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From 290da0472e3a0af01b242cd1d3dd6a24588db0e5 Mon Sep 17 00:00:00 2001
From: qiyunzhu <qiyunzhu@gmail.com>
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 <qiyunzhu@gmail.com>
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)
|
