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(define-module (genenetwork3-package)
#:use-module ((gn packages genenetwork)
#:select (genenetwork3) #:prefix gn:)
#:use-module ((gnu packages check) #:select (python-pylint))
#:use-module ((gnu packages python-check) #:select (python-mypy))
#:use-module ((gnu packages linux) #:select (procps))
#:use-module ((gnu packages databases) #:select (virtuoso-ose))
#:use-module (guix gexp)
#:use-module (guix utils)
#:use-module (guix git-download)
#:use-module (guix packages))
(define-public genenetwork3
(package
(inherit gn:genenetwork3)
(version (string-append (package-version gn:genenetwork3) "-git"))
(source (local-file ".."
"genenetwork3-checkout"
#:recursive? #t
#:select? (or (git-predicate (dirname (current-source-directory)))
(const #t))))))
(define-public genenetwork3-all-tests
(package
(inherit genenetwork3)
(arguments
(substitute-keyword-arguments (package-arguments genenetwork3)
((#:phases phases #~%standard-phases)
#~(modify-phases #$phases
(add-after
'unpack 'patch-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((virtuoso-ose (assoc-ref inputs "virtuoso-ose")))
(substitute* "tests/fixtures/rdf.py"
(("virtuoso-t")
(string-append #$virtuoso-ose "/bin/virtuoso-t"))))))
(add-after 'build 'rdf-tests
(lambda _
(invoke "pytest" "-k" "rdf")))
(add-before 'build 'pylint
(lambda _
(invoke "pylint" "main.py" "setup.py" "wsgi.py" "setup_commands"
"tests" "gn3" "scripts" "sheepdog")))
(add-after 'pylint 'mypy
(lambda _
(invoke "mypy" ".")))))))
(native-inputs
(modify-inputs (package-native-inputs genenetwork3)
(prepend procps)
(prepend python-pylint)
(prepend python-mypy)))))
genenetwork3
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