1 files changed, 0 insertions, 109 deletions
diff --git a/gnu/packages/patches/python-scikit-bio-1887.patch b/gnu/packages/patches/python-scikit-bio-1887.patch
deleted file mode 100644
index 7ee7518128..0000000000
--- a/gnu/packages/patches/python-scikit-bio-1887.patch
+++ /dev/null
@@ -1,109 +0,0 @@
-From 290da0472e3a0af01b242cd1d3dd6a24588db0e5 Mon Sep 17 00:00:00 2001
-From: qiyunzhu <[email protected]>
-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 <[email protected]>
-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)
-