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 [arguments]: Remove outdated substitutions; simplify check phase.master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