gnu: python-pybedtools: Streamline following Python build system changes.
* 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:
parent
3016f1f21a
commit
25798ca0e0
|
@ -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")
|
||||
|
|
Loading…
Reference in a new issue