Version 2 - **API breaking**

.github/workflows/test.yml

@@ -22,8 +22,11 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-        pip install pytest
+        pip install pytest ruff
         pip install -e .
 
+    - name: Run linting tests on files in src
+      run: ruff src
+
     - name: Run tests
       run: pytest

README.md

@@ -1,6 +1,6 @@
 [![PyPI version](https://badge.fury.io/py/fastkde.svg)](https://badge.fury.io/py/fastkde)
 ![GitHub Workflow Status (with event)](https://img.shields.io/github/actions/workflow/status/lbl-eesa/fastkde/test.yml?event=push&label=tests)
-<a target="_blank" href="https://colab.research.google.com/github/LBL-EESA/fastkde/blob/main/testing/readme_test.ipynb"> <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/> </a>
+<a target="_blank" href="https://colab.research.google.com/github/LBL-EESA/fastkde/blob/main/examples/readme_test.ipynb"> <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/> </a>
 
 # fastKDE
 
@@ -23,26 +23,20 @@ dimensionality).
 **For a standard PDF**
 
 ```python
+""" Demonstrate the first README example. """
 import numpy as np
-from fastkde import fastKDE
+import fastkde
 import matplotlib.pyplot as plt
 
-#Generate two random variables dataset (representing 100000 pairs of datapoints)
-N = int(2e5)
-var1 = 50*np.random.normal(size=N) + 0.1
-var2 = 0.01*np.random.normal(size=N) - 300
+#Generate two random variables dataset (representing 100,000 pairs of datapoints)
+N = int(1e5)
+x = 50*np.random.normal(size=N) + 0.1
+y = 0.01*np.random.normal(size=N) - 300
 
 #Do the self-consistent density estimate
-myPDF, values = fastKDE.pdf(var1,var2)
+PDF = fastkde.pdf(x, y, var_names = ['x', 'y'])
 
-#Extract the axes from the pdf values list
-v1,v2 = values
-
-#Plot contours of the PDF should be a set of concentric ellipsoids centered on
-#(0.1, -300) Comparitively, the y axis range should be tiny and the x axis range
-#should be large
-plt.contour(v1,v2,myPDF)
-plt.show()
+PDF.plot();
 ```
 
 
@@ -83,7 +77,7 @@ conditional
 #***************************
 # Calculate the conditional
 #***************************
-pOfYGivenX, values = fastKDE.conditional(y,x)
+cPDF = fastkde.conditional(y, x, var_names = ['y', 'x'])
 ```
 
 The following plot shows the results:
@@ -92,31 +86,20 @@ The following plot shows the results:
 #***************************
 # Plot the conditional
 #***************************
-fig,axs = plt.subplots(1,2,figsize=(10,5))
+fig,axs = plt.subplots(1,2,figsize=(10,5), sharex=True, sharey=True)
 
 #Plot a scatter plot of the incoming data
 axs[0].plot(x,y,'k.',alpha=0.1)
 axs[0].set_title('Original (x,y) data')
-
-#Set axis labels
-for i in (0,1):
-    axs[i].set_xlabel('x')
-    axs[i].set_ylabel('y')
+axs[0].set_xlabel('x')
+axs[0].set_ylabel('y')
 
 #Draw a contour plot of the conditional
-axs[1].contourf(values[0],values[1],pOfYGivenX,64)
+cPDF.plot(ax = axs[1], add_colorbar = False)
 #Overplot the original underlying relationship
-axs[1].plot(values[0],underlyingFunction(values[0]),linewidth=3,linestyle='--',alpha=0.5)
+axs[1].plot(cPDF.x,underlyingFunction(cPDF.x),linewidth=3,linestyle='--',alpha=0.5)
 axs[1].set_title('P(y|x)')
 
-#Set axis limits to be the same (limit to the range of the data)
-xlim = [x.min(),x.max()]
-ylim = [y.min(),y.max()]
-axs[1].set_xlim(xlim)
-axs[1].set_ylim(ylim)
-axs[0].set_xlim(xlim)
-axs[0].set_ylim(ylim)
-
 plt.savefig('conditional_demo.png')
 plt.show()
 ```
@@ -128,17 +111,16 @@ plt.show()
 To see the KDE values at specified points (not necessarily those that were used to generate the KDE):
 
 ```python
-import numpy as np
-from fastkde import fastKDE
-
+""" Demonstrate using the pdf_at_points function. """""
+import fastkde
 train_x = 50*np.random.normal(size=100) + 0.1
 train_y = 0.01*np.random.normal(size=100) - 300
 
 test_x = 50*np.random.normal(size=100) + 0.1
 test_y = 0.01*np.random.normal(size=100) - 300
 
 test_points = list(zip(test_x, test_y))
-test_point_pdf_values = fastKDE.pdf_at_points(train_x, train_y, list_of_points = test_points)
+test_point_pdf_values = fastkde.pdf_at_points(train_x, train_y, list_of_points = test_points)
 ```
 
 Note that this method can be significantly slower than calls to `fastkde.pdf()` since it does not benefit from using a fast Fourier transform during the final stage in which the PDF estimate is transformed from spectral space into data space, whereas `fastkde.pdf()` does.

requirements.txt

@@ -1,2 +1,3 @@
 numpy
-scipy
+scipy
+xarray

setup.py

@@ -1,4 +1,4 @@
-from setuptools import setup,Extension
+from setuptools import setup, Extension
 import numpy
 import os
 
@@ -9,27 +9,33 @@
 
 # set commands to build the c assistance modules
 extensions = [
-    Extension("fastkde.floodFillSearch", ["src/fastkde/floodFillSearch.pyx"],
-              libraries=libs,
-              library_dirs=lib_dirs,
-              include_dirs=inc_dirs,
-              runtime_library_dirs=lib_dirs),
-    Extension("fastkde.nufft", ["src/fastkde/nufft.pyx"],
-              libraries=libs,
-              library_dirs=lib_dirs,
-              include_dirs=inc_dirs,
-              runtime_library_dirs=lib_dirs),
+    Extension(
+        "fastkde.floodFillSearch",
+        ["src/fastkde/floodFillSearch.pyx"],
+        libraries=libs,
+        library_dirs=lib_dirs,
+        include_dirs=inc_dirs,
+        runtime_library_dirs=lib_dirs,
+    ),
+    Extension(
+        "fastkde.nufft",
+        ["src/fastkde/nufft.pyx"],
+        libraries=libs,
+        library_dirs=lib_dirs,
+        include_dirs=inc_dirs,
+        runtime_library_dirs=lib_dirs,
+    ),
 ]
 
 # get revision information
-with open('REVISION', 'r') as fin:
+with open("REVISION", "r") as fin:
     revision = fin.read().rstrip()
 
 # read the long description
-with open('README.md', 'r') as fin:
+with open("README.md", "r") as fin:
     long_description = fin.read()
 
-with open('requirements.txt', 'r') as fin:
+with open("requirements.txt", "r") as fin:
     install_requires = fin.read().split()
 
 extras = {
@@ -40,23 +46,27 @@
 extras["dev"] += extras["test"]
 
 setup(
-    name='fastkde',
-    packages=['fastkde'],
+    name="fastkde",
+    packages=["fastkde"],
     version=revision,
-    description='Tools for fast and robust univariate and multivariate kernel density estimation',
+    description="Tools for fast and robust univariate and multivariate kernel density estimation",
     long_description=long_description,
-    long_description_content_type='text/markdown',
+    long_description_content_type="text/markdown",
     author="Travis A. O'Brien",
     author_email="[email protected]",
     url="https://github.com/LBL-EESA/fastkde",
-    download_url="https://github.com/LBL-EESA/fastkde/archive/v{}.tar.gz".format(revision),
-    keywords=['statistics', 'probability', 'KDE', 'kernel density estimation'],
-    py_modules=['fastkde.fastKDE',
-                'fastkde.empiricalCharacteristicFunction',
-                'fastkde.plot'],
+    download_url="https://github.com/LBL-EESA/fastkde/archive/v{}.tar.gz".format(
+        revision
+    ),
+    keywords=["statistics", "probability", "KDE", "kernel density estimation"],
+    py_modules=[
+        "fastkde.fastKDE",
+        "fastkde.empiricalCharacteristicFunction",
+        "fastkde.plot",
+    ],
     classifiers=[],
     ext_modules=extensions,
     install_requires=install_requires,
     extras_require=extras,
-    where='src',
+    where="src",
 )

src/fastkde/__init__.py

@@ -4,3 +4,19 @@
     # if the user did `pip install -e .`, there will be no version.py file
     # therefore indicate that the version is "editable"
     __version__ = "editable"
+
+
+# make some core functions available at the package level
+import fastkde.fastKDE
+
+pdf = fastkde.fastKDE.pdf
+conditional = fastkde.fastKDE.conditional
+pdf_at_points = fastkde.fastKDE.pdf_at_points
+
+# import fastkde.plot if matplotlib is available
+try:
+    import fastkde.plot
+
+    pair_plot = fastkde.plot.pair_plot
+except ImportError:
+    pass