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| author | Efraim Flashner <efraim@flashner.co.il> | 2021-07-22 10:58:22 +0300 |
|---|---|---|
| committer | Efraim Flashner <efraim@flashner.co.il> | 2021-07-22 10:58:22 +0300 |
| commit | fd8aea010fee199b803c5613ff80212b009cb0d4 (patch) | |
| tree | 7c3df2195b2afeb4db511328750deefb028107e2 /gnu/packages/bioinformatics.scm | |
| parent | 877792a6a707012a4f1abadbd36cf23436660bbb (diff) | |
gnu: python-pysam: Make the check phase honor the tests? argument.
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 31 |
1 files changed, 16 insertions, 15 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d324424a58..a90a7fa9d4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2107,7 +2107,7 @@ has several key features: (setenv "CFLAGS" "-D_CURSES_LIB=1") #t)) (replace 'check - (lambda* (#:key inputs outputs #:allow-other-keys) + (lambda* (#:key tests? #:allow-other-keys) ;; Failing test removed in the next release. (delete-file "tests/AlignmentFile_test.py") ;; Add first subdirectory of "build" directory to PYTHONPATH. @@ -2117,20 +2117,21 @@ has several key features: ":" (getcwd) "/build/" (car (scandir "build" (negate (cut string-prefix? "." <>)))))) - ;; Step out of source dir so python does not import from CWD. - (with-directory-excursion "tests" - (setenv "HOME" "/tmp") - (invoke "make" "-C" "pysam_data") - (invoke "make" "-C" "cbcf_data") - (invoke "pytest" "-k" - (string-append - ;; requires network access. - "not FileHTTP" - ;; bug in test suite with samtools update - ;; https://github.com/pysam-developers/pysam/issues/961 - " and not TestHeaderBAM" - " and not TestHeaderCRAM" - " and not test_text_processing")))))))) + (when tests? + ;; Step out of source dir so python does not import from CWD. + (with-directory-excursion "tests" + (setenv "HOME" "/tmp") + (invoke "make" "-C" "pysam_data") + (invoke "make" "-C" "cbcf_data") + (invoke "pytest" "-k" + (string-append + ;; requires network access. + "not FileHTTP" + ;; bug in test suite with samtools update + ;; https://github.com/pysam-developers/pysam/issues/961 + " and not TestHeaderBAM" + " and not TestHeaderCRAM" + " and not test_text_processing"))))))))) (propagated-inputs `(("htslib" ,htslib-1.10))) ; Included from installed header files. (inputs |