Merge branch 'main' into 426-further-prune-postprocessing-code-specif…

…ically-plot_posterior-and-spread_draws

.github/workflows/website.yaml

@@ -14,41 +14,7 @@ permissions:
   id-token: write
 
 jobs:
-  render-docs:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: quarto-dev/quarto-actions/setup@v2
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-
-      - name: install poetry
-        run: pip install poetry
-
-      - name: install package
-        run: poetry install --with docs
-
-      # This section renders the quarto documents (and the README file)
-      # and moves them to the docs/source/_compiled_qmd directory
-      # which is then uploaded as an artifact.
-      - name: Render documents
-        run: |
-            cd docs
-            poetry run make tutorials_clean
-            poetry run make tutorials_md
-
-      # Upload
-      - name: Upload artifacts
-        uses: actions/upload-artifact@v4
-        with:
-          name: tutorials
-          path: docs/source/tutorials
-
   build:
-    needs: render-docs
     runs-on: ubuntu-latest
     permissions:
       contents: write
@@ -75,17 +41,11 @@ jobs:
       run: |
         cp README.md docs/source/index.md
 
-    # Download the rendered tutorials
-    - name: Download artifacts
-      uses: actions/download-artifact@v4
-      with:
-        name: tutorials
-        path: docs/source/tutorials/
-
     # Building
     - name: Build HTML using Poetry
       run: |
         cd docs
+        poetry run make tutorials_clean
         poetry run make html
 
     # Upload

.pre-commit-config.yaml

@@ -20,20 +20,17 @@ repos:
         language: script
         always_run: true
         files: "docs/source/tutorials/.*(qmd|md)$"
-  - repo: https://github.com/psf/black
-    rev: 23.10.0
-    hooks:
-      - id: black
-        args: ["--line-length", "79"]
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        args: ["--profile", "black", "--line-length", "79"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.0
+    rev: v0.6.8
     hooks:
+      # Sort imports
+      - id: ruff
+        args: ['check', '--select', 'I', '--fix']
+      # Run the linter
       - id: ruff
+      # Run the formatter
+      - id: ruff-format
+        args: ['--line-length', '79']
   - repo: https://github.com/numpy/numpydoc
     rev: v1.7.0
     hooks:

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
@@ -18,6 +16,7 @@
 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
@@ -23,6 +21,7 @@
 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