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gnu: multiqc: Update to 1.14.

* gnu/packages/bioinformatics.scm (multiqc): Update to 1.14.
[build-system]: Use pyproject-build-system.
[arguments]: Simplify check phase; restore sanity-check phase.
[propagated-inputs]: Add python-rich-click.
[native-inputs]: Update test data.
master
Ricardo Wurmus 2023-04-24 19:40:15 +02:00
parent 523e5ee2f1
commit bca1496f72
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GPG Key ID: 197A5888235FACAC
1 changed files with 8 additions and 14 deletions

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@ -10651,33 +10651,26 @@ replacement for strverscmp.")
(define-public multiqc
(package
(name "multiqc")
(version "1.10.1")
(version "1.14")
(source
(origin
(method url-fetch)
(uri (pypi-uri "multiqc" version))
(sha256
(base32
"0y9sgjca3bp0kk3ngry4zf4q2diyzp5bvzsx5l23nsysfbfkigm4"))))
(build-system python-build-system)
"0qlk2h0765hxp1w9hqf925rh8hq642lzgs6ppg91wln9y02s9fyw"))))
(build-system pyproject-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(lambda* (#:key inputs 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 "GUIX_PYTHONPATH"
(string-append here ":" (getenv "GUIX_PYTHONPATH")))
(invoke "python" "-munittest" "discover"))))))
;; TODO: importing the picard and gatk modules fails for unknown
;; reasons.
(delete 'sanity-check))))
(invoke "multiqc" "data" "--ignore" "data/modules")))))))))
(propagated-inputs
(list python-click
python-coloredlogs
@ -10691,12 +10684,13 @@ replacement for strverscmp.")
python-pyyaml
python-requests
python-rich
python-rich-click
python-simplejson
python-spectra))
(native-inputs
`(("python-pytest" ,python-pytest)
("tests"
,(let ((commit "02272d48a382beb27489fcf9e6308a0407dc3c2e"))
,(let ((commit "c3e7400affe3f3ca996973805797af61b93070ba"))
(origin
(method git-fetch)
(uri (git-reference
@ -10705,7 +10699,7 @@ replacement for strverscmp.")
(file-name (git-file-name "multiqc-test-data" commit))
(sha256
(base32
"1bha64wanrigczw4yn81din56396n61j5gqdrkslhslmskcafi91")))))))
"0wwqbkbfnqj5ax6l0da4csbmv1sw7ya7mwvdwryckaiqmkxy80va")))))))
(home-page "https://multiqc.info")
(synopsis "Aggregate bioinformatics analysis reports")
(description