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gnu: python-hicmatrix: Update to 15.

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* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[arguments]: Enabled tests. Remove 'relax-requirements phase.
[native-inputs]: Add python-pytest.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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Mădălin Ionel Patrașcu 2021-06-07 13:53:28 +02:00 • committed by Ricardo Wurmus
parent c03da7edb0
commit dd3698c1ac
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1 changed files with 18 additions and 19 deletions
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@ -11822,29 +11822,26 @@ such as Hi-C contact matrices.")
(define-public python-hicmatrix (define-public python-hicmatrix
(package (package
(name "python-hicmatrix") (name "python-hicmatrix")
(version "12") (version "15")
(source (source
(origin (origin
;; Version 12 is not available on pypi. ;;Pypi sources do not contain any test
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/deeptools/HiCMatrix") (url "https://github.com/deeptools/HiCMatrix")
(commit version))) (commit version)))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1xhdyx16f3brgxgxybixdi64ki8nbbkq5vk4h9ahi11pzpjfn1pj")))) "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:phases `(#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-after 'unpack 'relax-requirements (replace 'check
(lambda _ (lambda* (#:key tests? #:allow-other-keys)
(substitute* '("requirements.txt" (when tests?
"setup.py") (invoke "python" "-m" "pytest" "-v")))))))
(("cooler *=+ *0.8.5")
"cooler==0.8.*"))
#t)))))
(propagated-inputs (propagated-inputs
`(("python-cooler" ,python-cooler) `(("python-cooler" ,python-cooler)
("python-intervaltree" ,python-intervaltree) ("python-intervaltree" ,python-intervaltree)
@ -11852,6 +11849,8 @@ such as Hi-C contact matrices.")
("python-pandas" ,python-pandas) ("python-pandas" ,python-pandas)
("python-scipy" ,python-scipy) ("python-scipy" ,python-scipy)
("python-tables" ,python-tables))) ("python-tables" ,python-tables)))
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://github.com/deeptools/HiCMatrix/") (home-page "https://github.com/deeptools/HiCMatrix/")
(synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks") (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks")
(description (description