style: small doc and ci fixes

.github/workflows/deploy.yml

@@ -61,6 +61,6 @@ jobs:
       with:
         body_path: body.md
         tag_name: ${{ github.ref_name }}
-        files: dist/**
+        files: dist/*
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -1,12 +1,13 @@
 ![Logo](https://raw.githubusercontent.com/eckelsjd/uqtils/main/docs/assets/logo.svg)
+
 [![pdm-managed](https://img.shields.io/badge/pdm-managed-blueviolet)](https://pdm-project.org)
 [![Python version](https://img.shields.io/badge/python-3.11+-blue.svg?logo=python&logoColor=cccccc)](https://www.python.org/downloads/)
 [![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-orange.json)](https://github.com/eckelsjd/copier-numpy)
 [![PyPI](https://img.shields.io/pypi/v/uqtils?logo=python&logoColor=%23cccccc)](https://pypi.org/project/uqtils)
 ![build](https://img.shields.io/github/actions/workflow/status/eckelsjd/uqtils/deploy.yml?logo=github)
 ![docs](https://img.shields.io/github/actions/workflow/status/eckelsjd/uqtils/docs.yml?logo=materialformkdocs&logoColor=%2523cccccc&label=docs)
 ![tests](https://img.shields.io/github/actions/workflow/status/eckelsjd/uqtils/tests.yml?logo=github&logoColor=%2523cccccc&label=tests)
-![Code Coverage](https://img.shields.io/badge/coverage-87%25-yellowgreen?logo=codecov)
+![Code Coverage](https://img.shields.io/badge/coverage-88%25-yellowgreen?logo=codecov)
 
 Assorted utilities for uncertainty quantification and scientific computing.
 

src/uqtils/example.py

@@ -1,11 +1,11 @@
 """Examples for using the package."""
 # ruff: noqa: F841
+# ruff: noqa: I001
 
 def normal_example():
     """Sample and plot a normal pdf."""
     # --8<-- [start:normal]
     import numpy as np
-
     import uqtils as uq
 
     ndim = 3
@@ -25,7 +25,6 @@ def gradient_example():
     """Evaluate 1d and multivariate gradients."""
     # --8<-- [start:gradient]
     import numpy as np
-
     import uqtils as uq
 
     # 1d example
@@ -55,7 +54,6 @@ def mcmc_example():
     """Sample from a logpdf distribution using MCMC."""
     # --8<-- [start:mcmc]
     import numpy as np
-
     import uqtils as uq
 
     def fun(x):
@@ -78,12 +76,11 @@ def sobol_example():
     """Do Sobol' analysis on the Ishigami test function."""
     # --8<-- [start:sobol]
     import numpy as np
+    import uqtils as uq
 
-    from uqtils.sobol import ishigami, sobol_sa
-
-    model = lambda x: ishigami(x)['y']
+    model = lambda x: uq.ishigami(x)['y']
     sampler = lambda shape: np.random.rand(*shape, 3) * (2 * np.pi) - np.pi
     n_samples = 1000
 
-    S1, ST = sobol_sa(model, sampler, n_samples)
+    S1, ST = uq.sobol_sa(model, sampler, n_samples)
     # --8<-- [end:sobol]

src/uqtils/sobol.py

@@ -10,7 +10,7 @@
 
 from uqtils import ax_default
 
-__all__ = ['sobol_sa']
+__all__ = ['sobol_sa', 'ishigami']
 
 
 def sobol_sa(model, sampler, num_samples: int, qoi_idx: list[int] = None, qoi_labels: list[str] = None,
@@ -229,5 +229,5 @@ def sobol_sa(model, sampler, num_samples: int, qoi_idx: list[int] = None, qoi_la
 
 
 def ishigami(x, a=7.0, b=0.1):
-    """For testing Sobol indices: https://doi.org/10.1109/ISUMA.1990.151285"""
+    """For testing Sobol indices: [Ishigami function](https://doi.org/10.1109/ISUMA.1990.151285)"""
     return {'y': np.sin(x[..., 0:1]) + a*np.sin(x[..., 1:2])**2 + b*(x[..., 2:3]**4)*np.sin(x[..., 0:1])}