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gnu: python-cooler: Update to 0.8.11.

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* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
[arguments]: Add build phase "patch-tests"; replace "check" phase.
[native-inputs]: Add python-codecov, python-pytest-cov, and
python-pytest-flake8.
[propagated-inputs]: Add python-six and python-sparse.
This commit is contained in:
Mădălin Ionel Patrașcu 2021-06-06 02:06:51 +02:00 committed by Ricardo Wurmus
parent 78469645fd
commit d1e7b50dbf
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1 changed files with 36 additions and 6 deletions
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gnu/packages/bioinformatics.scm
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@ -11717,15 +11717,39 @@ (define-public python2-pyfaidx
(define-public python-cooler
(package
(name "python-cooler")
(version "0.8.7")
(version "0.8.11")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cooler" version))
(sha256
(base32
"01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp"))))
"1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-tests
(lambda _
(substitute* "tests/test_create.py"
(("def test_roundtrip")
(string-append "@pytest.mark.skip(reason=\"requires network "
"access to genome.ucsc.edu\")\n"
"def test_roundtrip")))
(substitute* "tests/test_util.py"
(("def test_fetch_chromsizes")
(string-append "@pytest.mark.skip(reason=\"requires network "
"access to genome.ucsc.edu\")\n"
"def test_fetch_chromsizes")))
;; This test depends on ipytree, which contains a lot of minified
;; JavaScript.
(substitute* "tests/test_fileops.py"
(("def test_print_trees")
"def _test_print_trees"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "-m" "pytest" "-v")))))))
(propagated-inputs
`(("python-asciitree" ,python-asciitree)
("python-biopython" ,python-biopython)
@ -11741,11 +11765,17 @@ (define-public python-cooler
("python-pysam" ,python-pysam)
("python-pyyaml" ,python-pyyaml)
("python-scipy" ,python-scipy)
("python-simplejson" ,python-simplejson)))
("python-simplejson" ,python-simplejson)
("python-six" ,python-six)
("python-sparse" ,python-sparse)))
(native-inputs
`(("python-mock" ,python-mock)
("python-pytest" ,python-pytest)))
(home-page "https://github.com/mirnylab/cooler")
`(("python-codecov" ,python-codecov)
("python-mock" ,python-mock)
("python-pytest" ,python-pytest)
("python-pytest-cov" ,python-pytest-cov)
("python-pytest-flake8" ,python-pytest-flake8)))
;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
(home-page "https://github.com/open2c/cooler")
(synopsis "Sparse binary format for genomic interaction matrices")
(description
"Cooler is a support library for a sparse, compressed, binary persistent