From 36bbc68fdc5a27ebfb0f5f8ed3058e20d89ed655 Mon Sep 17 00:00:00 2001
From: gileshd <gileshd@googlemail.com>
Date: Sun, 6 Oct 2024 19:54:33 +0100
Subject: [PATCH] Add further type annotations to categorical glm hmm

---
 .../models/categorical_glm_hmm.py             | 22 ++++++++++++++-----
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/dynamax/hidden_markov_model/models/categorical_glm_hmm.py b/dynamax/hidden_markov_model/models/categorical_glm_hmm.py
index ab30c094..c1127a89 100644
--- a/dynamax/hidden_markov_model/models/categorical_glm_hmm.py
+++ b/dynamax/hidden_markov_model/models/categorical_glm_hmm.py
@@ -5,7 +5,7 @@
 from dynamax.hidden_markov_model.models.abstractions import HMM, HMMEmissions, HMMParameterSet, HMMPropertySet
 from dynamax.hidden_markov_model.models.initial import StandardHMMInitialState, ParamsStandardHMMInitialState
 from dynamax.hidden_markov_model.models.transitions import StandardHMMTransitions, ParamsStandardHMMTransitions
-from dynamax.types import Scalar
+from dynamax.types import IntScalar, Scalar
 import optax
 from typing import NamedTuple, Optional, Tuple, Union
 
@@ -24,9 +24,9 @@ class ParamsCategoricalRegressionHMM(NamedTuple):
 class CategoricalRegressionHMMEmissions(HMMEmissions):
 
     def __init__(self,
-                 num_states,
-                 num_classes,
-                 input_dim,
+                 num_states: int,
+                 num_classes: int,
+                 input_dim: int,
                  m_step_optimizer=optax.adam(1e-2),
                  m_step_num_iters=50):
         """_summary_
@@ -50,7 +50,13 @@ def inputs_shape(self):
     def log_prior(self, params):
         return 0.0
 
-    def initialize(self, key=jr.PRNGKey(0), method="prior", emission_weights=None, emission_biases=None):
+    def initialize(
+            self,
+            key: Array=jr.PRNGKey(0),
+            method: str="prior",
+            emission_weights: Optional[Float[Array, "num_states num_classes input_dim"]]=None,
+            emission_biases: Optional[Float[Array, "num_states num_classes"]]=None,
+            ):
         """Initialize the model parameters and their corresponding properties.
 
         You can either specify parameters manually via the keyword arguments, or you can have
@@ -88,7 +94,11 @@ def initialize(self, key=jr.PRNGKey(0), method="prior", emission_weights=None, e
             biases=ParameterProperties())
         return params, props
 
-    def distribution(self, params, state, inputs=None):
+    def distribution(
+            self,
+            params: ParamsCategoricalRegressionHMMEmissions,
+            state: IntScalar,
+            inputs: Float[Array, " input_dim"]):
         logits = params.weights[state] @ inputs + params.biases[state]
         return tfd.Categorical(logits=logits)