gnu: python-scanpy: Update to 1.4.

* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.
[source]: Fetch from git.
[arguments]: Disable broken tests.
[native-inputs]: Add python-pytest.
[home-page]: Use HTTPS.
This commit is contained in:
Ricardo Wurmus 2019-03-26 18:05:27 +01:00
parent 8c9372c124
commit 28d32817d8
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@ -13266,15 +13266,41 @@ (define-public find-circ
(define-public python-scanpy
(package
(name "python-scanpy")
(version "1.2.2")
(version "1.4")
;; Fetch from git because the pypi tarball does not include tests.
(source
(origin
(method url-fetch)
(uri (pypi-uri "scanpy" version))
(method git-fetch)
(uri (git-reference
(url "https://github.com/theislab/scanpy.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1ak7bxms5a0yvf65prppq2g38clkv7c7jnjbnfpkh3xxv7q512jz"))))
"0zn6x6c0cnm1a20i6isigwb51g3pr9zpjk8r1minjqnxi5yc9pm4"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs #:allow-other-keys)
;; These tests require Internet access.
(delete-file-recursively "scanpy/tests/notebooks")
(delete-file "scanpy/tests/test_clustering.py")
;; TODO: No module named 'louvain'
(delete-file "scanpy/tests/test_rank_genes_groups_logreg.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")
(setenv "PYTHONPATH"
(string-append (getcwd) ":"
(getenv "PYTHONPATH")))
(invoke "pytest")
#t)))))
(propagated-inputs
`(("python-anndata" ,python-anndata)
("python-igraph" ,python-igraph)
@ -13290,7 +13316,9 @@ (define-public python-scanpy
("python-seaborn" ,python-seaborn)
("python-h5py" ,python-h5py)
("python-tables" ,python-tables)))
(home-page "http://github.com/theislab/scanpy")
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://github.com/theislab/scanpy")
(synopsis "Single-Cell Analysis in Python.")
(description "Scanpy is a scalable toolkit for analyzing single-cell gene
expression data. It includes preprocessing, visualization, clustering,