From a098b3498052e046c8338e0630e0166bcb12355d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 5 Mar 2020 21:46:12 +0100
Subject: gnu: python-anndata: Update to 0.7.1.

* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.1.
[arguments]: Move check phase after install phase; delete one test.
[propagated-inputs]: Add python-importlib-metadata, python-numcodecs,
python-packaging, and python-zarr.
[native-inputs]: Add python-joblib, python-pytest, and python-setuptools-scm.
---
 gnu/packages/python-xyz.scm | 27 ++++++++++++++++++++++++---
 1 file changed, 24 insertions(+), 3 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0505ad5f40..bf82f5934f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15819,20 +15819,41 @@ (define-public python-zarr
 (define-public python-anndata
   (package
     (name "python-anndata")
-    (version "0.6.18")
+    (version "0.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "anndata" version))
        (sha256
         (base32
-         "03x83yjaccbqszj7x4fwwmpil0ai59yx64d1zmf2691za3j03w73"))))
+         "0rnfbpr55j1a1bi2kd4mz444741hrn74kz90h5rnjr59jmpfnh09"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'delete-inconvenient-tests
+           (lambda _
+             ;; This test depends on python-scikit-learn.
+             (delete-file "anndata/tests/test_inplace_subset.py")
+             #t))
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "pytest" "-vv"))))))
     (propagated-inputs
      `(("python-h5py" ,python-h5py)
+       ("python-importlib-metadata" ,python-importlib-metadata)
        ("python-natsort" ,python-natsort)
+       ("python-numcodecs" ,python-numcodecs)
+       ("python-packaging" ,python-packaging)
        ("python-pandas" ,python-pandas)
-       ("python-scipy" ,python-scipy)))
+       ("python-scipy" ,python-scipy)
+       ("python-zarr" ,python-zarr)))
+    (native-inputs
+     `(("python-joblib" ,python-joblib)
+       ("python-pytest" ,python-pytest)
+       ("python-setuptools-scm" ,python-setuptools-scm)))
     (home-page "https://github.com/theislab/anndata")
     (synopsis "Annotated data for data analysis pipelines")
     (description "Anndata is a package for simple (functional) high-level APIs
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