Use doctest for testing python example docstrings (rapidsai#1073)

Similar to rapidsai/cudf#9815, this change uses doctest to test that the pylibraft example docstrings run without issue.

This caught several errors in the example docstrings, that are also fixed in this PR:
 *  a missing ‘device_ndarray’ import in kmeans fit when the centroids weren’t explicitly passed in
 *  an error in the fused_l2_nn_argmin docstring where output wasn’t defined
 *  An `AttributeError: module 'pylibraft.neighbors.ivf_pq' has no attribute 'np'` error in ivf_pq

Closes rapidsai#981

Authors:
  - Ben Frederickson (https://github.com/benfred)

Approvers:
  - Corey J. Nolet (https://github.com/cjnolet)

URL: rapidsai#1073

Author: benfred

python/pylibraft/pylibraft/cluster/__init__.py

@@ -13,4 +13,6 @@
 # limitations under the License.
 #
 
-from .kmeans import compute_new_centroids
+from .kmeans import KMeansParams, cluster_cost, compute_new_centroids, fit
+
+__all__ = ["KMeansParams", "cluster_cost", "compute_new_centroids", "fit"]

python/pylibraft/pylibraft/cluster/kmeans.pyx

@@ -27,7 +27,7 @@ from libcpp cimport nullptr
 from collections import namedtuple
 from enum import IntEnum
 
-from pylibraft.common import Handle, cai_wrapper
+from pylibraft.common import Handle, cai_wrapper, device_ndarray
 from pylibraft.common.handle import auto_sync_handle
 
 from pylibraft.common.handle cimport handle_t
@@ -81,33 +81,33 @@ def compute_new_centroids(X,
     --------
 
     >>> import cupy as cp
-    >>>
+
     >>> from pylibraft.common import Handle
     >>> from pylibraft.cluster.kmeans import compute_new_centroids
-    >>>
+
     >>> # A single RAFT handle can optionally be reused across
     >>> # pylibraft functions.
     >>> handle = Handle()
-    >>>
+
     >>> n_samples = 5000
     >>> n_features = 50
     >>> n_clusters = 3
-    >>>
+
     >>> X = cp.random.random_sample((n_samples, n_features),
-    >>>                               dtype=cp.float32)
-    >>>
+    ...                               dtype=cp.float32)
+
     >>> centroids = cp.random.random_sample((n_clusters, n_features),
-    >>>                                         dtype=cp.float32)
-    >>>
+    ...                                         dtype=cp.float32)
+    ...
     >>> labels = cp.random.randint(0, high=n_clusters, size=n_samples,
-    >>>                            dtype=cp.int32)
-    >>>
+    ...                            dtype=cp.int32)
+
     >>> new_centroids = cp.empty((n_clusters, n_features), dtype=cp.float32)
-    >>>
+
     >>> compute_new_centroids(
-    >>>     X, centroids, labels, new_centroids, handle=handle
-    >>> )
-    >>>
+    ...     X, centroids, labels, new_centroids, handle=handle
+    ... )
+
     >>> # pylibraft functions are often asynchronous so the
     >>> # handle needs to be explicitly synchronized
     >>> handle.sync()
@@ -211,22 +211,21 @@ def cluster_cost(X, centroids, handle=None):
     Examples
     --------
 
-    .. code-block:: python
-        import cupy as cp
-
-        from pylibraft.cluster.kmeans import cluster_cost
-
-        n_samples = 5000
-        n_features = 50
-        n_clusters = 3
-
-        X = cp.random.random_sample((n_samples, n_features),
-                                      dtype=cp.float32)
+    >>> import cupy as cp
+    >>>
+    >>> from pylibraft.cluster.kmeans import cluster_cost
+    >>>
+    >>> n_samples = 5000
+    >>> n_features = 50
+    >>> n_clusters = 3
+    >>>
+    >>> X = cp.random.random_sample((n_samples, n_features),
+    ...                             dtype=cp.float32)
 
-        centroids = cp.random.random_sample((n_clusters, n_features),
-                                                dtype=cp.float32)
+    >>> centroids = cp.random.random_sample((n_clusters, n_features),
+    ...                                      dtype=cp.float32)
 
-        inertia = cluster_cost(X, centroids)
+    >>> inertia = cluster_cost(X, centroids)
     """
     x_cai = X.__cuda_array_interface__
     centroids_cai = centroids.__cuda_array_interface__
@@ -434,21 +433,19 @@ def fit(
     Examples
     --------
 
-    .. code-block:: python
-
-        import cupy as cp
-
-        from pylibraft.cluster.kmeans import fit, KMeansParams
-
-        n_samples = 5000
-        n_features = 50
-        n_clusters = 3
-
-        X = cp.random.random_sample((n_samples, n_features),
-                                      dtype=cp.float32)
+    >>> import cupy as cp
+    >>>
+    >>> from pylibraft.cluster.kmeans import fit, KMeansParams
+    >>>
+    >>> n_samples = 5000
+    >>> n_features = 50
+    >>> n_clusters = 3
+    >>>
+    >>> X = cp.random.random_sample((n_samples, n_features),
+    ...                             dtype=cp.float32)
 
-        params = KMeansParams(n_clusters=n_clusters)
-        centroids, inertia, n_iter = fit(params, X)
+    >>> params = KMeansParams(n_clusters=n_clusters)
+    >>> centroids, inertia, n_iter = fit(params, X)
     """
     cdef handle_t *h = <handle_t*><size_t>handle.getHandle()
 

python/pylibraft/pylibraft/distance/__init__.py

@@ -15,3 +15,5 @@
 
 from .fused_l2_nn import fused_l2_nn_argmin
 from .pairwise_distance import DISTANCE_TYPES, distance as pairwise_distance
+
+__all__ = ["fused_l2_nn_argmin", "pairwise_distance"]

python/pylibraft/pylibraft/distance/fused_l2_nn.pyx

@@ -80,15 +80,15 @@ def fused_l2_nn_argmin(X, Y, out=None, sqrt=True, handle=None):
     >>> n_clusters = 5
     >>> n_features = 50
     >>> in1 = cp.random.random_sample((n_samples, n_features),
-    >>>                               dtype=cp.float32)
+    ...                               dtype=cp.float32)
     >>> in2 = cp.random.random_sample((n_clusters, n_features),
-    >>>                               dtype=cp.float32)
+    ...                               dtype=cp.float32)
     >>> # A single RAFT handle can optionally be reused across
     >>> # pylibraft functions.
     >>> handle = Handle()
-    >>> ...
-    >>> output = fused_l2_nn_argmin(in1, in2, output, handle=handle)
-    >>> ...
+
+    >>> output = fused_l2_nn_argmin(in1, in2, handle=handle)
+
     >>> # pylibraft functions are often asynchronous so the
     >>> # handle needs to be explicitly synchronized
     >>> handle.sync()
@@ -103,20 +103,20 @@ def fused_l2_nn_argmin(X, Y, out=None, sqrt=True, handle=None):
     >>> n_clusters = 5
     >>> n_features = 50
     >>> in1 = cp.random.random_sample((n_samples, n_features),
-    >>>                               dtype=cp.float32)
+    ...                               dtype=cp.float32)
     >>> in2 = cp.random.random_sample((n_clusters, n_features),
-    >>>                               dtype=cp.float32)
+    ...                               dtype=cp.float32)
     >>> output = cp.empty((n_samples, 1), dtype=cp.int32)
     >>> # A single RAFT handle can optionally be reused across
     >>> # pylibraft functions.
     >>> handle = Handle()
-    >>> ...
+
     >>> fused_l2_nn_argmin(in1, in2, out=output, handle=handle)
-    >>> ...
+    array(...)
+
     >>> # pylibraft functions are often asynchronous so the
     >>> # handle needs to be explicitly synchronized
     >>> handle.sync()
-
    """
 
     x_cai = cai_wrapper(X)

python/pylibraft/pylibraft/distance/pairwise_distance.pyx

@@ -124,9 +124,9 @@ def distance(X, Y, out=None, metric="euclidean", p=2.0, handle=None):
     >>> n_samples = 5000
     >>> n_features = 50
     >>> in1 = cp.random.random_sample((n_samples, n_features),
-    >>>                               dtype=cp.float32)
+    ...                               dtype=cp.float32)
     >>> in2 = cp.random.random_sample((n_samples, n_features),
-    >>>                               dtype=cp.float32)
+    ...                               dtype=cp.float32)
 
     A single RAFT handle can optionally be reused across
     pylibraft functions.
@@ -147,9 +147,9 @@ def distance(X, Y, out=None, metric="euclidean", p=2.0, handle=None):
     >>> n_samples = 5000
     >>> n_features = 50
     >>> in1 = cp.random.random_sample((n_samples, n_features),
-    >>>                              dtype=cp.float32)
+    ...                              dtype=cp.float32)
     >>> in2 = cp.random.random_sample((n_samples, n_features),
-    >>>                              dtype=cp.float32)
+    ...                              dtype=cp.float32)
     >>> output = cp.empty((n_samples, n_samples), dtype=cp.float32)
 
     A single RAFT handle can optionally be reused across
@@ -158,7 +158,8 @@ def distance(X, Y, out=None, metric="euclidean", p=2.0, handle=None):
     >>>
     >>> handle = Handle()
     >>> pairwise_distance(in1, in2, out=output,
-    >>>                  metric="euclidean", handle=handle)
+    ...                  metric="euclidean", handle=handle)
+    array(...)
 
     pylibraft functions are often asynchronous so the
     handle needs to be explicitly synchronized

python/pylibraft/pylibraft/neighbors/__init__.py

@@ -13,3 +13,5 @@
 # limitations under the License.
 #
 from .refine import refine
+
+__all__ = ["refine"]

python/pylibraft/pylibraft/neighbors/ivf_pq/__init__.py

@@ -14,3 +14,5 @@
 #
 
 from .ivf_pq import Index, IndexParams, SearchParams, build, extend, search
+
+__all__ = ["Index", "IndexParams", "SearchParams", "build", "extend", "search"]