gnu: python-scikit-bio: Update to 0.6.0.

* gnu/packages/patches/python-scikit-bio-1887.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.6.0.
[source]: Remove patch.
[arguments]: Disable skbio.diversity doctest; remove 'compatibility phase.
[propagated-inputs]: Add python-biom-format; remove python-ipython and
python-matplotlib.

Change-Id: I9bd9e0fd72f5f1b80ef6ff61c52da5fd56a715ed

gnu/local.mk

@@ -1952,7 +1952,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-robotframework-atest.patch	\
   %D%/packages/patches/python-robotframework-source-date-epoch.patch \
   %D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \
-  %D%/packages/patches/python-scikit-bio-1887.patch		\
   %D%/packages/patches/python-scikit-optimize-1148.patch	\
   %D%/packages/patches/python-scikit-optimize-1150.patch	\
   %D%/packages/patches/python-typing-inspect-fix.patch		\

gnu/packages/bioinformatics.scm

@@ -5278,25 +5278,24 @@ and record oriented data modeling and the Semantic Web.")
 (define-public python-scikit-bio
   (package
     (name "python-scikit-bio")
-    (version "0.5.9")
+    (version "0.6.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "scikit-bio" version))
               (sha256
                (base32
-                "0429060pkyq1pm19zb2n1la7czh7b633mp4a4h01j8zfigf49q3s"))
+                "03y1n91p6m44hhxm3rpb355j6ddalydz49s94h85kbhm7iy5l40h"))))
-              (patches (search-patches "python-scikit-bio-1887.patch"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
       ;; Accuracy problem
-      #:test-flags '(list "-k" "not test_fisher_alpha")
+      '(list "-k" (string-append "not test_fisher_alpha"
+                                 ;; UNEXPECTED EXCEPTION: ValueError("could
+                                 ;; not convert string to float: 'gut'")
+                                 " and not skbio.diversity"))
       #:phases
       '(modify-phases %standard-phases
-         (add-after 'unpack 'compatibility
-           (lambda _
-             (substitute* "skbio/diversity/__init__.py"
-               ((", numeric_only=True") ""))))
          (add-before 'check 'build-extensions
            (lambda _
              ;; Cython extensions have to be built before running the tests.
@@ -5306,11 +5305,10 @@ and record oriented data modeling and the Semantic Web.")
              (when tests?
                (apply invoke "python3" "-m" "skbio.test" test-flags)))))))
     (propagated-inputs
-     (list python-decorator
+     (list python-biom-format
+           python-decorator
            python-h5py
            python-hdmedians
-           python-ipython
-           python-matplotlib
            python-natsort
            python-numpy
            python-pandas

gnu/packages/patches/python-scikit-bio-1887.patch

@@ -1,109 +0,0 @@
-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)
-