execute workflow with steps and no processes

pyproject.toml

@@ -7,18 +7,17 @@ authors = [
 ]
 license = {text = "MIT"}
 readme = "README.md"
-requires-python = ">=3.10, <4.0"
+requires-python = ">=3.11, <4.0"
 packages = [
     {include = "simple_process_bigraph_runtime"},
     {include = "tests"}
 ]
 dependencies = [
     "process-bigraph (>=0.0.35, <1.0)",
     "typer (>=0.15.3, <1.0)",
-#    "process-bigraph-lang @ git+https://github.com/biosimulations/process-bigraph-lang.git#bind-to-object",
-    "process-bigraph-lang @ ../process-bigraph-lang",
-    "spatio-flux @ git+https://github.com/vivarium-collective/spatio-flux.git",
-    "vivarium-interface (>=0.0.5,<0.0.6)"
+    "process-bigraph-lang @ git+https://github.com/biosimulations/process-bigraph-lang.git#bind-to-object",
+#    "process-bigraph-lang @ ../process-bigraph-lang",
+    "spatio-flux @ git+https://github.com/vivarium-collective/spatio-flux.git"
 ]
 
 [tool.poetry]
@@ -30,6 +29,7 @@ deptry = "^0.23.0"
 mypy = "^1.15.0"
 pre-commit = "^4.2.0"
 tox = "^4.25.0"
+ipython = "^9.2.0"
 
 [build-system]
 requires = ["poetry-core>=2.0.0,<3.0.0"]

src/simple_process_bigraph_runtime/main.py

@@ -7,7 +7,6 @@
 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]
 
 import simple_process_bigraph_runtime.registry.spatio_flux_library as spatioflux
 import simple_process_bigraph_runtime.registry.toy_library as toy
@@ -54,8 +53,6 @@ def playground():
     pass
 
 def generatePythonModel(pblang_path: os.PathLike[str]) -> Model:
-    absolute_path: str = validate_pb_absolute_path(os.path.abspath(pblang_path))
-
     return dsl_adapter.generateModelAst(pblang_path)
 
 def validate_pb_absolute_path(absolute_path: str) -> str:

src/simple_process_bigraph_runtime/registry/spatio_flux_library.py

@@ -1,6 +1,5 @@
 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]
 
 from simple_process_bigraph_runtime.environment.process_bigraph_env import ProcessBigraphEnv
 

src/simple_process_bigraph_runtime/registry/toy_library.py

@@ -3,7 +3,6 @@
 
 from process_bigraph import Process, Step  # type: ignore[import-untyped]
 from process_bigraph.composite import SyncUpdate  # type: ignore[import-untyped]
-from vivarium import Vivarium  # type: ignore[import-untyped]
 
 from simple_process_bigraph_runtime.environment.process_bigraph_env import ProcessBigraphEnv
 

tests/conftest.py

@@ -1,3 +1,4 @@
 from tests.fixtures.model_fixtures import (  # noqa: F401
-    model_path_abc,
+    model_paths_abc_steps,
+    model_paths_abc_processes,
 )

tests/fixtures/data/abc_processes.pblang.json

@@ -0,0 +1,260 @@
+{
+  "obj_type": "Model",
+  "definitions": [],
+  "types": [
+    {
+      "name": "float",
+      "obj_type": "Type",
+      "builtin": "builtin",
+      "superType": null,
+      "default": null,
+      "update": null,
+      "subtypes": []
+    },
+    {
+      "name": "string",
+      "obj_type": "Type",
+      "builtin": "builtin",
+      "superType": null,
+      "default": null,
+      "update": null,
+      "subtypes": []
+    }
+  ],
+  "units": [],
+  "processDefs": [
+    {
+      "name": "add_nums",
+      "obj_type": "ProcessDef",
+      "params": [],
+      "vars": [
+        {
+          "name": "left_hand_addend",
+          "obj_type": "SchemaItem",
+          "type": {
+            "ref": "#/types@0",
+            "ref_text": "float"
+          },
+          "default": null,
+          "unit_ref": null
+        },
+        {
+          "name": "right_hand_addend",
+          "obj_type": "SchemaItem",
+          "type": {
+            "ref": "#/types@0",
+            "ref_text": "float"
+          },
+          "default": null,
+          "unit_ref": null
+        },
+        {
+          "name": "result",
+          "obj_type": "SchemaItem",
+          "type": {
+            "ref": "#/types@0",
+            "ref_text": "float"
+          },
+          "default": null,
+          "unit_ref": null
+        }
+      ],
+      "inputs": [
+        {
+          "ref": "#/processDefs@0/vars@0",
+          "ref_text": "left_hand_addend"
+        },
+        {
+          "ref": "#/processDefs@0/vars@1",
+          "ref_text": "right_hand_addend"
+        }
+      ],
+      "outputs": [
+        {
+          "ref": "#/processDefs@0/vars@2",
+          "ref_text": "result"
+        }
+      ],
+      "updates": [],
+      "python_path": {
+        "obj_type": "PythonPath",
+        "path": [
+          "toy",
+          "AddFloatsProcess"
+        ]
+      }
+    },
+    {
+      "name": "print_result",
+      "obj_type": "ProcessDef",
+      "params": [
+        {
+          "name": "output_file_path",
+          "obj_type": "SchemaItem",
+          "type": {
+            "ref": "#/types@1",
+            "ref_text": "string"
+          },
+          "default": {
+            "val": "~/abc_result.txt"
+          },
+          "unit_ref": null
+        }
+      ],
+      "vars": [
+        {
+          "name": "result",
+          "obj_type": "SchemaItem",
+          "type": {
+            "ref": "#/types@0",
+            "ref_text": "float"
+          },
+          "default": null,
+          "unit_ref": null
+        }
+      ],
+      "inputs": [
+        {
+          "ref": "#/processDefs@0/vars@2",
+          "ref_text": "result"
+        }
+      ],
+      "outputs": [],
+      "updates": [],
+      "python_path": {
+        "obj_type": "PythonPath",
+        "path": [
+          "toy",
+          "SaveFloatToFileStep"
+        ]
+      }
+    }
+  ],
+  "store_defs": [
+    {
+      "name": "left_hand",
+      "obj_type": "StoreDef",
+      "parent": null,
+      "states": [
+        {
+          "name": "left_hand_addend",
+          "obj_type": "SchemaItem",
+          "type": {
+            "ref": "#/types@0",
+            "ref_text": "float"
+          },
+          "default": {
+            "val": 2.07
+          },
+          "unit_ref": null
+        }
+      ]
+    },
+    {
+      "name": "right_hand",
+      "obj_type": "StoreDef",
+      "parent": null,
+      "states": [
+        {
+          "name": "right_hand_addend",
+          "obj_type": "SchemaItem",
+          "type": {
+            "ref": "#/types@0",
+            "ref_text": "float"
+          },
+          "default": {
+            "val": 3.5
+          },
+          "unit_ref": null
+        }
+      ]
+    },
+    {
+      "name": "resulting_calculation",
+      "obj_type": "StoreDef",
+      "parent": null,
+      "states": [
+        {
+          "name": "result",
+          "obj_type": "SchemaItem",
+          "type": {
+            "ref": "#/types@0",
+            "ref_text": "float"
+          },
+          "default": null,
+          "unit_ref": null
+        }
+      ]
+    }
+  ],
+  "compositeDefs": [
+    {
+      "name": "CellComposite",
+      "obj_type": "CompositeDef",
+      "stores": [
+        {
+          "name": "lhs",
+          "obj_type": "Store",
+          "store_def": {
+            "ref": "#/store_defs@0",
+            "ref_text": "left_hand"
+          }
+        },
+        {
+          "name": "rhs",
+          "obj_type": "Store",
+          "store_def": {
+            "ref": "#/store_defs@1",
+            "ref_text": "right_hand"
+          }
+        },
+        {
+          "name": "res",
+          "obj_type": "Store",
+          "store_def": {
+            "ref": "#/store_defs@2",
+            "ref_text": "resulting_calculation"
+          }
+        }
+      ],
+      "processes": [
+        {
+          "name": "addition",
+          "obj_type": "Process",
+          "process_def": {
+            "ref": "#/processDefs@0",
+            "ref_text": "add_nums"
+          },
+          "stores": [
+            {
+              "ref": "#/compositeDefs@0/stores@0",
+              "ref_text": "lhs"
+            },
+            {
+              "ref": "#/compositeDefs@0/stores@1",
+              "ref_text": "rhs"
+            },
+            {
+              "ref": "#/compositeDefs@0/stores@2",
+              "ref_text": "res"
+            }
+          ]
+        },
+        {
+          "name": "printing",
+          "obj_type": "Process",
+          "process_def": {
+            "ref": "#/processDefs@1",
+            "ref_text": "print_result"
+          },
+          "stores": [
+            {
+              "ref": "#/compositeDefs@0/stores@2",
+              "ref_text": "res"
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}