Renaming datautils to arrayutils (#154)

model/docs/extending_pyrenew.qmd

@@ -127,15 +127,15 @@ InfFeedbackSample = namedtuple(
 )
 ```
 
-The next step is to create the actual class. The bulk of its implementation lies in the function `pyrenew.latent.compute_infections_from_rt_with_feedback()`. We will also use the `pyrenew.datautils.pad_x_to_match_y()` function to ensure the passed vectors match their lengths. The following code-chunk shows most of the implementation of the `InfectionsWithFeedback` class:
+The next step is to create the actual class. The bulk of its implementation lies in the function `pyrenew.latent.compute_infections_from_rt_with_feedback()`. We will also use the `pyrenew.arrayutils.pad_x_to_match_y()` function to ensure the passed vectors match their lengths. The following code-chunk shows most of the implementation of the `InfectionsWithFeedback` class:
 
 ```{python}
 #| label: new-model-def
 #| code-line-numbers: true
 # Creating the class
 from pyrenew.metaclass import RandomVariable
 from pyrenew.latent import compute_infections_from_rt_with_feedback
-from pyrenew import datautils as du
+from pyrenew import arrayutils as au
 from jax.typing import ArrayLike
 import jax.numpy as jnp
 
@@ -181,7 +181,7 @@ class InfFeedback(RandomVariable):
         inf_feedback_strength, *_ = self.infection_feedback_strength.sample(
             **kwargs,
         )
-        inf_feedback_strength = du.pad_x_to_match_y(
+        inf_feedback_strength = au.pad_x_to_match_y(
             x=inf_feedback_strength, y=Rt, fill_value=inf_feedback_strength[0]
         )
 

model/src/pyrenew/datautils.py → model/src/pyrenew/arrayutils.py

@@ -1,5 +1,5 @@
 """
-Utility functions for data processing.
+Utility functions for processing arrays.
 """
 
 import jax.numpy as jnp

model/src/pyrenew/latent/infectionswithfeedback.py

@@ -5,7 +5,7 @@
 
 import jax.numpy as jnp
 import numpyro as npro
-import pyrenew.datautils as du
+import pyrenew.arrayutils as au
 import pyrenew.latent.infection_functions as inf
 from numpy.typing import ArrayLike
 from pyrenew.metaclass import RandomVariable, _assert_sample_and_rtype
@@ -160,7 +160,7 @@ def sample(
 
         # Making sure inf_feedback_strength spans the Rt length
         if inf_feedback_strength.size == 1:
-            inf_feedback_strength = du.pad_x_to_match_y(
+            inf_feedback_strength = au.pad_x_to_match_y(
                 x=inf_feedback_strength,
                 y=Rt,
                 fill_value=inf_feedback_strength[0],

model/src/pyrenew/model/rtinfectionsrenewalmodel.py

@@ -6,7 +6,7 @@
 from typing import NamedTuple
 
 import jax.numpy as jnp
-import pyrenew.datautils as du
+import pyrenew.arrayutils as au
 from numpy.typing import ArrayLike
 from pyrenew.deterministic import NullObservation
 from pyrenew.metaclass import Model, RandomVariable, _assert_sample_and_rtype
@@ -291,7 +291,7 @@ def sample(
         # is merged.
         # SEE ALSO:
         # https://github.com/CDCgov/multisignal-epi-inference/pull/123#discussion_r1612337288
-        i0 = du.pad_x_to_match_y(x=i0, y=gen_int, fill_value=0.0)
+        i0 = au.pad_x_to_match_y(x=i0, y=gen_int, fill_value=0.0)
 
         # Sampling from the latent process
         latent, *_ = self.sample_infections_latent(

model/src/test/test_datautils.py

@@ -1,29 +1,29 @@
 """
-Tests for the datautils module.
+Tests for the arrayutils module.
 """
 
 import jax.numpy as jnp
-import pyrenew.datautils as du
+import pyrenew.arrayutils as au
 import pytest
 
 
-def test_datautils_pad_to_match():
+def test_arrayutils_pad_to_match():
     """
     Verifies extension when required and error when `fix_y` is True.
     """
 
     x = jnp.array([1, 2, 3])
     y = jnp.array([1, 2])
 
-    x_pad, y_pad = du.pad_to_match(x, y)
+    x_pad, y_pad = au.pad_to_match(x, y)
 
     assert x_pad.size == y_pad.size
     assert x_pad.size == 3
 
     x = jnp.array([1, 2])
     y = jnp.array([1, 2, 3])
 
-    x_pad, y_pad = du.pad_to_match(x, y)
+    x_pad, y_pad = au.pad_to_match(x, y)
 
     assert x_pad.size == y_pad.size
     assert x_pad.size == 3
@@ -33,17 +33,17 @@ def test_datautils_pad_to_match():
 
     # Verify that the function raises an error when `fix_y` is True
     with pytest.raises(ValueError):
-        x_pad, y_pad = du.pad_to_match(x, y, fix_y=True)
+        x_pad, y_pad = au.pad_to_match(x, y, fix_y=True)
 
 
-def test_datautils_pad_x_to_match_y():
+def test_arrayutils_pad_x_to_match_y():
     """
     Verifies extension when required
     """
 
     x = jnp.array([1, 2])
     y = jnp.array([1, 2, 3])
 
-    x_pad = du.pad_x_to_match_y(x, y)
+    x_pad = au.pad_x_to_match_y(x, y)
 
     assert x_pad.size == 3