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gnu: python-pybedtools: Update to 0.8.1.

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* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.1.
[arguments]: Add another test to the 'disable-broken-tests phase.
(python2-pybedtools)[native-inputs]: Add python2-pathlib.
This commit is contained in:
Efraim Flashner 2020-03-11 16:31:33 +02:00
parent afb877847b
commit d9a2a255f9
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1 changed files with 12 additions and 3 deletions
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@ -785,13 +785,13 @@ intended to behave exactly the same as the original BWK awk.")
(define-public python-pybedtools (define-public python-pybedtools
(package (package
(name "python-pybedtools") (name "python-pybedtools")
(version "0.8.0") (version "0.8.1")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "pybedtools" version)) (uri (pypi-uri "pybedtools" version))
(sha256 (sha256
(base32 (base32
"1xl454ijvd4dzfvqgfahad49b49j7qy710fq9xh1rvk42z6x5ssf")))) "14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:modules ((ice-9 ftw) `(#:modules ((ice-9 ftw)
@ -818,6 +818,10 @@ intended to behave exactly the same as the original BWK awk.")
;; (see: https://github.com/daler/pybedtools/issues/192). ;; (see: https://github.com/daler/pybedtools/issues/192).
(("def test_getting_example_beds") (("def test_getting_example_beds")
"def _do_not_test_getting_example_beds")) "def _do_not_test_getting_example_beds"))
;; This issue still occurs on python2
(substitute* "pybedtools/test/test_issues.py"
(("def test_issue_303")
"def _test_issue_303"))
#t)) #t))
;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM. ;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM.
;; build system. ;; build system.
@ -886,7 +890,12 @@ Python.")
(license license:gpl2+))) (license license:gpl2+)))
(define-public python2-pybedtools (define-public python2-pybedtools
(package-with-python2 python-pybedtools)) (let ((pybedtools (package-with-python2 python-pybedtools)))
(package
(inherit pybedtools)
(native-inputs
`(("python2-pathlib" ,python2-pathlib)
,@(package-native-inputs pybedtools))))))
(define-public python-biom-format (define-public python-biom-format
(package (package