math-spec-mapping 0.4.1.2__py3-none-any.whl → 0.4.3__py3-none-any.whl

math_spec_mapping/Classes/MathSpec.py

@@ -1041,10 +1041,25 @@ using .Spaces: generate_space_type
         blocks,
         state_preperation_functions=[],
         parameter_preperation_functions=[],
+        fixed_parameters=None,
+        fixed_state=None,
     ):
         out = {}
         out["StateSpace"] = self._build_state_space()
+        if fixed_state:
+            for key in fixed_state:
+                assert (
+                    key in out["StateSpace"]
+                ), "The fixed parameter {} is not in the state space".format(key)
+                out["StateSpace"].pop(key)
+
         out["ParameterSpace"] = self._build_parameter_space()
+        if fixed_parameters:
+            for key in fixed_parameters:
+                assert (
+                    key in out["ParameterSpace"]
+                ), "The fixed parameter {} is not in the parameter space".format(key)
+                out["ParameterSpace"].pop(key)
         out["Model"] = cadCADModel(
             self,
             out["StateSpace"],
@@ -1052,6 +1067,8 @@ using .Spaces: generate_space_type
             blocks,
             state_preperation_functions=state_preperation_functions,
             parameter_preperation_functions=parameter_preperation_functions,
+            fixed_parameters=fixed_parameters,
+            fixed_state=fixed_state,
         )
         return out
 
@@ -1079,6 +1096,8 @@ class cadCADModel:
         blocks,
         state_preperation_functions=[],
         parameter_preperation_functions=[],
+        fixed_parameters=None,
+        fixed_state=None,
     ):
         self.ms = ms
         self.state_space = state_space
@@ -1086,10 +1105,18 @@ class cadCADModel:
         self.blocks = blocks
         self.state_preperation_functions = state_preperation_functions
         self.parameter_preperation_functions = parameter_preperation_functions
+        self.fixed_parameters = fixed_parameters
+        self.fixed_state = fixed_state
 
     def create_experiment(
         self, state, params, record_trajectory=False, use_deepcopy=True
     ):
+        if self.fixed_state:
+            for x in self.fixed_state:
+                state[x] = self.fixed_state[x]
+        if self.fixed_parameters:
+            for x in self.fixed_parameters:
+                params[x] = self.fixed_parameters[x]
         return Experiment(
             self,
             state,
@@ -1180,11 +1207,11 @@ class BatchExperiments:
     def step(self):
         for experiment in self.experiments:
             experiment.step()
-    
+
     def run(self, t):
         for experiment in self.experiments:
             experiment.run(t)
-    
+
     @property
     def trajectories(self):
         return [experiment.trajectories for experiment in self.experiments]

math_spec_mapping/Convenience/__init__.py

@@ -6,3 +6,4 @@ from .github import (
     create_priority_label_matrix,
     create_milestone_label_matrix,
 )
+from .cadCAD import get_nested_types

math_spec_mapping/Convenience/cadCAD.py

@@ -0,0 +1,21 @@
+from copy import deepcopy
+from typing import _TypedDictMeta, _GenericAlias
+
+
+def get_underlying_type(data):
+    if type(data) == _GenericAlias:
+        data = [get_underlying_type(x) for x in data.__args__]
+    elif type(data) == _TypedDictMeta:
+        data = get_nested_types(data.__annotations__)
+    return data
+
+
+def get_nested_types(data):
+    data = deepcopy(data)
+    for key in data:
+        if type(data[key]) == _TypedDictMeta:
+            data[key] = get_nested_types(data[key].__annotations__)
+        elif type(data[key]) == _GenericAlias:
+            data[key] = get_underlying_type(data[key])
+
+    return data

math_spec_mapping/Load/load.py

@@ -86,4 +86,8 @@ def load_from_json(json: Dict, spec_path=None) -> MathSpec:
     if spec_path:
         tree = load_spec_tree(spec_path, ms)
         ms._add_spec_tree(tree)
+    else:
+        print(
+            "Add spec path to load_from_json to load spec tree and allow linking to the code in Obsidian"
+        )
     return ms

math_spec_mapping/Reports/__init__.py

@@ -2,7 +2,7 @@ from .node_map import create_action_chains_graph
 from .boundary_actions import write_out_boundary_actions
 from .policies import write_out_policies
 from .mechanisms import write_out_mechanisms
-from .general import load_svg_graphviz
+from .general import load_svg_graphviz, convert_markdown_to_pdf
 from .html import (
     write_basic_report_full,
     write_action_chain_reports,
@@ -32,3 +32,4 @@ from .state import (
     write_initial_state_variables_tables,
 )
 from .parameters import write_parameter_table_markdown
+from .advanced import write_glossary_report

math_spec_mapping/Reports/advanced.py

@@ -0,0 +1,57 @@
+from ..Classes import MathSpec
+from .state import write_state_section
+
+
+def write_glossary_report(ms: MathSpec, directory: str) -> None:
+    """Function to write a report of each component and its description in MSML
+
+    Args:
+        ms (MathSpec): The mathematical specification object
+        directory (str): Directory to put reports into
+    """
+    out = "# Glossary\n\n"
+
+    out += "## Entities\n\n"
+    for entity in ms.entities:
+        if entity == "Global":
+            continue
+        entity = ms.entities[entity]
+        out += "**{}**: {}".format(entity.name, entity.notes)
+        out += "\n\n"
+    out += "\n"
+
+    out += "## State\n\n"
+    states = list(ms.state.keys())
+    states.remove("Global State")
+    states = ["Global State"] + states
+    for state in states:
+        out += "### {}\n\n".format(state)
+        out += write_state_section(ms.state[state])
+        out += "\n\n"
+    out += "\n\n"
+
+    for name, component in [
+        ["Types", ms.types],
+        ["Spaces", ms.spaces],
+        ["Boundary Actions", ms.boundary_actions],
+        ["Control Actions", ms.control_actions],
+        ["Policies", ms.policies],
+        ["Mechanisms", ms.mechanisms],
+        ["Wiring", ms.wiring],
+        ["Parameters", ms.parameters.parameter_map],
+        ["Stateful Metrics", ms.stateful_metrics],
+        ["Metrics", ms.metrics],
+    ]:
+        out += "## {}\n\n".format(name)
+        for key in component:
+            if hasattr(component[key], "description"):
+                desc = component[key].description
+            else:
+                desc = component[key].notes
+
+            out += "**{}**: {}\n\n".format(key, desc)
+        out += "\n\n"
+
+    path = directory + "/Glossary.md"
+    with open(path, "w") as f:
+        f.write(out)

math_spec_mapping/Reports/general.py

@@ -1,5 +1,6 @@
 from graphviz import Digraph
 import os
+import pypandoc
 
 
 def load_svg_graphviz(graph: Digraph, overwrite: bool = False) -> str:
@@ -23,7 +24,7 @@ def load_svg_graphviz(graph: Digraph, overwrite: bool = False) -> str:
         assert "{}.gv".format(graph.name) not in os.listdir(".")
 
     # Render the graph
-    graph.render(directory=".", format='svg')
+    graph.render(directory=".", format="svg")
 
     # Read the svg
     with open("./{}.gv.svg".format(graph.name), "r") as f:
@@ -35,6 +36,7 @@ def load_svg_graphviz(graph: Digraph, overwrite: bool = False) -> str:
 
     return svg
 
+
 def write_header() -> str:
     out = '<p>For explanations of generalized dynamical systems as well as how the mathematical specification library works in detail, please consult the documentation <a href="https://github.com/BlockScience/MSML/tree/main/docs">here</a></p>'
     out += "Graph Legend:<br/>"
@@ -43,4 +45,20 @@ def write_header() -> str:
     out += "Red Square: Policy<br/>"
     out += "Blue Circle: Mechanism<br/>"
     out += "Transparent Circle: State Variable"
-    return out
+    return out
+
+
+def convert_markdown_to_pdf(md_path, pdf_path, pdflatex_path=None):
+    if pdflatex_path:
+        pypandoc.convert_file(
+            md_path,
+            "pdf",
+            outputfile=pdf_path,
+            extra_args=["--pdf-engine={}".format(pdflatex_path)],
+        )
+    else:
+        pypandoc.convert_file(
+            md_path,
+            "pdf",
+            outputfile=pdf_path,
+        )

math_spec_mapping/Reports/markdown.py

@@ -70,7 +70,10 @@ 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"]
+        try:
+            file_path = component["Source Code Location"]
+        except:
+            file_path = None
     if file_path:
         file_path = os.path.relpath(file_path, path)
         text += "## Spec Source Code Location\n\n"

math_spec_mapping/__init__.py

@@ -28,6 +28,8 @@ from .Reports import (
     write_state_variable_table_markdown,
     write_initial_state_variables_tables,
     write_parameter_table_markdown,
+    write_glossary_report,
+    convert_markdown_to_pdf,
 )
 from .schema import schema
 from .Convenience import (
@@ -36,6 +38,7 @@ from .Convenience import (
     find_open_issues,
     create_priority_label_matrix,
     create_milestone_label_matrix,
+    get_nested_types,
 )
 
 # from .Convenience import write_top_level_json_description

{math_spec_mapping-0.4.1.2.dist-info → math_spec_mapping-0.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: math-spec-mapping
-Version: 0.4.1.2
+Version: 0.4.3
 Summary: A library for easy mapping of mathematical specifications.
 Author-email: Sean McOwen <Sean@Block.Science>
 Classifier: Programming Language :: Python :: 3
@@ -15,6 +15,7 @@ Requires-Dist: pandas>=1.4
 Requires-Dist: jsonschema>=4.21.1
 Requires-Dist: PyGithub==2.5.0
 Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: pypandoc>=1.15
 
 # Mathematical Specification Mapping Library (MSML)
 
@@ -30,7 +31,7 @@ One good example is the [wiring report](https://github.com/BlockScience/Predator
 
 ## Installing the library
 
-To install the library, simply pip install by running "pip install math_spec_mapping"
+To install the library, simply pip install by running "pip install math-spec-mapping". The pypi package can be found [here](https://pypi.org/project/math-spec-mapping/).
 
 ## Why MSML?
 

{math_spec_mapping-0.4.1.2.dist-info → math_spec_mapping-0.4.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-math_spec_mapping/__init__.py,sha256=7fGuxoSDYl61z0PZ_PzS6x5P8l174gOzobI9u0aoLVw,1260
+math_spec_mapping/__init__.py,sha256=8MbUccubjXcwkTrwi3AD8uFhokRYPwLXURNTLCnSbRM,1338
 math_spec_mapping/schema.py,sha256=6mrRqzEnTTSXjb19xJ63MBp0KjKH0s7i6TfT4MkAY9k,233
 math_spec_mapping/schema.schema.json,sha256=NyzUy899YR_5Y956ID5HQtgnRBrNTAN6QjrqCyBasRA,31005
 math_spec_mapping/Classes/ActionTransmissionChannel.py,sha256=zWMo5QsgPh5WGIWXl-xOrZNMXYJXmK6Vejw1dQvi0og,246
@@ -6,7 +6,7 @@ math_spec_mapping/Classes/Block.py,sha256=2VOBTPRafmtaLY847tEw3OJTrWNp2d0aSStC_u
 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=rXiAWuIxtdo4myvCNq7qkBPycCGErMQzVvBRq97HrJc,64548
+math_spec_mapping/Classes/MathSpec.py,sha256=i6-iWj7SnGWjqwWxiwZ0ysiiNPGHGsidCEgK1KMgumc,65605
 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
@@ -17,7 +17,8 @@ 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=cA5-5nOfjX6aHzTHM8M6mP5lsS7foumckRu7WDX610M,339
 math_spec_mapping/Classes/__init__.py,sha256=0zxgOqns_9JybD74HKMVh6aw8ij8WVbfQ4Q_1uWzof0,761
-math_spec_mapping/Convenience/__init__.py,sha256=BEZr1rXohKAknOa3wjNVx3EvSVxDcfftJsvtSw5mvmQ,264
+math_spec_mapping/Convenience/__init__.py,sha256=shG4kNPw3z9sSqHmRTLmqvUKMkK1Rq_9XNer2HIWZ9A,301
+math_spec_mapping/Convenience/cadCAD.py,sha256=t-d9FEvfcnjX326eMoCxV6eyE3qVqB0HldDNrrcYquQ,626
 math_spec_mapping/Convenience/documentation.py,sha256=1ziWVJznbCUxeAAt03nAdEYtMlXNo5TeedHfgs0vSBU,1625
 math_spec_mapping/Convenience/github.py,sha256=JMFJWyA3nRIMNYGvn9831BolnBthoa48HhgeZuENZm8,3772
 math_spec_mapping/Convenience/starter.py,sha256=dD1R9wcVFZV-BCTflxNkR6Ay6NF1TlVBdIaWmbJwMGE,17379
@@ -29,7 +30,7 @@ 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=Wjg0ESB80j9UwvoRB_-J8SBKq3KqCFZAKsuKNJFqkE4,4789
 math_spec_mapping/Load/implementations.py,sha256=a8YvumnyQvrnCo-o52Rv4yU8D7nmkMrV1iIA15fr6Bw,490
-math_spec_mapping/Load/load.py,sha256=Cm1IP_jIzWNGFVPcb1OOfQQYSNgyIfUdT--v1D1dkKE,2797
+math_spec_mapping/Load/load.py,sha256=65O8FlLbze5b8WDhbAMHF3B48IfcNijeX4k-WeEy864,2938
 math_spec_mapping/Load/mechanism.py,sha256=6tgISsxc-SXCYS5yxuIqnl0nX__t1k0uj9z0O0E1uC4,2367
 math_spec_mapping/Load/metrics.py,sha256=CcVM0_aN-aPnH5_AyEKzFCJGPbgMb0brw5nECsdNVeU,3936
 math_spec_mapping/Load/parameters.py,sha256=W4utm7to3s2fo4z3XgLH0TM1agaIad1qfM2I-lLMua4,1393
@@ -41,12 +42,13 @@ math_spec_mapping/Load/stateful_metrics.py,sha256=eNXIsNmezVN75L3zMXUl8_JORShm_o
 math_spec_mapping/Load/states.py,sha256=3YurI7eTNkN6nrXRFVrc58wH0VfM22XOuWE07HVpR7Y,1365
 math_spec_mapping/Load/type.py,sha256=pIo3lYAP6sxukvbFTDvaun1lslgShksZy2froNnwAfA,4973
 math_spec_mapping/Load/wiring.py,sha256=l1FhHNFRMKorn1oiRhsuMDsExcXnUmTjqQt5ElE-Bbk,3258
-math_spec_mapping/Reports/__init__.py,sha256=P3IuE1wiM1EO_yCSD73D4O0O6j7aVWmiwpKJM58ISEs,1121
+math_spec_mapping/Reports/__init__.py,sha256=OqmAKio9if1OknLoiTWTpaVq3PzfUCZdIEmZj3wS0z8,1190
+math_spec_mapping/Reports/advanced.py,sha256=Y75ZYPBpr_HOJ64BrsjA5Rc0vmqiiTcEQWx8orOT74Q,1767
 math_spec_mapping/Reports/boundary_actions.py,sha256=45BPp4QjWdD-3E9ZWwqgj_nI2-YdcI2ZZ19_Qv_K7Qk,1410
 math_spec_mapping/Reports/control_actions.py,sha256=NksekZKIPFSIkubttFstKFthc5AU9B9PWRLSl9j1wWs,1216
-math_spec_mapping/Reports/general.py,sha256=WOOn6Wlb8M4fsdN49FlKLwOka6vJPQ9aCUy88TL2ki0,1610
+math_spec_mapping/Reports/general.py,sha256=CSF5DZgZerUZ6Bdnt0mfzM-2QEUwnvC_JeveE7ngtTs,2024
 math_spec_mapping/Reports/html.py,sha256=MCVp_D1LuRoZrHtwzFOJGQviztGeahqsWf3Zue1Yz64,10134
-math_spec_mapping/Reports/markdown.py,sha256=q4dCzH6dDE0TLJ3XS7olUpDfPk8323IEPbT9ki7GEgE,30595
+math_spec_mapping/Reports/markdown.py,sha256=2WYZYzIubtNb-OyZCOK5nS_O9jPOsdwAtMMJJOt-ZDk,30657
 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
@@ -55,8 +57,8 @@ 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-0.4.1.2.dist-info/LICENSE,sha256=ObyEzSw8kgCaFbEfpu1zP4TrcAKLA0xhqHMZZfyh7N0,1069
-math_spec_mapping-0.4.1.2.dist-info/METADATA,sha256=T1RhgXo7hin7MtArY_9EfpZ358cHYt30BhS871mDgPk,6952
-math_spec_mapping-0.4.1.2.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-math_spec_mapping-0.4.1.2.dist-info/top_level.txt,sha256=AImhn9wgazkdV0a9vfiphtQR8uGe2nq-ZIOp-6yUk9o,18
-math_spec_mapping-0.4.1.2.dist-info/RECORD,,
+math_spec_mapping-0.4.3.dist-info/LICENSE,sha256=ObyEzSw8kgCaFbEfpu1zP4TrcAKLA0xhqHMZZfyh7N0,1069
+math_spec_mapping-0.4.3.dist-info/METADATA,sha256=6NFRaAlIrw6h_8802HicQ2P-8KUUrIDAOkWhY6Ys72w,7064
+math_spec_mapping-0.4.3.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+math_spec_mapping-0.4.3.dist-info/top_level.txt,sha256=AImhn9wgazkdV0a9vfiphtQR8uGe2nq-ZIOp-6yUk9o,18
+math_spec_mapping-0.4.3.dist-info/RECORD,,