Merge branch 'main' into geo_messaging

.vscode/settings.json

@@ -11,12 +11,15 @@
   },
   "files.insertFinalNewline": true,
   "files.trimFinalNewlines": true,
-
+
+  "editor.formatOnSave": true,
   "editor.codeActionsOnSave": {
     "source.organizeImports": "explicit"
   },
-  "editor.defaultFormatter": null,
-  "editor.formatOnSave": true,
+  "notebook.formatOnSave.enabled": true,
+  "notebook.codeActionsOnSave": {
+    "source.organizeImports": "explicit"
+  },
 
   "autopep8.importStrategy": "fromEnvironment",
   "isort.importStrategy": "fromEnvironment",
@@ -36,6 +39,7 @@
     "*_test.py"
   ],
 
+  "editor.defaultFormatter": null,
   "[python]": {
     "editor.detectIndentation": false,
     "editor.insertSpaces": true,

README.md

@@ -31,10 +31,12 @@ python3.11 -m venv .venv
 # activate it (after which `python` should be bound to the venv python)
 source .venv/bin/activate
 
-# then install the project in "editable" mode
-python -m pip install --editable .[dev]
+# then install the project in editable mode
+python -m pip install --editable ".[dev]"
 ```
 
+(The quotes in the last command are necessary on some platforms, but if the quotes give you issues you can also try without them.)
+
 ## Running from the command line
 
 The most basic task epymorph can perform is to run a spatial, compartmental disease simulation and output the time-series data of compartment populations (prevalence) as well as new events (incidence).

doc/devlog/README.md

@@ -35,12 +35,15 @@ This folder is a handy place to put Jupyter notebooks or other documents which h
 | 2023-10-26.ipynb | Tyler | | Describes a major Geo system refactor and introduces new systems. |
 | 2023-11-03-seirs-example.ipynb | Ajay | | Demonstrates the building and running of an SEIRS model. |
 | 2023-11-08.ipynb | Ajay | | Demonstration of using proxy geo to access data in parameter functions. |
+| 2023-11-08-age-ipm.ipynb | Jarom | | Initial prototyping of age-class IPMs. |
 | 2023-11-15.ipynb | Ajay | | Detailed description of parameter functions functionality. |
 | 2023-11-20-adrio-phase-2-demo.ipynb | Trevor | | Demonstrates the refactor work on DynamicGeos and the ADRIO system, and geo cache handling. |
 | 2023-11-22-ipm-probs.ipynb | Tyler | | Analyzing statistical correctness of our IPM processing algorithms. |
 | 2023-12-05.ipynb | Tyler | | A brief tour of changes to epymorph due to the refactor effort. |
 | 2024-01-08.ipynb | Tyler | | Another functional parameters demonstration, revisiting the Bonus Example from 2023-10-10. |
 | 2024-02-06-adrio-demo.ipynb | Trevor | | Demonstrates the ADRIO system using code updated for latest changes. |
+| 2024-02-06.ipynb | Tyler | | Revisiting age-class IPMs, and thinking about modularity of approach. |
+| 2024-02-12.ipynb | Tyler | | Continued age-class IPM work, this time in more than one geo node. |
 
 ## Contributing
 

epymorph/data/mm/flat.movement

@@ -0,0 +1,21 @@
+# This model evenly weights the probability of movement to all other nodes.
+# It uses parameter 'commuter_proportion' to determine how many people should
+# be moving, based on the total normal population of each node.
+
+[move-steps: per-day=2; duration=[1/3, 2/3]]
+
+[predef: function=
+def flat_predef():
+    ones = np.ones((dim.nodes, dim.nodes))
+    np.fill_diagonal(ones, 0)
+    dispersal_kernel = row_normalize(ones)
+    return { 'dispersal_kernel': dispersal_kernel }
+]
+
+# Assume a percentage of the population move around,
+# evenly weighted to all other locations.
+[mtype: days=all; leave=1; duration=0d; return=2; function=
+def flat_movement(t):
+    n_commuters = np.floor(geo['population'] * params['commuter_proportion']).astype(SimDType)
+    return np.multinomial(n_commuters, predef['dispersal_kernel'])
+]

epymorph/engine/context.py

@@ -104,7 +104,7 @@ def _create_attribute_getter(attr: AttributeDef) -> AttributeGetter:
             data_raw = self._get_attribute_value(attr)
             data = attr.shape.adapt(self.dim, data_raw, True)
             if data is None:
-                msg = f"Attribute '{attr.name}' could not be adpated to the required shape."
+                msg = f"Attribute '{attr.name}' could not be adapted to the required shape."
                 raise AttributeException(msg)
             return attr.shape.accessor(data)
 

epymorph/initializer.py

@@ -70,7 +70,7 @@ def _default_compartments(ctx: InitContext) -> NDArray[SimDType]:
 
 def _check_population(ctx: InitContext) -> None:
     try:
-        check_ndarray(ctx.geo['population'], dtype=np.integer, shape=(ctx.dim.nodes,))
+        check_ndarray(ctx.geo['population'], dtype=[np.int64], shape=(ctx.dim.nodes,))
     except KeyError as e:
         raise InitException.for_arg('population', 'No such value in the geo.') from e
     except NumpyTypeError as e:
@@ -95,7 +95,7 @@ def explicit(ctx: InitContext, initials: NDArray[SimDType]) -> NDArray[SimDType]
     return initials.copy()
 
 
-def proportional(ctx: InitContext, ratios: NDArray[np.integer | np.floating]) -> NDArray[SimDType]:
+def proportional(ctx: InitContext, ratios: NDArray[np.int64 | np.float64]) -> NDArray[SimDType]:
     """
     Set all compartments as a proportion of their population according to the geo.
     The parameter array provided to this initializer will be normalized, then multiplied
@@ -107,7 +107,7 @@ def proportional(ctx: InitContext, ratios: NDArray[np.integer | np.floating]) ->
 
     _, N, C, _ = ctx.dim.TNCE
     try:
-        check_ndarray(ratios, dtype=[np.integer, np.floating], shape=[(C,), (N, C)])
+        check_ndarray(ratios, dtype=[np.int64, np.float64], shape=[(C,), (N, C)])
     except NumpyTypeError as e:
         raise InitException.for_arg('ratios') from e
 

epymorph/movement/compile.py

@@ -134,6 +134,18 @@ def visit_Subscript(self, node: ast.Subscript) -> Any:
                 return node
         return self.generic_visit(node)
 
+    def visit_Attribute(self, node: ast.Attribute) -> Any:
+        """Modify references to objects that should be in context."""
+        if isinstance(node.value, ast.Name):
+            if node.value.id in ['dim']:
+                node.value = ast.Attribute(
+                    value=ast.Name(id='ctx', ctx=ast.Load()),
+                    attr=node.value.id,
+                    ctx=ast.Load(),
+                )
+                return node
+        return self.generic_visit(node)
+
     def visit_FunctionDef(self, node: ast.FunctionDef) -> Any:
         """Modify function parameters."""
         new_node = self.generic_visit(node)

epymorph/simulation.py

@@ -217,6 +217,7 @@ def epymorph_namespace() -> dict[str, Any]:
             'concatenate': partial(np.concatenate, dtype=SimDType),
             'sum': partial(np.sum, dtype=SimDType),
             'newaxis': np.newaxis,
+            'fill_diagonal': np.fill_diagonal,
             # numpy math functions
             'radians': np.radians,
             'degrees': np.degrees,

epymorph/util.py

@@ -33,6 +33,13 @@ def call_all(*fs: Callable[[], Any]) -> None:
         f()
 
 
+def or_raise(value: T | None, message: str) -> T:
+    """Enforce that the given value is not None, or else raise an exception."""
+    if value is None:
+        raise Exception(message)
+    return value
+
+
 # collection utilities