From 71dbf592c49e31b2f5e235278942b98f4ba99e72 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 22 Mar 2017 12:18:59 +0100 Subject: gnu: python-pysam: Run tests before installation. * gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check phase to be run before installation. --- gnu/packages/bioinformatics.scm | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8f0cd0ae77..51f0e0c0b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1430,7 +1430,11 @@ (define-public python-pysam '(delete-file-recursively "htslib")))) (build-system python-build-system) (arguments - `(#:phases + `(#:modules ((ice-9 ftw) + (srfi srfi-26) + (guix build python-build-system) + (guix build utils)) + #:phases (modify-phases %standard-phases (add-before 'build 'set-flags (lambda* (#:key inputs #:allow-other-keys) @@ -1442,23 +1446,21 @@ (define-public python-pysam (setenv "LDFLAGS" "-lncurses") (setenv "CFLAGS" "-D_CURSES_LIB=1") #t)) - (delete 'check) - (add-after 'install 'check + (replace 'check (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Add first subdirectory of "build" directory to PYTHONPATH. (setenv "PYTHONPATH" (string-append (getenv "PYTHONPATH") - ":" (assoc-ref outputs "out") - "/lib/python" - (string-take (string-take-right - (assoc-ref inputs "python") 5) 3) - "/site-packages")) + ":" (getcwd) "/build/" + (car (scandir "build" + (compose not (cut string-prefix? "." <>)))))) ;; Step out of source dir so python does not import from CWD. - (chdir "tests") - (setenv "HOME" "/tmp") - (and (zero? (system* "make" "-C" "pysam_data")) - (zero? (system* "make" "-C" "cbcf_data")) - (zero? (system* "nosetests" "-v")))))))) + (with-directory-excursion "tests" + (setenv "HOME" "/tmp") + (and (zero? (system* "make" "-C" "pysam_data")) + (zero? (system* "make" "-C" "cbcf_data")) + (zero? (system* "nosetests" "-v"))))))))) (propagated-inputs `(("htslib" ,htslib))) ; Included from installed header files. (inputs -- cgit v1.2.3