Format files using ruff

pyrenew/datasets/wastewater.py

@@ -4,7 +4,6 @@
 This module loads the package dataset named 'wastewater' and provides functions to manipulate the data. It uses the 'polars' library.
 """
 
-
 from importlib.resources import files
 
 import polars as pl

pyrenew/distutil.py

@@ -6,6 +6,7 @@
 found in renewal equation modeling,
 such as discrete time-to-event distributions
 """
+
 from __future__ import annotations
 
 import jax.numpy as jnp

test/test_forecast.py

@@ -1,7 +1,5 @@
 # numpydoc ignore=GL08
 
-from test.utils import SimpleRt
-
 import jax.numpy as jnp
 import jax.random as jr
 import numpyro
@@ -17,6 +15,7 @@
 from pyrenew.model import RtInfectionsRenewalModel
 from pyrenew.observation import PoissonObservation
 from pyrenew.randomvariable import DistributionalVariable
+from test.utils import SimpleRt
 
 
 def test_forecast():

test/test_integrate_discrete.py

@@ -2,6 +2,7 @@
 Test the integrate_discrete function
 used in DifferencedProcess and elsewhere
 """
+
 import jax
 import jax.numpy as jnp
 import pytest

test/test_latent_admissions.py

@@ -1,7 +1,5 @@
 # numpydoc ignore=GL08
 
-from test.utils import SimpleRt
-
 import jax.numpy as jnp
 import numpy.testing as testing
 import numpyro
@@ -10,6 +8,7 @@
 from pyrenew.deterministic import DeterministicPMF, DeterministicVariable
 from pyrenew.latent import HospitalAdmissions, Infections
 from pyrenew.randomvariable import DistributionalVariable
+from test.utils import SimpleRt
 
 
 def test_admissions_sample():

test/test_latent_infections.py

@@ -1,13 +1,12 @@
 # numpydoc ignore=GL08
 
-from test.utils import SimpleRt
-
 import jax.numpy as jnp
 import numpy.testing as testing
 import numpyro
 import pytest
 
 from pyrenew.latent import Infections
+from test.utils import SimpleRt
 
 
 def test_infections_as_deterministic():

test/test_model_basic_renewal.py

@@ -1,7 +1,5 @@
 # numpydoc ignore=GL08
 
-from test.utils import SimpleRt
-
 import jax.numpy as jnp
 import jax.random as jr
 import numpy as np
@@ -19,6 +17,7 @@
 from pyrenew.model import RtInfectionsRenewalModel
 from pyrenew.observation import PoissonObservation
 from pyrenew.randomvariable import DistributionalVariable
+from test.utils import SimpleRt
 
 
 def test_model_basicrenewal_no_timepoints_or_observations():

test/test_model_hosp_admissions.py

@@ -1,7 +1,5 @@
 # numpydoc ignore=GL08
 
-from test.utils import SimpleRt
-
 import jax.numpy as jnp
 import jax.random as jr
 import numpy as np
@@ -24,6 +22,7 @@
 from pyrenew.model import HospitalAdmissionsModel
 from pyrenew.observation import PoissonObservation
 from pyrenew.randomvariable import DistributionalVariable
+from test.utils import SimpleRt
 
 
 def test_model_hosp_no_timepoints_or_observations():

test/test_predictive.py

@@ -3,8 +3,6 @@
 when no posterior samples are available.
 """
 
-from test.utils import SimpleRt
-
 import jax.numpy as jnp
 import numpyro.distributions as dist
 import pytest
@@ -18,6 +16,7 @@
 from pyrenew.model import RtInfectionsRenewalModel
 from pyrenew.observation import PoissonObservation
 from pyrenew.randomvariable import DistributionalVariable
+from test.utils import SimpleRt
 
 pmf_array = jnp.array([0.25, 0.1, 0.2, 0.45])
 gen_int = DeterministicPMF(name="gen_int", value=pmf_array)

test/test_random_key.py

@@ -3,8 +3,6 @@
 with different random keys behave appropriately.
 """
 
-from test.utils import SimpleRt
-
 import jax.numpy as jnp
 import jax.random as jr
 import numpyro
@@ -20,6 +18,7 @@
 from pyrenew.model import RtInfectionsRenewalModel
 from pyrenew.observation import PoissonObservation
 from pyrenew.randomvariable import DistributionalVariable
+from test.utils import SimpleRt
 
 
 def create_test_model():  # numpydoc ignore=GL08

test/test_scan_rv_plate_compatibility.py

@@ -3,6 +3,7 @@
 classes behave as expected in a
 :func:`numpyro.plate` context.
 """
+
 import jax.numpy as jnp
 import numpyro
 import numpyro.distributions as dist