Add script for visualizing module dependencies as graph (#1471)

* Add script for visualizing module dependencies as graph

* Fix isort import order

src/scripts/dependencies/tlo_module_graph.py

@@ -0,0 +1,82 @@
+"""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)
+    disease_module_subgraph.set_node_defaults(**disease_module_node_defaults)
+    other_module_subgraph.set_node_defaults(**other_module_node_defaults)
+    for name, module_class in module_class_map.items():
+        node = pydot.Node(name)
+        if Metadata.DISEASE_MODULE in module_class.METADATA:
+            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",
+        "Tb",
+    }
+    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)