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gnu: python-pysam: Make the check phase honor the tests? argument.

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* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
This commit is contained in:
Efraim Flashner 2021-07-22 10:58:22 +03:00
parent 877792a6a7
commit fd8aea010f
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GPG Key ID: 41AAE7DCCA3D8351
1 changed files with 16 additions and 15 deletions
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gnu/packages/bioinformatics.scm
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@ -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