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gnu: multiqc: Update to 1.10.1.

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* gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1.
[arguments]: Remove build phase "relax-requirements"; replace "check" phase.
[propagated-inputs]: Add python-coloredlogs, python-future, python-networkx,
and python-rich; remove python-nose.
[native-inputs]: Add python-pytest and the test suite.
This commit is contained in:
Ricardo Wurmus 2021-06-07 10:51:26 +02:00
parent 856de4f61c
commit 1ac8f05103
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GPG key ID: 197A5888235FACAC
1 changed files with 41 additions and 25 deletions
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@ -8414,41 +8414,57 @@ (define-public filevercmp
(define-public multiqc
(package
(name "multiqc")
(version "1.5")
(version "1.10.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "multiqc" version))
(sha256
(base32
"02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy"))))
"0y9sgjca3bp0kk3ngry4zf4q2diyzp5bvzsx5l23nsysfbfkigm4"))))
(build-system python-build-system)
(propagated-inputs
`(("python-jinja2" ,python-jinja2)
("python-simplejson" ,python-simplejson)
("python-pyyaml" ,python-pyyaml)
("python-click" ,python-click)
("python-spectra" ,python-spectra)
("python-requests" ,python-requests)
("python-markdown" ,python-markdown)
("python-lzstring" ,python-lzstring)
("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
;; MultQC checks for the presence of nose at runtime.
("python-nose" ,python-nose)))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
(lambda _
(substitute* "setup.py"
;; MultiQC 1.5 ‘requires’ a version of python-matplotlib older
;; than the one in Guix, but should work fine with 2.2.2.
;; See <https://github.com/ewels/MultiQC/issues/725> and
;; <https://github.com/ewels/MultiQC/issues/732> for details.
(("['\"]matplotlib.*?['\"]")
"'matplotlib'"))
#t)))))
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(setenv "HOME" "/tmp")
(let ((here (getcwd)))
(copy-recursively (assoc-ref inputs "tests") "/tmp/tests")
;; ModuleNotFoundError: No module named 'multiqc.modules.ccs'
(delete-file "/tmp/tests/unit_tests/test_ccs.py")
(with-directory-excursion "/tmp/tests"
(setenv "PYTHONPATH" (string-append here ":" (getenv "PYTHONPATH")))
(invoke "python" "-munittest" "discover")))))))))
(propagated-inputs
`(("python-click" ,python-click)
("python-coloredlogs" ,python-coloredlogs)
("python-future" ,python-future)
("python-jinja2" ,python-jinja2)
("python-lzstring" ,python-lzstring)
("python-markdown" ,python-markdown)
("python-matplotlib" ,python-matplotlib)
("python-networkx" ,python-networkx)
("python-numpy" ,python-numpy)
("python-pyyaml" ,python-pyyaml)
("python-requests" ,python-requests)
("python-rich" ,python-rich)
("python-simplejson" ,python-simplejson)
("python-spectra" ,python-spectra)))
(native-inputs
`(("python-pytest" ,python-pytest)
("tests"
,(let ((commit "02272d48a382beb27489fcf9e6308a0407dc3c2e"))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ewels/MultiQC_TestData")
(commit commit)))
(file-name (git-file-name "multiqc-test-data" commit))
(sha256
(base32
"1bha64wanrigczw4yn81din56396n61j5gqdrkslhslmskcafi91")))))))
(home-page "https://multiqc.info")
(synopsis "Aggregate bioinformatics analysis reports")
(description