diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/patches/python-hdmedians-replace-nose.patch | 95 | ||||
| -rw-r--r-- | gnu/packages/statistics.scm | 20 |
3 files changed, 106 insertions, 10 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index e78792fdf8..0e56f89e52 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 0000000000..2341fee2cd --- /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 28a619e664..b33d99e29f 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 |