gnu: python-scikit-bio: Update to 0.5.9.
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.5.9. [source]: Add patch. [arguments]: Disable one test via #:test-flags; adjust 'compatibility phase; update 'check phase. [propagated-inputs]: Remove python-cachecontrol, python-lockfile, and python-scikit-learn; add python-requests. * gnu/packages/patches/python-scikit-bio-1887.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Change-Id: Ie57b0256cf695e5ea088545cd2102335303a93e7master
Ricardo Wurmus
parent
a8c1d812a0
commit
65d021a950
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@ -1926,6 +1926,7 @@ dist_patch_DATA = \
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%D%/packages/patches/python-robotframework-atest.patch \
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%D%/packages/patches/python-robotframework-source-date-epoch.patch \
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%D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \
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%D%/packages/patches/python-scikit-bio-1887.patch \
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%D%/packages/patches/python-scikit-optimize-1148.patch \
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%D%/packages/patches/python-scikit-optimize-1150.patch \
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%D%/packages/patches/python-typing-inspect-fix.patch \
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@ -4732,58 +4732,43 @@ and record oriented data modeling and the Semantic Web.")
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(define-public python-scikit-bio
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(package
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(name "python-scikit-bio")
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(version "0.5.7")
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(version "0.5.9")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "scikit-bio" version))
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(sha256
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(base32
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"1a8xbp3vrw8wfpm3pa2nb4rcar0643iqnb043ifwqbqyc86clhv3"))))
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"0429060pkyq1pm19zb2n1la7czh7b633mp4a4h01j8zfigf49q3s"))
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(patches (search-patches "python-scikit-bio-1887.patch"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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;; Accuracy problem
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#:test-flags '(list "-k" "not test_fisher_alpha")
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#:phases
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'(modify-phases %standard-phases
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;; See https://github.com/biocore/scikit-bio/pull/1826
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(add-after 'unpack 'compatibility
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(lambda _
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(substitute* "skbio/sequence/tests/test_sequence.py"
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(("def test_concat_strict_many")
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"def _do_not_test_concat_strict_many"))
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(substitute* "skbio/stats/distance/_mantel.py"
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(("from scipy.stats import PearsonRConstantInputWarning")
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"from scipy.stats import ConstantInputWarning")
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(("from scipy.stats import PearsonRNearConstantInputWarning")
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"from scipy.stats import NearConstantInputWarning")
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(("from scipy.stats import SpearmanRConstantInputWarning") "")
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(("warnings.warn\\(PearsonRConstantInputWarning\\(\\)\\)")
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"warnings.warn(ConstantInputWarning())")
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(("warnings.warn\\(PearsonRNearConstantInputWarning\\(\\)\\)")
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"warnings.warn(NearConstantInputWarning())")
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(("warnings.warn\\(SpearmanRConstantInputWarning\\(\\)\\)")
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"warnings.warn(ConstantInputWarning())"))
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(substitute* "skbio/diversity/alpha/tests/test_base.py"
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(("self.assertEqual\\(pielou_e")
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"self.assertAlmostEqual(pielou_e"))))
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(substitute* "skbio/diversity/__init__.py"
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((", numeric_only=True") ""))))
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(add-before 'check 'build-extensions
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(lambda _
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;; Cython extensions have to be built before running the tests.
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(invoke "python3" "setup.py" "build_ext" "--inplace")))
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests? (invoke "python3" "-m" "skbio.test")))))))
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(lambda* (#:key tests? test-flags #:allow-other-keys)
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(when tests?
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(apply invoke "python3" "-m" "skbio.test" test-flags)))))))
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(propagated-inputs
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(list python-cachecontrol
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python-decorator
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(list python-decorator
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python-h5py
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python-hdmedians
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python-ipython
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python-lockfile
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python-matplotlib
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python-natsort
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python-numpy
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python-pandas
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python-scikit-learn
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python-requests
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python-scipy))
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(native-inputs
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(list python-coverage python-pytest))
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@ -0,0 +1,109 @@
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From 290da0472e3a0af01b242cd1d3dd6a24588db0e5 Mon Sep 17 00:00:00 2001
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From: qiyunzhu <qiyunzhu@gmail.com>
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Date: Sat, 4 Nov 2023 12:59:54 -0700
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Subject: [PATCH 1/2] removed kulsinski
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---
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CHANGELOG.md | 6 ++++++
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ci/aarch64.conda_requirements.txt | 2 +-
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ci/conda_requirements.txt | 2 +-
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setup.py | 2 +-
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skbio/diversity/_driver.py | 2 --
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5 files changed, 9 insertions(+), 5 deletions(-)
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diff --git a/CHANGELOG.md b/CHANGELOG.md
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index 0ce69c2c6..cd9adea6c 100644
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--- a/CHANGELOG.md
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+++ b/CHANGELOG.md
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@@ -2,6 +2,12 @@
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## Version 0.5.10
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+### Features
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+* SciPy 1.11+ is now supported.
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+
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+### Backward-incompatible changes [experimental]
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+* Beta diversity metric `kulsinski` was removed. This was motivated by that SciPy replaced this distance metric with `kulczynski1` in version 1.11 (see SciPy issue [#2009](https://github.com/scipy/scipy/issues/2009)), and that both metrics do not return 0 on two identical vectors.
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+
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### Bug fixes
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* Re-enabled OpenMP support, which has been mistakenly disabled in 0.5.8 ([#1874](https://github.com/biocore/scikit-bio/pull/1874))
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diff --git a/ci/aarch64.conda_requirements.txt b/ci/aarch64.conda_requirements.txt
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index a329bc666..3564f4c3c 100644
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--- a/ci/aarch64.conda_requirements.txt
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+++ b/ci/aarch64.conda_requirements.txt
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@@ -5,5 +5,5 @@ matplotlib >= 1.4.3
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natsort >= 4.0.3
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numpy >= 1.9.2
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pandas >= 1.5.0
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-scipy <= 1.10.1
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+scipy >= 1.9.0
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h5py >= 3.6.0
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diff --git a/ci/conda_requirements.txt b/ci/conda_requirements.txt
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index 4402e4ebb..0f1bd715c 100644
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--- a/ci/conda_requirements.txt
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+++ b/ci/conda_requirements.txt
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@@ -5,6 +5,6 @@ matplotlib >= 1.4.3
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natsort >= 4.0.3
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numpy >= 1.9.2
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pandas >= 1.5.0
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-scipy <= 1.10.1
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+scipy >= 1.9.0
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h5py >= 3.6.0
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hdmedians >= 0.14.1
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diff --git a/setup.py b/setup.py
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index 36600e427..fa4d5e0a7 100644
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--- a/setup.py
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+++ b/setup.py
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@@ -221,7 +221,7 @@ def check_bin(ccbin, source, allow_dash):
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'natsort >= 4.0.3',
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'numpy >= 1.9.2',
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'pandas >= 1.5.0',
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- 'scipy <= 1.10.1',
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+ 'scipy >= 1.9.0',
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'h5py >= 3.6.0',
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'hdmedians >= 0.14.1',
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],
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diff --git a/skbio/diversity/_driver.py b/skbio/diversity/_driver.py
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index 016020743..1a792efb6 100644
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--- a/skbio/diversity/_driver.py
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+++ b/skbio/diversity/_driver.py
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@@ -296,7 +296,6 @@ def partial_beta_diversity(metric, counts, ids, id_pairs, validate=True,
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"dice",
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"hamming",
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"jaccard",
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- "kulsinski",
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"mahalanobis",
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"manhattan", # aliases to "cityblock" in beta_diversity
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"matching",
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@@ -314,7 +313,6 @@ def partial_beta_diversity(metric, counts, ids, id_pairs, validate=True,
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_qualitative_beta_metrics = [
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"dice",
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"jaccard",
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- "kulsinski",
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"matching",
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"rogerstanimoto",
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"russellrao",
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From 9dd9c6dd68a015f1159f884c57878b8a00fad14c Mon Sep 17 00:00:00 2001
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From: Qiyun Zhu <qiyunzhu@gmail.com>
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Date: Tue, 7 Nov 2023 22:42:10 -0700
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Subject: [PATCH 2/2] fixing numpy exception
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---
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skbio/stats/tests/test_composition.py | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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diff --git a/skbio/stats/tests/test_composition.py b/skbio/stats/tests/test_composition.py
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index 90921be5b..e720a594f 100644
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--- a/skbio/stats/tests/test_composition.py
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+++ b/skbio/stats/tests/test_composition.py
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@@ -1222,7 +1222,7 @@ def test_ancom_fail_alpha(self):
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ancom(self.table1, self.cats1, alpha=1.1)
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def test_ancom_fail_multiple_groups(self):
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- with self.assertRaises(TypeError):
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+ with self.assertRaises((TypeError, np.AxisError)):
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ancom(self.table4, self.cats4,
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significance_test=scipy.stats.ttest_ind)
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