diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 31 |
1 files changed, 22 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a99deeb0a6..9afb2c1197 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5602,25 +5602,38 @@ complexity samples.") (define-public python-screed (package (name "python-screed") - (version "0.9") + (version "1.0") (source (origin (method url-fetch) (uri (pypi-uri "screed" version)) (sha256 (base32 - "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0")))) + "148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx")))) (build-system python-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda _ - (setenv "PYTHONPATH" - (string-append (getenv "PYTHONPATH") ":.")) - (zero? (system* "nosetests" "--attr" "!known_failing"))))))) + ;; Tests must be run after installation, as the "screed" command does + ;; not exist right after building. + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (setenv "PYTHONPATH" + (string-append out "/lib/python" + (string-take (string-take-right + (assoc-ref inputs "python") + 5) 3) + "/site-packages:" + (getenv "PYTHONPATH"))) + (setenv "PATH" (string-append out "/bin:" (getenv "PATH")))) + (invoke "python" "setup.py" "test") + #t))))) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-runner" ,python-pytest-runner))) (inputs `(("python-bz2file" ,python-bz2file))) (home-page "https://github.com/dib-lab/screed/") |