From 290da0472e3a0af01b242cd1d3dd6a24588db0e5 Mon Sep 17 00:00:00 2001 From: qiyunzhu Date: Sat, 4 Nov 2023 12:59:54 -0700 Subject: [PATCH 1/2] removed kulsinski --- CHANGELOG.md | 6 ++++++ ci/aarch64.conda_requirements.txt | 2 +- ci/conda_requirements.txt | 2 +- setup.py | 2 +- skbio/diversity/_driver.py | 2 -- 5 files changed, 9 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0ce69c2c6..cd9adea6c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,12 @@ ## Version 0.5.10 +### Features +* SciPy 1.11+ is now supported. + +### Backward-incompatible changes [experimental] +* 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. + ### Bug fixes * Re-enabled OpenMP support, which has been mistakenly disabled in 0.5.8 ([#1874](https://github.com/biocore/scikit-bio/pull/1874)) diff --git a/ci/aarch64.conda_requirements.txt b/ci/aarch64.conda_requirements.txt index a329bc666..3564f4c3c 100644 --- a/ci/aarch64.conda_requirements.txt +++ b/ci/aarch64.conda_requirements.txt @@ -5,5 +5,5 @@ matplotlib >= 1.4.3 natsort >= 4.0.3 numpy >= 1.9.2 pandas >= 1.5.0 -scipy <= 1.10.1 +scipy >= 1.9.0 h5py >= 3.6.0 diff --git a/ci/conda_requirements.txt b/ci/conda_requirements.txt index 4402e4ebb..0f1bd715c 100644 --- a/ci/conda_requirements.txt +++ b/ci/conda_requirements.txt @@ -5,6 +5,6 @@ matplotlib >= 1.4.3 natsort >= 4.0.3 numpy >= 1.9.2 pandas >= 1.5.0 -scipy <= 1.10.1 +scipy >= 1.9.0 h5py >= 3.6.0 hdmedians >= 0.14.1 diff --git a/setup.py b/setup.py index 36600e427..fa4d5e0a7 100644 --- a/setup.py +++ b/setup.py @@ -221,7 +221,7 @@ def check_bin(ccbin, source, allow_dash): 'natsort >= 4.0.3', 'numpy >= 1.9.2', 'pandas >= 1.5.0', - 'scipy <= 1.10.1', + 'scipy >= 1.9.0', 'h5py >= 3.6.0', 'hdmedians >= 0.14.1', ], diff --git a/skbio/diversity/_driver.py b/skbio/diversity/_driver.py index 016020743..1a792efb6 100644 --- a/skbio/diversity/_driver.py +++ b/skbio/diversity/_driver.py @@ -296,7 +296,6 @@ def partial_beta_diversity(metric, counts, ids, id_pairs, validate=True, "dice", "hamming", "jaccard", - "kulsinski", "mahalanobis", "manhattan", # aliases to "cityblock" in beta_diversity "matching", @@ -314,7 +313,6 @@ def partial_beta_diversity(metric, counts, ids, id_pairs, validate=True, _qualitative_beta_metrics = [ "dice", "jaccard", - "kulsinski", "matching", "rogerstanimoto", "russellrao", From 9dd9c6dd68a015f1159f884c57878b8a00fad14c Mon Sep 17 00:00:00 2001 From: Qiyun Zhu Date: Tue, 7 Nov 2023 22:42:10 -0700 Subject: [PATCH 2/2] fixing numpy exception --- skbio/stats/tests/test_composition.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/skbio/stats/tests/test_composition.py b/skbio/stats/tests/test_composition.py index 90921be5b..e720a594f 100644 --- a/skbio/stats/tests/test_composition.py +++ b/skbio/stats/tests/test_composition.py @@ -1222,7 +1222,7 @@ def test_ancom_fail_alpha(self): ancom(self.table1, self.cats1, alpha=1.1) def test_ancom_fail_multiple_groups(self): - with self.assertRaises(TypeError): + with self.assertRaises((TypeError, np.AxisError)): ancom(self.table4, self.cats4, significance_test=scipy.stats.ttest_ind)