactant":
+            if not (is_species_node(u_data) and is_reaction_node(v_data)):
+                invalid_edges.append((u, v, role))
+        elif role == "product":
+            if not (is_reaction_node(u_data) and is_species_node(v_data)):
+                invalid_edges.append((u, v, role))
+        elif role is not None:
+            unknown_roles.append((u, v, role))
+
+    if invalid_edges:
+        msg = (
+            "Found edges whose direction is inconsistent with their role: "
+            f"{invalid_edges!r}."
+        )
+        if strict:
+            raise ValueError(msg)
+        logger.warning(msg)
+
+    if unknown_roles:
+        logger.warning(
+            "Found edges with unknown roles; they will be drawn with fallback style: %r",
+            unknown_roles,
+        )
+
+    return CRNGraphInfo(
+        species_nodes=species_nodes,
+        rule_nodes=rule_nodes,
+        is_dag=nx.is_directed_acyclic_graph(graph),
+    )