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-rw-r--r--gn/packages/python.scm193
1 files changed, 141 insertions, 52 deletions
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 60558a2..7e4786f 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -3,6 +3,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages attr)
#:use-module (gnu packages base)
+ #:use-module (gnu packages bioinformatics)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
@@ -30,6 +31,7 @@
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
+ #:use-module (gnu packages serialization)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tcl)
#:use-module (gnu packages tex)
@@ -228,25 +230,6 @@ until a value is returned.")
"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 (pypi-uri "typing_extensions" version))
- (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")
@@ -322,39 +305,6 @@ until a value is returned.")
(define-public python2-xlsxwriter
(package-with-python2 python-xlsxwriter))
-(define-public python-rdflib-jsonld ; guix ready
- (package
- (name "python-rdflib-jsonld")
- (version "0.4.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "rdflib-jsonld" version))
- (sha256
- (base32
- "0bdw2pbjmpy1l4p6slsjn54bqy6crk5hk4san84xxirgd9w78iql"))))
- (build-system python-build-system)
- (inputs
- `(("python-setuptools" ,python-setuptools)))
- (propagated-inputs
- `(("python-rdflib" ,python-rdflib)
- ("python-isodate" ,python-isodate)
- ("python-pyparsing" ,python-pyparsing)
- ("python-html5lib" ,python-html5lib)
- ("python-nose" ,python-nose)
-))
- (home-page
- "https://github.com/RDFLib/rdflib-jsonld")
- (synopsis
- "rdflib extension adding JSON-LD parser and serializer")
- (description
- "rdflib extension adding JSON-LD parser and serializer")
- (license license:bsd-3)))
-
-(define-public python2-rdflib-jsonld
- (package-with-python2 python-rdflib-jsonld))
-
-
(define-public python-rserve
(package
(name "python-rserve")
@@ -1094,3 +1044,142 @@ spreadsheets without the need for COM objects.")
(synopsis "")
(description "")
(license license:bsd-4)))
+
+(define-public python-admiral
+ (package
+ (name "python-admiral")
+ (version "0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "admiral" version))
+ (sha256
+ (base32
+ "1b2zjgyz94ld5wr7s4cm4x5sxijx3w0dmd7r2cq1s8iqjzz6rd1x"))))
+ (build-system python-build-system)
+ (arguments '(#:tests? #f)) ; No tests
+ (propagated-inputs
+ `(("python-humanfriendly" ,python-humanfriendly)))
+ (home-page "https://github.com/nspies/admiral")
+ (synopsis
+ "Simple python high-performance computing cluster batch submission")
+ (description
+ "Simple python high-performance computing cluster batch submission.")
+ (license #f))) ; No license in repository.
+
+(define-public python2-admiral
+ (package-with-python2 python-admiral))
+
+(define-public python-cachecontrol-0.11
+ (package
+ (inherit python-cachecontrol)
+ (name "python-cachecontrol")
+ (version "0.11.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "CacheControl" version))
+ (sha256
+ (base32
+ "07jsfhlbcwgqg6ayz8nznzaqg5rmxqblbzxz1qvg5wc44pcjjy4g"))))))
+
+(define-public python-ruamel.yaml-0.15
+ (package
+ (inherit python-ruamel.yaml)
+ (name "python-ruamel.yaml")
+ (version "0.15.77")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ruamel.yaml" version))
+ (sha256
+ (base32
+ "1mhzxkkiv3xmr9izrgk78x7f1r5gi8kd5ac7z3vn7j00q1ydn6da"))))))
+
+(define-public python-pbr-1.6.0
+ (package
+ (inherit python-pbr)
+ (name "python-pbr")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pbr" version))
+ (sha256
+ (base32
+ "1lg1klrczvzfan89y3bl9ykrknl3nb01vvai37fkww24apzyibjf"))))))
+
+(define-public python-arvados-python-client
+ (package
+ (name "python-arvados-python-client")
+ (version "2.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "arvados-python-client" version))
+ (sha256
+ (base32
+ "19l4w6m5426x5k2kick630dh2jx26j16ycs2nhbfgr4cd43d29y4"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f)) ; tests not included?
+ (propagated-inputs
+ `(("python-ciso8601" ,python-ciso8601)
+ ("python-future" ,python-future)
+ ;("python-google-api-python-client" ,python-google-api-python-client)
+ ("python-google-api-client" ,python-google-api-client)
+ ("python-httplib2" ,python-httplib2)
+ ("python-pycurl" ,python-pycurl)
+ ("python-ruamel.yaml" ,python-ruamel.yaml-0.15)
+ ("python-setuptools" ,python-setuptools)
+ ("python-ws4py" ,python-ws4py)))
+ (native-inputs
+ `(("python-mock" ,python-mock)
+ ("python-oauth2client" ,python-oauth2client)
+ ("python-pbr" ,python-pbr-1.6.0)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-uritemplate" ,python-uritemplate)))
+ (home-page "https://arvados.org")
+ (synopsis "Arvados client library")
+ (description "This package provides the arvados module, an API client for
+Arvados. It also includes higher-level functions to help you write Crunch
+scripts, and command-line tools to store and retrieve data in the Keep storage
+server.")
+ (license license:asl2.0)))
+
+(define-public python-schema-salad
+ (package
+ (name "python-schema-salad")
+ (version "5.0.20200416112825")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "schema-salad" version))
+ (sha256
+ (base32
+ "1pm6q266qrw4r0w0vnzhsvqgk5j8b3q61hxg99awhgpjsmcvkmsz"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-cachecontrol" ,python-cachecontrol-0.11)
+ ("python-lockfile" ,python-lockfile)
+ ("python-mistune" ,python-mistune)
+ ("python-rdflib" ,python-rdflib)
+ ("python-rdflib-jsonld" ,python-rdflib-jsonld)
+ ("python-requests" ,python-requests)
+ ("python-ruamel.yaml" ,python-ruamel.yaml)
+ ("python-setuptools" ,python-setuptools)
+ ("python-typing-extensions" ,python-typing-extensions)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)
+ ("python-pytest-runner" ,python-pytest-runner)))
+ (home-page "https://github.com/common-workflow-language/schema_salad")
+ (synopsis "Schema Annotations for Linked Avro Data (SALAD)")
+ (description
+ "Salad is a schema language for describing JSON or YAML structured linked
+data documents. Salad schema describes rules for preprocessing, structural
+validation, and hyperlink checking for documents described by a Salad schema.
+Salad supports rich data modeling with inheritance, template specialization,
+object identifiers, object references, documentation generation, code
+generation, and transformation to RDF. Salad provides a bridge between document
+and record oriented data modeling and the Semantic Web.")
+ (license license:asl2.0)))