Graphing property-level dependencies in disease modules (#1475)

* Updated modules so that all INIT_DEPENDENCIES and OPTIONAL_INIT_DEPENDENCIES are declared

* Updated modules so that all INIT_DEPENDENCIES and OPTIONAL_INIT_DEPENDENCIES and ADDITIONAL_DEPENDENCIES are declared

* Updated modules so that all INIT_DEPENDENCIES and OPTIONAL_INIT_DEPENDENCIES and ADDITIONAL_DEPENDENCIES are declared

* Updated modules so that all INIT_DEPENDENCIES and OPTIONAL_INIT_DEPENDENCIES and ADDITIONAL_DEPENDENCIES are declared

* Updated modules so that all INIT_DEPENDENCIES and OPTIONAL_INIT_DEPENDENCIES and ADDITIONAL_DEPENDENCIES are declared

* Updated modules so that all INIT_DEPENDENCIES and OPTIONAL_INIT_DEPENDENCIES and ADDITIONAL_DEPENDENCIES are declared

* Updated modules so that all INIT_DEPENDENCIES and OPTIONAL_INIT_DEPENDENCIES and ADDITIONAL_DEPENDENCIES are declared

* Moved all new dependencies to OPTIONAL_INIT_DEPENDENCIES

* Type

* Typo

* Updated circular dependencies

* Updated circular dependencies

* Changed to additional dependencies

* Added subgraphs

* Graph of properties from disease modules that contribute to other disease modules.

Process:  collects properties from each disease (+lifestyle) module, and compares them to the scripts of the remaining disease (+lifestyle) module.

* Delete src/scripts/longterm_projections/property_dependency_graph.py

Duplicate graph

* isort

* isort

* Changed names of functions to avoid overlap

* Updated docstring

* Initial attempt at creating module-level property graphs

* Fixed typo

* Graphs for each individual module

* Aesthetics - still needs colour

* reduced duplication

* Removed all additional dependencies

* typo

* Moved to get_properties folder

src/scripts/get_properties/module_dependencies_graph.py

@@ -0,0 +1,111 @@
+"""Construct a graph showing dependencies between modules."""
+
+import argparse
+from pathlib import Path
+from typing import Dict, Set
+
+from tlo.dependencies import DependencyGetter, get_all_dependencies, get_module_class_map
+from tlo.methods import Metadata
+
+try:
+    import pydot
+except ImportError:
+    pydot = None
+
+
+def construct_module_dependency_graph(
+    excluded_modules: Set[str],
+    disease_module_node_defaults: Dict,
+    other_module_node_defaults: Dict,
+    get_dependencies: DependencyGetter = get_all_dependencies,
+):
+    """Construct a pydot object representing module dependency graph.
+    :param excluded_modules: Set of ``Module`` subclass names to not included in graph.
+    :param disease_module_node_defaults: Any dot node attributes to apply to by default
+        to disease module nodes.
+    :param other_module_node_defaults: Any dot node attributes to apply to by default
+        to non-disease module nodes.
+    :param get_dependencies:  Function which given a module gets the set of module
+        dependencies. Defaults to extracting all dependencies.
+    :return: Pydot directed graph representing module dependencies.
+    """
+    if pydot is None:
+        raise RuntimeError("pydot package must be installed")
+
+    module_class_map = get_module_class_map(excluded_modules)
+    module_graph = pydot.Dot("modules", graph_type="digraph")
+    disease_module_subgraph = pydot.Subgraph("disease_modules")
+    module_graph.add_subgraph(disease_module_subgraph)
+    other_module_subgraph = pydot.Subgraph("other_modules")
+    module_graph.add_subgraph(other_module_subgraph)
+
+    # Set default styles for nodes
+    disease_module_node_defaults["style"] = "filled"
+    other_module_node_defaults["style"] = "filled"
+
+    for name, module_class in module_class_map.items():
+        # Determine attributes based on module type
+        node_attributes = {}
+
+        if Metadata.DISEASE_MODULE in module_class.METADATA and name.endswith("Cancer"):
+            node_attributes.update(disease_module_node_defaults)
+            node_attributes["color"] = "lightblue"  # Color for disease modules and Cancer
+        else:
+            node_attributes.update(other_module_node_defaults)
+            node_attributes["color"] = "lightgreen"  # Default color for other modules
+
+        # Create the node with determined attributes
+        node = pydot.Node(name, **node_attributes)
+
+        # Add the node to the appropriate subgraph
+        if Metadata.DISEASE_MODULE in module_class.METADATA or name.endswith("Cancer"):
+            disease_module_subgraph.add_node(node)
+        else:
+            other_module_subgraph.add_node(node)
+
+    for key, module in module_class_map.items():
+        for dependency in get_dependencies(module, module_class_map.keys()):
+            if dependency not in excluded_modules:
+                module_graph.add_edge(pydot.Edge(key, dependency))
+
+    return module_graph
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument(
+        "output_file", type=Path, help=(
+            "Path to output graph to. File extension will determine output format - for example: dot, dia, png, svg"
+        )
+    )
+    args = parser.parse_args()
+
+    excluded_modules = {
+        "Mockitis",
+        "ChronicSyndrome",
+        "Skeleton",
+        "AlriPropertiesOfOtherModules",
+        "DiarrhoeaPropertiesOfOtherModules",
+        "DummyHivModule",
+        "SimplifiedBirths",
+        "Demography",
+        "HealthBurden",
+        "SymptomManager",
+        "DummyTbModule",
+        "ImprovedHealthSystemAndCareSeekingScenarioSwitcher",
+        "HealthSeekingBehaviour",
+        "HealthSystem",
+        "Deviance",
+        "SimplifiedPregnancyAndLabour"
+    }
+
+    module_graph = construct_module_dependency_graph(
+        excluded_modules,
+        disease_module_node_defaults={"fontname": "Arial", "shape": "box"},
+        other_module_node_defaults={"fontname": "Arial", "shape": "ellipse"},
+    )
+
+    format = (
+        args.output_file.suffix[1:] if args.output_file.suffix else "raw"
+    )
+    module_graph.write(args.output_file, format=format)