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cwltools: updated

pull/2/head
Pjotr Prins 2 years ago
parent
commit
f129c4fc90
  1. 66
      gn/packages/cwl.scm
  2. 10
      gn/packages/python.scm

66
gn/packages/cwl.scm

@ -2,29 +2,61 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gn packages python)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix packages)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages check)
#:use-module (gnu packages graphviz)
#: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))
(define-public cwltool
(define-public python-pydot ;; can be updated in GNU Guix - this is a copy
(package
(name "cwltool")
(version "3.0.20200710214758")
(name "python-pydot")
(version "1.4.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cwltool" version))
(sha256
(base32
"1qbqkhinkhzg98jf24d5gnafsw23kng76rbi2hfvzl18bdsp1zz5"))))
(origin
(method url-fetch)
(uri (pypi-uri "pydot" version))
(sha256
(base32
"00az4cbf8bv447lkk9xi6pjm7gcc7ia33y4pm71fwfwis56rv76l"))))
(build-system python-build-system)
(native-inputs
;; For tests.
`(("python-chardet" ,python-chardet)))
(propagated-inputs
`(("python-pyparsing" ,python-pyparsing)))
(home-page "https://github.com/erocarrera/pydot")
(synopsis "Python interface to Graphviz's DOT language")
(description
"Pydot provides an interface to create, handle, modify and process
graphs in Graphviz's DOT language, written in pure Python.")
(license license:expat)))
(define-public cwltool
(let ((commit "78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf")
(revision "1"))
(package
(name "cwltool")
(version "3.0.20201117141248")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/common-workflow-language/cwltool.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1awf99n7aglxc5zszrlrv6jxp355jp45ws7wpsgjlgcdv7advn0w"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -38,9 +70,7 @@
(lambda _
;; Tries to connect to the internet.
(delete-file "tests/test_udocker.py")
(substitute* "tests/test_http_input.py"
(("https://raw.githubusercontent.com/common-workflow-language/cwltool/main")
"."))
(delete-file "tests/test_http_input.py")
(substitute* "tests/test_load_tool.py"
(("def test_load_graph_fragment_from_packed")
"@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_load_graph_fragment_from_packed"))
@ -53,10 +83,13 @@
"@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_v1_0_arg_empty_prefix_separate_false"))
#t)))))
(propagated-inputs
`(("python-bagit" ,python-bagit)
`(("git" ,git)
("python-argcomplete" ,python-argcomplete)
("python-bagit" ,python-bagit)
("python-coloredlogs" ,python-coloredlogs)
("python-mypy-extensions" ,python-mypy-extensions)
("python-prov" ,python-prov)
("python-pydot" ,python-pydot)
("python-psutil" ,python-psutil)
("python-rdflib" ,python-rdflib)
("python-requests" ,python-requests)
@ -85,7 +118,7 @@
(synopsis "Common workflow language reference implementation")
(description
"Common workflow language reference implementation.")
(license license:asl2.0)))
(license license:asl2.0))))
(define-public cwl-runner
(package
@ -105,5 +138,6 @@
"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)))
"Common workflow language alternate entry point to allow cwl-runner
script as an implementation-agnostic script interpreter.")
(license license:asl2.0)))

10
gn/packages/python.scm

@ -1100,14 +1100,14 @@ server.")
(define-public python-schema-salad
(package
(name "python-schema-salad")
(version "7.0.20200612160654")
(version "7.0.20200811075006")
(source
(origin
(method url-fetch)
(uri (pypi-uri "schema-salad" version))
(sha256
(base32
"15ma3lb6fkfc6sj75hnmmg0jj8q3pc5yrlyx15lpdd4dcp2jc39s"))))
"0wanbwmqb189x1m0vacnhpivfsr8rwbqknngivzxxs8j46yj80bg"))))
(build-system python-build-system)
(propagated-inputs
`(("python-cachecontrol" ,python-cachecontrol-0.11)
@ -1116,8 +1116,8 @@ server.")
("python-rdflib" ,python-rdflib)
("python-rdflib-jsonld" ,python-rdflib-jsonld)
("python-requests" ,python-requests)
;; This needs to be fixed before upstreaming
("python-ruamel.yaml" ,python38-ruaml.yaml-0.15.76)
;; This needs to be fixed before upstreaming - fixed?
("python-ruamel.yaml" ,python-ruamel.yaml)
("python-setuptools" ,python-setuptools)
("python-typing-extensions" ,python-typing-extensions)))
(native-inputs
@ -1528,7 +1528,7 @@ handles recursion and lists.")
(description "This package provides a SPARQL Slurper for rdflib.")
(license license:asl2.0)))
(define-public python38-ruaml.yaml-0.15.76
(define-public python38-ruaml.yaml-0.15.76 ;; no longer in use
(package
(inherit python-ruamel.yaml)
(name "python-ruamel.yaml")

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