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gnu: python-scanpy: Update to 1.7.2. 

* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
master
Roel Janssen 2021-06-01 10:25:12 +02:00
parent e639da604f
commit 7382aa00b8
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1 changed files with 21 additions and 4 deletions
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gnu/packages/bioinformatics.scm
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@ -122,6 +122,7 @@
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-compression)
#:use-module (gnu packages python-science)
@ -11328,14 +11329,14 @@ implementation differs in these ways:
(define-public python-scanpy
(package
(name "python-scanpy")
(version "1.4.6")
(version "1.7.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scanpy" version))
(sha256
(base32
"0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l"))))
"0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -11346,12 +11347,25 @@ implementation differs in these ways:
(delete-file-recursively "scanpy/tests/notebooks")
(delete-file "scanpy/tests/test_clustering.py")
(delete-file "scanpy/tests/test_datasets.py")
(delete-file "scanpy/tests/test_highly_variable_genes.py")
;; TODO: I can't get the plotting tests to work, even with Xvfb.
(delete-file "scanpy/tests/test_plotting.py")
(delete-file "scanpy/tests/test_preprocessing.py")
(delete-file "scanpy/tests/test_read_10x.py")
;; The following tests need anndata.tests, which aren't included
;; in the final python-anndata package.
(delete-file "scanpy/tests/test_combat.py")
(delete-file "scanpy/tests/test_embedding_plots.py")
(delete-file "scanpy/tests/test_normalization.py")
(delete-file "scanpy/tests/test_pca.py")
(delete-file "scanpy/tests/external/test_scrublet.py")
;; The following tests requires 'scanorama', which isn't
;; packaged yet.
(delete-file "scanpy/tests/external/test_scanorama_integrate.py")
(setenv "PYTHONPATH"
(string-append (getcwd) ":"
(getenv "PYTHONPATH")))
@ -11376,11 +11390,14 @@ implementation differs in these ways:
("python-seaborn" ,python-seaborn)
("python-statsmodels" ,python-statsmodels)
("python-tables" ,python-tables)
("python-pytoml" ,python-pytoml)
("python-tqdm" ,python-tqdm)
("python-umap-learn" ,python-umap-learn)))
(native-inputs
`(("python-pytest" ,python-pytest)
("python-setuptools-scm" ,python-setuptools-scm)))
`(("python-leidenalg" ,python-leidenalg)
("python-pytest" ,python-pytest)
("python-setuptools-scm" ,python-setuptools-scm)
("python-sinfo" ,python-sinfo)))
(home-page "https://github.com/theislab/scanpy")
(synopsis "Single-Cell Analysis in Python.")
(description "Scanpy is a scalable toolkit for analyzing single-cell gene