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gnu: python-pybedtools: Disable unreliable test. 

* gnu/packages/bioinformatics.scm (python-pybedtools)[arguments]: Disable
test_intron_exon_reads test; run tests verbosely.

test_intron_exon_reads
master
Ricardo Wurmus 2020-06-03 14:05:43 +02:00
parent 7277baf50d
commit 08542026ea
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GPG Key ID: 197A5888235FACAC
1 changed files with 5 additions and 4 deletions
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@ -806,12 +806,13 @@ intended to behave exactly the same as the original BWK awk.")
;; See https://github.com/daler/pybedtools/issues/192 ;; See https://github.com/daler/pybedtools/issues/192
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
;; See https://github.com/daler/pybedtools/issues/261
(add-after 'unpack 'disable-broken-tests (add-after 'unpack 'disable-broken-tests
(lambda _ (lambda _
;; This test (pybedtools.test.test_scripts.test_venn_mpl) needs a
;; graphical environment.
(substitute* "pybedtools/test/test_scripts.py" (substitute* "pybedtools/test/test_scripts.py"
;; This test freezes.
(("def test_intron_exon_reads")
"def _do_not_test_intron_exon_reads")
;; This test fails in the Python 2 build.
(("def test_venn_mpl") (("def test_venn_mpl")
"def _do_not_test_venn_mpl")) "def _do_not_test_venn_mpl"))
(substitute* "pybedtools/test/test_helpers.py" (substitute* "pybedtools/test/test_helpers.py"
@ -868,7 +869,7 @@ intended to behave exactly the same as the original BWK awk.")
(mkdir-p "/tmp/test") (mkdir-p "/tmp/test")
(copy-recursively "pybedtools/test" "/tmp/test") (copy-recursively "pybedtools/test" "/tmp/test")
(with-directory-excursion "/tmp/test" (with-directory-excursion "/tmp/test"
(invoke "pytest"))))))) (invoke "pytest" "-v" "--doctest-modules")))))))
(propagated-inputs (propagated-inputs
`(("bedtools" ,bedtools) `(("bedtools" ,bedtools)
("samtools" ,samtools) ("samtools" ,samtools)