Visualize combined actions by dashed lines

documentation/changelog.rst

@@ -11,6 +11,11 @@ Description of of all notable changes made per version.
 - Support writing and reading information about pathways to a binary file.
 - Support import / export between text and binary dataset formats. See ``ap_import`` and
   ``ap_export`` commands.
+- Visualize combinations of actions by dashed lines
+- Added documentations (manuals and API)
+- Moved repository to new location: https://github.com/Deltares-research/PathwaysGenerator
+- Configured continuous integration. Every time we make changes, the source code is checked
+  (style and functionality). https://github.com/Deltares-research/PathwaysGenerator/actions
 
 
 0.0.8

source/package/adaptation_pathways/desktop/application.py

@@ -23,19 +23,22 @@
 from ..plot import (
     pathway_graph_node_colours,
     pathway_map_edge_colours,
+    pathway_map_edge_styles,
     pathway_map_node_colours,
+    pathway_map_node_styles,
     plot_classic_pathway_map,
     plot_default_pathway_graph,
     plot_default_pathway_map,
     plot_default_sequence_graph,
     sequence_graph_node_colours,
 )
 from ..plot.colour import (
-    Colour,
     PlotColours,
     default_edge_colours,
+    default_edge_style,
     default_label_colour,
     default_node_edge_colours,
+    default_node_style,
     default_nominal_palette,
 )
 from ..plot.util import action_level_by_first_occurrence
@@ -126,7 +129,7 @@ def __init__(self, basename_pathname: str = ""):
         self.actions: list[list] = []  # type: ignore
         self.sequences: list[list[Action]] = []  # type: ignore
         self.tipping_point_by_action: alias.TippingPointByAction = {}  # type: ignore
-        self.colour_by_action_name: dict[str, Colour] = {}  # type: ignore
+        self.colour_by_action_name: dict[str, alias.Colour] = {}  # type: ignore
 
         self.ui.action_open.setIcon(QtGui.QIcon(Path.icon("folder-open-table.png")))
         self.ui.action_save.setIcon(QtGui.QIcon(Path.icon("disk.png")))
@@ -239,7 +242,9 @@ def eventFilter(self, object_, event):
     def _plot_sequence_graph(self, sequence_graph: SequenceGraph) -> None:
         plot_colours = PlotColours(
             sequence_graph_node_colours(sequence_graph, self.colour_by_action_name),
+            default_node_style(),
             default_edge_colours(sequence_graph),
+            default_edge_style(),
             default_node_edge_colours(sequence_graph),
             default_label_colour(),
         )
@@ -253,7 +258,9 @@ def _plot_sequence_graph(self, sequence_graph: SequenceGraph) -> None:
     def _plot_pathway_graph(self, pathway_graph: PathwayGraph) -> None:
         plot_colours = PlotColours(
             pathway_graph_node_colours(pathway_graph, self.colour_by_action_name),
+            default_node_style(),
             default_edge_colours(pathway_graph),
+            default_edge_style(),
             default_node_edge_colours(pathway_graph),
             default_label_colour(),
         )
@@ -267,7 +274,9 @@ def _plot_pathway_graph(self, pathway_graph: PathwayGraph) -> None:
     def _plot_pathway_map(self, pathway_map: PathwayMap) -> None:
         plot_colours = PlotColours(
             pathway_map_node_colours(pathway_map, self.colour_by_action_name),
+            default_node_style(),
             pathway_map_edge_colours(pathway_map, self.colour_by_action_name),
+            default_edge_style(),
             default_node_edge_colours(pathway_map),
             default_label_colour(),
         )
@@ -281,7 +290,9 @@ def _plot_pathway_map(self, pathway_map: PathwayMap) -> None:
     def _plot_pathway_classic_map(self, pathway_map: PathwayMap) -> None:
         plot_colours = PlotColours(
             pathway_map_node_colours(pathway_map, self.colour_by_action_name),
+            pathway_map_node_styles(pathway_map),
             pathway_map_edge_colours(pathway_map, self.colour_by_action_name),
+            pathway_map_edge_styles(pathway_map),
             default_node_edge_colours(pathway_map),
             default_label_colour(),
         )

source/package/adaptation_pathways/desktop/model/action.py

@@ -1,16 +1,18 @@
 from PySide6 import QtCore, QtGui
 from PySide6.QtCore import Qt
 
-from ...plot.colour import Colour
+from ... import alias
 
 
 class ActionModel(QtCore.QAbstractTableModel):
 
     _actions: list[list]
     _headers: tuple[str]
-    _colour_by_action_name: dict[str, Colour]
+    _colour_by_action_name: dict[str, alias.Colour]
 
-    def __init__(self, actions: list[list], colour_by_action_name: dict[str, Colour]):
+    def __init__(
+        self, actions: list[list], colour_by_action_name: dict[str, alias.Colour]
+    ):
 
         super().__init__()
         self._actions = actions

source/package/adaptation_pathways/desktop/model/sequence.py

@@ -3,20 +3,19 @@
 
 from ... import alias
 from ...action import Action
-from ...plot.colour import Colour
 
 
 class SequenceModel(QtCore.QAbstractTableModel):
     _sequences: list[list[Action]]
     _tipping_point_by_action: alias.TippingPointByAction
     _horizonal_headers: tuple[str, str, str]
-    _colour_by_action_name: dict[str, Colour]
+    _colour_by_action_name: dict[str, alias.Colour]
 
     def __init__(
         self,
         sequences: list[list[Action]],
         tipping_point_by_action: alias.TippingPointByAction,
-        colour_by_action_name: dict[str, Colour],
+        colour_by_action_name: dict[str, alias.Colour],
     ):
         super().__init__()
         self._sequences = sequences

source/package/adaptation_pathways/io/dataset.py

@@ -37,8 +37,8 @@ def read_dataset(
         else:
             message = (
                 f"Error while reading text dataset {basename_pathname}. "
-                "First tried reading a binary dataset with that name "
-                "but it does not exist."
+                "(First tried reading a binary dataset with that name "
+                "but it does not exist.)"
             )
         raise RuntimeError(message) from exception
 

source/package/adaptation_pathways/io/text.py

@@ -267,7 +267,9 @@ def read_sequences(
                         f"Found tipping point {tipping_point} "
                         f"for action {sequence[1]}, which already has "
                         f"tipping point {tipping_point_by_action[sequence[1]]}. "
-                        "Actions must be associated with exactly one tipping point."
+                        "Actions must be associated with exactly one tipping point. "
+                        f"Action editions ({sequence[1]}[1], {sequence[1]}[2]) can be used for "
+                        "multiple occurrences of the same action."
                     )
 
                 tipping_point_by_action[sequence[1]] = tipping_point

source/package/adaptation_pathways/plot/alias.py

@@ -3,8 +3,20 @@
 """
 
 from ..action import Action
-from .colour import Colour, Colours  # pylint: disable=unused-import
 
 
+# from .colour import Colour, Colours  # pylint: disable=unused-import
+
+Colour = tuple[float, float, float, float]
+"""
+A colour is represented by four floating point values [0, 1], representing RGBA values respectively
+"""
+
+Colours = list[Colour]
+Style = str | tuple[int, tuple[int, int]]
+Styles = list[Style]
+FillStyle = str
+FillStyles = list[Style]
+
 ColourByAction = dict[Action, Colour]
 ColourByActionName = dict[str, Colour]

source/package/adaptation_pathways/plot/colour.py

@@ -7,14 +7,7 @@
 from dataclasses import dataclass
 
 from ..graph import PathwayGraph, PathwayMap, SequenceGraph
-
-
-Colour = tuple[float, float, float, float]
-"""
-A colour is represented by four floating point values [0, 1], representing RGBA values respectively
-"""
-
-Colours = list[Colour]
+from . import alias
 
 
 @dataclass
@@ -23,15 +16,19 @@ class PlotColours:
     This class aggregates colours used when plotting graphs
 
     :param node_colours: Fill colours for nodes
+    :param node_style: Fill style for nodes
     :param edge_colours: Line colours for edges
+    :param edge_style: Line style for edges
     :param node_edge_colours: Line colours for node outline
     :param label_colour: Label colour for labels
     """
 
-    node_colours: Colours | None = None
-    edge_colours: Colours | None = None
-    node_edge_colours: Colours | None = None
-    label_colour: Colour | None = None
+    node_colours: list[alias.Colour | alias.Colours] | None = None
+    node_style: alias.FillStyle | list[alias.FillStyle | alias.FillStyles] | None = None
+    edge_colours: list[alias.Colour | alias.Colours] | None = None
+    edge_style: alias.Style | list[alias.Style | alias.Styles] | None = None
+    node_edge_colours: alias.Colours | None = None
+    label_colour: alias.Colour | None = None
 
 
 nord_palette_nominal = [
@@ -79,7 +76,7 @@ class PlotColours:
 """
 
 
-def default_nominal_palette() -> Colours:
+def default_nominal_palette() -> alias.Colours:
     """
     Return the default palette with nominal colours
     """
@@ -88,19 +85,28 @@ def default_nominal_palette() -> Colours:
 
 def default_edge_colours(
     graph: SequenceGraph | PathwayGraph,
-) -> Colours:
+) -> list[alias.Colour | alias.Colours]:
     """
     For each edge in the graph, return a colour
     """
     colour = nord_palette_dark[3]
-    colours = [colour] * len(list(graph.graph.edges))
+    colours: list[alias.Colour | alias.Colours] = [colour] * len(
+        list(graph.graph.edges)
+    )
 
     return colours
 
 
+def default_edge_style() -> alias.Style:
+    """
+    Return the default edge style
+    """
+    return "solid"
+
+
 def default_node_edge_colours(
     graph: SequenceGraph | PathwayGraph | PathwayMap,
-) -> Colours:
+) -> alias.Colours:
     """
     For each edge in the graph, return a colour
     """
@@ -110,25 +116,32 @@ def default_node_edge_colours(
     return colours
 
 
-def default_node_colour() -> Colour:
+def default_node_colour() -> alias.Colour:
     """
     Return the default node colour
     """
     return nord_palette_dark[3]
 
 
-def default_label_colour() -> Colour:
+def default_node_style() -> alias.FillStyle:
+    """
+    Return the default node style
+    """
+    return "full"
+
+
+def default_label_colour() -> alias.Colour:
     """
     Return the default label colour
     """
     return nord_palette_dark[0]
 
 
-def default_action_colours(nr_actions: int) -> Colours:
+def default_action_colours(nr_actions: int) -> alias.Colours:
     """
     For each action, return a colour
     """
-    colours: Colours = []
+    colours: alias.Colours = []
 
     while len(colours) < nr_actions:
         # Append the whole palette as many times as needed
@@ -138,7 +151,7 @@ def default_action_colours(nr_actions: int) -> Colours:
     return colours[:nr_actions]
 
 
-def rgba_to_hex(colour: Colour) -> str:
+def rgba_to_hex(colour: alias.Colour) -> str:
     """
     Return the hex representation of the colour in RGBA representation
     """
@@ -151,7 +164,7 @@ def rgba_to_hex(colour: Colour) -> str:
     return f"#{a:02x}{r:02x}{g:02x}{b:02x}"
 
 
-def hex_to_rgba(colour: str) -> Colour:
+def hex_to_rgba(colour: str) -> alias.Colour:
     """
     Return the RGBA representation of the colour in hex representation
     """

source/package/adaptation_pathways/plot/pathway_graph/colour.py

@@ -1,22 +1,23 @@
 from ...graph import PathwayGraph
 from ...graph.node import ActionConversion, ActionPeriod
+from .. import alias
 from ..colour import (
-    Colour,
-    Colours,
     PlotColours,
     default_edge_colours,
+    default_edge_style,
     default_label_colour,
     default_node_edge_colours,
+    default_node_style,
     default_nominal_palette,
     nord_palette_light,
 )
 
 
 def colour_by_node(
-    graph: PathwayGraph, colour_by_action_name: dict[str, Colour]
-) -> Colours:
+    graph: PathwayGraph, colour_by_action_name: dict[str, alias.Colour]
+) -> list[alias.Colour | alias.Colours]:
     # pylint: disable=redefined-outer-name
-    colours = []
+    colours: list[alias.Colour | alias.Colours] = []
     conversion_colour = nord_palette_light[0]
 
     # Use the same colour for conversions
@@ -31,7 +32,9 @@ def colour_by_node(
     return colours
 
 
-def colour_by_action_name(graph: PathwayGraph, palette: Colours) -> dict[str, Colour]:
+def colour_by_action_name(
+    graph: PathwayGraph, palette: alias.Colours
+) -> dict[str, alias.Colour]:
     palette_size = len(palette)
     result = {}
     idx = 0
@@ -46,7 +49,7 @@ def colour_by_action_name(graph: PathwayGraph, palette: Colours) -> dict[str, Co
     return result
 
 
-def default_node_colours(graph: PathwayGraph) -> Colours:
+def default_node_colours(graph: PathwayGraph) -> list[alias.Colour | alias.Colours]:
     colour_by_action_name_ = (
         graph.graph.graph["colour_by_action_name"]
         if "colour_by_action_name" in graph.graph.graph
@@ -59,7 +62,9 @@ def default_node_colours(graph: PathwayGraph) -> Colours:
 def default_colours(pathway_graph: PathwayGraph) -> PlotColours:
     return PlotColours(
         default_node_colours(pathway_graph),
+        default_node_style(),
         default_edge_colours(pathway_graph),
+        default_edge_style(),
         default_node_edge_colours(pathway_graph),
         default_label_colour(),
     )

source/package/adaptation_pathways/plot/pathway_map/__init__.py

@@ -4,6 +4,8 @@
 
 from .classic import plot as plot_classic_pathway_map
 from .colour import edge_colours as pathway_map_edge_colours
+from .colour import edge_styles as pathway_map_edge_styles
 from .colour import node_colours as pathway_map_node_colours
+from .colour import node_styles as pathway_map_node_styles
 from .default import plot as plot_default_pathway_map
 from .plot import PathwayMapLayout, plot_pathway_map