Merge pull request #49 from geoneric/gh41

Add support for spreading of vertical lines

source/package/adaptation_pathways/cli/plot_pathway_map.py

@@ -58,7 +58,7 @@ def main() -> int:
 
 Usage:
     {command} [--title=<title>] [--x_label=<label>] [--show_legend]
-        [--overshoot] <basename> <plot>
+        [--overshoot] [--spread=<spread>] <basename> <plot>
 
 Arguments:
     basename           Either, the name without postfix and extension of text
@@ -74,6 +74,10 @@ def main() -> int:
     --overshoot        Show tipping points as overshoots, extending a little
                        bit beyond the actual point
     --show_legend      Show legend
+    --spread=<spread>  Separate overlapping lines by a percentage [0, 1] of
+                       the range passed in. A value of 0.01 means 1% of the
+                       range of x-coordinates. Passing in a value > 0.02 is
+                       likely not useful.
     --title=<title>    Title
     --x_label=<label>  Label of x-axis
 
@@ -93,11 +97,13 @@ def main() -> int:
     x_label = arguments["--x_label"] if arguments["--x_label"] is not None else ""
     show_legend = arguments["--show_legend"]
     overshoot = arguments["--overshoot"]
+    overlapping_lines_spread = float(arguments["--spread"])
 
     plot_arguments: dict[str, typing.Any] = {
         "title": title,
         "x_label": x_label,
         "show_legend": show_legend,
+        "overlapping_lines_spread": overlapping_lines_spread,
     }
 
     if overshoot:

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

@@ -11,7 +11,7 @@
 from ...graph import PathwayMap
 from ...graph.node import ActionBegin, ActionEnd
 from .. import alias
-from ..util import add_position
+from ..util import add_position, distribute
 
 
 def _plot_action_lines(
@@ -104,11 +104,11 @@ def _plot_action_tipping_points(
     path_collection = mpl.collections.PathCollection(None)
 
     if len(nodes) > 0:
-        # The last "tipping point" is skipped
-        node_pos = np.asarray([layout[v] for v in nodes][:-1])
+        # TODO Skip the tipping point at the end of each individual path way
+        node_pos = np.asarray([layout[v] for v in nodes])
         x, y = zip(*node_pos)
         x = np.array(x) + tipping_point_overshoot
-        colours = [colour_by_action_name[node.action.name] for node in nodes][:-1]
+        colours = [colour_by_action_name[node.action.name] for node in nodes]
 
         if tipping_point_marker.is_filled():
             scatter_arguments = {
@@ -311,11 +311,57 @@ def _distribute_horizontally(
         _distribute_horizontally(pathway_map, action_begin_new, position_by_node)
 
 
+def _spread_vertically(
+    pathway_map: PathwayMap,
+    position_by_node: dict[ActionBegin | ActionEnd, np.ndarray],
+    overlapping_lines_spread: float,
+) -> None:
+
+    # - If vertical spreading is enabled
+    # - Assign all action_end / action_begin combinations to bins
+    # - For those bins that contain more than one elements, tweak the x-coordinates
+    # - Make the magnitude of the tweak configurable (dependent on line width?)
+
+    nodes_by_x: dict[float, list[tuple[ActionEnd, ActionBegin]]] = {}
+
+    for action_end in pathway_map.all_action_ends():
+        action_begins = pathway_map.action_begins(action_end)
+        x = position_by_node[action_end][0]
+
+        if x not in nodes_by_x:
+            nodes_by_x[x] = []
+
+        for action_begin in action_begins:
+            assert position_by_node[action_begin][0] == x
+            nodes_by_x[x].append((action_end, action_begin))
+
+    min_x = min(nodes_by_x.keys())
+    max_x = max(nodes_by_x.keys())
+    range_x = max_x - min_x
+
+    # Root action end. This x coordinate needs no tweaking.
+    del nodes_by_x[min_x]
+
+    for x, nodes in nodes_by_x.items():
+        nr_nodes = len(nodes)
+
+        if nr_nodes > 1:
+            x_coordinates = distribute(
+                nr_nodes * [x], overlapping_lines_spread * range_x
+            )
+
+            for idx in range(nr_nodes):
+                action_end, action_begin = nodes[idx]
+                position_by_node[action_end][0] = x_coordinates[idx]
+                position_by_node[action_begin][0] = x_coordinates[idx]
+
+
 # pylint: disable-next=too-many-locals, too-many-branches
 def _distribute_vertically(
     pathway_map: PathwayMap,
     root_action_begin: ActionBegin,
     position_by_node: dict[ActionBegin | ActionEnd, np.ndarray],
+    overlapping_lines_spread: float,
 ) -> None:
 
     action_end = pathway_map.action_end(root_action_begin)
@@ -438,9 +484,14 @@ def _distribute_vertically(
         assert np.isnan(position_by_node[action_end][1])
         position_by_node[action_end][1] = y_coordinate
 
+    if overlapping_lines_spread > 0:
+        _spread_vertically(pathway_map, position_by_node, overlapping_lines_spread)
+
 
 def _layout(
     pathway_map: PathwayMap,
+    *,
+    overlapping_lines_spread: float,
 ) -> dict[ActionBegin | ActionEnd, np.ndarray]:
     """
     Layout that replicates the pathway map layout of the original (pre-2024) pathway generator
@@ -460,7 +511,7 @@ def _layout(
 
     The graph in the pathway map passed in must contain an attribute called "level_by_action",
     with a numeric value per action, which corresponds with the position in the above mentioned
-    stack.  Low numbers correspond with a high position in the stack (large y-coordinate). Such
+    stack. Low numbers correspond with a high position in the stack (large y-coordinate). Such
     actions will be positioned at the top of the pathway map.
     """
     position_by_node: dict[ActionBegin | ActionEnd, np.ndarray] = {}
@@ -478,7 +529,9 @@ def _layout(
         add_position(position_by_node, root_action_begin, (x_coordinate, 0))
 
         _distribute_horizontally(pathway_map, root_action_begin, position_by_node)
-        _distribute_vertically(pathway_map, root_action_begin, position_by_node)
+        _distribute_vertically(
+            pathway_map, root_action_begin, position_by_node, overlapping_lines_spread
+        )
 
     return position_by_node
 
@@ -497,10 +550,12 @@ def plot(
     if legend_arguments is None:
         legend_arguments = {}
 
+    overlapping_lines_spread: float = arguments.get("overlapping_lines_spread", 0)
+
     classic_pathway_map_plotter(
         axes,
         pathway_map,
-        _layout(pathway_map),
+        _layout(pathway_map, overlapping_lines_spread=overlapping_lines_spread),
         arguments=arguments,
         legend_arguments=legend_arguments,
     )

source/test/ap_test/plot/pathway_map/layout_test.py

@@ -668,7 +668,7 @@ def test_empty(self):
         sequence_graph = SequenceGraph()
         pathway_map = sequence_graph_to_pathway_map(sequence_graph)
         pathway_map.assign_tipping_points({})
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
 
         self.assertEqual(len(positions), 0)
 
@@ -693,7 +693,7 @@ def test_single_period(self):
             }
         )
 
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 4)
 
         self.assert_equal_positions(
@@ -736,7 +736,7 @@ def test_serial_pathway(self):
             }
         )
 
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 8)
 
         self.assert_equal_positions(
@@ -783,7 +783,7 @@ def test_diverging_pathways(self):
             }
         )
 
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 8)
 
         self.assert_equal_positions(
@@ -845,7 +845,7 @@ def test_use_case_01(self):
         paths = list(pathway_map.all_paths())
         self.assertEqual(len(paths), 4)
 
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 24)
 
         self.assert_equal_positions(
@@ -937,7 +937,7 @@ def test_use_case_02(self):
         paths = list(pathway_map.all_paths())
         self.assertEqual(len(paths), 10)
 
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 32)
 
         self.assert_equal_positions(
@@ -1103,7 +1103,7 @@ def test_action_combination01(self):
                 d: 2100,
             }
         )
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 10)
 
         self.assert_equal_positions(
@@ -1159,7 +1159,7 @@ def test_action_combination02(self):
         paths = list(pathway_map.all_paths())
         self.assertEqual(len(paths), 3)
 
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 12)
 
         self.assert_equal_positions(
@@ -1234,7 +1234,7 @@ def test_action_combination03(self):
                 d: 2100,
             }
         )
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 12)
 
         self.assert_equal_positions(
@@ -1309,7 +1309,7 @@ def test_action_combination04(self):
                 d: 2100,
             }
         )
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 10)
 
         self.assert_equal_positions(
@@ -1365,7 +1365,7 @@ def test_action_combination05(self):
         paths = list(pathway_map.all_paths())
         self.assertEqual(len(paths), 3)
 
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 12)
 
         self.assert_equal_positions(
@@ -1422,7 +1422,7 @@ def test_action_combination06(self):
         paths = list(pathway_map.all_paths())
         self.assertEqual(len(paths), 3)
 
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 10)
 
         self.assert_equal_positions(
@@ -1490,7 +1490,7 @@ def test_action_edition_01(self):
                 a2: 2060,
             }
         )
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
         self.assertEqual(len(positions), 8)
 
         self.assert_equal_positions(
@@ -1539,7 +1539,7 @@ def test_vertical_action_order_01(self):
             b c 2040
             """
         pathway_map = configure_pathway_map(actions, sequences)
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
 
         y_coordinates_we_want = {
             "current": 0,
@@ -1568,7 +1568,7 @@ def test_vertical_action_order_02(self):
             current b 2030
             """
         pathway_map = configure_pathway_map(actions, sequences)
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
 
         y_coordinates_we_want = {
             "current": 0,
@@ -1599,7 +1599,7 @@ def test_vertical_action_order_03(self):
             current b 2030
             """
         pathway_map = configure_pathway_map(actions, sequences)
-        positions = classic_layout(pathway_map)
+        positions = classic_layout(pathway_map, overlapping_lines_spread=0)
 
         y_coordinates_we_want = {
             "current": 0,