From 53b2fe29734c58c0cf4a5ef0ae51a595998d7fa3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 1 May 2024 00:35:14 +0200 Subject: [PATCH] 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 | 1 - gnu/packages/bioinformatics.scm | 20 ++-- .../patches/python-scikit-bio-1887.patch | 109 ------------------ 3 files changed, 9 insertions(+), 121 deletions(-) delete mode 100644 gnu/packages/patches/python-scikit-bio-1887.patch diff --git a/gnu/local.mk b/gnu/local.mk index ca893bd0fa..eaefcc8d3d 100644 --- a/gnu/local.mk +++ b/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 \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4b6d85dfba..1d796e31a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5278,25 +5278,24 @@ (define-public python-schema-salad (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")) - (patches (search-patches "python-scikit-bio-1887.patch")))) + "03y1n91p6m44hhxm3rpb355j6ddalydz49s94h85kbhm7iy5l40h")))) (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 @@ (define-public python-scikit-bio (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 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 -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) -