Commit f65893ba authored by Pjotr Prins's avatar Pjotr Prins

CWL: updating

parent 4a1ef2cc
......@@ -3,6 +3,7 @@
(define-module (gn packages cwl)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages check)
#:use-module (gnu packages python)
#:use-module (gnu packages python-web)
#:use-module (gnu packages rdf)
......@@ -19,7 +20,7 @@
(define-public python-cwltool ; guix: needs work
(package
(name "python-cwltool")
(version "1.0.20150916041152")
(version "1.0.20181012180214")
(source
(origin
(method url-fetch)
......@@ -29,17 +30,23 @@
".tar.gz"))
(sha256
(base32
"1kqxc6nvq4nr8qdv39ycdi6fhzaipgjpmbghsz94ij6jhf5r3dq2"))))
"0pk0jlac2vl6vfihdq07agzz9dasw84yjz5ladcbwnmzzl022cg7"))))
(build-system python-build-system)
(inputs
`(("python-setuptools" ,python-setuptools)
`(("python-bagit" ,python-bagit)
("python-setuptools" ,python-setuptools)
("python-pytest-cov" ,python-pytest-cov)
("python-pytest-runner" ,python-pytest-runner)
("python-typing-extensions" ,python-typing-extensions)
("python-prov" ,python-prov)
("python-pyparsing" ,python-pyparsing)
("python-subprocess32" ,python-subprocess32)
))
(propagated-inputs
`(("python-schema-salad" ,python-schema-salad)
("python-html5lib" ,python-html5lib)
))
(arguments `(#:tests? #f)) ;; CWL includes no tests.
; (arguments `(#:tests? #f)) ;; CWL includes no tests.
(home-page
"https://github.com/common-workflow-language/common-workflow-language")
(synopsis
......@@ -54,17 +61,14 @@
(define-public python-schema-salad
(package
(name "python-schema-salad")
(version "1.0.2")
(version "3.0.20181129082112")
(source
(origin
(method url-fetch)
(uri (string-append
"https://pypi.python.org/packages/source/s/schema-salad/schema-salad-"
version
".tar.gz"))
(uri (pypi-uri "schema-salad" version))
(sha256
(base32
"09axiiirq73s1cs21n8mkdslaca2gxc2mlayyl6yiaq98cfgfh37"))))
"1xg70v82q053vz1sg8sc99alnkrm2kk05w6698vgmngl1767sk97"))))
(build-system python-build-system)
(arguments `(#:tests? #f)) ;; CWL includes no tests.
(inputs
......@@ -73,7 +77,7 @@
("python-rdflib-jsonld" ,python-rdflib-jsonld)
("python-mistune" ,python-mistune)))
(propagated-inputs
`(("python-rdflib-4.2" ,python-rdflib-4.2)
`(("python-rdflib" ,python-rdflib)
("python-avro" ,python-avro)
("python-pyyaml" ,python-pyyaml)
("python-requests" ,python-requests)
......
......@@ -26,6 +26,7 @@
#:use-module (gnu packages python)
#:use-module (gnu packages python-web)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tex)
......@@ -131,6 +132,92 @@ functions.")
(license license:expat))
)
(define-public python-bagit; guix candidate
(package
(name "python-bagit")
(version "1.7.0")
(source
(origin
(method url-fetch)
(uri "https://files.pythonhosted.org/packages/ee/11/7a7fa81c0d43fb4d449d418eba57fc6c77959754c5c2259a215152810555/bagit-1.7.0.tar.gz")
(sha256
(base32
"1m6y04qmig0b5hzb35lnaw3d2yfydb7alyr1579yblvgs3da6j7j"))))
(build-system python-build-system)
(inputs
`(("python-setuptools-scm" ,python-setuptools-scm)
("python-coverage" ,python-coverage)
("python-mock" ,python-mock)
))
(arguments `(#:tests? #f)) ;; No tests.
(home-page "https://pypi.python.org/pypi/bagit")
(synopsis
"Python bagit.")
(description
"Python bagit.")
(license license:gpl2))
)
(define-public python-prov ; guix candidate
(package
(name "python-prov")
(version "1.5.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "prov" version))
(sha256
(base32
"1a9h406laclxalmdny37m0yyw7y17n359akclbahimdggq853jd0"))))
(build-system python-build-system)
(home-page "https://github.com/trungdong/prov")
(synopsis
"A library for W3C Provenance Data Model supporting PROV-JSON, PROV-XML and PROV-O (RDF)")
(description
"A library for W3C Provenance Data Model supporting PROV-JSON, PROV-XML and PROV-O (RDF)")
(license license:expat)))
(define-public python-typing-extensions; guix candidate
(package
(name "python-typing-extensions")
(version "3.6.6")
(source
(origin
(method url-fetch)
(uri "https://files.pythonhosted.org/packages/fc/e6/3d2f306b12f01bde2861d67458d32c673e206d6fcc255537bf452db8f80c/typing_extensions-3.6.6.tar.gz")
(sha256
(base32
"07vhddjnd3mhdijyc3s0mwi9jgfjp3rr056nxqiavydbvkrvgrsi"))))
(build-system python-build-system)
(home-page "https://pypi.python.org/pypi/typing_extensions")
(synopsis
"Python typing_extensions.")
(description
"Python typing_extensions.")
(license license:gpl2))
)
(define-public python-subprocess32 ; guix candidate
(package
(name "python-subprocess32")
(version "0.2.9")
(source
(origin
(method url-fetch)
(uri "https://files.pythonhosted.org/packages/be/2b/beeba583e9877e64db10b52a96915afc0feabf7144dcbf2a0d0ea68bf73d/subprocess32-3.5.3.tar.gz")
(sha256
(base32
"1hr5fan8i719hmlmz73hf8rhq74014w07d8ryg7krvvf6692kj3b"))))
(build-system python-build-system)
(arguments `(#:tests? #f)) ;; No tests.
(home-page "https://pypi.python.org/pypi/subprocess32")
(synopsis
"Python subprocess32.")
(description
"Python subprocess32.")
(license license:gpl2))
)
(define-public python-inotify ; guix candidate
(package
(name "python-inotify")
......@@ -218,22 +305,20 @@ functions.")
(define-public python-rdflib-jsonld ; guix ready
(package
(name "python-rdflib-jsonld")
(version "0.3")
(version "0.4.0")
(source
(origin
(method url-fetch)
(uri (string-append
"https://pypi.python.org/packages/source/r/rdflib-jsonld/rdflib-jsonld-"
version
".tar.gz"))
(uri (pypi-uri "rdflib-jsonld" version))
(sha256
(base32
"121a876k49xl85jvikyh4hzvm34456ikw66cra5dfyr15br1qjll"))))
"0bdw2pbjmpy1l4p6slsjn54bqy6crk5hk4san84xxirgd9w78iql"))))
(build-system python-build-system)
(inputs
`(("python-setuptools" ,python-setuptools)))
(propagated-inputs
`(("python-rdflib-4.2" ,python-rdflib-4.2)
`(("python-rdflib" ,python-rdflib)
("python-isodate" ,python-isodate)
("python-pyparsing" ,python-pyparsing)
("python-html5lib" ,python-html5lib)
("python-nose" ,python-nose)
......@@ -250,50 +335,6 @@ functions.")
(package-with-python2 python-rdflib-jsonld))
(define-public python-rdflib-4.2
(package
(name "python-rdflib-4.2")
(version "4.2.0")
(source
(origin
(method url-fetch)
(uri (string-append
"https://pypi.python.org/packages/source/r/rdflib/rdflib-"
version
".tar.gz"))
(patches
;; The patch has no effect under Python 3.
(list (search-patch "python2-rdflib-drop-sparqlwrapper.patch")))
(sha256
(base32
"1h3f8yl9frjz8rsykjdjk83qsrcvld3qa7pkzh69s91h97ydl83l"))))
(build-system python-build-system)
(inputs
`(("python-html5lib" ,python-html5lib)
("python-isodate" ,python-isodate)
("python-pyparsing" ,python-pyparsing)
("python-setuptools" ,python-setuptools)))
(arguments `(#:tests? #f)) ;; No tests.
(home-page "https://github.com/RDFLib/rdflib")
(synopsis
"Python RDF library")
(description
"RDFLib is a Python library for working with RDF, a simple yet
powerful language for representing information.")
(license (license:non-copyleft "file://LICENSE"
"See LICENSE in the distribution."))))
(define-public python2-rdflib-4.2
(let ((base (package-with-python2 python-rdflib-4.2)))
(package
(inherit base)
(inputs
(append (package-inputs base)
`(("python-nose" ,python-nose))))
(arguments
`(#:python ,python-2
#:tests? #f))))) ; 3 tests fail, also outside Guix
(define-public python-rserve
(package
(name "python-rserve")
......@@ -326,20 +367,62 @@ powerful language for representing information.")
(define-public python2-rserve
(package-with-python2 python-rserve))
(define-public python-setuptools
(package
(name "python-setuptools")
(version "40.6.2")
(source
(origin
(method url-fetch)
(uri "https://files.pythonhosted.org/packages/37/1b/b25507861991beeade31473868463dad0e58b1978c209de27384ae541b0b/setuptools-40.6.3.zip"
)
(sha256
(base32
"1y085dnk574sxw9aymdng9gijvrsbw86hsv9hqnhv7y4d6nlsirv"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove included binaries which are used to build self-extracting
;; installers for Windows.
;; TODO: Find some way to build them ourself so we can include them.
(for-each delete-file (find-files "setuptools" "^(cli|gui).*\\.exe$"))
#t))))
(build-system python-build-system)
;; FIXME: Tests require pytest, which itself relies on setuptools.
;; One could bootstrap with an internal untested setuptools.
(arguments
`(#:tests? #f))
(home-page "https://pypi.python.org/pypi/setuptools")
(synopsis
"Library designed to facilitate packaging Python projects")
(description
"Setuptools is a fully-featured, stable library designed to facilitate
packaging Python projects, where packaging includes:
Python package and module definitions,
distribution package metadata,
test hooks,
project installation,
platform-specific details,
Python 3 support.")
;; TODO: setuptools now bundles the following libraries:
;; packaging, pyparsing, six and appdirs. How to unbundle?
(license (list license:psfl ; setuptools itself
license:expat ; six, appdirs, pyparsing
license:asl2.0 ; packaging is dual ASL2/BSD-2
license:bsd-2))))
(define-public python-avro ; guix ready - used by CWL
(package
(name "python-avro")
(version "1.7.7")
(version "1.8.2")
(source
(origin
(method url-fetch)
(uri (string-append
"https://pypi.python.org/packages/source/a/avro/avro-"
version
".tar.gz"))
(uri (pypi-uri "avro" version))
(sha256
(base32
"0n21lfclah7bmqnnqfqmpsrimz0s86qkxyn972jynq234n1lyynf"))))
"0nabn1hzj1880qsp7fkg7923c0xdqk4i35s15asmy2xp604f97lg"))))
(build-system python-build-system)
(inputs
`(("python-setuptools" ,python-setuptools)))
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment