Fix: np.matrix type not supported by sklearn

Some tests fail because the function `pairwise_distance` does not
support the `numpy.matrix` type. The error suggest to call
`numpy.asarray` first on the argument, so this patch does just that.

4 files changed, 36 insertions, 4 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 8002d5c3da78..236c6b35dc2b 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = python-pynndescent
 	pkgdesc = Simple fast approximate nearest neighbor search
 	pkgver = 0.5.8
-	pkgrel = 1
+	pkgrel = 2
 	url = https://github.com/lmcinnes/pynndescent
 	arch = any
 	license = BSD
@@ -12,6 +12,8 @@ pkgbase = python-pynndescent
 	depends = python-scikit-learn
 	depends = python-scipy
 	source = https://pypi.io/packages/source/p/pynndescent/pynndescent-0.5.8.tar.gz
+	source = asarray.patch
 	sha256sums = a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b
+	sha256sums = 240c9413befb3f7dd58a0f02a32e58a07c54abeef70cdaa222a3ec7bd8da7d63
 
 pkgname = python-pynndescent
diff --git a/.gitignore b/.gitignore
index 4785aa5f48e2..69004319df09 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,4 @@
 !/.SRCINFO
 !/PKGBUILD
 !/.gitignore
+!/*.patch
diff --git a/PKGBUILD b/PKGBUILD
index 10e5f65f7f32..83f65584feae 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,7 +1,7 @@
 # Maintainer: a821
 pkgname=python-pynndescent
 pkgver=0.5.8
-pkgrel=1
+pkgrel=2
 pkgdesc="Simple fast approximate nearest neighbor search"
 arch=('any')
 url="https://github.com/lmcinnes/pynndescent"
@@ -9,8 +9,15 @@ license=('BSD')
 depends=('python-joblib' 'python-numba' 'python-scikit-learn' 'python-scipy')
 makedepends=('python-setuptools')
 checkdepends=('python-pytest')
-source=("https://pypi.io/packages/source/p/pynndescent/pynndescent-${pkgver}.tar.gz")
-sha256sums=('a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b')
+source=("https://pypi.io/packages/source/p/pynndescent/pynndescent-${pkgver}.tar.gz"
+        "asarray.patch")
+sha256sums=('a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b'
+            '240c9413befb3f7dd58a0f02a32e58a07c54abeef70cdaa222a3ec7bd8da7d63')
+
+prepare() {
+  cd "pynndescent-$pkgver"
+  patch -p1 < ../asarray.patch
+}
 
 check() {
   cd "pynndescent-$pkgver"
diff --git a/asarray.patch b/asarray.patch
new file mode 100644
index 000000000000..9ba097b106f2
--- /dev/null
+++ b/asarray.patch
@@ -0,0 +1,22 @@
+diff --git a/pynndescent/tests/test_distances.py b/pynndescent/tests/test_distances.py
+index 101530b..9ad88b0 100644
+--- a/pynndescent/tests/test_distances.py
++++ b/pynndescent/tests/test_distances.py
+@@ -109,7 +109,7 @@ def test_binary_check(binary_data, metric):
+ def test_sparse_spatial_check(sparse_spatial_data, metric, decimal=6):
+     if metric in spdist.sparse_named_distances:
+         dist_matrix = pairwise_distances(
+-            sparse_spatial_data.todense().astype(np.float32), metric=metric
++            np.asarray(sparse_spatial_data.todense().astype(np.float32)), metric=metric
+         )
+     if metric in ("braycurtis", "dice", "sokalsneath", "yule"):
+         dist_matrix[np.where(~np.isfinite(dist_matrix))] = 0.0
+@@ -174,7 +174,7 @@ def test_sparse_spatial_check(sparse_spatial_data, metric, decimal=6):
+ )
+ def test_sparse_binary_check(sparse_binary_data, metric):
+     if metric in spdist.sparse_named_distances:
+-        dist_matrix = pairwise_distances(sparse_binary_data.todense(), metric=metric)
++        dist_matrix = pairwise_distances(np.asarray(sparse_binary_data.todense()), metric=metric)
+     if metric in ("jaccard", "dice", "sokalsneath"):
+         dist_matrix[np.where(~np.isfinite(dist_matrix))] = 0.0
+     if metric in ("kulsinski", "russellrao"):