math-spec-mapping 0.3.16__py3-none-any.whl → 0.3.18__py3-none-any.whl

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,
@@ -241,7 +241,9 @@ 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 +307,7 @@ 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 +437,10 @@ 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 +492,10 @@ 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/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()
@@ -440,6 +441,178 @@ class MathSpec:
         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]
 
+    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":
+                print("Displays not implemented")
+                # keys = [x["name"] for x in ms.displays["Wiring"]]
+            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"
         if not overwrite:

math_spec_mapping/Convenience/__init__.py

@@ -1,3 +1,8 @@
 # from .documentation import write_top_level_json_description
 from .starter import remove_dummy_repo_components
-from .github import write_scaffold_to_github_issues
+from .github import (
+    write_scaffold_to_github_issues,
+    find_open_issues,
+    create_priority_label_matrix,
+    create_milestone_label_matrix,
+)

math_spec_mapping/Convenience/github.py

@@ -1,5 +1,8 @@
 import os
 import requests
+from github import Github, Auth
+import pandas as pd
+from dotenv import load_dotenv
 
 
 def write_scaffold_to_github_issues(
@@ -32,3 +35,74 @@ def write_scaffold_to_github_issues(
             headers=headers,
             json={"title": issue_name, "body": checklist},
         )
+
+
+def find_open_issues():
+    load_dotenv()
+    g = Github(auth=Auth.Token(os.getenv("GITHUB_TOKEN")))
+    repo = g.get_repo("BlockScience/MSML")
+    open_issues = repo.get_issues(state="open")
+    open_issues = list(open_issues)
+
+    df = pd.DataFrame(
+        [[x.title, x.labels, x.html_url, x.milestone] for x in open_issues],
+        columns=["Name", "Labels", "URL", "Milestone"],
+    )
+    df["Milestone"] = df["Milestone"].apply(lambda x: x.title if x else None)
+    df = df.join(
+        df["Labels"]
+        .apply(lambda x: {y.name: True for y in x})
+        .apply(pd.Series)
+        .fillna(False)
+    )
+
+    empty = df[df["Labels"].apply(lambda x: len(x)) == 0]
+    empty = empty[~empty["URL"].str.contains("MSML/pull")]
+    assert len(empty) == 0, "Some issues do not have labels"
+
+    return df, open_issues
+
+
+def create_priority_label_matrix(df, exclude_milestones=None):
+    if exclude_milestones:
+        df = df[~df["Milestone"].isin(exclude_milestones)]
+    priority_labels = ["High Priority", "Medium Priority", "Low Priority"]
+    labels = list(df.columns[4:])
+    labels = sorted([x for x in labels if x not in priority_labels])
+
+    table = []
+    for label in labels:
+        row = []
+        for priority in priority_labels:
+            row.append(df[(df[priority]) & (df[label])])
+        table.append(row)
+    table = pd.DataFrame(table, index=labels, columns=priority_labels)
+    table = table.applymap(
+        lambda y: "\n".join(
+            y.apply(lambda x: "[{}]({})".format(x["Name"], x["URL"]), axis=1).values
+        )
+    )
+    return table
+
+
+def create_milestone_label_matrix(df, exclude_milestones=None):
+    if exclude_milestones:
+        df = df[~df["Milestone"].isin(exclude_milestones)]
+    priority_labels = ["High Priority", "Medium Priority", "Low Priority"]
+    labels = list(df.columns[4:])
+    labels = sorted([x for x in labels if x not in priority_labels])
+    milestones = sorted(list(df[~pd.isnull(df["Milestone"])]["Milestone"].unique()))
+
+    table = []
+    for label in labels:
+        row = []
+        for milestone in milestones:
+            row.append(df[(df["Milestone"] == milestone) & (df[label])])
+        table.append(row)
+    table = pd.DataFrame(table, index=labels, columns=milestones)
+    table = table.applymap(
+        lambda y: "\n".join(
+            y.apply(lambda x: "[{}]({})".format(x["Name"], x["URL"]), axis=1).values
+        )
+    )
+    return table

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/Load/__init__.py

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

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/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/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 +59,25 @@ 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):
+    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 +102,10 @@ 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 +143,11 @@ 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 +236,10 @@ 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 +328,10 @@ 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 +410,10 @@ 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 +447,22 @@ 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 +545,10 @@ 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 +664,10 @@ 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 +692,10 @@ 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 +731,25 @@ 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 +804,24 @@ 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)
 
 
@@ -788,6 +867,12 @@ def write_state_variables_markdown_reports(ms, path, state, add_metadata=True):
             out += variable.domain
         out += "\n\n"
 
+        out += "Updated By:\n"
+        for i, x in enumerate(sorted(variable.updated_by, key=lambda x: x.name)):
+            out += "{}. [[{}]]".format(i + 1, x.name)
+            out += "\n"
+        out += "\n"
+
         with open(
             "{}/State Variables/{}.md".format(
                 path, "{}-{}".format(state.name, variable.name)

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,
@@ -30,6 +30,12 @@ from .Reports import (
     write_parameter_table_markdown,
 )
 from .schema import schema
-from .Convenience import remove_dummy_repo_components, write_scaffold_to_github_issues
+from .Convenience import (
+    remove_dummy_repo_components,
+    write_scaffold_to_github_issues,
+    find_open_issues,
+    create_priority_label_matrix,
+    create_milestone_label_matrix,
+)
 
 # from .Convenience import write_top_level_json_description

{math_spec_mapping-0.3.16.dist-info → math_spec_mapping-0.3.18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: math-spec-mapping
-Version: 0.3.16
+Version: 0.3.18
 Summary: A library for easy mapping of mathematical specifications.
 Author-email: Sean McOwen <Sean@Block.Science>
 Classifier: Programming Language :: Python :: 3

{math_spec_mapping-0.3.16.dist-info → math_spec_mapping-0.3.18.dist-info}/RECORD

@@ -1,12 +1,12 @@
-math_spec_mapping/__init__.py,sha256=LvuIbfILQf3UGyHympLJyncfnnpZpEyvN5UDOpi8bWw,1140
+math_spec_mapping/__init__.py,sha256=7fGuxoSDYl61z0PZ_PzS6x5P8l174gOzobI9u0aoLVw,1260
 math_spec_mapping/schema.py,sha256=6mrRqzEnTTSXjb19xJ63MBp0KjKH0s7i6TfT4MkAY9k,233
 math_spec_mapping/schema.schema.json,sha256=hJP2TcV5WPFPmx4u_A5U1xtnpkE1LeYaTeYOXadTot0,30916
 math_spec_mapping/Classes/ActionTransmissionChannel.py,sha256=zWMo5QsgPh5WGIWXl-xOrZNMXYJXmK6Vejw1dQvi0og,246
-math_spec_mapping/Classes/Block.py,sha256=x5eYzuWp6C_n1tUVMxECpdYi4w_Tv0NLyxg0m8pHjMo,19602
+math_spec_mapping/Classes/Block.py,sha256=D-UNvG7kYJa3iVgBH9KUaaldnFL4RVjCQQvrjjm00k4,20082
 math_spec_mapping/Classes/BoundaryAction.py,sha256=_rFvEZ4LNxmlM59js4SuQ9n5CgVmITw4YWKs0-q0r-4,560
 math_spec_mapping/Classes/ControlAction.py,sha256=4AzMSA8fbnUf-fGlvMJXHJFbz32G1h1QVWf2yzrXrLA,493
 math_spec_mapping/Classes/Entity.py,sha256=fA0-b128_OHHxfCg4pzqyQV083EYev1HlVpy86S5igg,1226
-math_spec_mapping/Classes/MathSpec.py,sha256=jOWfO5mx_7RjAy4SF9Faiw-tGEhL2HeyzV9lKk0pVDQ,43432
+math_spec_mapping/Classes/MathSpec.py,sha256=GVyRz_a-afJcmj3W5fqqFYlX1YmxpmbjLFdLpFZGN60,51282
 math_spec_mapping/Classes/Mechanism.py,sha256=2sLm3wYBIeTQaMBcsJ9btqIWsbS895Ra8NY6Y9_G_Dg,379
 math_spec_mapping/Classes/Metric.py,sha256=iQhH4g8Z60QlM22nPX9ytGmidOsZSiSs0KjqwmsScwU,636
 math_spec_mapping/Classes/Parameter.py,sha256=ZuJ_w0sChvRElJ4sOnXZ2EV4Ell2xXFulKLjVOpgz2E,1237
@@ -17,11 +17,11 @@ math_spec_mapping/Classes/StateUpdateTransmissionChannel.py,sha256=3hBLvD1lE64Pk
 math_spec_mapping/Classes/StatefulMetric.py,sha256=plMFMAFEk1y2t4DR5lA2SRC9UrYArsx_W33l3mZSdgE,804
 math_spec_mapping/Classes/Type.py,sha256=2KFY8d3cv1PzJJ7SSMHJf1zcfQ3ZbqxotK2KgTaLZdM,289
 math_spec_mapping/Classes/__init__.py,sha256=0zxgOqns_9JybD74HKMVh6aw8ij8WVbfQ4Q_1uWzof0,761
-math_spec_mapping/Convenience/__init__.py,sha256=P8WgrbpJkH08GeyOdhF-ITfT4Yd4ny8QJEvZK0fSljc,164
+math_spec_mapping/Convenience/__init__.py,sha256=BEZr1rXohKAknOa3wjNVx3EvSVxDcfftJsvtSw5mvmQ,264
 math_spec_mapping/Convenience/documentation.py,sha256=1ziWVJznbCUxeAAt03nAdEYtMlXNo5TeedHfgs0vSBU,1625
-math_spec_mapping/Convenience/github.py,sha256=mMOhIH3Nvh_91fNTOPjz1oQq1iDq2m5hNLMhtcrr5FU,1025
-math_spec_mapping/Convenience/starter.py,sha256=9dBKU3EHscut2wA6Nx1XUmehrFIdr4dCjP9V1BbTF6s,12567
-math_spec_mapping/Load/__init__.py,sha256=_ga5nHi7U5rY5lCF36_XI9Qmybq4P8R4m5I5mmjLBk8,33
+math_spec_mapping/Convenience/github.py,sha256=Wddr1FCxcIxaFeiKyvx3mvVDbzjcgTxs4rU8ulc4qXk,3539
+math_spec_mapping/Convenience/starter.py,sha256=dD1R9wcVFZV-BCTflxNkR6Ay6NF1TlVBdIaWmbJwMGE,17379
+math_spec_mapping/Load/__init__.py,sha256=QfHMLatZAKqj4up-LkDL_r42tO7Mo_-qdqPQYLYY5l0,49
 math_spec_mapping/Load/action_transmission_channel.py,sha256=9Wer7g2s5SSOcUYuZ0PqSKUVVnW3EvGQJZNXJTwW__0,2561
 math_spec_mapping/Load/boundary_actions.py,sha256=cDN0pjkkWfYY3HHmgSrD__-weGD4DXElnG8w1pRc5Lc,2933
 math_spec_mapping/Load/control_actions.py,sha256=Y9LeEJuVj2OwxdTfnHZ57UV48j6PYCfyQWux4uXp1Mo,2371
@@ -29,12 +29,13 @@ math_spec_mapping/Load/displays.py,sha256=uQvs0Jhp8-9SXGex8SG3ibxHJu7ahAV3xLeBFb
 math_spec_mapping/Load/entities.py,sha256=Ds7VQY_govWEn1vSHYVrLa8IadSNyOQzaCK18JPYPKk,1289
 math_spec_mapping/Load/general.py,sha256=2q6aGKxXhebiHHTZhtACvM4nWIkTben0o5rXuvfv2Vw,4463
 math_spec_mapping/Load/implementations.py,sha256=a8YvumnyQvrnCo-o52Rv4yU8D7nmkMrV1iIA15fr6Bw,490
-math_spec_mapping/Load/load.py,sha256=oC-CuqbVqqhWw0kK7iiNKexAB_djgVNbjXSQfTsj2FA,2647
+math_spec_mapping/Load/load.py,sha256=Cm1IP_jIzWNGFVPcb1OOfQQYSNgyIfUdT--v1D1dkKE,2797
 math_spec_mapping/Load/mechanism.py,sha256=VRjkR2McsSJh2oq8n9JkeewirdlVjPRA-T5SRSKWPPQ,2293
 math_spec_mapping/Load/metrics.py,sha256=CcVM0_aN-aPnH5_AyEKzFCJGPbgMb0brw5nECsdNVeU,3936
 math_spec_mapping/Load/parameters.py,sha256=W4utm7to3s2fo4z3XgLH0TM1agaIad1qfM2I-lLMua4,1393
 math_spec_mapping/Load/policy.py,sha256=QTIcslHKgdYjjG69cqkJbW20CPvEL-B8R5u51rd2Puo,2697
 math_spec_mapping/Load/spaces.py,sha256=5nJto38BVMED5KuMXOqavYj8gcSTKiNSTdMOOp5ThTA,1186
+math_spec_mapping/Load/spec_tree.py,sha256=4If9twlH30tDFxmZSRkwrRnfLlG_dTWOHbzvVrn42Bg,2481
 math_spec_mapping/Load/state_update_transmission_channels.py,sha256=FJWp5n4HdtHAfof5BUQ6BnRakljatL2h8dWCapaVSc0,2238
 math_spec_mapping/Load/stateful_metrics.py,sha256=3Lq1ZGMaDd5OcGeqR2p5c_znkYw7ETTNPFjUVdZAHKk,2384
 math_spec_mapping/Load/states.py,sha256=3YurI7eTNkN6nrXRFVrc58wH0VfM22XOuWE07HVpR7Y,1365
@@ -45,7 +46,7 @@ math_spec_mapping/Reports/boundary_actions.py,sha256=45BPp4QjWdD-3E9ZWwqgj_nI2-Y
 math_spec_mapping/Reports/control_actions.py,sha256=NksekZKIPFSIkubttFstKFthc5AU9B9PWRLSl9j1wWs,1216
 math_spec_mapping/Reports/general.py,sha256=WOOn6Wlb8M4fsdN49FlKLwOka6vJPQ9aCUy88TL2ki0,1610
 math_spec_mapping/Reports/html.py,sha256=RpyQQON8pDnMmfcyxOsm8UAD5Ad8VKnnW-OyOarTmzA,9711
-math_spec_mapping/Reports/markdown.py,sha256=LCc9pbph0vcDvavCAWt1Z4uF2whnS8sVF87Aiyv4o_M,27592
+math_spec_mapping/Reports/markdown.py,sha256=ErQYnMtl1yxvFVS1Y4AuhifQYEmEab-75HN5kVRFAMo,30114
 math_spec_mapping/Reports/mechanisms.py,sha256=d2Rxt3JBYvqAOAYUynl0buYVoXEHrO8EGq7GK6hK8NA,1322
 math_spec_mapping/Reports/node_map.py,sha256=FdSMDQG16NX6n9sZcH-T5xwsvgjrV9OqBHc9J_VlNK0,3129
 math_spec_mapping/Reports/parameters.py,sha256=-ucL71lolqU0xvV7yb0sXl4pFMRl5tXNWdoBfUjLOaQ,1944
@@ -54,8 +55,8 @@ math_spec_mapping/Reports/spaces.py,sha256=-76hR5wQBv4lsG000ypBJ-OprjsNjI-rNRMYd
 math_spec_mapping/Reports/state.py,sha256=QYeCvX5cHeZBrbvMeDsTqJcUDTuDFJSLvPbasjLspk8,3643
 math_spec_mapping/Reports/tables.py,sha256=O0CNuqh3LMECq5uLjBOoxMUk5hUvkUK660FNnwWUxDY,1505
 math_spec_mapping/Reports/wiring.py,sha256=u9SvKWy6T-WJUEgFI6-zgZanoOaTTs_2YwmEceDLsV8,1618
-math_spec_mapping-0.3.16.dist-info/LICENSE,sha256=ObyEzSw8kgCaFbEfpu1zP4TrcAKLA0xhqHMZZfyh7N0,1069
-math_spec_mapping-0.3.16.dist-info/METADATA,sha256=Bm-QWdPR6T4sJDJpc8omA2pKf8Zd_QdEOtwYSK9wHNc,6498
-math_spec_mapping-0.3.16.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-math_spec_mapping-0.3.16.dist-info/top_level.txt,sha256=AImhn9wgazkdV0a9vfiphtQR8uGe2nq-ZIOp-6yUk9o,18
-math_spec_mapping-0.3.16.dist-info/RECORD,,
+math_spec_mapping-0.3.18.dist-info/LICENSE,sha256=ObyEzSw8kgCaFbEfpu1zP4TrcAKLA0xhqHMZZfyh7N0,1069
+math_spec_mapping-0.3.18.dist-info/METADATA,sha256=hQL3NZ1h1AWYGEQvanepfsOHymyzJbwks-puwjMI0Ho,6498
+math_spec_mapping-0.3.18.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+math_spec_mapping-0.3.18.dist-info/top_level.txt,sha256=AImhn9wgazkdV0a9vfiphtQR8uGe2nq-ZIOp-6yUk9o,18
+math_spec_mapping-0.3.18.dist-info/RECORD,,