fix mypy typing errors

Author: jcschaff

src/simple_process_bigraph_runtime/generation/composite_generator.py

@@ -1,7 +1,7 @@
 from typing import Any, cast
 
 from process_bigraph_lang.dsl.model import Model, StoreDef, ProcessDef, Store, Type
-from vivarium import Vivarium
+from vivarium import Vivarium  # type: ignore[import-untyped]
 
 
 def process_composite(model: Model, assembler: Vivarium):
@@ -32,18 +32,22 @@ def process_composite(model: Model, assembler: Vivarium):
                 store_path_str: str = composite_def.name + "::" + store.name
                 store_path = [composite_def.name, store.name]
 
-                for state_def in store_def.states:
-                    state_type = cast(Type, state_def.type.ref_object)
-                    assert isinstance(state_type, Type)
-                    store_path_to_value_map[store_path_str] = state_def.default.val \
-                        if state_def.default is not None \
-                        else _determine_builtin_default(state_type)
-
-                for state_def in store_def.states:
-                    if state_def.name in input_bindings:
-                        input_bindings[state_def.name] = store_path
-                    if state_def.name in output_bindings:
-                        output_bindings[state_def.name] = store_path
+                if store_def.states:
+                    for state_def in store_def.states:
+                        state_type = cast(Type, state_def.type.ref_object)
+                        assert isinstance(state_type, Type)
+                        store_path_to_value_map[store_path_str] = state_def.default.val \
+                            if state_def.default is not None \
+                            else _determine_builtin_default(state_type)
+
+                    for state_def in store_def.states:
+                        if state_def.name in input_bindings:
+                            input_bindings[state_def.name] = store_path
+                        if state_def.name in output_bindings:
+                            output_bindings[state_def.name] = store_path
+
+            if not process_def.python_path:
+                raise ValueError(f"Process definition {process_def.name} has no python path")
 
             assembler.add_process(
                 name=process.name,

src/simple_process_bigraph_runtime/generation/process_generator.py

@@ -1,11 +1,14 @@
 from process_bigraph_lang.dsl.model import ProcessDef
-from vivarium import Vivarium
+from vivarium import Vivarium  # type: ignore[import-untyped]
+from vivarium.vivarium import VivariumTypes  # type: ignore[import-untyped]
 
 
 def register_process_defs(assembler: Vivarium, process_defs: list[ProcessDef]) -> None:
     # note: does not actually dynamically build processes...yet
-    registry = assembler.core
+    registry: VivariumTypes = assembler.core
     for process_def in process_defs:
+        if not process_def.python_path:
+            raise ValueError(f"Process definition {process_def.name} has no python path")
         python_path = ".".join(process_def.python_path.path)
         if not registry.process_registry.find(python_path):
             raise ValueError(f"Unknown process definition {process_def.name}")

src/simple_process_bigraph_runtime/generation/type_generator.py

@@ -1,5 +1,5 @@
 from process_bigraph_lang.dsl.model import Type
-from vivarium import Vivarium
+from vivarium import Vivarium  # type: ignore[import-untyped]
 
 
 def register_types(assembler: Vivarium, types_to_register: list[Type]):

src/simple_process_bigraph_runtime/generation/unit_generator.py

@@ -1,5 +1,5 @@
 from process_bigraph_lang.dsl.model import Unit
-from vivarium import Vivarium
+from vivarium import Vivarium  # type: ignore[import-untyped]
 
 def register_units(assembler: Vivarium, units_to_register: list[Unit]) -> None:
     for unit_to_register in units_to_register:

src/simple_process_bigraph_runtime/main.py

@@ -1,29 +1,23 @@
-import sys
 import os
-import warnings
+import sys
+from pathlib import Path
 
 import typer
+from bigraph_viz import plot_bigraph  # type: ignore[import-untyped]
+from process_bigraph import Composite, ProcessTypes  # type: ignore[import-untyped]
 from process_bigraph_lang.dsl.model import Model
 from typing_extensions import Annotated
+from vivarium import Vivarium  # type: ignore[import-untyped]
 
-from simple_process_bigraph_runtime.generation.process_generator import register_process_defs
-
-with warnings.catch_warnings(): # Temporary minimal_impact bug in process_bigraphs
-    warnings.simplefilter("ignore", SyntaxWarning)
-    #warnings.filterwarnings("error", category=SyntaxWarning)
-    from process_bigraph import ProcessTypes
+import simple_process_bigraph_runtime.registry.spatio_flux_library as spatioflux
+import simple_process_bigraph_runtime.registry.toy_library as toy
 from simple_process_bigraph_runtime import dsl_adapter
-from vivarium import Vivarium
-from process_bigraph import Composite
-
+from simple_process_bigraph_runtime.generation.composite_generator import process_composite
+from simple_process_bigraph_runtime.generation.process_generator import register_process_defs
 from simple_process_bigraph_runtime.generation.type_generator import register_types
 from simple_process_bigraph_runtime.generation.unit_generator import register_units
-from simple_process_bigraph_runtime.generation.composite_generator import process_composite
-import simple_process_bigraph_runtime.registry.spatio_flux_library as spatioflux
-import simple_process_bigraph_runtime.registry.toy_library as toy
-from bigraph_viz import plot_bigraph
 
-plot_settings = {
+plot_settings: dict[str, str | bool] = {
     'remove_process_place_edges': True
 }
 save_images = True
@@ -37,7 +31,7 @@
 
 @app.command()
 def validate(pblang_path: Annotated[str, typer.Argument(help="Path to the pblang file to validate")]):
-    ast_model: Model = generatePythonModel(pblang_path)
+    ast_model: Model = generatePythonModel(Path(pblang_path))
     _, pb_doc, pb_core = performConversion(ast_model)
     plot_bigraph(state=pb_doc['state'], schema=pb_doc['composition'],
                  core=pb_core,
@@ -48,7 +42,7 @@ def validate(pblang_path: Annotated[str, typer.Argument(help="Path to the pblang
 
 @app.command()
 def execute(duration: float, pblang_path: Annotated[str, typer.Argument(help="Path to the pblang file to validate")]):
-    ast_model: Model = generatePythonModel(pblang_path)
+    ast_model: Model = generatePythonModel(Path(pblang_path))
     pb_composite, _0, _1 = performConversion(ast_model)
 
     pb_composite.run(duration)

src/simple_process_bigraph_runtime/registry/spatio_flux_library.py

@@ -1,8 +1,7 @@
-from typing import Any
-from process_bigraph import Process, Composite, ProcessTypes, pp
-from bigraph_schema import default
-from vivarium import Vivarium
-from spatio_flux import processes
+from bigraph_schema import default  # type: ignore[import-untyped]
+from spatio_flux import processes  # type: ignore[import-untyped]
+from vivarium import Vivarium  # type: ignore[import-untyped]
+
 
 def apply_non_negative(schema, current, update, top_schema, top_state, path, core):
     new_value = current + update

src/simple_process_bigraph_runtime/registry/toy_library.py

@@ -1,7 +1,7 @@
 import os.path
 
-from process_bigraph import Process, Step
-from vivarium import Vivarium
+from process_bigraph import Process, Step  # type: ignore[import-untyped]
+from vivarium import Vivarium  # type: ignore[import-untyped]
 
 complex_number = {
     "real" : "float",

tests/test_add.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 from process_bigraph_lang.dsl.model import Model, ProcessDef
-from vivarium import Vivarium
+from vivarium import Vivarium  # type: ignore[import-untyped]
 
 import simple_process_bigraph_runtime.registry.toy_library as toy
 from simple_process_bigraph_runtime.generation.composite_generator import process_composite
@@ -31,11 +31,13 @@ def test_add(model_path_abc: Path) -> None:
     print(core)
 
     add_num: ProcessDef = ast_model.processDefs[0]
+    assert add_num.python_path
     assert ".".join(add_num.python_path.path) == 'toy.AddFloatsRepeatedly'
     assert ".".join(add_num.python_path.path) in core.process_registry.registry
 
     print(core.process_registry.registry)
 
     print_results: ProcessDef = ast_model.processDefs[1]
+    assert print_results.python_path
     assert ".".join(print_results.python_path.path) == 'toy.SaveFloatToFile'
     assert ".".join(print_results.python_path.path) in core.process_registry.registry