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.
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@ -2107,7 +2107,7 @@ has several key features:
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(setenv "CFLAGS" "-D_CURSES_LIB=1")
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(setenv "CFLAGS" "-D_CURSES_LIB=1")
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#t))
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#t))
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(replace 'check
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(replace 'check
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(lambda* (#:key tests? #:allow-other-keys)
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;; Failing test removed in the next release.
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;; Failing test removed in the next release.
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(delete-file "tests/AlignmentFile_test.py")
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(delete-file "tests/AlignmentFile_test.py")
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;; Add first subdirectory of "build" directory to PYTHONPATH.
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;; Add first subdirectory of "build" directory to PYTHONPATH.
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@ -2117,6 +2117,7 @@ has several key features:
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":" (getcwd) "/build/"
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":" (getcwd) "/build/"
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(car (scandir "build"
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(car (scandir "build"
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(negate (cut string-prefix? "." <>))))))
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(negate (cut string-prefix? "." <>))))))
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(when tests?
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;; Step out of source dir so python does not import from CWD.
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;; Step out of source dir so python does not import from CWD.
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(with-directory-excursion "tests"
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(with-directory-excursion "tests"
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(setenv "HOME" "/tmp")
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(setenv "HOME" "/tmp")
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@ -2130,7 +2131,7 @@ has several key features:
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;; https://github.com/pysam-developers/pysam/issues/961
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;; https://github.com/pysam-developers/pysam/issues/961
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" and not TestHeaderBAM"
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" and not TestHeaderBAM"
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" and not TestHeaderCRAM"
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" and not TestHeaderCRAM"
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" and not test_text_processing"))))))))
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" and not test_text_processing")))))))))
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(propagated-inputs
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(propagated-inputs
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`(("htslib" ,htslib-1.10))) ; Included from installed header files.
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`(("htslib" ,htslib-1.10))) ; Included from installed header files.
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(inputs
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(inputs
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