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;; Experimental packaging for the Common Workflow Language (started by Bruno)
(define-module (gn packages cwl)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages check)
#:use-module (gnu packages databases)
#:use-module (gnu packages python)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages node)
#:use-module (gnu packages rdf)
#:use-module (gnu packages serialization)
#:use-module (gnu packages time)
#:use-module (gnu packages version-control)
#:use-module (gnu packages xml)
#:use-module (gn packages python)
#:use-module (guix download)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix utils)
; #:use-module (guix build-system gnu)
#:use-module (guix build-system python)
; #:use-module (guix build-system trivial)
#:use-module (srfi srfi-1))
(define-public cwltool ; guix: needs work
(let ((commit "15539fba76993f951af9eba913bea6d677c74005"))
(package
(name "cwltool")
(version "1.0.20181012180214")
(source
(origin
; (method url-fetch)
; (uri (string-append
; "https://pypi.python.org/packages/source/c/cwltool/cwltool-"
; version
; ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/genenetwork/cwltool.git") ;; my repo for Python 3.7
(commit commit)))
(file-name (git-file-name name (string-append version "-" (string-take commit 7))))
(sha256
(base32
"1qwfa82car7477sy0cb5bj4964w7zq7dcw2bdcls6c2i9qdp0586"))))
(build-system python-build-system)
(propagated-inputs ; a lot of these are used for testing
`(("git" ,git)
("node" ,node)
("python-bagit" ,python-bagit)
("python-arcp" ,python-arcp)
("python-setuptools" ,python-setuptools)
("python-dateutil" ,python-dateutil)
("python-pytest-cov" ,python-pytest-cov)
("python-prov" ,python-prov)
("python-pytest-runner" ,python-pytest-runner)
("python-rdflib" ,python-rdflib)
("python-pyparsing" ,python-pyparsing)
("python-pytest-mock" ,python-pytest-mock)
("python-mock" ,python-mock)
("python-subprocess32" ,python-subprocess32)
("python-ruamel.yaml" ,python-ruamel.yaml)
("python-cachecontrol" ,python-cachecontrol)
("python-lxml" ,python-lxml)
("python-mypy-extensions" ,python-mypy-extensions)
("python-mistune" ,python-mistune)
("python-networkx" ,python-networkx)
("python-schema-salad" ,python-schema-salad)
("python-html5lib" ,python-html5lib)
("python-rdflib-jsonld" ,python-rdflib-jsonld)
("python-scandir" ,python-scandir)
("python-psutil" ,python-psutil)
))
; (arguments `(#:tests? #f)) ;; CWL includes no tests.
(arguments
`(;#:phases
; (modify-phases %standard-phases
; (replace 'check
; (lambda* (#:key inputs outputs #:allow-other-keys)
; (invoke "python" "-m" "pytest")
; )))
#:tests? #f)) ; Disable for now
(home-page
"https://github.com/common-workflow-language/common-workflow-language")
(synopsis
"Common workflow language reference implementation")
(description
"Common workflow language reference implementation")
(license license:asl2.0))))
(define-public python-cachecontrol
(package
(name "python-cachecontrol")
(version "0.11.7")
(source
(origin
(method url-fetch)
;; Pypi does not have tests.
(uri (string-append
"https://github.com/ionrock/cachecontrol/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1yfhwihx1b1xjsx0r19va2m0r2s91im03x4d7pwzp87368f2lkkp"))))
(build-system python-build-system)
(arguments
`(#:tests? #f)) ;; Recent version breaks on cherrypy
(native-inputs
`(("python-pytest" ,python-pytest)
("python-redis" ,python-redis)
("python-webtest" ,python-webtest)
("python-mock" ,python-mock)))
(propagated-inputs
`(("python-requests" ,python-requests)
("python-lockfile" ,python-lockfile)))
(home-page "https://github.com/ionrock/cachecontrol")
(synopsis "The httplib2 caching algorithms for use with requests")
(description "CacheControl is a port of the caching algorithms in
@code{httplib2} for use with @code{requests} session objects.")
(license license:asl2.0)))
(define-public python-schema-salad
(let ((commit "eb85c3d49b99b7643e8a12248e2dc05504910c1e"))
(package
(name "python-schema-salad")
(version "3.0.20181129082112")
(source
(origin
; (method url-fetch)
; (uri (pypi-uri "schema-salad" version))
(method git-fetch)
(uri (git-reference
(url "https://github.com/genenetwork/schema_salad.git") ;; my repo for Python3.7
(commit commit)))
(file-name (git-file-name name (string-append version "-" (string-take commit 7))))
(sha256
(base32
"174f224zzjr0nbjlq3ypciyfijnibasysrgjswvx8yhan2dizlhr"))))
(build-system python-build-system)
(arguments `(#:tests? #f)) ;; CWL includes no tests.
(inputs
`(("python-cython" ,python-cython)
("python-setuptools" ,python-setuptools)
("python-rdflib-jsonld" ,python-rdflib-jsonld)
("python-mistune" ,python-mistune)))
(propagated-inputs
`(("python-rdflib" ,python-rdflib)
("python-avro" ,python-avro)
("python-pyyaml" ,python-pyyaml)
("python-requests" ,python-requests)
("python-shellescape" ,python-shellescape)
))
(home-page
"https://github.com/common-workflow-language/common-workflow-language")
(synopsis
"Schema Annotations for Linked Avro Data (SALAD)")
(description
"Schema Annotations for Linked Avro Data (SALAD)")
(license license:asl2.0))))
; (define-public python2-schema-salad
; (package-with-python2 python-schema-salad))
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