Update doc

README.md

@@ -4,6 +4,5 @@
 
 - [Developer manual](documentation/develop/index.rst)
 - [User manual](documentation/use/index.rst)
-- [Tester manual](documentation/test/index.rst)
 
 <img src="documentation/use/generator.png"/>

documentation/develop/example/ex_05_sequence_graph/05_plot_serial_sequence_graph.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_sequence_graph as plot
@@ -34,7 +34,7 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
+sequence_graph = SequenceGraph(sequences)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_05_sequence_graph/10_plot_diverging_sequence_graph.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_sequence_graph as plot
@@ -34,7 +34,7 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
+sequence_graph = SequenceGraph(sequences)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_05_sequence_graph/15_plot_converging_sequence_graph.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_sequence_graph as plot
@@ -38,7 +38,7 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
+sequence_graph = SequenceGraph(sequences)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_05_sequence_graph/20_plot_example_sequence_graph.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_sequence_graph as plot
@@ -45,7 +45,7 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
+sequence_graph = SequenceGraph(sequences)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_05_sequence_graph/25_plot_example_sequence_graph.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_sequence_graph as plot
@@ -51,7 +51,7 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
+sequence_graph = SequenceGraph(sequences)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_10_pathway_graph/05_plot_serial_pathway_graph.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_graph
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_pathway_graph as plot
@@ -34,8 +34,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_graph = conversion.sequence_graph_to_pathway_graph(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_graph = sequence_graph_to_pathway_graph(sequence_graph)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_10_pathway_graph/10_plot_diverging_pathway_graph.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_graph
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_pathway_graph as plot
@@ -34,8 +34,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_graph = conversion.sequence_graph_to_pathway_graph(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_graph = sequence_graph_to_pathway_graph(sequence_graph)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_10_pathway_graph/15_plot_converging_pathway_graph.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_graph
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_pathway_graph as plot
@@ -38,8 +38,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_graph = conversion.sequence_graph_to_pathway_graph(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_graph = sequence_graph_to_pathway_graph(sequence_graph)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_10_pathway_graph/20_plot_example_pathway_graph.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_graph
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_pathway_graph as plot
@@ -45,8 +45,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_graph = conversion.sequence_graph_to_pathway_graph(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_graph = sequence_graph_to_pathway_graph(sequence_graph)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_10_pathway_graph/25_plot_example_pathway_graph.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_graph
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_pathway_graph as plot
@@ -51,8 +51,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_graph = conversion.sequence_graph_to_pathway_graph(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_graph = sequence_graph_to_pathway_graph(sequence_graph)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_15_pathway_map/05_plot_serial_pathway_map.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_pathway_map as plot
@@ -34,8 +34,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_15_pathway_map/10_plot_diverging_pathway_map.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_pathway_map as plot
@@ -34,8 +34,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_15_pathway_map/15_plot_converging_pathway_map.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_pathway_map as plot
@@ -38,8 +38,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_15_pathway_map/20_plot_example_pathway_map.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_pathway_map as plot
@@ -45,8 +45,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/develop/example/ex_15_pathway_map/25_plot_example_pathway_map.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import init_axes
 from adaptation_pathways.plot import plot_default_pathway_map as plot
@@ -51,8 +51,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
 
 colour_by_action_name = {
     action.name: colour for action, colour in colour_by_action.items()

documentation/use/example/ex_10_pathway_map/05_plot_serial_pathway_map_classic.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import action_level_by_first_occurrence, init_axes
 from adaptation_pathways.plot import plot_classic_pathway_map as plot
@@ -34,8 +34,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
 
 level_by_action = action_level_by_first_occurrence(sequences)
 colour_by_action_name = {

documentation/use/example/ex_10_pathway_map/10_plot_diverging_pathway_map_classic.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import action_level_by_first_occurrence, init_axes
 from adaptation_pathways.plot import plot_classic_pathway_map as plot
@@ -34,8 +34,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
 
 level_by_action = action_level_by_first_occurrence(sequences)
 colour_by_action_name = {

documentation/use/example/ex_10_pathway_map/15_plot_converging_pathway_map_classic.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import action_level_by_first_occurrence, init_axes
 from adaptation_pathways.plot import plot_classic_pathway_map as plot
@@ -38,8 +38,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
 
 level_by_action = action_level_by_first_occurrence(sequences)
 colour_by_action_name = {

documentation/use/example/ex_10_pathway_map/20_plot_example_pathway_map_classic.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import action_level_by_first_occurrence, init_axes
 from adaptation_pathways.plot import plot_classic_pathway_map as plot
@@ -45,8 +45,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
 
 level_by_action = action_level_by_first_occurrence(sequences)
 colour_by_action_name = {

documentation/use/example/ex_10_pathway_map/25_plot_example_pathway_map_classic.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from adaptation_pathways.graph import conversion
+from adaptation_pathways.graph import SequenceGraph, sequence_graph_to_pathway_map
 from adaptation_pathways.io import text
 from adaptation_pathways.plot import action_level_by_first_occurrence, init_axes
 from adaptation_pathways.plot import plot_classic_pathway_map as plot
@@ -51,8 +51,8 @@
     ),
     actions,
 )
-sequence_graph = conversion.sequences_to_sequence_graph(sequences)
-pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+sequence_graph = SequenceGraph(sequences)
+pathway_map = sequence_graph_to_pathway_map(sequence_graph)
 
 level_by_action = action_level_by_first_occurrence(sequences)
 colour_by_action_name = {