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authorRicardo Wurmus <rekado@elephly.net>2022-12-13 16:29:48 +0100
committerRicardo Wurmus <rekado@elephly.net>2022-12-13 16:31:55 +0100
commitb339e181e1f9138c59934cdff330a73cc490cf32 (patch)
tree7800bb0dbbc632092024491bda085eb10034b3fc
parentde30c74b639c8739263973d0e49344b727b2c163 (diff)
gnu: python-bx-python: Update to 0.9.0.
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.9.0. [build-system]: Use pyproject-build-system. [arguments]: Add phase 'build-extensions and 'disable-cython-doctests. [native-inputs]: Replace python-nose with python-pytest.
-rw-r--r--gnu/packages/bioinformatics.scm21
1 files changed, 16 insertions, 5 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f9a51910d9..1dae5982ea 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2252,23 +2252,34 @@ off-target reads for a capture method that targets CpG-rich region.")
(define-public python-bx-python
(package
(name "python-bx-python")
- (version "0.8.12")
+ (version "0.9.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bxlab/bx-python")
- (commit "f4e6a5c93e719db69b5798b6fdd9b167da358316")))
+ (commit "4f4a48d3f227ae390c1b22072867ba86e347bdef")))
(file-name (git-file-name name version))
(sha256
(base32
- "0mclahslz34vq9x424jmzsxk0nmpm1j716fa8h3zwr9ssvch7skc"))))
- (build-system python-build-system)
+ "1c914rw8phiw7zwzngz9i9hdciz5lq53drwdbpl2bd2sf5bj2biy"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-before 'check 'build-extensions
+ (lambda _
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python" "setup.py" "build_ext" "--inplace")))
+ ;; Unrecognized argument.
+ (add-after 'unpack 'disable-cython-doctests
+ (lambda _ (substitute* "pytest.ini" (("--doctest-cython") "")))))))
(propagated-inputs
(list python-numpy))
(inputs
(list zlib))
(native-inputs
- (list python-lzo python-nose python-cython))
+ (list python-cython python-lzo python-pytest))
(home-page "https://github.com/bxlab/bx-python")
(synopsis "Tools for manipulating biological data")
(description