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gnu: python-pybedtools: Streamline following Python build system changes.

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* gnu/packages/bioinformatics.scm (python-pybedtools): Remove trailing #t.
[phases]{check}: Do not manually set PYTHONPATH.
[arguments]: Remove the '#:modules' argument.
This commit is contained in:
Maxim Cournoyer 2021-01-22 15:39:14 -05:00
parent 3016f1f21a
commit 25798ca0e0
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GPG key ID: 1260E46482E63562
1 changed files with 3 additions and 26 deletions
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29
gnu/packages/bioinformatics.scm
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@ -816,9 +816,7 @@ (define-public python-pybedtools
"14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0"))))
(build-system python-build-system)
(arguments
`(#:modules ((ice-9 ftw)
(srfi srfi-1)
(srfi srfi-26)
`(#:modules ((srfi srfi-26)
(guix build utils)
(guix build python-build-system))
;; See https://github.com/daler/pybedtools/issues/192
@ -844,10 +842,7 @@ (define-public python-pybedtools
;; This issue still occurs on python2
(substitute* "pybedtools/test/test_issues.py"
(("def test_issue_303")
"def _test_issue_303"))
#t))
;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM.
;; build system.
"def _test_issue_303"))))
;; Force the Cythonization of C++ files to guard against compilation
;; problems.
(add-after 'unpack 'remove-cython-generated-files
@ -859,30 +854,12 @@ (define (strip-extension filename)
(string-take filename (string-index-right filename #\.)))
(define (cythonized? c/c++-file)
(member (strip-extension c/c++-file) cython-sources))
(for-each delete-file (filter cythonized? c/c++-files))
#t)))
(for-each delete-file (filter cythonized? c/c++-files)))))
(add-after 'remove-cython-generated-files 'generate-cython-extensions
(lambda _
(invoke "python" "setup.py" "cythonize")))
(replace 'check
(lambda _
(let* ((cwd (getcwd))
(build-root-directory (string-append cwd "/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)))))
(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"))))
;; The tests need to be run from elsewhere...
(mkdir-p "/tmp/test")
(copy-recursively "pybedtools/test" "/tmp/test")