From 7c78efdce60ca3c65a59c28ef806b4904e5ed6b5 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 20 Mar 2022 08:56:33 +0200
Subject: gn: upstream python-scikit-allel

---
 gn/packages/bioinformatics.scm | 49 ------------------------------------------
 1 file changed, 49 deletions(-)

(limited to 'gn/packages/bioinformatics.scm')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 6dde766..01e4c59 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -3137,52 +3137,3 @@ from a VCF.  In particular, pixy facilitates the use of VCFs containing
 invariant (monomorphic) sites, which are essential for the correct computation
 of π and dxy in the face of missing data (i.e. always).")
     (license license:expat)))
-
-(define-public python-scikit-allel
-  (package
-    (name "python-scikit-allel")
-    (version "1.3.5")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "scikit-allel" version))
-        (sha256
-         (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
-    (build-system python-build-system)
-    (arguments
-     (list
-       #:phases
-       #~(modify-phases %standard-phases
-           (replace 'check
-             (lambda* (#:key tests? #:allow-other-keys)
-               (when tests?
-                 (invoke "python" "setup.py" "build_ext" "--inplace")
-                 (invoke "python" "-m" "pytest" "-v" "allel"
-                         ;; AttributeError: 'Dataset' object has no attribute 'asstr'
-                         ;; Perhaps need python-h5py@3?
-                         "-k" (string-append
-                                "not test_vcf_to_hdf5"
-                                " and not test_vcf_to_hdf5_exclude"
-                                " and not test_vcf_to_hdf5_rename"
-                                " and not test_vcf_to_hdf5_group"
-                                " and not test_vcf_to_hdf5_ann"))))))))
-    (propagated-inputs
-     (list python-dask
-           python-numpy))
-    (native-inputs
-     (list python-cython
-           ;; The following are all needed for the tests
-           htslib
-           python-h5py
-           python-hmmlearn
-           python-numexpr
-           python-pytest
-           python-scipy
-           python-setuptools-scm
-           python-zarr))
-    (home-page "https://github.com/cggh/scikit-allel")
-    (synopsis "Explore and analyze genetic variation data")
-    (description
-     "This package provides utilities for exploratory analysis of large scale
-genetic variation data.")
-    (license license:expat)))
-- 
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