diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 39 | ||||
| -rw-r--r-- | gnu/packages/patches/python-scikit-bio-1887.patch | 109 |
3 files changed, 122 insertions, 27 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index d2e2843372..ed4e82772e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1926,6 +1926,7 @@ 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 \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c05ca19022..462dd54bc9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4732,58 +4732,43 @@ and record oriented data modeling and the Semantic Web.") (define-public python-scikit-bio (package (name "python-scikit-bio") - (version "0.5.7") + (version "0.5.9") (source (origin (method url-fetch) (uri (pypi-uri "scikit-bio" version)) (sha256 (base32 - "1a8xbp3vrw8wfpm3pa2nb4rcar0643iqnb043ifwqbqyc86clhv3")))) + "0429060pkyq1pm19zb2n1la7czh7b633mp4a4h01j8zfigf49q3s")) + (patches (search-patches "python-scikit-bio-1887.patch")))) (build-system pyproject-build-system) (arguments (list + ;; Accuracy problem + #:test-flags '(list "-k" "not test_fisher_alpha") #:phases '(modify-phases %standard-phases - ;; See https://github.com/biocore/scikit-bio/pull/1826 (add-after 'unpack 'compatibility (lambda _ - (substitute* "skbio/sequence/tests/test_sequence.py" - (("def test_concat_strict_many") - "def _do_not_test_concat_strict_many")) - (substitute* "skbio/stats/distance/_mantel.py" - (("from scipy.stats import PearsonRConstantInputWarning") - "from scipy.stats import ConstantInputWarning") - (("from scipy.stats import PearsonRNearConstantInputWarning") - "from scipy.stats import NearConstantInputWarning") - (("from scipy.stats import SpearmanRConstantInputWarning") "") - (("warnings.warn\\(PearsonRConstantInputWarning\\(\\)\\)") - "warnings.warn(ConstantInputWarning())") - (("warnings.warn\\(PearsonRNearConstantInputWarning\\(\\)\\)") - "warnings.warn(NearConstantInputWarning())") - (("warnings.warn\\(SpearmanRConstantInputWarning\\(\\)\\)") - "warnings.warn(ConstantInputWarning())")) - (substitute* "skbio/diversity/alpha/tests/test_base.py" - (("self.assertEqual\\(pielou_e") - "self.assertAlmostEqual(pielou_e")))) + (substitute* "skbio/diversity/__init__.py" + ((", numeric_only=True") "")))) (add-before 'check 'build-extensions (lambda _ ;; Cython extensions have to be built before running the tests. (invoke "python3" "setup.py" "build_ext" "--inplace"))) (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? (invoke "python3" "-m" "skbio.test"))))))) + (lambda* (#:key tests? test-flags #:allow-other-keys) + (when tests? + (apply invoke "python3" "-m" "skbio.test" test-flags))))))) (propagated-inputs - (list python-cachecontrol - python-decorator + (list python-decorator python-h5py python-hdmedians python-ipython - python-lockfile python-matplotlib python-natsort python-numpy python-pandas - python-scikit-learn + python-requests python-scipy)) (native-inputs (list python-coverage python-pytest)) diff --git a/gnu/packages/patches/python-scikit-bio-1887.patch b/gnu/packages/patches/python-scikit-bio-1887.patch new file mode 100644 index 0000000000..7ee7518128 --- /dev/null +++ b/gnu/packages/patches/python-scikit-bio-1887.patch @@ -0,0 +1,109 @@ +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) + |