From 7e04c9e67dca1303c9d1fa912047587efe5cd9c4 Mon Sep 17 00:00:00 2001
From: gileshd <gileshd@googlemail.com>
Date: Fri, 20 Sep 2024 16:23:45 +0100
Subject: [PATCH] Add further type annotations to arhmm

---
 dynamax/hidden_markov_model/models/arhmm.py | 28 +++++++++++----------
 1 file changed, 15 insertions(+), 13 deletions(-)

diff --git a/dynamax/hidden_markov_model/models/arhmm.py b/dynamax/hidden_markov_model/models/arhmm.py
index e6614e10..b7d1fa61 100644
--- a/dynamax/hidden_markov_model/models/arhmm.py
+++ b/dynamax/hidden_markov_model/models/arhmm.py
@@ -1,8 +1,10 @@
+from typing import NamedTuple, Optional, Tuple, Union
 import jax.numpy as jnp
 import jax.random as jr
 from jax import lax
 from jax.tree_util import tree_map
-from jaxtyping import Float, Array
+from jaxtyping import Int, Float, Array
+
 from dynamax.hidden_markov_model.models.abstractions import HMM, HMMParameterSet, HMMPropertySet
 from dynamax.hidden_markov_model.models.initial import StandardHMMInitialState, ParamsStandardHMMInitialState
 from dynamax.hidden_markov_model.models.transitions import StandardHMMTransitions, ParamsStandardHMMTransitions
@@ -11,7 +13,6 @@
 from dynamax.types import Scalar
 from dynamax.utils.bijectors import RealToPSDBijector
 from tensorflow_probability.substrates import jax as tfp
-from typing import NamedTuple, Optional, Tuple, Union
 
 tfd = tfp.distributions
 tfb = tfp.bijectors
@@ -25,21 +26,22 @@ class ParamsLinearAutoregressiveHMM(NamedTuple):
 
 class LinearAutoregressiveHMMEmissions(LinearRegressionHMMEmissions):
     def __init__(self,
-                 num_states,
-                 emission_dim,
-                 num_lags=1):
+                 num_states: int,
+                 emission_dim: int,
+                 num_lags: int=1):
         self.num_lags = num_lags
         self.emission_dim = emission_dim
         input_dim = num_lags * emission_dim
         super().__init__(num_states, input_dim, emission_dim)
 
     def initialize(self,
-                   key=jr.PRNGKey(0),
-                   method="prior",
-                   emission_weights=None,
-                   emission_biases=None,
-                   emission_covariances=None,
-                   emissions=None):
+                   key: Array=jr.PRNGKey(0),
+                   method: str="prior",
+                   emission_weights: Optional[Float[Array, "num_states emission_dim input_dim"]]=None,
+                   emission_biases: Optional[Float[Array, "num_states emission_dim"]]=None,
+                   emission_covariances: Optional[Float[Array, "num_states emission_dim emission_dim"]]=None,
+                   emissions: Optional[Float[Array, "num_timesteps emission_dim"]]=None
+                   ) -> Tuple[ParamsLinearRegressionHMMEmissions, ParamsLinearRegressionHMMEmissions]:
         if method.lower() == "kmeans":
             assert emissions is not None, "Need emissions to initialize the model with K-Means!"
             from sklearn.cluster import KMeans
@@ -166,7 +168,7 @@ def sample(self,
                key: Array,
                num_timesteps: int,
                prev_emissions: Optional[Float[Array, "num_lags emission_dim"]]=None,
-    ) -> Tuple[Float[Array, "num_timesteps state_dim"], Float[Array, "num_timesteps emission_dim"]]:
+    ) -> Tuple[Int[Array, " num_timesteps"], Float[Array, "num_timesteps emission_dim"]]:
         r"""Sample states $z_{1:T}$ and emissions $y_{1:T}$ given parameters $\theta$.
 
         Args:
@@ -211,7 +213,7 @@ def _step(carry, key):
     def compute_inputs(self,
                        emissions: Float[Array, "num_timesteps emission_dim"],
                        prev_emissions: Optional[Float[Array, "num_lags emission_dim"]]=None
-    ) -> Float[Array, "num_timesteps emission_dim_times_num_lags"]:
+    ) -> Float[Array, "num_timesteps {self.num_lags}*{self.emission_dim}"]:
         r"""Helper function to compute the matrix of lagged emissions.
 
         Args: