docs update

.github/workflows/docs.yml

@@ -25,5 +25,6 @@ jobs:
           path: .cache
           restore-keys: |
             mkdocs-material-
-      - run: pip install mkdocs-material "mkdocstrings[python]"
-      - run: mkdocs gh-deploy --force
+      - run: pip install mkdocs-material "mkdocstrings[python]" mike
+      - name: Build Docs
+        run: mike deploy --push main

docs/components/composite_ported_objects.md

@@ -1,6 +1,6 @@
 # Defining composite models
 
-A composite model consists of collections of functions and differential equations composed together by [functional substitution](functional_substitution.md) and [variable aggregation](variable_aggregation.md). Composite models in `psymple` are captured by [composite ported objects](../mathematics/ported_objects/#composite-ported-objects).
+A composite model consists of collections of functions and differential equations composed together by [functional substitution](../mathematics/functional_substitution.md) and [variable aggregation](../mathematics/variable_aggregation.md). Composite models in `psymple` are captured by [composite ported objects](../mathematics/ported_objects.md/#composite-ported-objects).
 
 The functions and differential equations to be composed come from ported objects added as children. The ports of these child objects are then connected to the ports of the parent ported object by [directed wires](../mathematics/functional_substitution.md/#implementation-detail) to capture functional substitution, and [variable wires](../mathematics/variable_aggregation.md/#implementation-detail) to capture variable aggregation.
 

docs/components/functional_ported_objects.md

@@ -1,12 +1,12 @@
 # Defining functions
 
-Functions in `psymple` are captured by [functional ported objects](../mathematics/ported_objects/#functional-ported-objects). A system of multivariate functions of the form 
+Functions in `psymple` are captured by [functional ported objects](../mathematics/ported_objects.md/#functional-ported-objects). A system of multivariate functions of the form 
 
 $$
 \underline{y} = \underline{f}(t, \underline{d})
 $$
 
-is captured by a functional ported object with a set of [parameter assignments](../mathematics/variables_parameters/#parameter-assignments) modelling $y_i = f_i(t,\underline{d}_i)$ for each $i$, where $\underline{d}_i \subseteq \underline{d}$.
+is captured by a functional ported object with a set of [parameter assignments](../mathematics/variables_parameters.md/#parameter-assignments) modelling $y_i = f_i(t,\underline{d}_i)$ for each $i$, where $\underline{d}_i \subseteq \underline{d}$.
 
 ## Example
 

docs/components/variable_ported_objects.md

@@ -1,12 +1,12 @@
 # Defining ODEs
 
-Differential equations in `psymple` are captured by [variable ported objects](../mathematics/ported_objects/#variable-ported-objects). A system of differential equations of the form 
+Differential equations in `psymple` are captured by [variable ported objects](../mathematics/ported_objects.md/#variable-ported-objects). A system of differential equations of the form 
 
 $$ 
 \frac{d \underline{x}}{dt} = \underline{f}(\underline{x}, t, \underline{b})
 $$
 
-is captured by a variable ported object with a set of [differential assignments](../mathematics/variables_parameters/#differential-assignments) modelling $\frac{dx_i}{dt} = f_i (\underline{x}, t, \underline{b}_i)$ for each $i$, where $\underline{b}_i \subseteq \underline{b}$. 
+is captured by a variable ported object with a set of [differential assignments](../mathematics/variables_parameters.md/#differential-assignments) modelling $\frac{dx_i}{dt} = f_i (\underline{x}, t, \underline{b}_i)$ for each $i$, where $\underline{b}_i \subseteq \underline{b}$. 
 
 ## Example
 

mkdocs.yml

@@ -1,6 +1,9 @@
 # mkdocs.yml
 site_name: Psymple Docs
 
+repo_url: https://github.com/casasglobal-org/psymple
+repo_name: casasglobal-org/psymple
+
 theme:
   name: "material"
   icon:
@@ -12,6 +15,8 @@ theme:
     - navigation.tabs
     - navigation.tabs.sticky
     - navigation.sections
+    - search.suggest
+    - search.highlight
 
 markdown_extensions:
   - admonition
@@ -31,12 +36,13 @@ markdown_extensions:
   - pymdownx.tabbed:
       alternate_style: true
 
-
 extra_javascript:
   - javascripts/mathjax.js
   - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
 
 plugins:
+- autorefs:
+    resolve_closest: true
 - mkdocstrings:
     handlers:
       python:
@@ -47,6 +53,11 @@ plugins:
           show_root_heading: true
           show_root_full_path: false
           docstring_section_style: spacy
+- search
+
+extra:
+  version:
+    provider: mike
 
 nav:
   - Introduction: index.md

psymple/build/abstract.py

@@ -44,13 +44,13 @@ def __init__(
 
         Args:
             name: a string which must be unique for each `PortedObject` inside a common
-                [`CompositePortedObject`][psymple.ported_objects.CompositePortedObject].
+                [`CompositePortedObject`][psymple.build.CompositePortedObject].
             input_ports: list of input ports to expose. 
-                See [add_input_ports][psymple.ported_objects.abstract.PortedObject.add_input_ports].
+                See [add_input_ports][psymple.build.abstract.PortedObject.add_input_ports].
             output_ports: list of output ports to expose. 
-                See [add_output_ports][psymple.ported_objects.abstract.PortedObject.add_input_ports].
+                See [add_output_ports][psymple.build.abstract.PortedObject.add_input_ports].
             variable_ports: list of variable ports to expose. 
-                See [add_variable_ports][psymple.ported_objects.abstract.PortedObject.add_variable_ports].
+                See [add_variable_ports][psymple.build.abstract.PortedObject.add_variable_ports].
             parsing_locals: a dictionary mapping strings to `sympy` objects.
         """
         self.name = name

psymple/build/ported_objects.py

@@ -210,8 +210,8 @@ def __init__(
     def add_variable_assignments(
         self,
         *assignments: DifferentialAssignment | dict | tuple,
-        create_variable_ports=True,
-        create_input_ports=True,
+        create_variable_ports: bool = True,
+        create_input_ports: bool = True,
     ):
         """
         Add variable assignments to self.
@@ -456,7 +456,7 @@ def add_parameter_assignments(
             self.assignments[parameter_name] = assignment
             self.output_ports[parameter_name] = OutputPort(parameter_name)
 
-    def compile(self, prefix_names=False):
+    def compile(self, prefix_names: bool = False):
         """
         Generate a [`CompiledPortedObject`][psymple.build.ported_objects.CompiledPortedObject] with:
 
@@ -587,7 +587,7 @@ def __init__(
         variable_ports: list[VariablePort | dict | str] = [],
         variable_wires: list[dict | tuple] = [],
         directed_wires: list[dict | tuple] = [],
-        parsing_locals = {},
+        parsing_locals: dict = {},
     ):
         """
         Construct a CompositePortedObject.
@@ -799,7 +799,7 @@ def add_variable_wire(
         Add a variable wire to self.
 
         Args:
-            source_ports: a list of strings identifying variable ports to aggregate 
+            child_ports: a list of strings identifying variable ports to aggregate 
             parent_port: a string identifying the parent variable port of self to identify with
             output_name: a string identifying the aggregation internally if a parent port 
                 is not specified.
@@ -880,7 +880,7 @@ def _get_child(self, name: str):
                 raise KeyError(f"{name} is not a child of {self.name}")
 
 
-    def compile(self, prefix_names=False):
+    def compile(self, prefix_names: bool = False):
         """
         Generate a [`CompiledPortedObject`][psymple.build.ported_objects.CompiledPortedObject] with:
 
@@ -1117,7 +1117,7 @@ def _dump_directed_wires(self):
         ]
         return directed_wires
 
-    def to_data(self):
+    def to_data(self) -> PortedObjectData:
         """
         A dismantler method such that every instance X of `CompositePortedObject`
         can be recreated by calling `X.to_data().to_ported_object()`

psymple/build/system.py

@@ -399,7 +399,7 @@ def __init__(
             ported_object: instance of `PortedObject` or `PortedObjectData defining the system model.
             utility_functions: list of the utility functions available in the system. See documentation
                 for [`add_utility_function`][psymple.build.System.add_utility_function] for acceptable values.
-            system_paramters: list of the system parameters available in the system. See documentation
+            system_parameters: list of the system parameters available in the system. See documentation
                 for [`add_system_paramter`][psymple.build.System.add_system_parameter] for acceptable values.
             time_symbol: The symbol used for the independent variable time in the system.
             compile: If `True` and `ported_object` is provided, then system will be compiled automatically.
@@ -525,7 +525,7 @@ def set_initial_values(self, values: dict[str, int | float]):
         Initial values must be `int` or `float` instances only.
 
         Args:
-            initial_values: a dictionary of `variable: value` pairs where `variable` is the string
+            values: a dictionary of `variable: value` pairs where `variable` is the string
                 identifier of a variable in `self.variables` and `value` is `int` or `float`.
         """
         if not self.compiled:
@@ -584,8 +584,8 @@ def _check_required_parameters(self):
 
     def create_simulation(
         self,
-        name=None,
-        solver="continuous",
+        name: str = None,
+        solver: str = "continuous",
         initial_values: dict = {},
         input_parameters: dict = {},
     ) -> Simulation:

psymple/build/wires.py

@@ -29,8 +29,8 @@ class VariableAggregationWiring:
 
     warning: Warning
         This class should not be instantiated on its own. Instead, use
-        [`psymple.ported_objects.CompositePortedObject.add_variable_wire`][] or 
-        [`psymple.ported_objects.CompositePortedObject.add_wires`][].
+        [`psymple.build.CompositePortedObject.add_variable_wire`][] or 
+        [`psymple.build.CompositePortedObject.add_wires`][].
     """
 
     def __init__(self, child_ports: list[str], parent_port: str, output_name: str):
@@ -63,8 +63,8 @@ class DirectedWire:
 
     warning: Warning
         This class should not be instantiated on its own. Instead, use
-        [`psymple.ported_objects.CompositePortedObject.add_directed_wire`][] or 
-        [`psymple.ported_objects.CompositePortedObject.add_wires`][].
+        [`psymple.build.CompositePortedObject.add_directed_wire`][] or 
+        [`psymple.build.CompositePortedObject.add_wires`][].
     """
 
     def __init__(self, source_port: str, destination_ports: list[str]):