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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[arguments]: Remove outdated substitutions; simplify check phase.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
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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@ -849,13 +849,13 @@ 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 "0.8.1") (version "0.8.2")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "pybedtools" version)) (uri (pypi-uri "pybedtools" version))
(sha256 (sha256
(base32 (base32
"14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0")))) "0wc7z8g8prgdx7n5chjva2fdq03wiwhqisjjxzkjg1j5k5ha7151"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:modules ((ice-9 ftw) `(#:modules ((ice-9 ftw)
@ -868,13 +868,6 @@ intended to behave exactly the same as the original BWK awk.")
(modify-phases %standard-phases (modify-phases %standard-phases
(add-after 'unpack 'disable-broken-tests (add-after 'unpack 'disable-broken-tests
(lambda _ (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" (substitute* "pybedtools/test/test_helpers.py"
;; Requires internet access. ;; Requires internet access.
(("def test_chromsizes") (("def test_chromsizes")
@ -886,8 +879,7 @@ intended to behave exactly the same as the original BWK awk.")
;; This issue still occurs on python2 ;; This issue still occurs on python2
(substitute* "pybedtools/test/test_issues.py" (substitute* "pybedtools/test/test_issues.py"
(("def test_issue_303") (("def test_issue_303")
"def _test_issue_303")) "def _test_issue_303"))))
#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.
;; Force the Cythonization of C++ files to guard against compilation ;; 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"))) (invoke "python" "setup.py" "cythonize")))
(replace 'check (replace 'check
(lambda _ (lambda _
(let* ((cwd (getcwd)) (let* ((build-root-directory (string-append (getcwd) "/build/"))
(build-root-directory (string-append cwd "/build/"))
(build (string-append (build (string-append
build-root-directory build-root-directory
(find (cut string-prefix? "lib" <>) (find (cut string-prefix? "lib" <>)
(scandir (string-append (scandir build-root-directory)))))
build-root-directory)))))
(scripts (string-append
build-root-directory
(find (cut string-prefix? "scripts" <>)
(scandir build-root-directory)))))
(setenv "PYTHONPATH" (setenv "PYTHONPATH"
(string-append build ":" (getenv "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"))))
;; The tests need to be run from elsewhere... ;; The tests need to be run from elsewhere...
(mkdir-p "/tmp/test") (mkdir-p "/tmp/test")
(copy-recursively "pybedtools/test" "/tmp/test") (copy-recursively "pybedtools/test" "/tmp/test")