math-spec-mapping 0.3.17__tar.gz → 0.3.19__tar.gz

{math_spec_mapping-0.3.17/src/math_spec_mapping.egg-info → math_spec_mapping-0.3.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: math-spec-mapping
-Version: 0.3.17
+Version: 0.3.19
 Summary: A library for easy mapping of mathematical specifications.
 Author-email: Sean McOwen <Sean@Block.Science>
 Classifier: Programming Language :: Python :: 3

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 [project]
 name = "math-spec-mapping"
-version = "0.3.17"
+version = "0.3.19"
 authors = [
   { name="Sean McOwen", email="Sean@Block.Science" },
 ]

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Classes/Block.py

@@ -73,7 +73,7 @@ class Block:
         i += 1
         out = 'X{}["{}"]'.format(i, self.name)
         if self.block_type == "Mechanism":
-            for u in self.updates:
+            for u in sorted(self.updates, key=lambda x: x[0].name + "-" + x[1].name):
                 out += "\n"
                 out += "X{} --> {}".format(
                     i,
@@ -172,6 +172,9 @@ class Block:
         out = list(set(out))
         return out
 
+    def __repr__(self):
+        return "<{}>".format(self.name)
+
 
 class ParallelBlock(Block):
     def __init__(self, data: Dict):
@@ -241,7 +244,9 @@ class ParallelBlock(Block):
         elif go_deep == False:
             i += 1
             out = 'X{}["{}"]'.format(i, self.name)
-            for u in self.all_updates:
+            for u in sorted(
+                self.all_updates, key=lambda x: x[0].name + "-" + x[1].name
+            ):
                 out += "\n"
                 out += "X{} --> {}".format(
                     i,
@@ -305,6 +310,7 @@ class ParallelBlock(Block):
             d = domain_map[ix1]
             if len(d) > 0:
                 d_length = len(d)
+                d = ["<a href='{}' class=internal-link>{}</a>".format(x, x) for x in d]
                 d = "\n".join(d)
                 d = '"{}"'.format(d)
                 out += "X{} --{}{}-> X{}".format(domain_i, d, "-" * d_length, ix1)
@@ -434,7 +440,10 @@ class StackBlock(Block):
         elif go_deep == False:
             i += 1
             out = 'X{}["{}"]'.format(i, self.name)
-            for u in self.all_updates:
+
+            for u in sorted(
+                self.all_updates, key=lambda x: x[0].name + "-" + x[1].name
+            ):
                 out += "\n"
                 out += "X{} --> {}".format(
                     i,
@@ -486,6 +495,10 @@ class StackBlock(Block):
                     optional = global_optional
                     if len(d) > 0:
                         d_length = len(d)
+                        d = [
+                            "<a href='{}' class=internal-link>{}</a>".format(x, x)
+                            for x in d
+                        ]
                         d = "\n".join(d)
                         d = '"{}"'.format(d)
                         if optional:

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Classes/MathSpec.py

@@ -33,6 +33,7 @@ class MathSpec:
         ]
         self.stateful_metrics = ms_dict["Stateful Metrics"]
         self.wiring = ms_dict["Wiring"]
+        self.tree = None
         # self.blocks = ms_dict["Blocks"]
         self._load_blocks()
         self._load_components()
@@ -438,7 +439,195 @@ class MathSpec:
 
         self._used_spaces = list(set().union(*self._used_spaces))
         us_names = [y.name for y in self._used_spaces]
-        self._unused_spaces = [self.spaces[x] for x in self.spaces if x not in us_names]
+        self._unused_spaces = [
+            self.spaces[x]
+            for x in self.spaces
+            if x not in us_names and x not in ["Terminating Space", "Empty Space"]
+        ]
+
+        if len(self._unused_spaces) > 0:
+            print("The following spaces are not used: {}".format(self._unused_spaces))
+
+    def _add_spec_tree(self, tree):
+        self.tree = tree
+        for folder in [
+            "StatefulMetrics",
+            "Metrics",
+            "Mechanisms",
+            "BoundaryActions",
+            "Types",
+            "ControlActions",
+            "Displays",
+            "Spaces",
+            "State",
+            "Policies",
+            "Wiring",
+            "Parameters",
+            "Entities",
+        ]:
+            tree = self.tree[folder]
+            if folder == "StatefulMetrics":
+                for component in self.stateful_metrics_map:
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.stateful_metrics_map[component].source_code_location = None
+                    else:
+                        self.stateful_metrics_map[component].source_code_location = (
+                            tree[component]
+                        )
+            elif folder == "Metrics":
+                for component in self.metrics:
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.metrics[component].source_code_location = None
+                    else:
+                        self.metrics[component].source_code_location = tree[component]
+            elif folder == "Mechanisms":
+                for component in self.mechanisms:
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.mechanisms[component].source_code_location = None
+                    else:
+                        self.mechanisms[component].source_code_location = tree[
+                            component
+                        ]
+            elif folder == "BoundaryActions":
+                for component in self.boundary_actions:
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.boundary_actions[component].source_code_location = None
+                    else:
+                        self.boundary_actions[component].source_code_location = tree[
+                            component
+                        ]
+            elif folder == "Types":
+                for component in self.types:
+                    if component not in tree:
+
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.types[component].source_code_location = None
+                    else:
+                        self.types[component].source_code_location = tree[component]
+            elif folder == "ControlActions":
+                for component in self.control_actions:
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.control_actions[component].source_code_location = None
+                    else:
+                        self.control_actions[component].source_code_location = tree[
+                            component
+                        ]
+            elif folder == "Displays":
+
+                for component in self.displays["Wiring"]:
+                    if component["name"] not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component["name"]
+                            )
+                        )
+                        component["Source Code Location"] = None
+                    else:
+                        component["Source Code Location"] = tree[component["name"]]
+            elif folder == "Spaces":
+                for component in self.spaces:
+                    if component in ["Terminating Space", "Empty Space"]:
+                        self.spaces[component].source_code_location = None
+                        continue
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.spaces[component].source_code_location = None
+                    else:
+                        self.spaces[component].source_code_location = tree[component]
+            elif folder == "State":
+                for component in self.state:
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.state[component].source_code_location = None
+                    else:
+                        self.state[component].source_code_location = tree[component]
+            elif folder == "Policies":
+                for component in self.policies:
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.policies[component].source_code_location = None
+                    else:
+                        self.policies[component].source_code_location = tree[component]
+            elif folder == "Wiring":
+                for component in self.wiring:
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.wiring[component].source_code_location = None
+                    else:
+                        self.wiring[component].source_code_location = tree[component]
+            elif folder == "Parameters":
+                for component in self.parameters.parameter_map:
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.parameters.parameter_map[
+                            component
+                        ].source_code_location = None
+                    else:
+                        self.parameters.parameter_map[
+                            component
+                        ].source_code_location = tree[component]
+            elif folder == "Entities":
+                for component in self.entities:
+                    if component not in tree:
+                        print(
+                            "Can't find component code source in {} for {}".format(
+                                folder, component
+                            )
+                        )
+                        self.entities[component].source_code_location = None
+                    else:
+                        self.entities[component].source_code_location = tree[component]
+            else:
+                assert False
 
     def metaprogramming_python_types(self, model_directory, overwrite=False):
         path = model_directory + "/types.py"
@@ -837,6 +1026,14 @@ class MathSpecImplementation:
                     )
                 else:
                     control_actions[ca.name] = opt.implementations["python"]
+
+                for opt_i in [x for x in ca.control_action_options if x != opt]:
+                    if "python" not in opt_i.implementations:
+                        print(
+                            "No python implementation for {} / {}. To fix this, go to Implementations/Python/ControlActions and add {}".format(
+                                ca.name, opt_i.name, opt_i.name
+                            )
+                        )
         return control_actions
 
     def load_boundary_actions(self):
@@ -868,6 +1065,14 @@ class MathSpecImplementation:
                     )
                 else:
                     boundary_actions[ba.name] = opt.implementations["python"]
+
+                for opt_i in [x for x in ba.boundary_action_options if x != opt]:
+                    if "python" not in opt_i.implementations:
+                        print(
+                            "No python implementation for {} / {}. To fix this, go to Implementations/Python/BoundaryActions and add {}".format(
+                                ba.name, opt_i.name, opt_i.name
+                            )
+                        )
         return boundary_actions
 
     def load_mechanisms(self):
@@ -964,6 +1169,14 @@ class MathSpecImplementation:
                     )
                 else:
                     policies[p.name] = opt.implementations["python"]
+            for opt_i in [x for x in p.policy_options if x != opt]:
+                if "python" not in opt_i.implementations:
+                    print(
+                        "No python implementation for {} / {}. To fix this, go to Implementations/Python/Policies and add {}".format(
+                            p.name, opt_i.name, opt_i.name
+                        )
+                    )
+
         return policies
 
     def load_stateful_metrics(self):

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Convenience/starter.py

@@ -33,9 +33,9 @@ def remove_dummy_repo_components(path):
         if "__init__.py" in contents:
             with open(path2 + "/__init__.py", "r") as f:
                 contents = f.read()
-                contents = contents.replace("from .Dummy import metrics_x\n", "")
-                contents = contents.replace("metrics.extend(metrics_x)\n", "")
-                contents = contents.replace("metrics.extend(metrics_x)", "")
+                contents = contents.replace("from .Dummy import dummy_metrics\n", "")
+                contents = contents.replace("metrics.extend(dummy_metrics)\n", "")
+                contents = contents.replace("metrics.extend(dummy_metrics)", "")
             with open(path2 + "/__init__.py", "w") as f:
                 f.write(contents)
 
@@ -46,17 +46,17 @@ def remove_dummy_repo_components(path):
             with open(path2 + "/wiring.py", "r") as f:
                 contents = f.read()
 
-                contents = contents.replace('"Dummy Boundary Wiring 2",\n', "")
-                contents = contents.replace('"Dummy Boundary Wiring 2",', "")
-                contents = contents.replace('"Dummy Boundary Wiring 2"', "")
+                contents = contents.replace('"DUMMY Length-1 Boundary Wiring",\n', "")
+                contents = contents.replace('"DUMMY Length-1 Boundary Wiring",', "")
+                contents = contents.replace('"DUMMY Length-1 Boundary Wiring"', "")
 
-                contents = contents.replace('"Dummy Boundary Wiring",\n', "")
-                contents = contents.replace('"Dummy Boundary Wiring",', "")
-                contents = contents.replace('"Dummy Boundary Wiring"', "")
+                contents = contents.replace('"DUMMY Length-2 Boundary Wiring",\n', "")
+                contents = contents.replace('"DUMMY Length-2 Boundary Wiring",', "")
+                contents = contents.replace('"DUMMY Length-2 Boundary Wiring"', "")
 
-                contents = contents.replace('"Dummy Control Wiring",\n', "")
-                contents = contents.replace('"Dummy Control Wiring",', "")
-                contents = contents.replace('"Dummy Control Wiring"', "")
+                contents = contents.replace('"DUMMY Control Wiring",\n', "")
+                contents = contents.replace('"DUMMY Control Wiring",', "")
+                contents = contents.replace('"DUMMY Control Wiring"', "")
 
             with open(path2 + "/wiring.py", "w") as f:
                 f.write(contents)
@@ -188,6 +188,32 @@ def remove_dummy_repo_components(path):
                 contents = contents.replace("dummy_state", "")
             with open(path2 + "/__init__.py", "w") as f:
                 f.write(contents)
+        contents = os.listdir(path2)
+        if "Global.py" in contents:
+            with open(path2 + "/Global.py", "r") as f:
+                contents = f.read()
+            for x in [
+                """        {
+            "type": "DUMMY Integer Type",
+            "name": "Time",
+            "description": "The clock time",
+            "symbol": None,
+            "domain": None,
+        }""",
+                """        {
+            "type": "Entity Type",
+            "name": "Dummy",
+            "description": "The dummy entity",
+            "symbol": None,
+            "domain": None,
+        }""",
+            ]:
+                contents = contents.replace("{},\n".format(x), "")
+                contents = contents.replace("{}\n".format(x), "")
+                contents = contents.replace("{},".format(x), "")
+                contents = contents.replace("{}".format(x), "")
+            with open(path2 + "/Global.py", "w") as f:
+                f.write(contents)
 
     if "Parameters" in directory_folders:
         path2 = path + "/Parameters"
@@ -257,12 +283,15 @@ def remove_dummy_repo_components(path):
         if "types.py" in contents:
             with open(path2 + "/types.py", "r") as f:
                 contents = f.read()
-                contents = contents.replace(
-                    """    "DummyType1": str,
-    "DummyType2": int,
-    "DummyCompoundType": {"A": "Dummy Type 1", "B": "Dummy Type 2"},""",
-                    "",
-                )
+                for x in [
+                    '"DummyABCDEFType": str',
+                    '"DummyIntegerType": int',
+                    '"DummyDecimalType": float',
+                ]:
+                    contents = contents.replace("{},\n".format(x), "")
+                    contents = contents.replace("{}\n".format(x), "")
+                    contents = contents.replace("{},".format(x), "")
+                    contents = contents.replace("{}".format(x), "")
 
             with open(path2 + "/types.py", "w") as f:
                 f.write(contents)
@@ -271,7 +300,7 @@ def remove_dummy_repo_components(path):
         path2 = path + "/TypeMappings"
         contents = os.listdir(path2)
 
-        if "types.py" in contents:
+        if "types.jl" in contents:
             with open(path2 + "/types.jl", "r") as f:
                 contents = f.read()
                 contents = contents.replace(
@@ -295,11 +324,102 @@ end""",
             with open(path2 + "/types.ts", "r") as f:
                 contents = f.read()
                 contents = contents.replace(
-                    """type DummyType1 = string
-type DummyType2 = number
-type DummyCompoundType = {"A": DummyType1, "B": DummyType2}""",
+                    """type DummyABCDEFType = string""",
+                    "",
+                )
+                contents = contents.replace(
+                    """type DummyIntegerType = number""",
+                    "",
+                )
+                contents = contents.replace(
+                    """type DummyDecimalType = number""",
                     "",
                 )
 
             with open(path2 + "/types.ts", "w") as f:
                 f.write(contents)
+
+    remove_dummy_repo_implementations(path)
+
+
+def remove_implementation_folder(path, folder, component_names, import_statement):
+    path = path + "/" + folder
+    contents = os.listdir(path)
+    if "Dummy.py" in contents:
+        os.remove(path + "/Dummy.py")
+    if "__init__.py" in contents:
+        with open(path + "/__init__.py", "r") as f:
+            contents = f.read()
+            contents = contents.replace(import_statement + "\n", "")
+            contents = contents.replace(import_statement, "")
+            for x in component_names:
+                contents = contents.replace("{},\n".format(x), "")
+                contents = contents.replace("{}\n".format(x), "")
+                contents = contents.replace("{},".format(x), "")
+                contents = contents.replace("{}".format(x), "")
+        with open(path + "/__init__.py", "w") as f:
+            f.write(contents)
+
+
+def remove_dummy_repo_implementations(path):
+    path = path + "/Implementations/Python"
+    directory_folders = os.listdir(path)
+
+    if "BoundaryActions" in directory_folders:
+        remove_implementation_folder(
+            path,
+            "BoundaryActions",
+            [
+                '"Length-1 ABC Equal Weight Option": v1_dummy_boundary',
+                '"DUMMY Length-2 ABC Equal Weight Option": v1_dummy_boundary2',
+                '"DUMMY Length-2 ABC Equal Weight 2 Option": v2_dummy_boundary2',
+            ],
+            "from .Dummy import v1_dummy_boundary, v1_dummy_boundary2, v2_dummy_boundary2",
+        )
+    if "ControlActions" in directory_folders:
+        remove_implementation_folder(
+            path,
+            "ControlActions",
+            [
+                '"DUMMY Length-1 DEF Equal Weight Option": v1_dummy_control',
+                '"DUMMY Length-1 DEF D Probability Option": v2_dummy_control',
+            ],
+            "from .Dummy import v1_dummy_control, v2_dummy_control",
+        )
+    if "Policies" in directory_folders:
+        remove_implementation_folder(
+            path,
+            "Policies",
+            ['"DUMMY Letter Count Policy V1": dummy_letter_count_policy'],
+            "from .Dummy import dummy_letter_count_policy",
+        )
+    if "Mechanisms" in directory_folders:
+        remove_implementation_folder(
+            path,
+            "Mechanisms",
+            [
+                '"DUMMY Update Dummy Entity Mechanism": dummy_update_dummy_entity_mechanism',
+                '"DUMMY Increment Time Mechanism": dummy_increment_time_mechanism',
+                '"DUMMY Log Simulation Data Mechanism": dummy_log_simulation_data_mechanism',
+            ],
+            """from .Dummy import (
+    dummy_update_dummy_entity_mechanism,
+    dummy_increment_time_mechanism,
+    dummy_log_simulation_data_mechanism,
+)""",
+        )
+
+    if "StatefulMetrics" in directory_folders:
+        remove_implementation_folder(
+            path,
+            "StatefulMetrics",
+            ['"DUMMY Nominal Length Stateful Metric": dummy_metric'],
+            """from .Dummy import dummy_metric""",
+        )
+    if "Metrics" in directory_folders:
+        remove_implementation_folder(
+            path,
+            "Metrics",
+            ['"DUMMY Multiplied Length Metric": dummy_multiplied_length_metric'],
+            """from .Dummy import dummy_multiplied_length_metric""",
+        )

math_spec_mapping-0.3.19/src/math_spec_mapping/Load/__init__.py

@@ -0,0 +1 @@
+from .load import load_from_json, load_spec_tree

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Load/action_transmission_channel.py

@@ -50,8 +50,14 @@ def convert_action_transmission_channel(
         data["target"] = ms["Mechanisms"][target]
 
     # Add in called by and called here with origin and target
-    data["origin"].calls.append((data["target"], data["optional"], data["space"]))
-    data["target"].called_by.append((data["origin"], data["optional"], data["space"]))
+    if (data["target"], data["optional"], data["space"]) not in data["origin"].calls:
+        data["origin"].calls.append((data["target"], data["optional"], data["space"]))
+    if (data["origin"], data["optional"], data["space"]) not in data[
+        "target"
+    ].called_by:
+        data["target"].called_by.append(
+            (data["origin"], data["optional"], data["space"])
+        )
 
     # Build the action transmission channel object
     return ActionTransmissionChannel(data)

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Load/boundary_actions.py

@@ -1,6 +1,6 @@
 from typing import Dict
 from ..Classes import BoundaryAction, BoundaryActionOption
-from .general import check_json_keys
+from .general import check_json_keys, check_domain_codomain_spaces
 
 
 def convert_boundary_action(data: Dict, ms: Dict) -> BoundaryAction:
@@ -24,6 +24,8 @@ def convert_boundary_action(data: Dict, ms: Dict) -> BoundaryAction:
         data["name"]
     )
 
+    check_domain_codomain_spaces(data, ms)
+
     if len(data["codomain"]) == 0:
         data["codomain"] = ("Empty Space",)
 

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Load/control_actions.py

@@ -1,6 +1,6 @@
 from typing import Dict
 from ..Classes import ControlAction, ControlActionOption
-from .general import check_json_keys
+from .general import check_json_keys, check_domain_codomain_spaces
 
 
 def convert_control_action(data: Dict, ms: Dict) -> ControlAction:
@@ -25,6 +25,8 @@ def convert_control_action(data: Dict, ms: Dict) -> ControlAction:
         data["name"]
     )
 
+    check_domain_codomain_spaces(data, ms)
+
     if len(data["codomain"]) == 0:
         data["codomain"] = ("Empty Space",)
 

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Load/general.py

@@ -159,3 +159,12 @@ def check_json_keys(json: Dict, check_set_key: str) -> None:
 
 def validate_json_schema(json):
     validate(json, schema)
+
+
+def check_domain_codomain_spaces(json: Dict, ms) -> None:
+    if "domain" in json:
+        for key in json["domain"]:
+            assert key in ms["Spaces"], "{} not in spaces".format(key)
+    if "codomain" in json:
+        for key in json["codomain"]:
+            assert key in ms["Spaces"], "{} not in spaces".format(key)

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Load/load.py

@@ -17,9 +17,10 @@ from .type import load_types, load_type_keys
 from .metrics import load_metrics
 from .displays import load_displays
 from .implementations import load_implementations
+from .spec_tree import load_spec_tree
 
 
-def load_from_json(json: Dict) -> MathSpec:
+def load_from_json(json: Dict, spec_path=None) -> MathSpec:
     """Function to load a math spec from a json format
 
     Args:
@@ -81,4 +82,8 @@ def load_from_json(json: Dict) -> MathSpec:
     for space in ms.spaces.values():
         space.domain_blocks = list(set(space.domain_blocks))
         space.codomain_blocks = list(set(space.codomain_blocks))
+
+    if spec_path:
+        tree = load_spec_tree(spec_path, ms)
+        ms._add_spec_tree(tree)
     return ms

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Load/mechanism.py

@@ -1,6 +1,6 @@
 from typing import Dict
 from ..Classes import Mechanism
-from .general import check_json_keys
+from .general import check_json_keys, check_domain_codomain_spaces
 
 
 def convert_mechanism(data: Dict, ms: Dict) -> Mechanism:
@@ -26,6 +26,8 @@ def convert_mechanism(data: Dict, ms: Dict) -> Mechanism:
     if len(data["domain"]) == 0:
         data["domain"] = ("Empty Space",)
 
+    check_domain_codomain_spaces(data, ms)
+
     # Copy
     data = data.copy()
 

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Load/policy.py

@@ -2,7 +2,7 @@ from typing import Dict
 from ..Classes import Policy, PolicyOption
 
 
-from .general import check_json_keys
+from .general import check_json_keys, check_domain_codomain_spaces
 
 
 def convert_policy_options(data: Dict, ms) -> PolicyOption:
@@ -58,6 +58,7 @@ def convert_policy(data: Dict, ms: Dict) -> Policy:
     assert type(data["domain"]) == tuple, "{} domain is not a tuple".format(
         data["name"]
     )
+    check_domain_codomain_spaces(data, ms)
 
     if len(data["codomain"]) == 0:
         data["codomain"] = ("Empty Space",)

math_spec_mapping-0.3.19/src/math_spec_mapping/Load/spec_tree.py

@@ -0,0 +1,71 @@
+import ast
+import os
+
+
+def load_spec_tree(path, ms):
+    tree = {}
+    for folder in [
+        "StatefulMetrics",
+        "Metrics",
+        "Mechanisms",
+        "BoundaryActions",
+        "Types",
+        "ControlActions",
+        "Displays",
+        "Spaces",
+        "State",
+        "Policies",
+        "Wiring",
+        "Parameters",
+        "Entities",
+    ]:
+        if folder == "StatefulMetrics":
+            keys = ms.get_all_stateful_metric_names()
+        elif folder == "Metrics":
+            keys = ms.metrics.keys()
+        elif folder == "Mechanisms":
+            keys = ms.mechanisms.keys()
+        elif folder == "BoundaryActions":
+            keys = ms.boundary_actions.keys()
+        elif folder == "Types":
+            keys = ms.types.keys()
+        elif folder == "ControlActions":
+            keys = ms.control_actions.keys()
+        elif folder == "Displays":
+            keys = [x["name"] for x in ms.displays["Wiring"]]
+        elif folder == "Spaces":
+            keys = ms.spaces.keys()
+        elif folder == "State":
+            keys = ms.state.keys()
+        elif folder == "Policies":
+            keys = ms.policies.keys()
+        elif folder == "Wiring":
+            keys = ms.wiring.keys()
+        elif folder == "Parameters":
+            keys = ms.parameters.all_parameters
+        elif folder == "Entities":
+            keys = ms.entities.keys()
+        else:
+            assert False
+        keys = list(keys)
+        tree[folder] = {}
+
+        init_path = path + "/" + folder + "/__init__.py"
+        with open(init_path, "r") as file:
+            tree2 = ast.parse(file.read(), filename=init_path)
+            imports = []
+            for node in ast.walk(tree2):
+                if isinstance(node, ast.Import):
+                    for alias in node.names:
+                        imports.append(alias.name)
+                    assert False, "Not implemented for imports that are not import from"
+                elif isinstance(node, ast.ImportFrom):
+                    if node.module:
+                        for name in node.names:
+                            file_path = "{}/{}/{}.py".format(path, folder, node.module)
+                            with open(file_path, "r") as file2:
+                                contents = file2.read()
+                            for key in keys:
+                                if key in contents:
+                                    tree[folder][key] = os.path.abspath(file_path)
+    return tree

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Load/stateful_metrics.py

@@ -40,6 +40,12 @@ def convert_stateful_metric(ms, data: Dict) -> StatefulMetricSet:
                 x[1]
             )
 
+        assert (
+            var["type"] in ms["Types"]
+        ), "{} type referenced by {} is not present in math spec".format(
+            var["type"], var["name"]
+        )
+
         var["implementations"] = {}
         if "python" in ms["Implementations"]:
             if "stateful_metrics" in ms["Implementations"]["python"]:

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Reports/html.py

@@ -169,6 +169,13 @@ cssclasses:
             else:
                 out += symbol3 + "{}".format(var.name) + "\n"
 
+    out += symbol1 + "**Metrics**\n"
+    for name in ms.metrics.keys():
+        if linking:
+            out += symbol2 + "[[{}]]".format(name) + "\n"
+        else:
+            out += symbol2 + "{}".format(name) + "\n"
+
     out += symbol1 + "**Types**\n"
     for name in ms.types.keys():
         if linking:
@@ -221,6 +228,12 @@ cssclasses:
             out += symbol2 + "[[{}]]".format(name) + "\n"
         else:
             out += symbol2 + name + "\n"
+    out += symbol1 + "**Wirings**\n"
+    for name in ms.wiring.keys():
+        if linking:
+            out += symbol2 + "[[{}]]".format(name) + "\n"
+        else:
+            out += symbol2 + name + "\n"
 
     if add_tabbing:
         out = out.split("\n")

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/Reports/markdown.py

@@ -3,7 +3,11 @@ from .state import write_state_section
 from inspect import signature, getsource, getfile
 
 
-def get_source_code(ms, component_type, implementation_name):
+def get_source_code(
+    ms,
+    component_type,
+    implementation_name,
+):
     if implementation_name in ms.implementations["python"][component_type]:
         code = ms.implementations["python"][component_type][implementation_name]
     else:
@@ -55,10 +59,28 @@ def write_entity_markdown_report(ms, path, entity, add_metadata=True):
         out += "### [[{}]]".format(ac.name)
         out += "\n"
 
-    with open("{}/Entities/{}.md".format(path, entity.name), "w") as f:
+    path = "{}/Entities/{}.md".format(path, entity.name)
+    out = write_source_code_block(entity, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
+def write_source_code_block(component, text, path):
+    if hasattr(component, "source_code_location"):
+        file_path = component.source_code_location
+    else:
+        file_path = component["Source Code Location"]
+    if file_path:
+        file_path = os.path.relpath(file_path, path)
+        text += "## Spec Source Code Location\n\n"
+        text += "Spec Path (only works if vault is opened at level including the src folder): [{}]({})".format(
+            file_path, file_path
+        )
+        text += "\n\n"
+    return text
+
+
 def write_state_markdown_report(ms, path, state, add_metadata=True):
     state = ms.state[state]
     if "States" not in os.listdir(path):
@@ -83,7 +105,10 @@ def write_state_markdown_report(ms, path, state, add_metadata=True):
         out += "### [[{}]]".format(ba.name)
         out += "\n"
 
-    with open("{}/States/{}.md".format(path, state.name), "w") as f:
+    path = "{}/States/{}.md".format(path, state.name)
+    out = write_source_code_block(state, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -121,8 +146,11 @@ def write_types_markdown_report(ms, path, t, add_metadata=True):
     out += "## Notes"
     out += "\n\n"
     out += t.notes
+    out += "\n"
 
-    with open("{}/Types/{}.md".format(path, t.name), "w") as f:
+    path = "{}/Types/{}.md".format(path, t.name)
+    out = write_source_code_block(t, out, path)
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -211,9 +239,10 @@ def write_boundary_action_markdown_report(ms, path, boundary_action, add_metadat
 
             out += "\n"
 
-    with open(
-        "{}/Boundary Actions/{}.md".format(path, boundary_action.label), "w"
-    ) as f:
+    path = "{}/Boundary Actions/{}.md".format(path, boundary_action.label)
+    out = write_source_code_block(boundary_action, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -302,7 +331,10 @@ def write_policy_markdown_report(ms, path, policy, add_metadata=True):
 
             out += "\n"
 
-    with open("{}/Policies/{}.md".format(path, policy.label), "w") as f:
+    path = "{}/Policies/{}.md".format(path, policy.label)
+    out = write_source_code_block(policy, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -381,7 +413,10 @@ def write_mechanism_markdown_report(ms, path, mechanism, add_metadata=True):
 
     out += "\n"
 
-    with open("{}/Mechanisms/{}.md".format(path, mechanism.label), "w") as f:
+    path = "{}/Mechanisms/{}.md".format(path, mechanism.label)
+    out = write_source_code_block(mechanism, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -415,19 +450,22 @@ def write_space_markdown_report(ms, path, space, add_metadata=True):
 
     out += "## Blocks with Space in Domain"
     out += "\n"
-    for i, x in enumerate(space.domain_blocks):
+    for i, x in enumerate(sorted(space.domain_blocks, key=lambda x: x.name)):
         out += "{}. [[{}]]".format(i + 1, x.name)
         out += "\n"
     out += "\n"
 
     out += "## Blocks with Space in Codomain"
     out += "\n"
-    for i, x in enumerate(space.codomain_blocks):
+    for i, x in enumerate(sorted(space.codomain_blocks, key=lambda x: x.name)):
         out += "{}. [[{}]]".format(i + 1, x.name)
         out += "\n"
     out += "\n"
 
-    with open("{}/Spaces/{}.md".format(path, space.name), "w") as f:
+    path = "{}/Spaces/{}.md".format(path, space.name)
+    out = write_source_code_block(space, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -510,7 +548,10 @@ def write_control_action_markdown_report(ms, path, control_action, add_metadata=
 
             out += "\n"
 
-    with open("{}/Control Actions/{}.md".format(path, control_action.label), "w") as f:
+    path = "{}/Control Actions/{}.md".format(path, control_action.label)
+    out = write_source_code_block(control_action, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -626,7 +667,10 @@ def write_wiring_markdown_report(ms, path, wiring, add_metadata=True):
         out += "\n"
     out += "\n"
 
-    with open("{}/Wiring/{}.md".format(path, wiring.name), "w") as f:
+    path = "{}/Wiring/{}.md".format(path, wiring.name)
+    out = write_source_code_block(wiring, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -651,7 +695,10 @@ def write_parameter_markdown_report(ms, path, parameter, add_metadata=True):
     out += "Domain: {}\n\n".format(param.domain)
     out += "Parameter Class: {}\n\n".format(param.parameter_class)
 
-    with open("{}/Parameters/{}.md".format(path, param.name), "w") as f:
+    path = "{}/Parameters/{}.md".format(path, param.name)
+    out = write_source_code_block(param, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -687,7 +734,25 @@ def write_stateful_metrics_markdown_report(ms, path, metric, add_metadata=True):
         out += "\n"
     out += "\n"
 
-    with open("{}/Stateful Metrics/{}.md".format(path, metric.name), "w") as f:
+    temp = get_source_code(ms, "stateful_metrics", metric.name)
+    if temp:
+        source_code, file_path = temp
+        file_path = os.path.relpath(file_path, "{}/Stateful Metrics".format(path))
+        out += "## Python Implementation\n"
+        out += source_code
+        out += "\n"
+        out += "Implementation Path (only works if vault is opened at level including the src folder): [{}]({})".format(
+            file_path, file_path
+        )
+        out += "\n"
+
+    out += "\n"
+
+    path = "{}/Stateful Metrics/{}.md".format(path, metric.name)
+
+    out = write_source_code_block(metric, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -742,7 +807,24 @@ def write_metrics_markdown_report(ms, path, metric, add_metadata=True):
         out += "{}. [[{}]]".format(i + 1, x.name)
         out += "\n"
 
-    with open("{}/Metrics/{}.md".format(path, metric.name), "w") as f:
+    temp = get_source_code(ms, "metrics", metric.name)
+    if temp:
+        source_code, file_path = temp
+        file_path = os.path.relpath(file_path, "{}/Metrics".format(path))
+        out += "## Python Implementation\n"
+        out += source_code
+        out += "\n"
+        out += "Implementation Path (only works if vault is opened at level including the src folder): [{}]({})".format(
+            file_path, file_path
+        )
+        out += "\n"
+
+    out += "\n"
+
+    path = "{}/Metrics/{}.md".format(path, metric.name)
+    out = write_source_code_block(metric, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 
@@ -860,7 +942,10 @@ def write_wiring_display_markdown_report(ms, path, wiring, add_metadata=True):
         out += "\n"
     out += "\n"
 
-    with open("{}/Displays/Wiring/{}.md".format(path, wiring["name"]), "w") as f:
+    path = "{}/Displays/Wiring/{}.md".format(path, wiring["name"])
+    out = write_source_code_block(wiring, out, path)
+
+    with open(path, "w") as f:
         f.write(out)
 
 

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping/__init__.py

@@ -1,4 +1,4 @@
-from .Load import load_from_json
+from .Load import load_from_json, load_spec_tree
 from .Reports import (
     create_action_chains_graph,
     write_out_boundary_actions,

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19/src/math_spec_mapping.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: math-spec-mapping
-Version: 0.3.17
+Version: 0.3.19
 Summary: A library for easy mapping of mathematical specifications.
 Author-email: Sean McOwen <Sean@Block.Science>
 Classifier: Programming Language :: Python :: 3

{math_spec_mapping-0.3.17 → math_spec_mapping-0.3.19}/src/math_spec_mapping.egg-info/SOURCES.txt

@@ -43,6 +43,7 @@ src/math_spec_mapping/Load/metrics.py
 src/math_spec_mapping/Load/parameters.py
 src/math_spec_mapping/Load/policy.py
 src/math_spec_mapping/Load/spaces.py
+src/math_spec_mapping/Load/spec_tree.py
 src/math_spec_mapping/Load/state_update_transmission_channels.py
 src/math_spec_mapping/Load/stateful_metrics.py
 src/math_spec_mapping/Load/states.py

math_spec_mapping-0.3.17/src/math_spec_mapping/Load/__init__.py

@@ -1 +0,0 @@
-from .load import load_from_json