gnu: python-hdmedians: Switch to Pytest backend.

* gnu/packages/statistics.scm (python-hdmedians)[source]<patch>: Add
patch fixing tests.
[arguments] <test-flags>: Provide "--pyargs" option to tests against
compiled module.
<phases>: Remove 'build-extensions.
[native-inputs]: Remove python-nose; add python-pytest.

* gnu/packages/patches/python-hdmedians-replace-nose.patch: New file
* gnu/local.mk (dist_patch_DATA): Register new patch.

Change-Id: I86c577a55c2c273bd6504d225af8056f65593f77

3 files changed, 106 insertions, 10 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index e78792fdf81..0e56f89e52b 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2039,6 +2039,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-clarabel-blas.patch		\
   %D%/packages/patches/python-docrepr-fix-tests.patch		\
   %D%/packages/patches/python-feedparser-missing-import.patch	\
+  %D%/packages/patches/python-hdmedians-replace-nose.patch	\
   %D%/packages/patches/python-louvain-fix-test.patch		\
   %D%/packages/patches/python-matplotlib-fix-legend-loc-best-test.patch	\
   %D%/packages/patches/python-mohawk-pytest.patch	\
diff --git a/gnu/packages/patches/python-hdmedians-replace-nose.patch b/gnu/packages/patches/python-hdmedians-replace-nose.patch
new file mode 100644
index 00000000000..2341fee2cdb
--- /dev/null
+++ b/gnu/packages/patches/python-hdmedians-replace-nose.patch
@@ -0,0 +1,95 @@
+This patch is from the upstream pull request.
+https://github.com/daleroberts/hdmedians/pull/10.
+It adds compatibility with Pytest and drops Nose.
+
+diff --git a/hdmedians/tests/test_geomedian.py b/hdmedians/tests/test_geomedian.py
+index 0bc37e9..ff5f938 100644
+--- a/hdmedians/tests/test_geomedian.py
++++ b/hdmedians/tests/test_geomedian.py
+@@ -4,9 +4,9 @@ Tests.
+ 
+ import numpy as np
+ import hdmedians as hd
++import pytest
+ 
+ from numpy.testing import assert_equal, assert_array_almost_equal
+-from nose.tools import assert_true, assert_raises
+ 
+ # shape (6, 25)
+ DATA1 = np.array([[693, 990, 1281, 2101, 3524, 2577],
+@@ -124,10 +124,12 @@ def test_nangeomedian_axis_one_two_good():
+ def test_nangeomedian_axis_bad():
+     data = np.array([[1.0, np.nan, 1.0],
+                      [2.0, 1.0, 1.0]])
+-    assert_raises(IndexError, hd.nangeomedian, data, axis=2)
++    with pytest.raises(IndexError):
++        hd.nangeomedian(data, axis=2)
+ 
+ 
+ def test_nangeomedian_all_nan():
+     data = np.array([[np.nan, np.nan, np.nan],
+                      [np.nan, np.nan, np.nan]])
+-    assert_raises(ValueError, hd.nangeomedian, data)
++    with pytest.raises(ValueError):
++        hd.nangeomedian(data)
+diff --git a/hdmedians/tests/test_medoid.py b/hdmedians/tests/test_medoid.py
+index c5e0a7f..4fbdf80 100644
+--- a/hdmedians/tests/test_medoid.py
++++ b/hdmedians/tests/test_medoid.py
+@@ -4,9 +4,9 @@ Tests.
+ 
+ import numpy as np
+ import hdmedians as hd
++import pytest
+ 
+ from numpy.testing import assert_equal, assert_array_almost_equal
+-from nose.tools import assert_true, assert_raises
+ 
+ # shape (6, 25)
+ DATA1 = np.array([[693, 990, 1281, 2101, 3524, 2577],
+@@ -59,7 +59,7 @@ def test_medoid_in_set_random():
+     s = [list(x) for x in a.T]
+     m = hd.medoid(a)
+     idx = s.index(list(m))
+-    assert_true(idx > -1)
++    assert(idx > -1)
+ 
+ 
+ def test_medoid_noaxis():
+@@ -85,7 +85,8 @@ def test_medoid_axis_one():
+ 
+ 
+ def test_medoid_axis_bad():
+-    assert_raises(IndexError, hd.medoid, DATA1, axis=2)
++    with pytest.raises(IndexError):
++        hd.medoid(DATA1, axis=2)
+ 
+ 
+ def test_medoid_noaxis_indexonly():
+@@ -136,7 +137,8 @@ def test_nanmedoid_two_obs():
+ def test_nanmedoid_all_nan():
+     data = np.array([[np.nan, np.nan, np.nan],
+                      [np.nan, np.nan, np.nan]])
+-    assert_raises(ValueError, hd.nanmedoid, data)
++    with pytest.raises(ValueError):
++        hd.nanmedoid(data)
+ 
+ 
+ def test_nanmedoid_axis_zero():
+@@ -170,7 +172,8 @@ def test_nanmedoid_axis_one_indexonly():
+ 
+ 
+ def test_nanmedoid_axis_bad():
+-    assert_raises(IndexError, hd.nanmedoid, DATA1, axis=2)
++    with pytest.raises(IndexError):
++        hd.nanmedoid(DATA1, axis=2)
+ 
+ 
+ def test_nanmedoid_two_obs():
+@@ -184,4 +187,5 @@ def test_nanmedoid_two_obs():
+ def test_nanmedoid_all_nan():
+     data = np.array([[np.nan, np.nan, np.nan],
+                      [np.nan, np.nan, np.nan]])
+-    assert_raises(ValueError, hd.nanmedoid, data)
++    with pytest.raises(ValueError):
++        hd.nanmedoid(data)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 28a619e6641..b33d99e29f8 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1100,19 +1100,19 @@ correlated samples from Markov Chain Monte Carlo (MCMC).")
               (uri (pypi-uri "hdmedians" version))
               (sha256
                (base32
-                "1mn2k8srnmfy451l7zvb2l4hn9701bc5awjm6q3vmqbicyqyqyml"))))
+                "1mn2k8srnmfy451l7zvb2l4hn9701bc5awjm6q3vmqbicyqyqyml"))
+       (patches (search-patches "python-hdmedians-replace-nose.patch"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:phases
-      '(modify-phases %standard-phases
-         (add-before 'check 'build-extensions
-           (lambda _
-             ;; Cython extensions have to be built before running the tests.
-             (invoke "python" "setup.py" "build_ext" "--inplace"))))))
-    (propagated-inputs (list python-cython python-numpy python-setuptools
-                             python-wheel))
-    (native-inputs (list python-nose))
+      #:test-flags #~(list "--pyargs" "hdmedians")))
+    (native-inputs
+     (list python-pytest))
+    (propagated-inputs
+     (list python-cython
+           python-numpy
+           python-setuptools
+           python-wheel))
     (home-page "http://github.com/daleroberts/hdmedians")
     (synopsis "High-dimensional medians")
     (description "Various definitions for a high-dimensional median exist and