Doc page fixes

climatecritters/core/forcing.py

@@ -25,11 +25,11 @@
     f   = seq.compile()              # → Forcing
 
     # Register with a model
-    model.register_forcing('S', f, attachment_style='additive', timing='pre')
+    cc.Model.register_forcing('S', f, attachment_style='additive', timing='pre')
 
     # Superpose two indefinite signals
     combined = cc.Forcing(orbital_func) + cc.Forcing(noise_func)
-    model.register_forcing('S0', combined)
+    cc.Model.register_forcing('S0', combined)
 """
 
 from __future__ import annotations

climatecritters/core/model.py

@@ -76,7 +76,7 @@ def _format_value(v):
 class Model:
     """The overarching model structure for ClimateCritters.
 
-    CCModel serves as the archetype/parent class for models within the
+    Model serves as the archetype/parent class for models within the
     ``model_critters`` directory.  It is not meant to be instantiated directly.
 
     Parameter handling
@@ -580,7 +580,7 @@ def sde_noise(self, t, y):
 
     def integrate(self, t_span=None, y0=None, method='RK45', dt=None,
                   output_time=None, run_name=None, kwargs=None):
-        """Integrate the model over a time span and return a :class:`CCOutput`.
+        """Integrate the model over a time span and return an `Output`.
 
         Parameters
         ----------
@@ -608,7 +608,7 @@ def integrate(self, t_span=None, y0=None, method='RK45', dt=None,
             Fixed timestep for ``euler``, ``euler_maruyama``, ``heun_maruyama``,
             ``milstein``, and ``rk4``.  Required for those methods.
         output_time : array-like, optional
-            If provided, the returned ``CCOutput`` is immediately reframed onto
+            If provided, the returned ``Output`` is immediately reframed onto
             this time axis (e.g. to exclude a spin-up period).
             ``output.model_time`` always retains the raw solver grid.
         run_name : str, optional

climatecritters/core/output.py

@@ -1,4 +1,4 @@
-"""CCOutput — container for a single CCModel integration run.
+"""Output — container for a single Model integration run.
 
 Separating run output from model configuration lets the same model instance
 be re-run with different parameters or initial conditions while keeping each
@@ -13,9 +13,9 @@
 
 
 class Output:
-    """Container for the results of one call to ``CCModel.integrate()``.
+    """Container for the results of one call to ``Model.integrate()``.
 
-    ``CCOutput`` carries the full trajectory produced by the solver and
+    ``Output`` carries the full trajectory produced by the solver and
     exposes output-focused operations (noise addition, pyleoclim export,
     time resampling).  Keeping these on the output rather than on the model
     means a single model instance can produce multiple independent outputs

climatecritters/model_critters/box_model.py

@@ -2,13 +2,13 @@
 
 """Generic box-model utilities for ClimateCritters.
 
-This module provides a small declarative layer on top of :class:`CCModel` for
+This module provides a small declarative layer on top of `Model` for
 building simple ODE box models without writing a full bespoke subclass each
 time.
 
 Two styles are supported:
 
-1. Explicit callable tendencies via :class:`BoxModelSpec.register_tendency`
+1. Explicit callable tendencies via `BoxModelSpec.register_tendency`
 2. Automatic box-network assembly via reciprocal exchange and directed
    transport relations
 
@@ -87,7 +87,7 @@ class BoxModelContext:
     The context exposes a compact, box-model-friendly API:
 
     - ``ctx["A"]`` for direct state lookup
-    - ``ctx.param("k")`` for parameters resolved through ``CCModel.get_param``
+    - ``ctx.param("k")`` for parameters resolved through ``Model.get_param``
     - ``ctx.input("R")`` for external prescribed inputs
     - ``ctx.volume("SP")`` and ``ctx.concentration("SP")`` for box-network
       models
@@ -128,7 +128,7 @@ class BoxModelSpec:
     inputs, diagnostics, and either:
 
     - explicit callable tendencies registered via
-      :meth:`register_tendency` / :meth:`register_relations`, or
+      `BoxModelSpec.register_tendency` / `BoxModelSpec.register_relations`, or
     - an automatic box network assembled from volumes, reciprocal exchange,
       and directed transport terms
 
@@ -140,13 +140,13 @@ class BoxModelSpec:
 
     Notes
     -----
-    Call :meth:`validate` (or :meth:`make_boxmodel`) before integrating.
+    Call `BoxModelSpec.validate` (or `make_boxmodel`) before integrating.
     Validation checks that every state variable has a tendency relation
     (explicit mode) or a registered volume (automatic mode).
 
     See also
     --------
-    GenericBoxModel : The ``CCModel`` subclass produced by :meth:`make_boxmodel`.
+    GenericBoxModel : The ``Model`` subclass produced by `make_boxmodel`.
     BoxModelContext : Evaluation context passed to callable tendencies.
 
     Examples
@@ -218,7 +218,7 @@ def register_parameters(self, **parameters):
         """Register default parameter values.
 
         Values may be constants, callables, or ``Forcing``-like objects
-        compatible with ``CCModel.get_param``.
+        compatible with ``Model.get_param``.
         """
         self.parameter_defaults.update(parameters)
         return self
@@ -280,7 +280,7 @@ def register_input(self, name, fallback_param=None):
     def register_tendency(self, state_variable, relation):
         """Register a callable tendency for one state variable.
 
-        ``relation`` must accept a :class:`BoxModelContext` and return the
+        ``relation`` must accept a `BoxModelContext` and return the
         tendency for ``state_variable``.
         """
         self.tendency_relations[str(state_variable)] = relation
@@ -376,7 +376,7 @@ def validate(self):
             raise ValueError(f"Missing tendency relations for state variables: {missing}")
 
     def make_model(self, var_name=None, **parameter_overrides):
-        """Instantiate a :class:`GenericBoxModel` from this spec."""
+        """Instantiate a `GenericBoxModel` from this spec."""
         self.validate()
         return GenericBoxModel(
             self,
@@ -389,9 +389,9 @@ def make_boxmodel(self, var_name=None, **parameter_overrides):
 
 
 class GenericBoxModel(Model):
-    """``CCModel`` subclass produced by :class:`BoxModelSpec`.
+    """``Model`` subclass produced by `BoxModelSpec`.
 
-    Users construct this via :meth:`BoxModelSpec.make_boxmodel` rather than
+    Users construct this via `make_boxmodel` rather than
     instantiating it directly.  The resulting model integrates with
     ``model.integrate(...)``, exports to Pyleoclim via ``output.to_pyleo()``,
     and computes diagnostics from solved history via
@@ -427,7 +427,7 @@ def __init__(self, spec, var_name=None, *args, **kwargs):
             setattr(self, name, value)
 
     def uses_post_history(self):
-        """Route diagnostics through CCModel's post-history hooks."""
+        """Route diagnostics through Model's post-history hooks."""
         return True
 
     def resolve_input(self, name, t, state):

climatecritters/model_critters/damped_spring.py

@@ -111,7 +111,7 @@ def __init__(
         self.params = ()
 
     # ------------------------------------------------------------------
-    # CCModel interface
+    # Model interface
     # ------------------------------------------------------------------
 
     def uses_post_history(self):

climatecritters/model_critters/ebm.py

@@ -11,7 +11,7 @@
 
 # ---------------------------------------------------------------------------
 # Module-level physics helpers
-# All callables comply with the CCModel contract: (t), (t, state), or
+# All callables comply with the Model contract: (t), (t, state), or
 # (t, state, model) with the first positional arg named 't' or 'time'.
 # ---------------------------------------------------------------------------
 
@@ -49,7 +49,7 @@ def OLR_func(pRad=650, ps=1000):
     Returns
     -------
     func : callable
-        A ``(t, state)`` callable compliant with the CCModel parameter
+        A ``(t, state)`` callable compliant with the Model parameter
         contract (see ``contracts/signal_model_contract.md``).  Returns OLR
         in W m⁻².
     """
@@ -93,7 +93,7 @@ def albedo_func1D(t, state, model, *, a2=0.25, alpha_ice=0.6, alpha_0=0.1, T1=26
     """P2-corrected latitudinal albedo using a Legendre polynomial parameterization.
 
     Uses the global-mean temperature to set the base albedo via the same
-    quadratic ice-line transition as :func:`albedo_func`, then adds a
+    quadratic ice-line transition as `albedo_func`, then adds a
     second-order Legendre polynomial correction to capture the equator-to-pole
     gradient.  Requires the model to expose a ``phi`` attribute (degrees).
 
@@ -150,7 +150,7 @@ class EBMBase(Model):
 
     See also
     --------
-    climatecritters.core.CCModel : Base class for all ClimateCritters models.
+    climatecritters.core.Model : Base class for all ClimateCritters models.
     EBM0D : Zero-dimensional EBM subclass.
     EBM1DLat : Latitudinally-resolved diffusive EBM subclass.
     """
@@ -477,7 +477,7 @@ def __init__(self, var_name='ebm1d_lat', grid_n=50, C=10.0, D=0.55,
     def validate_initial_state(self, y0):
         """Validate and normalize the initial temperature profile.
 
-        Overrides :meth:`CCModel.validate_initial_state` to accept a scalar
+        Overrides `Model.validate_initial_state` to accept a scalar
         initial condition and broadcast it uniformly across the latitude grid.
 
         Parameters
@@ -503,7 +503,7 @@ def validate_initial_state(self, y0):
     def calc_albedo(self, T, t):
         """Compute the latitudinal ice-albedo with a linear transition zone.
 
-        Overrides :meth:`EBMBase.calc_albedo`.  Each grid point is assigned
+        Overrides `EBMBase.calc_albedo`.  Each grid point is assigned
         an albedo based on local temperature: 0.6 below -10 °C, 0.3 above
         0 °C, and a linear blend in between.
 
@@ -533,7 +533,7 @@ def calc_albedo(self, T, t):
     def calc_OLR(self, T, t):
         """Compute the Budyko linear OLR: ``(A - CO2_forcing) + B * T``.
 
-        Overrides :meth:`EBMBase.calc_OLR`.  Parameters ``A``, ``B``, and
+        Overrides `EBMBase.calc_OLR`.  Parameters ``A``, ``B``, and
         ``CO2_forcing`` are resolved through ``get_param_value``, so they can
         be time-varying or Forcing objects.
 
@@ -699,7 +699,7 @@ def dydt(self, t, state):
 
         This method has **no side effects**: because ``uses_post_history = True``,
         all output is derived from the full solved trajectory in
-        :meth:`populate_diagnostics_from_history` rather than accumulated here.
+        `EBM1DLat.populate_diagnostics_from_history` rather than accumulated here.
 
         Parameters
         ----------
@@ -725,7 +725,7 @@ def dydt(self, t, state):
     def populate_diagnostics_from_history(self, time, history):
         """Compute diagnostic variables from the full solved trajectory.
 
-        Called automatically by :meth:`CCModel.post_integrate` after the
+        Called automatically by `Model.post_integrate` after the
         solver completes.  Populates ``self.diagnostic_variables`` with the
         global-mean temperature and ice-line latitude at every timestep.
 

climatecritters/model_critters/enso_recharge.py

@@ -9,8 +9,8 @@ def seasonal_forcing(A=0.5, period=6.0):
     """Return a sinusoidal seasonal forcing callable for the ENSO recharge oscillator.
 
     The returned function computes ``A * sin(2π t / period)`` and can be
-    wrapped in a :class:`~climatecritters.core.Forcing` or passed directly to
-    :meth:`~climatecritters.core.CCModel.register_forcing`::
+    wrapped in a `Forcing` or passed directly to
+    `Model.register_forcing`::
 
         import climatecritters as cc
         from climatecritters.model_critters.enso_recharge import (
@@ -64,7 +64,7 @@ class ENSORechargeOscillator(Model):
     where ``b = b0*mu`` and ``R = gamma*b - c``.
 
     Seasonal or any other external forcing is added through the standard
-    :meth:`~climatecritters.core.CCModel.register_forcing` interface::
+    `Model.register_forcing` interface::
 
         from climatecritters.utils.forcing import create_sinusoid_forcing
 

climatecritters/model_critters/g24.py

@@ -48,7 +48,7 @@ class Model3(Model):
         model.register_forcing('insolation', cc.Forcing(calc_f))
 
     The internal derivative of forcing ``dfdt`` is computed via
-    :func:`calc_df` by default; supply a custom callable or
+    `calc_df` by default; supply a custom callable or
     ``cc.Forcing`` to override.
 
     Parameter defaults are taken from Ganopolski (2024).  Time-varying

climatecritters/model_critters/melcher25.py

@@ -110,7 +110,7 @@ class Melcher25(Model):
 
     See also
     --------
-    cc.core.CCModel : Base class.
+    cc.core.Model : Base class.
     classify_bistable_states : Reclassify a Δb signal post-hoc without
         re-running the SDE.
 
@@ -267,7 +267,7 @@ def sde_noise(self, t, y):
     def populate_diagnostics_from_history(self, time, history):
         """Classify states and compute thresholds from the full solved trajectory.
 
-        Called automatically by ``CCModel.post_integrate`` after every
+        Called automatically by ``Model.post_integrate`` after every
         ``integrate()`` call. Populates ``diagnostic_variables['states']``
         with the hysteresis classification and sets
         ``self.stadial_threshold`` / ``self.interstadial_threshold``.

climatecritters/model_critters/pendulum.py

@@ -487,7 +487,7 @@ def cartesian_positions(self):
 
 @dataclass
 class PendulumRodBeta:
-    """Properties of one rod in a :class:`MultiPendulumBeta` chain.
+    """Properties of one rod in a `MultiPendulumBeta` chain.
 
     Parameters
     ----------
@@ -504,7 +504,7 @@ class PendulumRodBeta:
     Notes
     -----
     ``forcing`` is resolved at runtime using the same contract as
-    :class:`CCModel` parameters, so constants, ``lambda t: ...`` callables,
+    `Model` parameters, so constants, ``lambda t: ...`` callables,
     ``lambda t, state: ...`` callables, and forcing objects are all accepted.
     """
 
@@ -545,7 +545,7 @@ class MultiPendulumBeta(Model):
     Parameters
     ----------
     rods:
-        Sequence of :class:`PendulumRodBeta` in pivot-to-tip order. Must
+        Sequence of `PendulumRodBeta` in pivot-to-tip order. Must
         contain at least two rods.
     g:
         Gravitational acceleration in m/s^2. Must be > 0.