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gnu: python-pybedtools: Update to 0.8.2.

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* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.2.
[arguments]: Remove outdated substitutions; simplify check phase.
This commit is contained in:
Ricardo Wurmus 2021-05-05 16:18:13 +02:00
parent 75af43162e
commit da7f89c737
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GPG key ID: 197A5888235FACAC
1 changed files with 6 additions and 24 deletions
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gnu/packages/bioinformatics.scm
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@ -849,13 +849,13 @@ intended to behave exactly the same as the original BWK awk.")
(define-public python-pybedtools
(package
(name "python-pybedtools")
(version "0.8.1")
(version "0.8.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "pybedtools" version))
(sha256
(base32
"14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0"))))
"0wc7z8g8prgdx7n5chjva2fdq03wiwhqisjjxzkjg1j5k5ha7151"))))
(build-system python-build-system)
(arguments
`(#:modules ((ice-9 ftw)
@ -868,13 +868,6 @@ intended to behave exactly the same as the original BWK awk.")
(modify-phases %standard-phases
(add-after 'unpack 'disable-broken-tests
(lambda _
(substitute* "pybedtools/test/test_scripts.py"
;; This test freezes.
(("def test_intron_exon_reads")
"def _do_not_test_intron_exon_reads")
;; This test fails in the Python 2 build.
(("def test_venn_mpl")
"def _do_not_test_venn_mpl"))
(substitute* "pybedtools/test/test_helpers.py"
;; Requires internet access.
(("def test_chromsizes")
@ -886,8 +879,7 @@ intended to behave exactly the same as the original BWK awk.")
;; This issue still occurs on python2
(substitute* "pybedtools/test/test_issues.py"
(("def test_issue_303")
"def _test_issue_303"))
#t))
"def _test_issue_303"))))
;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM.
;; build system.
;; Force the Cythonization of C++ files to guard against compilation
@ -908,23 +900,13 @@ intended to behave exactly the same as the original BWK awk.")
(invoke "python" "setup.py" "cythonize")))
(replace 'check
(lambda _
(let* ((cwd (getcwd))
(build-root-directory (string-append cwd "/build/"))
(let* ((build-root-directory (string-append (getcwd) "/build/"))
(build (string-append
build-root-directory
(find (cut string-prefix? "lib" <>)
(scandir (string-append
build-root-directory)))))
(scripts (string-append
build-root-directory
(find (cut string-prefix? "scripts" <>)
(scandir build-root-directory)))))
(scandir build-root-directory)))))
(setenv "PYTHONPATH"
(string-append build ":" (getenv "PYTHONPATH")))
;; Executable scripts such as 'intron_exon_reads.py' must be
;; available in the PATH.
(setenv "PATH"
(string-append scripts ":" (getenv "PATH"))))
(string-append build ":" (getenv "PYTHONPATH"))))
;; The tests need to be run from elsewhere...
(mkdir-p "/tmp/test")
(copy-recursively "pybedtools/test" "/tmp/test")